From 2540e941207c70fc3af589985b35e875ff7de334 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Sun, 28 Oct 2018 14:38:46 +0100 Subject: [PATCH 001/468] ENH: support WRF and WPS v4.0.1 (intel-2018b) --- .../w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb | 34 +++ .../w/WPS/WPS-4.0.1_find-wrfdir.patch | 20 ++ ...S-4.0.1_netCDF-Fortran_seperate_path.patch | 70 +++++ .../w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 38 +++ ...F-4.0.1_netCDF-Fortran_separate_path.patch | 254 ++++++++++++++++++ 5 files changed, 416 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb new file mode 100644 index 00000000000..4528b3ee5fd --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb @@ -0,0 +1,34 @@ +name = 'WPS' +version = '4.0.1' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'opt': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/wrf-model/WPS/archive/'] + +checksums = ['1379cee8029818e7a69376a7c425d1a00801284182dd0f56a58a753703d5fb2b'] + +patches = [ + 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_find-wrfdir.patch', +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, '%s' % versionsuffix), + ('JasPer', '2.0.14'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('zlib', '1.2.11'), + ('libpng', '1.6.34'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch new file mode 100644 index 00000000000..982ddd0845b --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch @@ -0,0 +1,20 @@ +diff -uNr WPS-4.0.1.orig/arch/preamble WPS-4.0.1/arch/preamble +--- WPS-4.0.1.orig/arch/preamble 2018-10-02 18:21:14.000000000 +0200 ++++ WPS-4.0.1/arch/preamble 2018-10-26 16:05:10.676021080 +0200 +@@ -39,13 +39,13 @@ + # repository, or an older WRF v3.x tar file. + # To override the path to the compiled WRF code, just set the WRF_DIR variable after the "endif" below + # +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0.1), ) # Check for WRF v4.0.1 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0.1), ) # Check for WRF v4.0.1 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0.1 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0), ) # Check for WRF v4.0 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0), ) # Check for WRF v4.0 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF), ) # Check for clone of the WRF repository ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF), ) # Check for clone of the WRF repository + WRF_DIR = ../WRF + else # Check for old WRF v3.x directory + WRF_DIR = ../WRFV3 diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch new file mode 100644 index 00000000000..d4584dde87c --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch @@ -0,0 +1,70 @@ +diff -uNr WPS.orig/arch/Config.pl WPS/arch/Config.pl +--- WPS.orig/arch/Config.pl 2017-07-13 01:16:49.000000000 +0200 ++++ WPS/arch/Config.pl 2017-10-05 15:09:46.656317470 +0200 +@@ -36,6 +36,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -uNr WPS.orig/configure WPS/configure +--- WPS.orig/configure 2017-07-13 01:16:49.000000000 +0200 ++++ WPS/configure 2017-10-05 15:11:12.749218059 +0200 +@@ -119,9 +119,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -151,7 +156,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach + + + #Checking cross-compiling capability for some particular environment +@@ -317,9 +322,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +diff -uNr WPS.orig/util/src/Makefile WPS/util/src/Makefile +--- WPS.orig/util/src/Makefile 2017-07-13 01:16:50.000000000 +0200 ++++ WPS/util/src/Makefile 2017-10-05 15:12:07.359886380 +0200 +@@ -41,11 +41,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb new file mode 100644 index 00000000000..19bb8bc2cda --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -0,0 +1,38 @@ +name = 'WRF' +version = '4.0.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/wrf-model/WRF/archive/'] + +checksums = ['a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe'] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.20.00')] + +dependencies = [ + ('JasPer', '2.0.14'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +# 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..607bfdad074 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch @@ -0,0 +1,254 @@ +diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl +--- WRF-4.0.1.orig/arch/Config.pl 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/arch/Config.pl 2018-10-25 00:03:03.060958813 +0200 +@@ -8,6 +8,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib might be in a different path + $sw_pnetcdf_path = "" ; + $sw_hdf5_path=""; + $sw_phdf5_path=""; +@@ -90,6 +91,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -117,6 +122,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -439,6 +445,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; + $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ; +@@ -485,7 +492,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -uNr WRF-4.0.1.orig/arch/configure.defaults WRF-4.0.1/arch/configure.defaults +--- WRF-4.0.1.orig/arch/configure.defaults 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/arch/configure.defaults 2018-10-19 17:57:23.437418176 +0200 +@@ -1598,6 +1598,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -uNr WRF-4.0.1.orig/arch/conf_tokens WRF-4.0.1/arch/conf_tokens +--- WRF-4.0.1.orig/arch/conf_tokens 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/arch/conf_tokens 2018-10-23 10:19:00.867135754 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -uNr WRF-4.0.1.orig/arch/postamble WRF-4.0.1/arch/postamble +--- WRF-4.0.1.orig/arch/postamble 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/arch/postamble 2018-10-24 08:53:53.042677598 +0200 +@@ -47,7 +47,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ +- -I$(NETCDFPATH)/include \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + CONFIGURE_RTTOV_INC + REGISTRY = Registry + CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE +@@ -70,6 +70,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -101,13 +102,13 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_grib_share : +diff -uNr WRF-4.0.1.orig/configure WRF-4.0.1/configure +--- WRF-4.0.1.orig/configure 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/configure 2018-10-19 18:39:36.232467326 +0200 +@@ -183,12 +183,20 @@ + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then ++ if [ -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else +- USENETCDF=" " ++ if [ -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then ++ USENETCDF="-L$NETCDF/lib!-L$NETCDF/lib64!-lnetcdf" # ! will be replaced with space ++ else ++ USENETCDF=" " ++ fi + fi + export USENETCDF=$USENETCDF + export USENETCDFF=$USENETCDFF +@@ -629,14 +637,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -uNr WRF-4.0.1.orig/external/io_netcdf/makefile WRF-4.0.1/external/io_netcdf/makefile +--- WRF-4.0.1.orig/external/io_netcdf/makefile 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/external/io_netcdf/makefile 2018-10-19 18:11:19.135941823 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -uNr WRF-4.0.1.orig/external/io_pnetcdf/Makefile WRF-4.0.1/external/io_pnetcdf/Makefile +--- WRF-4.0.1.orig/external/io_pnetcdf/Makefile 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/external/io_pnetcdf/Makefile 2018-10-19 18:11:49.369236552 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -uNr WRF-4.0.1.orig/Makefile WRF-4.0.1/Makefile +--- WRF-4.0.1.orig/Makefile 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/Makefile 2018-10-19 18:23:30.857876650 +0200 +@@ -906,7 +906,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1036,7 +1036,7 @@ + + # rule used by configure to test if this will compile with netcdf4 + nc4_test: +- @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib $(USENETCDF) ; cd .. ++ @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 $(USENETCDF) ; cd .. + + # rule used by configure to test if Fortran 2003 IEEE signaling is available + fortran_2003_ieee_test: From e567a1f07173fb9f9c5d3047df680827e226bb89 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Sun, 28 Oct 2018 15:58:52 +0100 Subject: [PATCH 002/468] ENH: add tcsh-6.20.00 (GCCcore-7.3.0) --- .../t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..a4366a50622 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.20.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.30', '', True)] + +dependencies = [('ncurses', '6.1')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' From 57f2286570e804a53ff97bb07a4a357344d1364f Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Sun, 28 Oct 2018 18:56:07 +0100 Subject: [PATCH 003/468] STY: fix style, add checksums --- .../t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb | 6 +++--- .../w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb | 10 ++++++---- .../w/WPS/WPS-4.0.1_find-wrfdir.patch | 8 ++++++++ ...S-4.0.1_netCDF-Fortran_seperate_path.patch | 5 +++++ .../w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 20 ++++++++++--------- ...F-4.0.1_netCDF-Fortran_separate_path.patch | 5 +++++ 6 files changed, 38 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb index a4366a50622..5bd9169ede5 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb @@ -22,14 +22,14 @@ description = """Tcsh is an enhanced, but completely compatible version of the B toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'ftp://ftp.astron.com/pub/%(namelower)s', 'ftp://ftp.astron.com/pub/%(namelower)s/old', ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b89de7064ab54dac454a266cfe5d8bf66940cb5ed048d0c30674ea62e7ecef9d'] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30')] dependencies = [('ncurses', '6.1')] diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb index 4528b3ee5fd..5a74b38bd1f 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb @@ -9,15 +9,17 @@ description = """WRF Preprocessing System (WPS) for WRF. The Weather Research an toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'opt': True} -sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/wrf-model/WPS/archive/'] - -checksums = ['1379cee8029818e7a69376a7c425d1a00801284182dd0f56a58a753703d5fb2b'] - +sources = ['v%(version)s.tar.gz'] patches = [ 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', 'WPS-%(version)s_find-wrfdir.patch', ] +checksums = [ + '1379cee8029818e7a69376a7c425d1a00801284182dd0f56a58a753703d5fb2b', # v4.0.1.tar.gz + 'ca8e931847658b0fe24283dc16a87479c8093571f4bae9a04fa1ab6cad49bcb1', # WPS-4.0.1_netCDF-Fortran_seperate_path.patch + '279fc79909a3eb0370fea0bdf5690e0d5bfb9c5d04350f10ae0bf48680238111', # WPS-4.0.1_find-wrfdir.patch +] buildtype = "dmpar" versionsuffix = '-%s' % buildtype diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch index 982ddd0845b..50413e35aff 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch @@ -1,3 +1,11 @@ +# Allow WRF source code directory to be located in EasyBuild module tree +# ============================================================================ +# Since WPS v4.0, the WPS build system seems to make strong assumptions on +# where to find the WRF source code. This patch allows the WRF source code to +# be found also when WRF is located in the EasyBuild module tree. $WRF_DIR_PRE +# is being set from the wps EasyBlock. +# Patch written by @andreas-h (Oct 2018) + diff -uNr WPS-4.0.1.orig/arch/preamble WPS-4.0.1/arch/preamble --- WPS-4.0.1.orig/arch/preamble 2018-10-02 18:21:14.000000000 +0200 +++ WPS-4.0.1/arch/preamble 2018-10-26 16:05:10.676021080 +0200 diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch index d4584dde87c..432299fbcaf 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch @@ -1,3 +1,8 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. + diff -uNr WPS.orig/arch/Config.pl WPS/arch/Config.pl --- WPS.orig/arch/Config.pl 2017-07-13 01:16:49.000000000 +0200 +++ WPS/arch/Config.pl 2017-10-05 15:09:46.656317470 +0200 diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index 19bb8bc2cda..0b5fb87e213 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -9,10 +9,18 @@ description = """The Weather Research and Forecasting (WRF) Model is a next-gene toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 -sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/wrf-model/WRF/archive/'] - -checksums = ['a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + # 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 + ] +checksums = [ + 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + 'c5287268f0f1f4f8816c3384a59ff10649f68ceee11d24238149ea27620f5ba1', # WRF-4.0.1_netCDF-Fortran_separate_path.patch +] # csh is used by WRF install scripts builddependencies = [('tcsh', '6.20.00')] @@ -23,12 +31,6 @@ dependencies = [ ('netCDF-Fortran', '4.4.4'), ] -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', -# 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 -] - # limit parallel build to 20 maxparallel = 20 diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch index 607bfdad074..3196108ca09 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch @@ -1,3 +1,8 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. + diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl --- WRF-4.0.1.orig/arch/Config.pl 2018-10-03 00:17:21.000000000 +0200 +++ WRF-4.0.1/arch/Config.pl 2018-10-25 00:03:03.060958813 +0200 From d30fffc2a70871438bedd6c857c08c1303c64f5d Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Sun, 28 Oct 2018 20:49:50 +0100 Subject: [PATCH 004/468] STY: pep8 --- easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index 0b5fb87e213..ca86ca58b68 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -15,7 +15,7 @@ patches = [ 'WRF_parallel_build_fix.patch', 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', # 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 - ] +] checksums = [ 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch From 132be7b2be46e1347c0a4a49a44b6178cb983dfa Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Wed, 7 Nov 2018 12:17:12 +0100 Subject: [PATCH 005/468] STY: fix minor issues --- easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb | 2 +- easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb index 5a74b38bd1f..f4728ca2a06 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb @@ -25,7 +25,7 @@ buildtype = "dmpar" versionsuffix = '-%s' % buildtype dependencies = [ - ('WRF', version, '%s' % versionsuffix), + ('WRF', version, versionsuffix), ('JasPer', '2.0.14'), ('netCDF', '4.6.1'), ('netCDF-Fortran', '4.4.4'), diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index ca86ca58b68..1dce8c20568 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -14,7 +14,6 @@ sources = ['v%(version)s.tar.gz'] patches = [ 'WRF_parallel_build_fix.patch', 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', - # 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 ] checksums = [ 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz From ec41e4b1fbfd61622384e2f69743ce122164cfd7 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Wed, 21 Nov 2018 17:20:37 +0100 Subject: [PATCH 006/468] BUG: fix WRFv4 and WPSv4 build problems on some platforms Using the easyblocks from easybuilders/easybuild-easyblocks#1592, this fixes build problems occurring on some platforms. I can successfully build on Debian/Buster (my laptop) using foss-2018b, and on our HPC using both intel-2018b and foss-2018b. --- .../w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb | 4 +- .../w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb | 36 +++++++++++++++++ .../w/WPS/WPS-4.0.2_find-wrfdir.patch | 24 ++++++++++++ ... WPSv4_netCDF-Fortran_seperate_path.patch} | 20 ++++++++-- .../w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 4 +- .../w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb | 39 +++++++++++++++++++ ... WRFv4_netCDF-Fortran_separate_path.patch} | 35 +++++++++-------- 7 files changed, 138 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch rename easybuild/easyconfigs/w/WPS/{WPS-4.0.1_netCDF-Fortran_seperate_path.patch => WPSv4_netCDF-Fortran_seperate_path.patch} (76%) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb rename easybuild/easyconfigs/w/WRF/{WRF-4.0.1_netCDF-Fortran_separate_path.patch => WRFv4_netCDF-Fortran_separate_path.patch} (90%) diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb index f4728ca2a06..2c7853c159f 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb @@ -12,12 +12,12 @@ toolchainopts = {'opt': True} source_urls = ['https://github.com/wrf-model/WPS/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ - 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPSv4_netCDF-Fortran_seperate_path.patch', 'WPS-%(version)s_find-wrfdir.patch', ] checksums = [ '1379cee8029818e7a69376a7c425d1a00801284182dd0f56a58a753703d5fb2b', # v4.0.1.tar.gz - 'ca8e931847658b0fe24283dc16a87479c8093571f4bae9a04fa1ab6cad49bcb1', # WPS-4.0.1_netCDF-Fortran_seperate_path.patch + '495341f7ae883ba4eb1fbeb41f336745d55d6b63e79360d35680c3f7f29f01ec', # WPSv4_netCDF-Fortran_seperate_path.patch '279fc79909a3eb0370fea0bdf5690e0d5bfb9c5d04350f10ae0bf48680238111', # WPS-4.0.1_find-wrfdir.patch ] diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb new file mode 100644 index 00000000000..24257a43d60 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb @@ -0,0 +1,36 @@ +name = 'WPS' +version = '4.0.2' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPSv4_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_find-wrfdir.patch', +] +checksums = [ + 'e053b3348d942288d04aca642ec700d97ec6895d6ef96ffa6168581c127dac00', # v4.0.2.tar.gz + '495341f7ae883ba4eb1fbeb41f336745d55d6b63e79360d35680c3f7f29f01ec', # WPSv4_netCDF-Fortran_seperate_path.patch + '4c8ac67526c3600a5252f2fe8efbe706a556af1b3f58e206a734f31899fbeee9', # WPS-4.0.2_find-wrfdir.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, versionsuffix), + ('JasPer', '2.0.14'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('zlib', '1.2.11'), + ('libpng', '1.6.34'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch new file mode 100644 index 00000000000..fc1a67d5426 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch @@ -0,0 +1,24 @@ +diff -uNr WPS-4.0.2.orig/arch/preamble WPS-4.0.2/arch/preamble +--- WPS-4.0.2.orig/arch/preamble 2018-11-10 01:13:04.000000000 +0100 ++++ WPS-4.0.2/arch/preamble 2018-11-21 16:42:38.066848290 +0100 +@@ -39,16 +39,16 @@ + # repository, or an older WRF v3.x tar file. + # To override the path to the compiled WRF code, just set the WRF_DIR variable after the "endif" below + # +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0.2), ) # Check for WRF v4.0.2 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0.2), ) # Check for WRF v4.0.2 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0.2 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0.1), ) # Check for WRF v4.0.1 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0.1), ) # Check for WRF v4.0.1 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0.1 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0), ) # Check for WRF v4.0 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0), ) # Check for WRF v4.0 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF), ) # Check for clone of the WRF repository ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF), ) # Check for clone of the WRF repository + WRF_DIR = ../WRF + else # Check for old WRF v3.x directory + WRF_DIR = ../WRFV3 diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPSv4_netCDF-Fortran_seperate_path.patch similarity index 76% rename from easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch rename to easybuild/easyconfigs/w/WPS/WPSv4_netCDF-Fortran_seperate_path.patch index 432299fbcaf..22d13491dfc 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch +++ b/easybuild/easyconfigs/w/WPS/WPSv4_netCDF-Fortran_seperate_path.patch @@ -1,7 +1,7 @@ # Allow netCDF library with separate directories for C and Fortran # ============================================================================ # This patch has been around in EasyBuild since 2013; it was committed by -# @boegel then. +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain diff -uNr WPS.orig/arch/Config.pl WPS/arch/Config.pl --- WPS.orig/arch/Config.pl 2017-07-13 01:16:49.000000000 +0200 @@ -14,9 +14,21 @@ diff -uNr WPS.orig/arch/Config.pl WPS/arch/Config.pl } if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") { -diff -uNr WPS.orig/configure WPS/configure ---- WPS.orig/configure 2017-07-13 01:16:49.000000000 +0200 -+++ WPS/configure 2017-10-05 15:11:12.749218059 +0200 +diff -uNr WPS-4.0.1.orig/arch/preamble WPS-4.0.1.ncff/arch/preamble +--- WPS-4.0.1.orig/arch/preamble 2018-10-02 18:21:14.000000000 +0200 ++++ WPS-4.0.1.ncff/arch/preamble 2018-11-20 17:25:13.005578671 +0100 +@@ -59,7 +59,7 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include -I$(NETCDFF)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ +diff -uNr WPS-4.0.1.orig/configure WPS-4.0.1.ncff/configure +--- WPS-4.0.1.orig/configure 2018-10-02 18:21:14.000000000 +0200 ++++ WPS-4.0.1.ncff/configure 2018-11-20 17:59:14.299417528 +0100 @@ -119,9 +119,14 @@ echo "Will use NETCDF in dir: $NETCDF" # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index 1dce8c20568..da0969fb160 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -13,12 +13,12 @@ source_urls = ['https://github.com/wrf-model/WRF/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ 'WRF_parallel_build_fix.patch', - 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + 'WRFv4_netCDF-Fortran_separate_path.patch', ] checksums = [ 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch - 'c5287268f0f1f4f8816c3384a59ff10649f68ceee11d24238149ea27620f5ba1', # WRF-4.0.1_netCDF-Fortran_separate_path.patch + '3b9b1334b4611f924961008181d0202d2e3160af67d67b2ab5869d0db968cac9', # WRFv4_netCDF-Fortran_separate_path.patch ] # csh is used by WRF install scripts diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb new file mode 100644 index 00000000000..984cd3a1abe --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '4.0.2' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRFv4_netCDF-Fortran_separate_path.patch', +] +checksums = [ + '161637aded4c1b30105cee66d3dee5d0f5bd57a78a4a8704d1dde1734f83a17e', # v4.0.2.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + '3b9b1334b4611f924961008181d0202d2e3160af67d67b2ab5869d0db968cac9', # WRFv4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.20.00')] + +dependencies = [ + ('JasPer', '2.0.14'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch similarity index 90% rename from easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch rename to easybuild/easyconfigs/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch index 3196108ca09..a7527b42d44 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch +++ b/easybuild/easyconfigs/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch @@ -1,11 +1,11 @@ # Allow netCDF library with separate directories for C and Fortran # ============================================================================ # This patch has been around in EasyBuild since WRF3.5; it was committed by -# @boegel then. +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl --- WRF-4.0.1.orig/arch/Config.pl 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/arch/Config.pl 2018-10-25 00:03:03.060958813 +0200 ++++ WRF-4.0.1/arch/Config.pl 2018-11-19 14:20:04.776144494 +0100 @@ -8,6 +8,7 @@ select((select(STDOUT), $|=1)[0]); $sw_perl_path = perl ; @@ -46,7 +46,7 @@ diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; } else { - $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; -+ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; } } else @@ -116,8 +116,8 @@ diff -uNr WRF-4.0.1.orig/arch/postamble WRF-4.0.1/arch/postamble wrfio_grib_share : diff -uNr WRF-4.0.1.orig/configure WRF-4.0.1/configure --- WRF-4.0.1.orig/configure 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/configure 2018-10-19 18:39:36.232467326 +0200 -@@ -183,12 +183,20 @@ ++++ WRF-4.0.1/configure 2018-11-20 12:08:49.040926889 +0100 +@@ -183,10 +183,14 @@ if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then USENETCDFF="-lnetcdff" else @@ -129,19 +129,22 @@ diff -uNr WRF-4.0.1.orig/configure WRF-4.0.1/configure + fi fi - if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then -+ if [ -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then - USENETCDF="-lnetcdf" +- USENETCDF="-lnetcdf" ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then ++ USENETCDF="-lnetcdf" else -- USENETCDF=" " -+ if [ -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then -+ USENETCDF="-L$NETCDF/lib!-L$NETCDF/lib64!-lnetcdf" # ! will be replaced with space -+ else -+ USENETCDF=" " -+ fi + USENETCDF=" " fi - export USENETCDF=$USENETCDF - export USENETCDFF=$USENETCDFF -@@ -629,14 +637,14 @@ +@@ -549,7 +553,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -629,14 +633,14 @@ echo "If you wish to change the default options, edit the file:" echo " arch/configure.defaults" From bbb992f670d43a015e8418651ce288736796d933 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 18 Jan 2019 16:44:05 -0300 Subject: [PATCH 007/468] Configs for horton-2.1.1 and dependencies --- .../horton-2.1.1-foss-2018b-Python-2.7.15.eb | 50 +++++++++++++++++++ .../horton-2.1.1-intel-2018b-Python-2.7.15.eb | 50 +++++++++++++++++++ .../l/Libint/Libint-2.0.3-foss-2018b.eb | 14 ++++++ .../l/Libint/Libint-2.0.3-intel-2018b.eb | 14 ++++++ .../l/libxc/libxc-2.2.3-foss-2018b.eb | 27 ++++++++++ .../l/libxc/libxc-2.2.3-intel-2018b.eb | 30 +++++++++++ 6 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..9ca0c72698a --- /dev/null +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'horton' +version = '2.1.1' + +homepage = 'http://theochem.github.io/horton' +description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written + primarily in the Python programming language. (HORTON is named after the helpful + pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON + is to provide a platform for testing new ideas on the quantum many-body problem + at a reasonable computational cost. Although HORTON is primarily designed to be + a quantum-chemistry program, it can perform computations involving model + Hamiltonians, and could be extended for computations in nuclear physics.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.15' +pyversuffix = '-Python-%s' % pyver +dependencies = [ + ('Python', pyver), + ('h5py', '2.8.0', pyversuffix), + ('matplotlib', '2.2.3', pyversuffix), + ('Libint', '2.0.3'), + ('libxc', '2.2.3'), +] + +prebuildopts = ' '.join([ + 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', + 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', + 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', +]) + +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +#runtest = ' '.join([ +# 'export MATPLOTLIBRC=$PWD;', +# 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', +# '%s python setup.py build_ext -i; ' % prebuildopts, +# 'nosetests -v', +#]) + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..f45e9bb1eef --- /dev/null +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'horton' +version = '2.1.1' + +homepage = 'http://theochem.github.io/horton' +description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written + primarily in the Python programming language. (HORTON is named after the helpful + pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON + is to provide a platform for testing new ideas on the quantum many-body problem + at a reasonable computational cost. Although HORTON is primarily designed to be + a quantum-chemistry program, it can perform computations involving model + Hamiltonians, and could be extended for computations in nuclear physics.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.15' +pyversuffix = '-Python-%s' % pyver +dependencies = [ + ('Python', pyver), + ('h5py', '2.8.0', pyversuffix), + ('matplotlib', '2.2.3', pyversuffix), + ('Libint', '2.0.3'), + ('libxc', '2.2.3'), +] + +prebuildopts = ' '.join([ + 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', + 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', + 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', +]) + +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +#runtest = ' '.join([ +# 'export MATPLOTLIBRC=$PWD;', +# 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', +# '%s python setup.py build_ext -i; ' % prebuildopts, +# 'nosetests -v', +#]) + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb new file mode 100644 index 00000000000..456e6b3c095 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -0,0 +1,14 @@ +name = 'Libint' +version = '2.0.3' + +homepage = 'https://sourceforge.net/p/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +sources = ['libint-%(version)s-stable.tgz'] +source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb new file mode 100644 index 00000000000..329f8d37121 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb @@ -0,0 +1,14 @@ +name = 'Libint' +version = '2.0.3' + +homepage = 'https://sourceforge.net/p/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +sources = ['libint-%(version)s-stable.tgz'] +source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb new file mode 100644 index 00000000000..561661417d2 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb new file mode 100644 index 00000000000..85d607baacc --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +# Tests also fail with Intel Compilers on Haswell when optarch is enabled. +toolchainopts = {'lowopt': True, 'optarch': False} + +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' From 4842ac5b02374bb8cb6ac24de97e2ebd0e45886c Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Wed, 30 Jan 2019 08:13:32 -0300 Subject: [PATCH 008/468] Cleanup and add checksums --- ...2018b-Python-2.7.15.eb => horton-2.1.1-foss-2018b.eb} | 9 +-------- ...018b-Python-2.7.15.eb => horton-2.1.1-intel-2018b.eb} | 9 +-------- .../easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb | 3 ++- .../easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb | 3 ++- 4 files changed, 6 insertions(+), 18 deletions(-) rename easybuild/easyconfigs/h/horton/{horton-2.1.1-foss-2018b-Python-2.7.15.eb => horton-2.1.1-foss-2018b.eb} (84%) rename easybuild/easyconfigs/h/horton/{horton-2.1.1-intel-2018b-Python-2.7.15.eb => horton-2.1.1-intel-2018b.eb} (84%) diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb similarity index 84% rename from easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb rename to easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb index 9ca0c72698a..3bfb0b5491c 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] sources = [SOURCE_TAR_GZ] +checksums = ['13e3381dea62e5877c6cde94515e99c8b7872f0a9498961b0766bdeae4506fe6'] pyver = '2.7.15' pyversuffix = '-Python-%s' % pyver @@ -33,14 +34,6 @@ prebuildopts = ' '.join([ 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', ]) -# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc -#runtest = ' '.join([ -# 'export MATPLOTLIBRC=$PWD;', -# 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', -# '%s python setup.py build_ext -i; ' % prebuildopts, -# 'nosetests -v', -#]) - pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb similarity index 84% rename from easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb rename to easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb index f45e9bb1eef..ec4dd619733 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] sources = [SOURCE_TAR_GZ] +checksums = ['13e3381dea62e5877c6cde94515e99c8b7872f0a9498961b0766bdeae4506fe6'] pyver = '2.7.15' pyversuffix = '-Python-%s' % pyver @@ -33,14 +34,6 @@ prebuildopts = ' '.join([ 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', ]) -# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc -#runtest = ' '.join([ -# 'export MATPLOTLIBRC=$PWD;', -# 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', -# '%s python setup.py build_ext -i; ' % prebuildopts, -# 'nosetests -v', -#]) - pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 456e6b3c095..4ae37c37d5e 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -8,7 +8,8 @@ description = """Libint library is used to evaluate the traditional (electron re toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'pic': True} -sources = ['libint-%(version)s-stable.tgz'] source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] +sources = ['libint-%(version)s-stable.tgz'] +checksums = ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb index 329f8d37121..80ca6acb553 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb @@ -8,7 +8,8 @@ description = """Libint library is used to evaluate the traditional (electron re toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'pic': True} -sources = ['libint-%(version)s-stable.tgz'] source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] +sources = ['libint-%(version)s-stable.tgz'] +checksums = ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'] moduleclass = 'chem' From 7141c090e87fc73ee5989a8eb2518748eda27d5a Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Tue, 12 Feb 2019 12:04:05 +0100 Subject: [PATCH 009/468] Requeted changes in horton eb and other fixes --- ... horton-2.1.1-foss-2018b-Python-2.7.15.eb} | 24 ++++++++++++------- ...horton-2.1.1-intel-2018b-Python-2.7.15.eb} | 24 ++++++++++++------- ...oss-2018b.eb => libxc-2.2.2-foss-2018b.eb} | 4 ++-- ...el-2018b.eb => libxc-2.2.2-intel-2018b.eb} | 4 ++-- 4 files changed, 34 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/h/horton/{horton-2.1.1-foss-2018b.eb => horton-2.1.1-foss-2018b-Python-2.7.15.eb} (66%) rename easybuild/easyconfigs/h/horton/{horton-2.1.1-intel-2018b.eb => horton-2.1.1-intel-2018b-Python-2.7.15.eb} (67%) rename easybuild/easyconfigs/l/libxc/{libxc-2.2.3-foss-2018b.eb => libxc-2.2.2-foss-2018b.eb} (88%) rename easybuild/easyconfigs/l/libxc/{libxc-2.2.3-intel-2018b.eb => libxc-2.2.2-intel-2018b.eb} (90%) diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb similarity index 66% rename from easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb rename to easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb index 3bfb0b5491c..b1b552d8b8d 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'horton' version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://theochem.github.io/horton' description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written @@ -16,16 +17,14 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] sources = [SOURCE_TAR_GZ] -checksums = ['13e3381dea62e5877c6cde94515e99c8b7872f0a9498961b0766bdeae4506fe6'] +checksums = ['4b3f87920d881030ba80f097326a744de2cfee5316aa4499cc9a6501f64b5060'] -pyver = '2.7.15' -pyversuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), - ('h5py', '2.8.0', pyversuffix), - ('matplotlib', '2.2.3', pyversuffix), + ('Python', '2.7.15'), + ('h5py', '2.8.0', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), ('Libint', '2.0.3'), - ('libxc', '2.2.3'), + ('libxc', '2.2.2'), ] prebuildopts = ' '.join([ @@ -34,10 +33,17 @@ prebuildopts = ' '.join([ 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', ]) -pyshortver = '.'.join(pyver.split('.')[:2]) +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +runtest = ' '.join([ + 'export MATPLOTLIBRC=$PWD;', + 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', + '%s python setup.py build_ext -i; ' % prebuildopts, + 'nosetests -v', +]) + sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/horton'], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb similarity index 67% rename from easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb rename to easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb index ec4dd619733..2f77a2c0bf3 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'horton' version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://theochem.github.io/horton' description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written @@ -16,16 +17,14 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] sources = [SOURCE_TAR_GZ] -checksums = ['13e3381dea62e5877c6cde94515e99c8b7872f0a9498961b0766bdeae4506fe6'] +checksums = ['4b3f87920d881030ba80f097326a744de2cfee5316aa4499cc9a6501f64b5060'] -pyver = '2.7.15' -pyversuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), - ('h5py', '2.8.0', pyversuffix), - ('matplotlib', '2.2.3', pyversuffix), + ('Python', '2.7.15'), + ('h5py', '2.8.0', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), ('Libint', '2.0.3'), - ('libxc', '2.2.3'), + ('libxc', '2.2.2'), ] prebuildopts = ' '.join([ @@ -34,10 +33,17 @@ prebuildopts = ' '.join([ 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', ]) -pyshortver = '.'.join(pyver.split('.')[:2]) +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +runtest = ' '.join([ + 'export MATPLOTLIBRC=$PWD;', + 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', + '%s python setup.py build_ext -i; ' % prebuildopts, + 'nosetests -v', +]) + sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/horton'], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb similarity index 88% rename from easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb rename to easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb index 561661417d2..6cd124752b3 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libxc' -version = '2.2.3' +version = '2.2.2' homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] sources = [SOURCE_TAR_GZ] -checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] +checksums = ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'] configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb similarity index 90% rename from easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb rename to easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb index 85d607baacc..5dfa0de3524 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libxc' -version = '2.2.3' +version = '2.2.2' homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. @@ -14,7 +14,7 @@ toolchainopts = {'lowopt': True, 'optarch': False} source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] sources = [SOURCE_TAR_GZ] -checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] +checksums = ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'] configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' From 3156df36464b57c3e133c7fe589ce6ebc1b575d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Feb 2019 10:53:04 +0100 Subject: [PATCH 010/468] add -mno-fma to for Libint 2.0.3 with foss/2018b --- easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 4ae37c37d5e..9a8217520b3 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -12,4 +12,7 @@ source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc' sources = ['libint-%(version)s-stable.tgz'] checksums = ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'] +# need to prevent GCC from emiting FMA instructions due to bugs in include/vector_x86.h for Libint 2.0.x +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -mno-fma" && ' + moduleclass = 'chem' From 1702667b468038cb5e6359f6510090c41ceabda6 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 22 Feb 2019 11:05:40 +0100 Subject: [PATCH 011/468] Patch for FMA issues in Libint --- .../l/Libint/Libint-2.0.3-foss-2018b.eb | 12 ++- .../l/Libint/Libint-2.0.3-stable-fma.patch | 95 +++++++++++++++++++ 2 files changed, 103 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 9a8217520b3..769fd172792 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -10,9 +10,13 @@ toolchainopts = {'pic': True} source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] sources = ['libint-%(version)s-stable.tgz'] -checksums = ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'] - -# need to prevent GCC from emiting FMA instructions due to bugs in include/vector_x86.h for Libint 2.0.x -preconfigopts = 'export CXXFLAGS="$CXXFLAGS -mno-fma" && ' +# Remove some problematic (and not very useful) FMA header code that does not compile with GCC. +# This is done with a patch, because it also affects anything that links against Libint. +# This way, FMA compilert optimization can remain enabled. +patches = ['Libint-2.0.3-stable-fma.patch'] +checksums = [ + '5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02', # libint-2.0.3-stable.tgz + '4db3795818bc37340a45453e8cc9d1d8ab7e08c0c2e9e5b64df2dfc7f0322390', # Libint-2.0.3-stable-fma.patch +] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch new file mode 100644 index 00000000000..bd670511e7c --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch @@ -0,0 +1,95 @@ +--- libint-2.0.3-stable.orig/include/vector_x86.h 2019-02-22 09:16:11.718287697 +0100 ++++ libint-2.0.3-stable/include/vector_x86.h 2019-02-22 09:17:37.628678533 +0100 +@@ -141,30 +141,6 @@ + return c; + } + +-#if defined(__FMA__) +- inline VectorSSEDouble fma_plus(VectorSSEDouble a, VectorSSEDouble b, VectorSSEDouble c) { +- VectorSSEDouble d; +- d.d = _mm_fmadd_pd(a.d, b.d, c.d); +- return d; +- } +- inline VectorSSEDouble fma_minus(VectorSSEDouble a, VectorSSEDouble b, VectorSSEDouble c) { +- VectorSSEDouble d; +- d.d = _mm_fmsub_pd(a.d, b.d, c.d); +- return d; +- } +-#elif defined(__FMA4__) +- inline VectorSSEDouble fma_plus(VectorSSEDouble a, VectorSSEDouble b, VectorSSEDouble c) { +- VectorSSEDouble d; +- d.d = _mm_macc_pd(a.d, b.d, c.d); +- return d; +- } +- inline VectorSSEDouble fma_minus(VectorSSEDouble a, VectorSSEDouble b, VectorSSEDouble c) { +- VectorSSEDouble d; +- d.d = _mm_msub_pd(a.d, b.d, c.d); +- return d; +- } +-#endif +- + //@} + + //@{ standard functions +@@ -365,30 +341,6 @@ + return c; + } + +-#if defined(__FMA__) +- inline VectorSSEFloat fma_plus(VectorSSEFloat a, VectorSSEFloat b, VectorSSEFloat c) { +- VectorSSEFloat d; +- d.d = _mm_fmadd_ps(a.d, b.d, c.d); +- return d; +- } +- inline VectorSSEFloat fma_minus(VectorSSEFloat a, VectorSSEFloat b, VectorSSEFloat c) { +- VectorSSEFloat d; +- d.d = _mm_fmsub_ps(a.d, b.d, c.d); +- return d; +- } +-#elif defined(__FMA4__) +- inline VectorSSEFloat fma_plus(VectorSSEFloat a, VectorSSEFloat b, VectorSSEFloat c) { +- VectorSSEFloat d; +- d.d = _mm_macc_ps(a.d, b.d, c.d); +- return d; +- } +- inline VectorSSEFloat fma_minus(VectorSSEFloat a, VectorSSEFloat b, VectorSSEFloat c) { +- VectorSSEFloat d; +- d.d = _mm_msub_ps(a.d, b.d, c.d); +- return d; +- } +-#endif +- + //@} + + //@{ standard functions +@@ -591,30 +543,6 @@ + return c; + } + +-#if defined(__FMA__) +- inline VectorAVXDouble fma_plus(VectorAVXDouble a, VectorAVXDouble b, VectorAVXDouble c) { +- VectorAVXDouble d; +- d.d = _mm256_fmadd_pd(a.d, b.d, c.d); +- return d; +- } +- inline VectorAVXDouble fma_minus(VectorAVXDouble a, VectorAVXDouble b, VectorAVXDouble c) { +- VectorAVXDouble d; +- d.d = _mm256_fmsub_pd(a.d, b.d, c.d); +- return d; +- } +-#elif defined(__FMA4__) +- inline VectorAVXDouble fma_plus(VectorAVXDouble a, VectorAVXDouble b, VectorAVXDouble c) { +- VectorAVXDouble d; +- d.d = _mm256_facc_pd(a.d, b.d, c.d); +- return d; +- } +- inline VectorAVXDouble fma_minus(VectorAVXDouble a, VectorAVXDouble b, VectorAVXDouble c) { +- VectorAVXDouble d; +- d.d = _mm256_fsub_pd(a.d, b.d, c.d); +- return d; +- } +-#endif +- + //@} + + //@{ standard functions From 271ac25abc26b0e78847e4951d135fe970330605 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 23 Feb 2019 11:40:13 +0100 Subject: [PATCH 012/468] Clean up Libint-2.0.3 config and patch --- easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb | 7 ++----- .../easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch | 3 +++ 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 769fd172792..249cb59796f 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -10,13 +10,10 @@ toolchainopts = {'pic': True} source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] sources = ['libint-%(version)s-stable.tgz'] -# Remove some problematic (and not very useful) FMA header code that does not compile with GCC. -# This is done with a patch, because it also affects anything that links against Libint. -# This way, FMA compilert optimization can remain enabled. -patches = ['Libint-2.0.3-stable-fma.patch'] +patches = ['Libint-%(version)s-stable-fma.patch'] checksums = [ '5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02', # libint-2.0.3-stable.tgz - '4db3795818bc37340a45453e8cc9d1d8ab7e08c0c2e9e5b64df2dfc7f0322390', # Libint-2.0.3-stable-fma.patch + '948388d66e898fb8fdb4964b7852fd7d13999bcfb97339bf8e69ef471ca982b1', # Libint-2.0.3-stable-fma.patch ] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch index bd670511e7c..7ec9c500202 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch @@ -1,3 +1,6 @@ +Remove some problematic (and not very useful) FMA header code that does not compile with GCC. +This is done with a patch, because this problem also affects anything that links against Libint. +This way, FMA compiler optimization can remain enabled. --- libint-2.0.3-stable.orig/include/vector_x86.h 2019-02-22 09:16:11.718287697 +0100 +++ libint-2.0.3-stable/include/vector_x86.h 2019-02-22 09:17:37.628678533 +0100 @@ -141,30 +141,6 @@ From f0dbbe23b3971c3addad87699faade0528888317 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sun, 24 Feb 2019 13:03:09 +0100 Subject: [PATCH 013/468] Add author to patch for Libint --- easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch index 7ec9c500202..9c0ef2eba11 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch @@ -1,6 +1,7 @@ Remove some problematic (and not very useful) FMA header code that does not compile with GCC. This is done with a patch, because this problem also affects anything that links against Libint. This way, FMA compiler optimization can remain enabled. +Author: Toon Verstraelen (UGent, toon.verstraelen@ugent.be) --- libint-2.0.3-stable.orig/include/vector_x86.h 2019-02-22 09:16:11.718287697 +0100 +++ libint-2.0.3-stable/include/vector_x86.h 2019-02-22 09:17:37.628678533 +0100 @@ -141,30 +141,6 @@ From 3115fc1f8892eaba76ec56e83ffc8cc3411ef557 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Mon, 25 Feb 2019 10:27:37 +0100 Subject: [PATCH 014/468] Fix checksum in Libint eb --- easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 249cb59796f..ff6129c1666 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -13,7 +13,7 @@ sources = ['libint-%(version)s-stable.tgz'] patches = ['Libint-%(version)s-stable-fma.patch'] checksums = [ '5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02', # libint-2.0.3-stable.tgz - '948388d66e898fb8fdb4964b7852fd7d13999bcfb97339bf8e69ef471ca982b1', # Libint-2.0.3-stable-fma.patch + 'e8dad3b3da0df26dc64677f56af25923158a2414a4d85b72a8068470d28ced4c', # Libint-2.0.3-stable-fma.patch ] moduleclass = 'chem' From 10619ab314cbfd6914f1fc6df439c34e6f43b5e4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 12 Aug 2019 17:31:33 +0200 Subject: [PATCH 015/468] adding easyconfigs: fiji-20170530.eb, fiji-20190803.eb --- easybuild/easyconfigs/f/fiji/fiji-20170530.eb | 44 ++++++++++++++++++ easybuild/easyconfigs/f/fiji/fiji-20190803.eb | 46 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/f/fiji/fiji-20170530.eb create mode 100644 easybuild/easyconfigs/f/fiji/fiji-20190803.eb diff --git a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb new file mode 100644 index 00000000000..e52698bf09b --- /dev/null +++ b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb @@ -0,0 +1,44 @@ +easyblock = 'PackedBinary' + +name = 'fiji' +version = '20170530' + +homepage = 'https://fiji.sc/' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-1.51n""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://downloads.imagej.net/fiji/Life-Line/'] +sources = ['%(name)s-nojre-%(version)s.zip'] +checksums = ['cf9fb45c48b22a7888b479968477f1f7a300a9c833e47244cbe0d1e93890bd20'] + +dependencies = [('Java', '1.8', '', True)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe,ImageJ-linux32}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' http://sites.imagej.net/Tboudier/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' http://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64. + Plugins can be installed in your $HOME/.plugins folder. + If you need any other update sites to be enabled, please contact support.""" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fiji/fiji-20190803.eb b/easybuild/easyconfigs/f/fiji/fiji-20190803.eb new file mode 100644 index 00000000000..f11e7bb19ca --- /dev/null +++ b/easybuild/easyconfigs/f/fiji/fiji-20190803.eb @@ -0,0 +1,46 @@ +easyblock = 'PackedBinary' + +name = 'fiji' +version = '20190803' + +homepage = 'https://fiji.sc/' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-1.52p and fiji-2.0.0-pre8""" + +toolchain = {'name': 'dummy', 'version': ''} + +# There are no sane releases of fiji, only a tarball of the *latest* version is available. +# Manually download the 'nojre' version and check the versions of ImageJ and fiji in the folder 'jars' +# source_urls = ['https://downloads.imagej.net/fiji/latest/'] +# sources = ['%(name)s-nojre.tar.gz'] +sources = ['%(name)s-nojre-%(version)s.tar.gz'] + +dependencies = [('Java', '1.8', '', True)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe,ImageJ-linux32}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' http://sites.imagej.net/Tboudier/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' http://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64. + Plugins can be installed in your $HOME/.plugins folder. + If you need any other update sites to be enabled, please contact support.""" + +moduleclass = 'vis' From fdd2895f662fe3ea8ad35cd973cf2c6422980752 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 12 Aug 2019 18:05:11 +0200 Subject: [PATCH 016/468] fiji-20190803: Add checksums --- easybuild/easyconfigs/f/fiji/fiji-20190803.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/fiji/fiji-20190803.eb b/easybuild/easyconfigs/f/fiji/fiji-20190803.eb index f11e7bb19ca..06672498902 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20190803.eb +++ b/easybuild/easyconfigs/f/fiji/fiji-20190803.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'dummy', 'version': ''} # source_urls = ['https://downloads.imagej.net/fiji/latest/'] # sources = ['%(name)s-nojre.tar.gz'] sources = ['%(name)s-nojre-%(version)s.tar.gz'] +checksums = ['a0508869dd123727fee0c9a5b91baf504e07686251cd5047d93affd27cab9bfe'] dependencies = [('Java', '1.8', '', True)] From 29d552ae3c99d822881c8a674168b13a8290d948 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 25 Sep 2019 17:45:01 +0200 Subject: [PATCH 017/468] fiji-20170530: add scripts to MATLABPATH and add comment about the available latest release --- easybuild/easyconfigs/f/fiji/fiji-20170530.eb | 6 +++ easybuild/easyconfigs/f/fiji/fiji-20190803.eb | 47 ------------------- 2 files changed, 6 insertions(+), 47 deletions(-) delete mode 100644 easybuild/easyconfigs/f/fiji/fiji-20190803.eb diff --git a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb index e52698bf09b..543d480b185 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb +++ b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb @@ -10,6 +10,10 @@ This release is based on ImageJ-1.51n""" toolchain = {'name': 'dummy', 'version': ''} +# More recent releases of fiji can be found in the non-versioned tarballs available at +# source_urls = ['https://downloads.imagej.net/fiji/latest/'] +# Manually download the 'nojre' version and check the versions of ImageJ and fiji in the folder 'jars' +# sources = ['%(name)s-nojre.tar.gz'] source_urls = ['https://downloads.imagej.net/fiji/Life-Line/'] sources = ['%(name)s-nojre-%(version)s.zip'] checksums = ['cf9fb45c48b22a7888b479968477f1f7a300a9c833e47244cbe0d1e93890bd20'] @@ -37,6 +41,8 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = {'MATLABPATH': 'scripts'} + modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64. Plugins can be installed in your $HOME/.plugins folder. If you need any other update sites to be enabled, please contact support.""" diff --git a/easybuild/easyconfigs/f/fiji/fiji-20190803.eb b/easybuild/easyconfigs/f/fiji/fiji-20190803.eb deleted file mode 100644 index 06672498902..00000000000 --- a/easybuild/easyconfigs/f/fiji/fiji-20190803.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'fiji' -version = '20190803' - -homepage = 'https://fiji.sc/' -description = """Fiji is an image processing package—a 'batteries-included' distribution of - ImageJ, bundling a lot of plugins which facilitate scientific image analysis. -This release is based on ImageJ-1.52p and fiji-2.0.0-pre8""" - -toolchain = {'name': 'dummy', 'version': ''} - -# There are no sane releases of fiji, only a tarball of the *latest* version is available. -# Manually download the 'nojre' version and check the versions of ImageJ and fiji in the folder 'jars' -# source_urls = ['https://downloads.imagej.net/fiji/latest/'] -# sources = ['%(name)s-nojre.tar.gz'] -sources = ['%(name)s-nojre-%(version)s.tar.gz'] -checksums = ['a0508869dd123727fee0c9a5b91baf504e07686251cd5047d93affd27cab9bfe'] - -dependencies = [('Java', '1.8', '', True)] - -postinstallcmds = [ - # Remove binaries for other platforms - 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe,ImageJ-linux32}', - # Enable any update site (edit existing site with same parameters to enable it) - # Full list at https://imagej.github.io/list-of-update-sites/ - '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' - ' https://sites.imagej.net/ImageScience/', - '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' - ' http://sites.imagej.net/Tboudier/', - # Add a new update site - # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' - # ' http://site.url/NewName/', - # Update the installation - '%(installdir)s/ImageJ-linux64 --headless --update update', -] - -sanity_check_paths = { - 'files': ['ImageJ-linux64'], - 'dirs': [], -} - -modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64. - Plugins can be installed in your $HOME/.plugins folder. - If you need any other update sites to be enabled, please contact support.""" - -moduleclass = 'vis' From e790e172cc2a287ba387a4dddbf0e53de246f033 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 25 Sep 2019 17:50:19 +0200 Subject: [PATCH 018/468] fiji-20170530: clarify comments about update sites --- easybuild/easyconfigs/f/fiji/fiji-20170530.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb index 543d480b185..bbe193264bf 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb +++ b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb @@ -23,8 +23,8 @@ dependencies = [('Java', '1.8', '', True)] postinstallcmds = [ # Remove binaries for other platforms 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe,ImageJ-linux32}', - # Enable any update site (edit existing site with same parameters to enable it) - # Full list at https://imagej.github.io/list-of-update-sites/ + # Enable an update site (edit an existing site with same parameters to enable it) + # Full list available at https://imagej.github.io/list-of-update-sites/ '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' ' https://sites.imagej.net/ImageScience/', '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' @@ -43,7 +43,7 @@ sanity_check_paths = { modextrapaths = {'MATLABPATH': 'scripts'} -modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64. +modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64 Plugins can be installed in your $HOME/.plugins folder. If you need any other update sites to be enabled, please contact support.""" From 8ff091470edffcde36f173d6a717f503fdbee78c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 26 Sep 2019 14:54:24 +0200 Subject: [PATCH 019/468] fiji-20170530: switch to SYSTEM toolchain --- easybuild/easyconfigs/f/fiji/fiji-20170530.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb index bbe193264bf..080fb56b339 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb +++ b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb @@ -8,7 +8,7 @@ description = """Fiji is an image processing package—a 'batteries-included' di ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-1.51n""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # More recent releases of fiji can be found in the non-versioned tarballs available at # source_urls = ['https://downloads.imagej.net/fiji/latest/'] From 14531d1de0e48a9280a48f94bafe374a9e40e799 Mon Sep 17 00:00:00 2001 From: alozano Date: Fri, 15 Nov 2019 16:00:48 +0100 Subject: [PATCH 020/468] adding easyconfigs: MACS2-2.2.5-foss-2018b-Python-3.6.6.eb --- .../MACS2-2.2.5-foss-2018b-Python-3.6.6.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..76b791b9366 --- /dev/null +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'MACS2' +version = '2.2.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/taoliu/MACS/' +description = "Model Based Analysis for ChIP-Seq data" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/taoliu/MACS/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2434d5170facaeb7fd59c6a2040e000e49a77bd50767643e3b60996985d0a516'] + +dependencies = [('Python', '3.6.6')] + +options = {'modulename': name} + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/macs2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('%(namelower)s --version')] + +moduleclass = 'bio' From 1b23019e00a5a23d14c48b85415c4a2a7d60d6b3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 18 Nov 2019 11:51:21 +0100 Subject: [PATCH 021/468] adding easyconfigs: CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb, LEMON-1.3.1-GCC-8.2.0-2.31.1.eb --- .../CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb | 43 +++++++++++++++++++ .../l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb | 32 ++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..9df41b2e44a --- /dev/null +++ b/easybuild/easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'CNT-ILP' +version = '20171031' +local_commit = '637029b' + +homepage = 'http://compbio.cs.brown.edu/projects/cnt-ilp/' +description = """ Integer Linear Program for the Copy-Number Tree Problem """ + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/raphael-group/CNT-ILP/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['2798ae15f671f944dd1a5050d28a8475fd94a4a3a598ab936cce1e2dae51cc38'] + +dependencies = [ + ('CPLEX', '12.9'), + ('LEMON', '1.3.1'), +] + +builddependencies = [('CMake', '3.13.3')] + +separate_build_dir = True + +configopts = '-DLIBLEMON_ROOT=$EBROOTLEMON ' +configopts += '-DCPLEX_INC_DIR=$EBROOTCPLEX/cplex/include/ ' +configopts += '-DCPLEX_LIB_DIR=$EBROOTCPLEX/cplex/lib/x86-64_linux/static_pic ' +configopts += '-DCONCERT_INC_DIR=$EBROOTCPLEX/concert/include/ ' +configopts += '-DCONCERT_LIB_DIR=$EBROOTCPLEX/concert/lib/x86-64_linux/static_pic ' +configopts += '-DCMAKE_EXE_LINKER_FLAGS=-ldl ' + +install_cmd = 'mkdir %(installdir)s/bin && cp -a cnt compare visualize %(installdir)s/bin/ && ' +install_cmd += 'cd ../%(name)s-* && cp -a data utils contributors.txt LICENSE.txt README.md %(installdir)s' + +sanity_check_paths = { + 'files': ['bin/cnt', 'bin/compare', 'bin/visualize'], + 'dirs': [], +} + +sanity_check_commands = ['cnt -s 2 %(installdir)s/data/20160430/simC_c1_k4_n10_u1_s1_del02.input'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..5bf9e1fc226 --- /dev/null +++ b/easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'LEMON' +version = '1.3.1' + +homepage = 'https://lemon.cs.elte.hu' +description = """ LEMON stands for Library for Efficient Modeling and Optimization in Networks. + It is a C++ template library providing efficient implementations of common data structures and algorithms + with focus on combinatorial optimization tasks connected mainly with graphs and networks. """ + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://lemon.cs.elte.hu/pub/sources/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['71b7c725f4c0b4a8ccb92eb87b208701586cf7a96156ebd821ca3ed855bad3c8'] + +builddependencies = [('CMake', '3.13.3')] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=TRUE'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['dimacs-solver', 'dimacs-to-lgf', 'lemon-0.x-to-1.x.sh', 'lgf-gen']] + + ['lib/libemon.a', 'lib/libemon.%s' % SHLIB_EXT], + 'dirs': ['include/lemon'], +} + +moduleclass = 'lib' From d737fac5b3f46819424d1e39201240ad3eb97679 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 18 Nov 2019 13:52:58 +0100 Subject: [PATCH 022/468] use https --- .../easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb index 9df41b2e44a..f657288a00a 100644 --- a/easybuild/easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/c/CNT-ILP/CNT-ILP-20171031-GCC-8.2.0-2.31.1.eb @@ -4,7 +4,7 @@ name = 'CNT-ILP' version = '20171031' local_commit = '637029b' -homepage = 'http://compbio.cs.brown.edu/projects/cnt-ilp/' +homepage = 'https://compbio.cs.brown.edu/projects/cnt-ilp/' description = """ Integer Linear Program for the Copy-Number Tree Problem """ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} From ee801a9bcd4a917c191a9107aecde819ffecae3b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 24 Nov 2019 14:34:54 +0100 Subject: [PATCH 023/468] make changes to work with easyblock for SCOOP --- easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb index dff08c16f03..e89b49d0c60 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb @@ -29,8 +29,9 @@ exts_list = [ ('greenlet', '0.4.14', { 'checksums': ['f1cc268a15ade58d9a0c04569fe6613e19b8b0345b64453064e2c3c6d79051af'], }), - ('scoop', version, { - 'patches': ['SCOOP-%(version)s_fix-localhost.patch'], + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'patches': ['%(name)s-%(version)s_fix-localhost.patch'], 'checksums': [ 'd8b6444c7bac901171e3327a97e241dde63f060354e162a65551fd8083ca62b4', # scoop-0.7.1.1.tar.gz '3299c905aefa1b53afa5887361ca6db3ddf31e35739453c7563fc0ecfe9ba97f', # SCOOP-0.7.1.1_fix-localhost.patch From 3b0c45b5999ce17bf12fdabfcf0ce5492af0fca9 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 26 Nov 2019 15:03:25 +0100 Subject: [PATCH 024/468] Add new FSL EasyConfig and patches for FSL-6.0.2. It only runs in conjunction with an updated EasyBlock from this PR https://github.com/easybuilders/easybuild-easyblocks/pull/1860 --- ...-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb | 86 + .../f/FSL/FSL-6.0.2_Build_extras.patch | 11 + .../f/FSL/FSL-6.0.2_Enable_GPU_build.patch | 16 + .../f/FSL/FSL-6.0.2_Makefile_fixes.patch | 245 ++ ....2_probtrackx2_gpu_large_mri_support.patch | 3883 +++++++++++++++++ 5 files changed, 4241 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb new file mode 100644 index 00000000000..475d022425c --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb @@ -0,0 +1,86 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Some tools like icmp are missing since they are built with the fslpython_install.sh script +# which locally installs Miniconda and creates a virtual environment. This is too messy and +# an alternative solution is necessary to install them. +# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 +# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation + +name = 'FSL' +version = '6.0.2' +local_python_suffix = '-Python-2.7.15' +local_CUDA_suffix = '-CUDA-10.0.130' +versionsuffix = '{0}{1}'.format(local_python_suffix, local_CUDA_suffix) + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-6.0.2_Makefile_fixes.patch', + 'FSL-6.0.2_Build_extras.patch', + 'FSL-6.0.1_Melodic-use-ifstream-good.patch', + 'FSL-6.0.2_Enable_GPU_build.patch', + # Fixes https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1911&L=FSL&P=R2783 + 'FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', +] +checksums = [ + 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz + '3a14d9c3ea75d90fa3e4beb5da3cd11a60c6859441acaece02b32ccab6aa278f', # FSL-6.0.2_Makefile_fixes.patch + '2b7ade2146fadbba6c983370bb030ac4e2b11d8bf5259eacc8f3054d3d11003f', # FSL-6.0.2_Build_extras.patch + 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch + '4870f20e84c24331418ea9d5ee67d5ba9cf075bcc85b053d4d8b7a276a96a1a5', # FSL-6.0.2_Enable_GPU_build.patch + # FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch + '05f6ddf6b149e234ea7428bd5b510a72aa8f131a00fda0e369f854b722d88b19', + '4479aa501a7e6e9f1a0063e4ddb680836147ba08673d3fccb9e1db3c4d910672', # FSL-6.0.1_Fix_fsl_exec_script.patch +] + +builddependencies = [ + ('Boost', '1.67.0'), +] + +dependencies = [ + ('libgd', '2.2.5'), + ('libxml2', '2.9.8'), + ('libxml++', '2.40.1'), + ('SQLite', '3.24.0'), + ('libpng', '1.6.34'), + ('Tk', '8.6.8'), + ('NLopt', '2.4.2'), + ('freeglut', '3.0.0'), + ('expat', '2.2.5'), + ('zlib', '1.2.11'), + ('VTK', '8.1.1', local_python_suffix), + ('GSL', '2.5'), + ('Qwt', '6.1.4'), + ('CUDA', '10.0.130'), +] + +# FSLDIR needs to be defined when running postinstall to get the correct shebang +# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 +postinstallcmds = [( + 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH' + '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' +)] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +# Adding the bin from the virtualenv was the only way to get things working... +modextrapaths = { + 'PATH': 'fsl/fslpython/bin', + 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch new file mode 100644 index 00000000000..9f133c9daca --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch @@ -0,0 +1,11 @@ +--- fsl.orig/extras/build 2019-11-15 10:48:52.249162071 +0100 ++++ fsl/extras/build 2019-11-15 17:19:51.859063451 +0100 +@@ -106,6 +106,8 @@ + fi + PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" + PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat" ++# For EasyBuild ++PROJECTS="libgdc libprob libcprob cprob newran ../include/armawrap/dummy_newmat" + for projname in $PROJECTS; do + if [ -d $FSLESRCDIR/$projname ] ; then + buildIt $FSLESRCDIR $projname 1 diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch new file mode 100644 index 00000000000..8c908e9b7b0 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch @@ -0,0 +1,16 @@ +diff -Nru fsl.orig/src/fdt/fslconfig fsl/src/fdt/fslconfig +--- fsl.orig/src/fdt/fslconfig 2019-10-11 13:50:36.336062960 +0200 ++++ fsl/src/fdt/fslconfig 2019-10-11 18:09:38.260806371 +0200 +@@ -1,3 +1 @@ +-if [ `hostname` == "caper.fmrib.ox.ac.uk" -o `hostname` == "jalapeno19.fmrib.ox.ac.uk" ]; then +- export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; +-fi ++export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; +diff -Nru fsl.orig/src/ptx2/fslconfig fsl/src/ptx2/fslconfig +--- fsl.orig/src/ptx2/fslconfig 2019-10-11 13:50:36.310062989 +0200 ++++ fsl/src/ptx2/fslconfig 2019-10-11 18:09:19.874825110 +0200 +@@ -1,3 +1 @@ +-if [ `hostname` == "caper.fmrib.ox.ac.uk" -o `hostname` == "jalapeno19.fmrib.ox.ac.uk" ]; then +- export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; +-fi ++export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch new file mode 100644 index 00000000000..43f133d60ab --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch @@ -0,0 +1,245 @@ +diff -Nru fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk +--- fsl.orig/config/buildSettings.mk 2019-03-20 15:06:00.000000000 +0100 ++++ fsl/config/buildSettings.mk 2019-11-18 18:23:47.688894797 +0100 +@@ -18,7 +18,7 @@ + CHMOD = /bin/chmod + MKDIR = /bin/mkdir + INSTALL = install -p +-TCLSH = ${FSLDIR}/bin/fsltclsh ++TCLSH = tclsh + DEPENDFLAGS = -MM + MACHDBGFLAGS = -g + ##################################################################### +@@ -33,17 +33,17 @@ + LIB_CEPHES = ${FSLEXTLIB} + INC_CEPHES = ${FSLEXTINC}/cephes + # GD library +-LIB_GD = ${FSLEXTLIB} +-INC_GD = ${FSLEXTINC} ++LIB_GD = ${EBROOTLIBGD}/lib ++INC_GD = ${EBROOTLIBGD}/include + # GDC library + LIB_GDC = ${FSLEXTLIB} + INC_GDC = ${FSLEXTINC}/libgdc + # GSL library +-LIB_GSL = ${FSLEXTLIB} +-INC_GSL = ${FSLEXTINC}/gsl ++LIB_GSL = ${EBROOTGSL}/lib ++INC_GSL = ${EBROOTGSL}/include + # PNG library +-LIB_PNG = ${FSLEXTLIB} +-INC_PNG = ${FSLEXTINC} ++LIB_PNG = ${EBROOTLIBPNG}/lib ++INC_PNG = ${EBROOTLIBPNG}/include + # PROB library + LIB_PROB = ${FSLEXTLIB} + INC_PROB = ${FSLEXTINC}/libprob +@@ -54,21 +54,21 @@ + LIB_NEWRAN = ${FSLEXTLIB} + INC_NEWRAN = ${FSLEXTINC}/newran + # BOOST library +-BOOSTDIR = ${FSLEXTINC}/boost +-LIB_BOOST = ${BOOSTDIR} +-INC_BOOST = ${BOOSTDIR} ++BOOSTDIR = ${EBROOTBOOST} ++LIB_BOOST = ${BOOSTDIR}/lib ++INC_BOOST = ${BOOSTDIR}/include + # QWT library +-QWTDIR = /usr/local/qwt ++QWTDIR = ${EBROOTQWT} + INC_QWT = ${QWTDIR}/include + LIB_QWT = ${QWTDIR}/lib + # FFTW3 library +-LIB_FFTW3 = ${FSLEXTLIB} +-INC_FFTW3 = ${FSLEXTINC}/fftw3 ++LIB_FFTW3 = ${EBROOTFFTW}/lib ++INC_FFTW3 = ${EBROOTFFTW}/include + # LIBXML2 library +-INC_XML2 = ${FSLEXTINC}/libxml2 ++INC_XML2 = ${EBROOTLIBXML2}/include + # LIBXML++ library +-INC_XML++ = ${FSLEXTINC}/libxml++-2.6 +-INC_XML++CONF = ${FSLEXTLIB}/libxml++-2.6/include ++INC_XML++ = ${EBROOTLIBXMLPLUSPLUS}/include/libxml++-2.6 ++INC_XML++CONF = ${EBROOTLIBXMLPLUSPLUS}/lib/libxml++-2.6/include + # NEWMAT library/armadillo + INC_NEWMAT = ${FSLEXTINC}/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD + ##################################################################### +@@ -124,16 +124,16 @@ + ##################################################################### + ifeq ($(SYSTYPE), Linux) + ############### System Vars ##################################### +-CC = gcc +-CXX = c++ +-CXX11 = c++ ++CC := ${CC} ++CXX := ${CXX} ++CXX11 := ${CXX} -std=c++11 + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + ARCHFLAGS = -m64 + ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib' + PARALLELFLAGS = -fopenmp +-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} +-GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long ++OPTFLAGS := ${OPTFLAGS} ${ARCHFLAGS} ++GNU_ANSI_FLAGS = -Wall -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn + ANSI_FLAGS = ${GNU_ANSI_FLAGS} + RANLIB = echo +@@ -141,23 +141,23 @@ + # CUDA development environment + CUDAVER := $(or $(CUDAVER),9.1) + #$(info $$CUDAVER is [${CUDAVER}]) +-CUDA_INSTALLATION = /opt/cuda-${CUDAVER} ++CUDA_INSTALLATION := ${EBROOTCUDA} + GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION}) + LIB_CUDA = ${CUDA_INSTALLATION}/lib64 + INC_CUDA = ${CUDA_INSTALLATION}/include + NVCC = ${CUDA_INSTALLATION}/bin/nvcc + ############### External Libs ##################################### + # ZLIB library +-LIB_ZLIB = /lib64 +-INC_ZLIB = /usr/include ++LIB_ZLIB = ${EBROOTZLIB}/lib ++INC_ZLIB = ${EBROOTZLIB}/include + # QT library +-QTDIR = /usr/lib/qt3 ++QTDIR = ${EBROOTQT} + LIB_QT = ${QTDIR}/lib + INC_QT = ${QTDIR}/include + # VTK library +-VTKDIR_INC = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/include/vtk-7.0 +-VTKDIR_LIB = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/lib +-VTKSUFFIX = -7.0 ++VTKDIR_INC = ${EBROOTVTK}/include/vtk-`echo ${EBVERSIONVTK} | cut -f1-2 -d.` ++VTKDIR_LIB = ${EBROOTVTK}/lib ++VTKSUFFIX = -`echo ${EBVERSIONVTK} | cut -f1-2 -d.` + # openblas + LIB_NEWMAT = ${FSLEXTLIB} -lopenblas + # get and then parse gcc version to run context specific builds +diff -Nru fsl.orig/config/common/vars.mk fsl/config/common/vars.mk +--- fsl.orig/config/common/vars.mk 2019-03-20 15:06:00.000000000 +0100 ++++ fsl/config/common/vars.mk 2019-11-18 18:23:11.774679091 +0100 +@@ -24,14 +24,14 @@ + USRCFLAGS = + USRCXXFLAGS = + +-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ++LDFLAGS = ${EBVARLDFLAGS} ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} + +-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ++AccumulatedIncFlags = ${EBVARCPPFLAGS} -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} + +-CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ ++CFLAGS = ${EBVARCFLAGS} ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ + ${AccumulatedIncFlags} + +-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ ++CXXFLAGS = ${EBVARCXXFLAGS} ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ + ${AccumulatedIncFlags} + + HFILES = *.h +diff -Nru fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh +--- fsl.orig/etc/fslconf/fsl.csh 2019-05-20 14:37:06.000000000 +0200 ++++ fsl/etc/fslconf/fsl.csh 2019-11-18 18:23:11.775679125 +0100 +@@ -25,8 +25,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-setenv FSLTCLSH $FSLDIR/bin/fsltclsh +-setenv FSLWISH $FSLDIR/bin/fslwish ++setenv FSLTCLSH tclsh ++setenv FSLWISH wish + + # The following variables are used for running code in parallel across + # several machines ( i.e. for FDT ) +diff -Nru fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh +--- fsl.orig/etc/fslconf/fsl-devel.sh 2019-05-20 14:37:06.000000000 +0200 ++++ fsl/etc/fslconf/fsl-devel.sh 2019-11-18 18:23:11.775679125 +0100 +@@ -26,8 +26,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-FSLTCLSH=$FSLDIR/bin/fsltclsh +-FSLWISH=$FSLDIR/bin/fslwish ++FSLTCLSH=tclsh ++FSLWISH=wish + + export FSLTCLSH FSLWISH + +diff -Nru fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh +--- fsl.orig/etc/fslconf/fsl.sh 2019-05-20 14:37:06.000000000 +0200 ++++ fsl/etc/fslconf/fsl.sh 2019-11-18 18:23:11.775679125 +0100 +@@ -26,8 +26,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-FSLTCLSH=$FSLDIR/bin/fsltclsh +-FSLWISH=$FSLDIR/bin/fslwish ++FSLTCLSH=tclsh ++FSLWISH=wish + + export FSLTCLSH FSLWISH + +diff -Nru fsl.orig/src/film/Makefile fsl/src/film/Makefile +--- fsl.orig/src/film/Makefile 2018-10-01 14:56:21.000000000 +0200 ++++ fsl/src/film/Makefile 2019-11-18 18:23:11.775679125 +0100 +@@ -28,7 +28,7 @@ + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} + + film_gls:${OBJS} film_gls.o +- ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -l giftiio ++ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -lgiftiio + + film_gls_res:${OBJS} film_gls_res.o + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} +diff -Nru fsl.orig/src/fslsurface/Makefile fsl/src/fslsurface/Makefile +--- fsl.orig/src/fslsurface/Makefile 2014-12-16 15:52:05.000000000 +0100 ++++ fsl/src/fslsurface/Makefile 2019-11-18 18:23:11.775679125 +0100 +@@ -37,7 +37,7 @@ + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} + + +-LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass ++LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass -lglapi + + APPLY_ZLIB = -DHAVE_ZLIB + +diff -Nru fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile +--- fsl.orig/src/libmeshutils/Makefile 2014-12-16 15:20:18.000000000 +0100 ++++ fsl/src/libmeshutils/Makefile 2019-11-18 18:23:11.775679125 +0100 +@@ -3,7 +3,7 @@ + + PROJNAME = meshUtils + +-LD_LIBRARY_PATH=${FSLDIR}/lib ++#LD_LIBRARY_PATH=${FSLDIR}/lib + + USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} + USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} +diff -Nru fsl.orig/src/mist-clean/Makefile fsl/src/mist-clean/Makefile +--- fsl.orig/src/mist-clean/Makefile 2019-01-07 15:22:09.000000000 +0100 ++++ fsl/src/mist-clean/Makefile 2019-11-18 18:23:11.775679125 +0100 +@@ -1,16 +1,16 @@ + include ${FSLCONFDIR}/default.mk + +-NLOPT_INC = ${FSLEXTINC} +-NLOPT_LIB = ${FSLEXTLIB} +-SQLITE_INC = ${FSLEXTINC}/libsqlite +-SQLITE_LIB = ${FSLEXTLIB} ++NLOPT_INC = ${EBROOTNLOPT}/include ++NLOPT_LIB = ${EBROOTNLOPT}/lib ++SQLITE_INC = ${EBROOTSQLITE}/include ++SQLITE_LIB = ${EBROOTSQLITE}/lib + + PROJNAME = mist + + XFILES = mist/mist + SCRIPTS = bin/mist_1_train bin/mist_2_fit bin/mist_FA_reg bin/mist_display bin/mist_mesh_utils + +-USRCXXFLAGS = -std=c++11 ++USRCXXFLAGS = -std=c++11 -DBOOST_LOG_DYN_LINK + USRINCFLAGS = -I${FSLDIR}/include/newimage -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_GDC} -I${INC_GD} -I${SQLITE_INC} -I${NLOPT_INC} -I${VTKDIR_INC} -Icommon + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_BOOST} -L${LIB_GDC} -L${LIB_GD} -L${NLOPT_LIB} -L${VTKDIR_LIB} + diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch new file mode 100644 index 00000000000..8d76f676392 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch @@ -0,0 +1,3883 @@ +# This should fix what was described in this thread https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1911&L=FSL&O=D&X=C89E84F6301F100D81&Y=caspar.vanleeuwen%40surfsara.nl&P=96399 +# In addition, I included a change in tractographyInput.cc to explicitely call 'round' from the namespace 'MISCMATHS'. +diff -Nru fsl.orig/src/ptx2/CUDA/intersectionsDevice.cu fsl/src/ptx2/CUDA/intersectionsDevice.cu +--- fsl.orig/src/ptx2/CUDA/intersectionsDevice.cu 2019-11-15 10:47:30.358790161 +0100 ++++ fsl/src/ptx2/CUDA/intersectionsDevice.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include + +diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_gpu.cu +--- fsl.orig/src/ptx2/CUDA/memManager_gpu.cu 2019-11-15 10:47:30.376790024 +0100 ++++ fsl/src/ptx2/CUDA/memManager_gpu.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,70 +4,11 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + +-cudaError_t checkCuda(cudaError_t result){ ++cudaError_t checkCuda(cudaError_t result, const char *msg=NULL){ + if (result != cudaSuccess) { ++ if (msg) fprintf(stderr, "Error: %s\n", msg); + fprintf(stderr, "CUDA Runtime Error: %s\n", + cudaGetErrorString(result)); + exit(1); +@@ -468,62 +409,155 @@ + } + } + ++size_t calculate_mem_required(tractographyData& data_host){ ++ probtrackxOptions& opts =probtrackxOptions::getInstance(); ++ size_t total_mem_required; ++ total_mem_required = sizeof(tractographyData); ++ total_mem_required += data_host.nseeds*3*sizeof(float); // seeds ++ if(opts.network.value()) total_mem_required += data_host.nseeds*sizeof(float); // network ++ total_mem_required += 2*data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float); //mask & lut_vol2mat ++ total_mem_required += 3*data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float); // samples ++ ++ size_t seedVolSize=data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]*sizeof(float); ++ size_t voxFacesIndexSize = (data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int); ++ if(data_host.avoid.NVols) total_mem_required += seedVolSize; ++ if(data_host.avoid.NSurfs){ ++ size_t surfSize = size_t(data_host.avoid.sizesStr[1]*sizeof(float)) + data_host.avoid.sizesStr[2]*sizeof(int) ++ + data_host.avoid.sizesStr[3]*sizeof(int) + voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.stop.NVols) total_mem_required += seedVolSize; ++ if(data_host.stop.NSurfs){ ++ size_t surfSize = size_t(data_host.stop.sizesStr[1]*sizeof(float)) + data_host.stop.sizesStr[2]*sizeof(int) ++ + data_host.stop.sizesStr[3]*sizeof(int) + voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.wtstop.NVols) total_mem_required += data_host.wtstop.NVols * seedVolSize; ++ if(data_host.wtstop.NSurfs){ ++ size_t surfSize = size_t(data_host.wtstop.sizesStr[1]*sizeof(float)) + data_host.wtstop.sizesStr[2]*sizeof(int) ++ + data_host.wtstop.sizesStr[3]*sizeof(int) + data_host.wtstop.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.network.NVols) total_mem_required += data_host.network.NVols * seedVolSize; ++ if(data_host.network.NSurfs){ ++ size_t surfSize = size_t(data_host.network.sizesStr[1]*sizeof(float)) + data_host.network.sizesStr[2]*sizeof(int) ++ + data_host.network.sizesStr[3]*sizeof(int) + data_host.network.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.network.NVols||data_host.network.NSurfs){ ++ total_mem_required += data_host.network.NVols+data_host.network.NSurfs*sizeof(int); ++ } ++ if(data_host.networkREF.NVols) total_mem_required += seedVolSize; ++ if(data_host.networkREF.NSurfs){ ++ size_t surfSize = size_t(data_host.networkREF.sizesStr[1]*sizeof(float)) + data_host.networkREF.sizesStr[2]*sizeof(int) ++ + data_host.networkREF.sizesStr[3]*sizeof(int) + voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.waypoint.NVols) total_mem_required += data_host.waypoint.NVols * seedVolSize; ++ if(data_host.waypoint.NSurfs){ ++ size_t surfSize = size_t(data_host.waypoint.sizesStr[1]*sizeof(float)) + data_host.waypoint.sizesStr[2]*sizeof(int) ++ + data_host.waypoint.sizesStr[3]*sizeof(int) + data_host.waypoint.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.waypoint.NVols||data_host.waypoint.NSurfs){ ++ total_mem_required += data_host.waypoint.NVols+data_host.waypoint.NSurfs*sizeof(int); ++ } ++ if(data_host.targets.NVols) total_mem_required += data_host.targets.NVols * seedVolSize; ++ if(data_host.targets.NSurfs){ ++ size_t surfSize = size_t(data_host.targets.sizesStr[1]*sizeof(float)) + data_host.targets.sizesStr[2]*sizeof(int) ++ + data_host.targets.sizesStr[3]*sizeof(int) + data_host.targets.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.targets.NVols||data_host.targets.NSurfs){ ++ total_mem_required += data_host.targets.NVols+data_host.targets.NSurfs*sizeof(int); ++ } ++ if(data_host.targetsREF.NVols) total_mem_required += seedVolSize; ++ if(data_host.targetsREF.NSurfs){ ++ size_t surfSize = size_t(data_host.targetsREF.sizesStr[1]*sizeof(float)) + data_host.targetsREF.sizesStr[2]*sizeof(int) ++ + data_host.targetsREF.sizesStr[3]*sizeof(int) + voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.lrmatrix1.NVols){ ++ if(opts.matrix2out.value()) ++ total_mem_required += data_host.lrmatrix1.NVols*data_host.M2sizes[0]*data_host.M2sizes[1]*data_host.M2sizes[2]*sizeof(float); ++ else ++ total_mem_required += data_host.lrmatrix1.NVols * seedVolSize; ++ } ++ if(data_host.lrmatrix1.NSurfs){ ++ size_t surfSize = size_t(data_host.lrmatrix1.sizesStr[0]*sizeof(int)) ++ + data_host.lrmatrix1.sizesStr[1]*sizeof(float) + data_host.lrmatrix1.sizesStr[2]*sizeof(int) ++ + data_host.lrmatrix1.sizesStr[3]*sizeof(int) + data_host.lrmatrix1.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.matrix3.NVols) total_mem_required += data_host.matrix3.NVols * seedVolSize; ++ if(data_host.matrix3.NSurfs){ ++ size_t surfSize = size_t(data_host.matrix3.sizesStr[0]*sizeof(int)) ++ + data_host.matrix3.sizesStr[1]*sizeof(float) + data_host.matrix3.sizesStr[2]*sizeof(int) ++ + data_host.matrix3.sizesStr[3]*sizeof(int) + data_host.matrix3.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.lrmatrix3.NVols) total_mem_required += data_host.lrmatrix3.NVols * seedVolSize; ++ if(data_host.lrmatrix3.NSurfs){ ++ size_t surfSize = size_t(data_host.lrmatrix3.sizesStr[0]*sizeof(int)) ++ + data_host.lrmatrix3.sizesStr[1]*sizeof(float) + data_host.lrmatrix3.sizesStr[2]*sizeof(int) ++ + data_host.lrmatrix3.sizesStr[3]*sizeof(int) + data_host.lrmatrix3.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ return total_mem_required; ++} ++ + + void copy_to_gpu( tractographyData& data_host, +- tractographyData*& data_gpu) ++ tractographyData*& data_gpu) + { + probtrackxOptions& opts =probtrackxOptions::getInstance(); + ++ size_t total_mem_required = calculate_mem_required(data_host); ++ cout << "Memory required for allocating data (MB): "<< total_mem_required/1048576 << endl; ++ ++ size_t free,total; ++ cudaMemGetInfo(&free,&total); ++ if(total_mem_required > free){ ++ cout << "Not enough Memory available on device. Exiting ..." << endl; ++ terminate(); ++ } ++ + checkCuda(cudaMalloc((void**)&data_gpu,sizeof(tractographyData))); + checkCuda(cudaMemcpy(data_gpu,&data_host,sizeof(tractographyData),cudaMemcpyHostToDevice)); + + int* auxI; + float* auxF; +- +- // sizes and dims .... now in Constant memory +- ++ + // seeds +- checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*3*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*3*sizeof(float)), "Allocating seeds"); + checkCuda(cudaMemcpy(auxF,data_host.seeds,data_host.nseeds*3*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->seeds,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + if(opts.network.value()){ +- checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*sizeof(float)), "Allocating Network ROIs"); + checkCuda(cudaMemcpy(auxF,data_host.seeds_ROI,data_host.nseeds*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->seeds_ROI,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + // mask +- checkCuda(cudaMalloc((void**)&auxF,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float)), "Allocating mask"); + checkCuda(cudaMemcpy(auxF,data_host.mask,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float),cudaMemcpyHostToDevice)); +- checkCuda(cudaMemcpy(&data_gpu->mask,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMemcpy(&data_gpu->mask,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + // th_samples +- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating th_samples"); + checkCuda(cudaMemcpy(auxF,data_host.thsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); +- checkCuda(cudaMemcpy(&data_gpu->thsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMemcpy(&data_gpu->thsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + // ph_samples +- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating ph_samples"); + checkCuda(cudaMemcpy(auxF,data_host.phsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); +- checkCuda(cudaMemcpy(&data_gpu->phsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMemcpy(&data_gpu->phsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + // f_samples +- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating f_samples"); + checkCuda(cudaMemcpy(auxF,data_host.fsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); +- checkCuda(cudaMemcpy(&data_gpu->fsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMemcpy(&data_gpu->fsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + // lut_vol2mat +- checkCuda(cudaMalloc((void**)&auxI,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int))); ++ checkCuda(cudaMalloc((void**)&auxI,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int)), "Allocating lut_vol2mat"); + checkCuda(cudaMemcpy(auxI,data_host.lut_vol2mat,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lut_vol2mat,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + +- //Seeds_to_DTI...... now in Constant memory +- +- //DTI_to_Seeds...... now in Constant memory +- +- //VOX2MM...... now in Constant memory +- +- //NON-LINEAR ...... now in Constant memory and Texture Memory +- +- //Warp sizes.... now in constant memory +- +- //Sampling Inverse.... now in constant memory +- + //Avoid mask + if(data_host.avoid.NVols){ + checkCuda(cudaMalloc((void**)&auxF,data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]*sizeof(float))); +@@ -531,10 +565,6 @@ + checkCuda(cudaMemcpy(&data_gpu->avoid.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.avoid.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.avoid.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.avoid.locs,data_host.avoid.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->avoid.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); +- // no deed locs + checkCuda(cudaMalloc((void**)&auxF,data_host.avoid.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.avoid.vertices,data_host.avoid.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->avoid.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -555,10 +585,6 @@ + checkCuda(cudaMemcpy(&data_gpu->stop.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.stop.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.stop.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.stop.locs,data_host.stop.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->stop.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); +- // no need locs + checkCuda(cudaMalloc((void**)&auxF,data_host.stop.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.stop.vertices,data_host.stop.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->stop.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -579,10 +605,6 @@ + checkCuda(cudaMemcpy(&data_gpu->wtstop.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.wtstop.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.wtstop.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.wtstop.locs,data_host.wtstop.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->wtstop.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); +- // no need locs + checkCuda(cudaMalloc((void**)&auxF,data_host.wtstop.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.wtstop.vertices,data_host.wtstop.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->wtstop.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -592,8 +614,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.wtstop.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFaces,data_host.wtstop.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->wtstop.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.wtstop.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFacesIndex,(data_host.wtstop.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.wtstop.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFacesIndex,(data_host.wtstop.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->wtstop.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + } + // Network mask +@@ -603,10 +625,6 @@ + checkCuda(cudaMemcpy(&data_gpu->network.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.network.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.network.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.network.locs,data_host.network.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->network.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); +- // no locs + checkCuda(cudaMalloc((void**)&auxF,data_host.network.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.network.vertices,data_host.network.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->network.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -616,8 +634,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.network.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.network.VoxFaces,data_host.network.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->network.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.network.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.network.VoxFacesIndex,(data_host.network.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.network.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.network.VoxFacesIndex,(data_host.network.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->network.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + } + if(data_host.network.NVols||data_host.network.NSurfs){ +@@ -654,9 +672,6 @@ + checkCuda(cudaMemcpy(&data_gpu->waypoint.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.waypoint.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.waypoint.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.waypoint.locs,data_host.waypoint.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->waypoint.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); + checkCuda(cudaMalloc((void**)&auxF,data_host.waypoint.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.waypoint.vertices,data_host.waypoint.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->waypoint.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -666,8 +681,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.waypoint.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFaces,data_host.waypoint.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->waypoint.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.waypoint.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFacesIndex,(data_host.waypoint.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.waypoint.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFacesIndex,(data_host.waypoint.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->waypoint.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + } + if(data_host.waypoint.NVols||data_host.waypoint.NSurfs){ +@@ -692,8 +707,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.targets.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFaces,data_host.targets.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->targets.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.targets.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFacesIndex,(data_host.targets.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.targets.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFacesIndex,(data_host.targets.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->targets.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + } + if(data_host.targets.NVols||data_host.targets.NSurfs){ +@@ -748,8 +763,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.lrmatrix1.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFaces,data_host.lrmatrix1.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lrmatrix1.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix1.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFacesIndex,(data_host.lrmatrix1.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix1.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFacesIndex,(data_host.lrmatrix1.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lrmatrix1.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + //cudaMalloc((void**)&auxI,data_host.lrmatrix1.sizesStr[4]*sizeof(int)); + //cudaMemcpy(auxI,data_host.lrmatrix1.IndexRoi,data_host.lrmatrix1.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); +@@ -774,8 +789,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.matrix3.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFaces,data_host.matrix3.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->matrix3.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.matrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFacesIndex,(data_host.matrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.matrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFacesIndex,(data_host.matrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->matrix3.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + //cudaMalloc((void**)&auxI,data_host.matrix3.sizesStr[4]*sizeof(int)); + //cudaMemcpy(auxI,data_host.matrix3.IndexRoi,data_host.matrix3.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); +@@ -800,8 +815,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.lrmatrix3.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFaces,data_host.lrmatrix3.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lrmatrix3.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFacesIndex,(data_host.lrmatrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFacesIndex,(data_host.lrmatrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lrmatrix3.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + //cudaMalloc((void**)&auxI,data_host.lrmatrix3.sizesStr[4]*sizeof(int)); + //cudaMemcpy(auxI,data_host.lrmatrix3.IndexRoi,data_host.lrmatrix3.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); +diff -Nru fsl.orig/src/ptx2/CUDA/streamlinesDevice.cu fsl/src/ptx2/CUDA/streamlinesDevice.cu +--- fsl.orig/src/ptx2/CUDA/streamlinesDevice.cu 2019-11-15 10:47:30.363790122 +0100 ++++ fsl/src/ptx2/CUDA/streamlinesDevice.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2005 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #define DIVRND 1.00000001f + #define LCRAT 5.0f //box for loopcheck is five times smaller than brain mask +diff -Nru fsl.orig/src/ptx2/CUDA/tractography_CallKernels.cu fsl/src/ptx2/CUDA/tractography_CallKernels.cu +--- fsl.orig/src/ptx2/CUDA/tractography_CallKernels.cu 2019-11-15 10:47:30.381789984 +0100 ++++ fsl/src/ptx2/CUDA/tractography_CallKernels.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + void initialise_SeedsGPU( + curandState*& devStates, +diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.cc fsl/src/ptx2/CUDA/tractographyData.cc +--- fsl.orig/src/ptx2/CUDA/tractographyData.cc 2019-11-15 10:47:30.365790108 +0100 ++++ fsl/src/ptx2/CUDA/tractographyData.cc 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #ifndef EXPOSE_TREACHEROUS + #define EXPOSE_TREACHEROUS 1 +diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.h fsl/src/ptx2/CUDA/tractographyData.h +--- fsl.orig/src/ptx2/CUDA/tractographyData.h 2019-11-15 10:47:30.383789969 +0100 ++++ fsl/src/ptx2/CUDA/tractographyData.h 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + + #ifndef Data_gpu_ptx_H +@@ -99,7 +39,7 @@ + int nvoxels; + int nsamples; + int nfibres; +- int nseeds; ++ size_t nseeds; + int nparticles; + int nsteps; + +diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractography_gpu.cu +--- fsl.orig/src/ptx2/CUDA/tractography_gpu.cu 2019-11-15 10:47:30.374790038 +0100 ++++ fsl/src/ptx2/CUDA/tractography_gpu.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include + #include +@@ -92,7 +32,7 @@ + init_gpu(); + size_t free,total; + cudaMemGetInfo(&free,&total); +- cout << "Free memory at the beginning: "<< free << " ---- Total memory: " << total << "\n"; ++ cout << "Device memory available (MB): "<< free/1048576 << " ---- Total device memory(MB): " << total/1048576 << "\n"; + + probtrackxOptions& opts=probtrackxOptions::getInstance(); + +@@ -103,7 +43,7 @@ + copy_ToTextureMemory(data_host); // Set Texture memory + + cuMemGetInfo(&free,&total); +- cout << "Free memory after copying masks: "<< free << " ---- Total memory: " << total << "\n"; ++ cout << "Device memory available after copying data (MB): "<< free/1048576 << "\n"; + + int MAX_SLs; + int THREADS_STREAM; // MAX_Streamlines and NSTREAMS must be multiples +@@ -219,7 +159,6 @@ + + checkCuda(cudaDeviceSynchronize()); + cuMemGetInfo(&free,&total); +- cout << "Free memory before running iterations: "<< free << " ---- Total memory: " << total << "\n"; + + // run iterations + for(int iter=0;iter0||lengths_host[0][pos+1]>0){ + vector tmp; +- bool included_seed=false; + if(lengths_host[0][pos]>0){ + int posSEED=i*data_host.nsteps*3; + int posCURRENT=0; +@@ -365,12 +303,10 @@ + tmp.push_back(paths_host[0][posSEED+posCURRENT*3+1]); + tmp.push_back(paths_host[0][posSEED+posCURRENT*3+2]); + } +- included_seed=true; + } + if(lengths_host[0][pos+1]>0){ + int pos2=i*data_host.nsteps*3+((data_host.nsteps/2)*3); + int co=0; +- //if(included_seed) co=1; + for(;co0||lengths_host[0][pos+1]>0){ + vector tmp; +- bool included_seed=false; + if(lengths_host[0][pos]>0){ + int posSEED=i*data_host.nsteps*3; + int posCURRENT=0; +@@ -466,12 +401,10 @@ + tmp.push_back(paths_host[0][posSEED+posCURRENT*3+1]); + tmp.push_back(paths_host[0][posSEED+posCURRENT*3+2]); + } +- included_seed=true; + } + if(lengths_host[0][pos+1]>0){ + int pos2=i*data_host.nsteps*3+((data_host.nsteps/2)*3); + int co=0; +- //if(included_seed) co=1; + for(;co + #include +diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractographyInput.cc +--- fsl.orig/src/ptx2/CUDA/tractographyInput.cc 2019-11-15 10:47:30.368790085 +0100 ++++ fsl/src/ptx2/CUDA/tractographyInput.cc 2019-11-15 15:03:45.388788544 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #ifndef EXPOSE_TREACHEROUS + #define EXPOSE_TREACHEROUS +@@ -85,26 +25,15 @@ + coords[1] = MISCMATHS::round(v(2)); + coords[2] = MISCMATHS::round(v(3)); + } +-/*void applycoordchange(Matrix& coordvol, const Matrix& old2new_mat) +-{ +- for (int n=1; n<=coordvol.Nrows(); n++) { +- ColumnVector v(4); +- v << coordvol(n,1) << coordvol(n,2) << coordvol(n,3) << 1.0; +- v = old2new_mat * v; +- coordvol(n,1) = MISCMATHS::round(v(1)); +- coordvol(n,2) = MISCMATHS::round(v(2)); +- coordvol(n,3) = MISCMATHS::round(v(3)); +- } +- }*/ +- +-void tractographyInput::load_mesh( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords) ++ ++void tractographyInput::load_mesh( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { + int type=meshFileType(filename); + if (type==ASCII){ +@@ -119,14 +48,14 @@ + } + } + +-void tractographyInput::load_mesh_ascii( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords) ++void tractographyInput::load_mesh_ascii( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { + // load a freesurfer ascii mesh + ifstream f(filename.c_str()); +@@ -139,10 +68,10 @@ + cerr<<"Loading ascii file: error in the header"<>NVertices>>NFaces; + +- int posV,posF,initV,posLV; ++ size_t posV,posF,initV,posLV; + posV=vertices.size(); // maybe there were some more vertices before + posLV=locs.size(); + initV=posV; +@@ -162,7 +91,7 @@ + values.resize(NVertices); + bool zeros=false; + bool nonzeros=false; +- for (int i=0; i>vertices[posV]>>vertices[posV+1]>>vertices[posV+2]>>values[i]; // write from file to vector + if(values[i]==0) zeros=true; + else nonzeros=true; +@@ -171,30 +100,30 @@ + if (zeros&&nonzeros) allMesh=false; // then some values should be ignored + + // storing locations: use same structure for active-nonactive vertex +- int auxCount=posV-NVertices*3; +- int local_loc=1; +- for (int i=0; i>p0>>p1>>p2>>val; +@@ -208,14 +137,14 @@ + }else {cout<<"Loading ascii file: error opening file: "<& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords) ++void tractographyInput::load_mesh_vtk(string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { + ifstream f(filename.c_str()); + if (f.is_open()){ +@@ -229,9 +158,9 @@ + getline(f,header); + getline(f,header); + getline(f,header); +- int NVertices, NFaces; ++ size_t NVertices, NFaces; + f>>header>>NVertices>>header; +- int posV,posF,initV,posLV; ++ size_t posV,posF,initV,posLV; + posV=vertices.size(); + posLV=locs.size(); + initV=posV; +@@ -241,16 +170,16 @@ + // reading the points + // if is not possible to define values, then all vertices are activated + int local_loc=1; +- for (int i=0; i>vertices[posV]>>vertices[posV+1]>>vertices[posV+2]; + locs[posLV]=nlocs; + if (wcoords){ +- coords.push_back(MISCMATHS::round(vertices[posV])); +- coords.push_back(MISCMATHS::round(vertices[posV+1])); +- coords.push_back(MISCMATHS::round(vertices[posV+2])); +- coords.push_back(nroi); +- coords.push_back(local_loc); +- local_loc++; ++ coords.push_back(MISCMATHS::round(vertices[posV])); ++ coords.push_back(MISCMATHS::round(vertices[posV+1])); ++ coords.push_back(MISCMATHS::round(vertices[posV+2])); ++ coords.push_back(nroi); ++ coords.push_back(local_loc); ++ local_loc++; + } + posV=posV+3; + posLV++; +@@ -261,7 +190,7 @@ + faces.resize(posF+NFaces*3); + + // reading the triangles +- for (int i=0; i>j>>p0>>p1>>p2; +@@ -278,22 +207,22 @@ + } + } + +-void tractographyInput::load_mesh_gifti( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords) ++void tractographyInput::load_mesh_gifti(string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { + fslsurface_name::fslSurface surf; + read_surface(surf,filename); +- int posV,posF,initV,posLV; ++ size_t posV,posF,initV,posLV; + posV=vertices.size(); + posLV=locs.size(); + initV=posV; +- int count=0; ++ size_t count=0; + for (vector< fslsurface_name::vertex >::iterator i= surf.vbegin(); i!= surf.vend();++i){ + vertices.resize(posV+3); + vertices[posV]=i->x; +@@ -326,42 +255,42 @@ + } + if (zeros&&nonzeros) allMesh=false; + int local_loc=1; +- int auxCount=posV-count*3; +- for (int i=0; i& coords) ++ int* Ssizes, ++ float* Vout, ++ int& nlocs, ++ bool reset, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { ++ //reset: if true, it sets -1 voxels not present in mask, ++ //reset must be false if mixed volume: stop / exclusion / targetREF, networkREF + int local_loc=1; + volume tmpvol; + read_volume(tmpvol,filename); + for (int z=0;z=0 && voxX=0 && voxY=0 && voxZ t(1); +- t[0]=j; // this position is relative to this portion of faces !!!!!! +- triangles.push_back(t); // add to set of triangles that cross voxels +- surfvol(voxX,voxY,voxZ)=triangles.size()-1; +- total++; +- }else{ // voxel already labeled as "crossed" +- triangles[val].push_back(j); // add this triangle to the set that cross this voxel +- total++; +- } ++ int val = surfvol(voxX,voxY,voxZ); ++ if (val==-1){ // this voxel hasn't been labeled yet ++ vector t(1); ++ t[0]=j; // this position is relative to this portion of faces !!!!!! ++ triangles.push_back(t); // add to set of triangles that cross voxels ++ surfvol(voxX,voxY,voxZ)=triangles.size()-1; ++ total++; ++ }else{ // voxel already labeled as "crossed" ++ triangles[val].push_back(j); // add this triangle to the set that cross this voxel ++ total++; ++ } + }else{ +- printf("Warning: Ignoring some vertices because they are defined outside the limits\n"); +- printf("Please check that your meshspace is defined correctly\n"); ++ printf("Warning: Ignoring some vertices because they are defined outside the limits\n"); ++ printf("Please check that your meshspace is defined correctly\n"); + } + } + } +@@ -471,41 +404,41 @@ + for (int z=0;z t; +- t.insert(t.end(),triangles[val].begin(),triangles[val].end()); // get position of the triangles (faces) crossed by this voxel +- for (unsigned int i=0;i add initfaces) +- count++; +- } +- voxFacesIndex[index+1]=voxFacesIndex[index]+t.size(); +- }else{ +- voxFacesIndex[index+1]=voxFacesIndex[index]; +- } +- index++; ++ int val = surfvol(x,y,z); ++ if (val!=-1){ ++ vector t; ++ t.insert(t.end(),triangles[val].begin(),triangles[val].end()); // get position of the triangles (faces) crossed by this voxel ++ for (unsigned int i=0;i add initfaces) ++ count++; ++ } ++ voxFacesIndex[index+1]=voxFacesIndex[index]+t.size(); ++ }else{ ++ voxFacesIndex[index+1]=voxFacesIndex[index]; ++ } ++ index++; + } + } + } + } + + void tractographyInput::csv_tri_crossed_voxels( float tri[3][3], +- vector& crossed) ++ vector& crossed) + { +- int minx=(int)round(tri[0][0]); +- int miny=(int)round(tri[0][1]); +- int minz=(int)round(tri[0][2]); ++ int minx=(int)MISCMATHS::round(tri[0][0]); ++ int miny=(int)MISCMATHS::round(tri[0][1]); ++ int minz=(int)MISCMATHS::round(tri[0][2]); + int maxx=minx,maxy=miny,maxz=minz; + crossed.clear(); + int i=0;int tmpi; + do{ +- tmpi=(int)round(tri[i][0]); ++ tmpi=(int)MISCMATHS::round(tri[i][0]); + minx=tmpimaxx?tmpi:maxx; +- tmpi=(int)round(tri[i][1]); ++ tmpi=(int)MISCMATHS::round(tri[i][1]); + miny=tmpimaxy?tmpi:maxy; +- tmpi=(int)round(tri[i][2]); ++ tmpi=(int)MISCMATHS::round(tri[i][2]); + minz=tmpimaxz?tmpi:maxz; + i++; +@@ -516,26 +449,26 @@ + for (int x=minx-s;x<=maxx+s;x+=1){ + for (int y=miny-s;y<=maxy+s;y+=1){ + for (int z=minz-s;z<=maxz+s;z+=1){ +- boxcentre[0]=(float)x; +- boxcentre[1]=(float)y; +- boxcentre[2]=(float)z; +- if (triBoxOverlap(boxcentre,boxhalfsize,tri)){ +- v< voxFacesVec; + vector nullV; + ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; ++ + if (fsl_imageexists(filename)){ + // filename is a volume +- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; +- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); ++ data.volume=new float[sizeVol]; ++ //memset(data.volume,-1,sizeVol*sizeof(float)); + load_volume(filename,Ssizes,data.volume,data.nlocs,true,false,0,nullV); + data.NVols=1; + }else if (meshExists(filename)){ +@@ -567,8 +502,8 @@ + if (fs){ + fs>>tmp; + do{ +- fnames.push_back(tmp); +- fs>>tmp; ++ fnames.push_back(tmp); ++ fs>>tmp; + }while (!fs.eof()); + }else{ + cerr<& refVol, +- // Output +- MaskData& data, +- Matrix& coords) ++void tractographyInput::load_rois( // Input ++ string filename, ++ Matrix mm2vox, ++ float* Sdims, // Or Matrix2 sizes ++ int* Ssizes, ++ int wcoords, ++ volume& refVol, ++ // Output ++ MaskData& data, ++ Matrix& coords) + { ++ //wcoords:0 do not write, 1 write only coords, 2 write also ROI-id and position ++ + data.sizesStr=new int[3]; + data.sizesStr[0]=0; + data.sizesStr[1]=0; +@@ -644,10 +579,12 @@ + vector voxFacesVec; + vector coordsV; + ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; ++ + if (fsl_imageexists(filename)){ + // filename is a volume +- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; +- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); ++ data.volume=new float[sizeVol]; ++ //memset(data.volume,-1,sizeSeed*sizeof(float)); + load_volume(filename,Ssizes,data.volume,data.nlocs,true,wcoords,0,coordsV); + data.NVols=1; + data.IndexRoi=new int[1]; +@@ -655,7 +592,8 @@ + data.sizesStr[4]=1; + }else if (meshExists(filename)){ + load_mesh(filename,verticesVec,facesVec,locsVec,data.nlocs,wcoords,0,coordsV); +- data.VoxFacesIndex=new int[Ssizes[0]*Ssizes[1]*Ssizes[2]+1]; ++ size_t sizeVox2Face = sizeVol+1; ++ data.VoxFacesIndex=new int[sizeVox2Face]; + init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[0],facesVec.size(), + 0,voxFacesVec,data.VoxFacesIndex,locsVec); + data.NSurfs=1; +@@ -670,20 +608,21 @@ + if (fs){ + fs>>tmp; + do{ +- fnames.push_back(tmp); +- if (fsl_imageexists(tmp)) data.NVols++; +- if (meshExists(tmp)) data.NSurfs++; +- fs>>tmp; ++ fnames.push_back(tmp); ++ if (fsl_imageexists(tmp)) data.NVols++; ++ if (meshExists(tmp)) data.NSurfs++; ++ fs>>tmp; + }while (!fs.eof()); + }else{ + cerr<(nv)*sizeVol; ++ load_volume(fnames[i],Ssizes,&data.volume[posSeedvol],data.nlocs,true,wcoords,nroi,coordsV); ++ data.IndexRoi[nv]=nroi; ++ nv++; ++ nroi++; + }else if (meshExists(fnames[i])){ +- load_mesh(fnames[i],verticesVec,facesVec,locsVec,data.nlocs,wcoords,nroi,coordsV); +- init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[lastfacesSize],facesVec.size()-lastfacesSize,lastfacesSize, +- voxFacesVec,&data.VoxFacesIndex[ns*(Ssizes[0]*Ssizes[1]*Ssizes[2]+1)],locsVec); +- data.IndexRoi[data.NVols+ns]=nroi; +- ns++; +- nroi++; +- lastfacesSize=facesVec.size(); ++ size_t posSeedsurf = size_t(ns)*(sizeVol+1); ++ load_mesh(fnames[i],verticesVec,facesVec,locsVec,data.nlocs,wcoords,nroi,coordsV); ++ init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[lastfacesSize],facesVec.size()-lastfacesSize,lastfacesSize, ++ voxFacesVec,&data.VoxFacesIndex[posSeedsurf],locsVec); ++ data.IndexRoi[data.NVols+ns]=nroi; ++ ns++; ++ nroi++; ++ lastfacesSize=facesVec.size(); + }else{ +- cerr<<"load_rois: Unknown file type: "< facesVec, +- // Output +- int* matrix1_locs, +- int* matrix1_idTri, +- int* matrix1_Ntri) ++ int id_vertex, ++ int id_search, ++ vector facesVec, ++ // Output ++ int* matrix1_locs, ++ int* matrix1_idTri, ++ int* matrix1_Ntri) + { + int id=id_search*3; + int num_triangles=0; +@@ -783,21 +721,19 @@ + matrix1_Ntri[id_vertex]=num_triangles; + } + +- +- + void tractographyInput::load_rois_matrix1( tractographyData& tData, +- // Input +- string filename, +- Matrix mm2vox, +- float* Sdims, +- int* Ssizes, +- bool wcoords, +- volume& refVol, +- // Output +- MaskData& data, +- Matrix& coords) ++ // Input ++ string filename, ++ Matrix mm2vox, ++ float* Sdims, ++ int* Ssizes, ++ bool wcoords, ++ volume& refVol, ++ // Output ++ MaskData& data, ++ Matrix& coords) + { +- // a maximum of 12 triangles per seed ? ++ // a maximum of 12 triangles per seed + tData.matrix1_locs=new int[12*tData.nseeds]; + tData.matrix1_idTri=new int[12*tData.nseeds]; + tData.matrix1_Ntri=new int[tData.nseeds]; +@@ -815,10 +751,12 @@ + vector voxFacesVec; + vector coordsV; + ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; ++ + if (fsl_imageexists(filename)){ + // filename is a volume +- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; +- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); ++ data.volume=new float[sizeVol]; ++ //memset(data.volume,-1,sizeVol*sizeof(float)); + load_volume(filename,Ssizes,data.volume,data.nlocs,true,wcoords,0,coordsV); + data.NVols=1; + data.IndexRoi=new int[1]; +@@ -832,7 +770,7 @@ + } + }else if (meshExists(filename)){ + load_mesh(filename,verticesVec,facesVec,locsVec,data.nlocs,wcoords,0,coordsV); +- data.VoxFacesIndex=new int[Ssizes[0]*Ssizes[1]*Ssizes[2]+1]; ++ data.VoxFacesIndex=new int[sizeVol+1]; + init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[0],facesVec.size(), + 0,voxFacesVec,data.VoxFacesIndex,locsVec); + data.NSurfs=1; +@@ -850,20 +788,19 @@ + if (fs){ + fs>>tmp; + do{ +- fnames.push_back(tmp); +- if (fsl_imageexists(tmp)) data.NVols++; +- if (meshExists(tmp)) data.NSurfs++; +- fs>>tmp; ++ fnames.push_back(tmp); ++ if (fsl_imageexists(tmp)) data.NVols++; ++ if (meshExists(tmp)) data.NSurfs++; ++ fs>>tmp; + }while (!fs.eof()); + }else{ + cerr<*& m_prob, +- bool initialize_m_prob, +- volume*& m_prob2, +- bool initialize_m_prob2, +- volume4D*& m_localdir, +- volume& refVol) // reference ++size_t tractographyInput::load_seeds_rois( tractographyData& tData, ++ string seeds_filename, ++ string ref_filename, ++ float* Sdims, ++ int* Ssizes, ++ int convention, ++ float*& seeds, ++ int*& seeds_ROI, ++ Matrix& mm2vox, ++ float* vox2mm, ++ volume*& m_prob, ++ bool initialize_m_prob, ++ volume*& m_prob2, ++ bool initialize_m_prob2, ++ volume4D*& m_localdir, ++ volume& refVol) // reference + { + Log& logger = LogSingleton::getInstance(); + probtrackxOptions& opts=probtrackxOptions::getInstance(); + vector nullV; +- int nseeds=0; ++ size_t nseeds=0; ++ + if (fsl_imageexists(seeds_filename)){ + // a volume file + if(opts.network.value()){ +@@ -981,19 +918,20 @@ + Ssizes[0]=seedsVol.xsize(); + Ssizes[1]=seedsVol.ysize(); + Ssizes[2]=seedsVol.zsize(); ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; + set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); + +- seeds=new float[3*Ssizes[0]*Ssizes[1]*Ssizes[2]]; //max ++ seeds=new float[3*sizeVol]; + for (int z=0;zreinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(refVol,*m_prob); +- *m_prob=0; +- } +- if (initialize_m_prob2){ +- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(refVol,*m_prob2); +- *m_prob2=0; +- } +- if(opts.opathdir.value()){ // OPATHDIR +- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); +- copybasicproperties(refVol,*m_localdir); +- *m_localdir=0; +- } ++ read_volume(refVol,ref_filename); ++ Sdims[0]=refVol.xdim(); ++ Sdims[1]=refVol.ydim(); ++ Sdims[2]=refVol.zdim(); ++ Ssizes[0]=refVol.xsize(); ++ Ssizes[1]=refVol.ysize(); ++ Ssizes[2]=refVol.zsize(); ++ set_vox2mm(convention,Sdims,Ssizes,refVol,mm2vox,vox2mm); ++ if (initialize_m_prob){ ++ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(refVol,*m_prob); ++ *m_prob=0; ++ } ++ if (initialize_m_prob2){ ++ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(refVol,*m_prob2); ++ *m_prob2=0; ++ } ++ if(opts.opathdir.value()){ // OPATHDIR ++ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); ++ copybasicproperties(refVol,*m_localdir); ++ *m_localdir=0; ++ } + }else{ +- cerr<<"Reference volume "< locs; +@@ -1059,38 +997,38 @@ + int loc=0; + float c1,c2,c3; + for (unsigned int vertex=0;vertex>tmp; + do{ +- fnames.push_back(tmp); +- fs>>tmp; ++ fnames.push_back(tmp); ++ fs>>tmp; + }while (!fs.eof()); + }else{ + cerr<<"Seed file "< seedsVol; +- read_volume(seedsVol,fnames[i]); +- if (!found_vol){ +- refVol=seedsVol; +- Sdims[0]=seedsVol.xdim(); +- Sdims[1]=seedsVol.ydim(); +- Sdims[2]=seedsVol.zdim(); +- Ssizes[0]=seedsVol.xsize(); +- Ssizes[1]=seedsVol.ysize(); +- Ssizes[2]=seedsVol.zsize(); +- set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); +- if (initialize_m_prob){ +- m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(seedsVol,*m_prob); +- *m_prob=0; +- } +- if (initialize_m_prob2){ +- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(seedsVol,*m_prob2); +- *m_prob2=0; +- } +- if(opts.opathdir.value()){ // OPATHDIR +- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); +- copybasicproperties(seedsVol,*m_localdir); +- *m_localdir=0; +- } +- }else{ +- if (Sdims[0]!=seedsVol.xdim()||Sdims[1]!=seedsVol.ydim()||Sdims[2]!=seedsVol.zdim()|| +- Ssizes[0]!=seedsVol.xsize()||Ssizes[1]!=seedsVol.ysize()||Ssizes[2]!=seedsVol.zsize()){ +- cerr<<"Seed volumes must have same dimensions"< seedsVol; ++ read_volume(seedsVol,fnames[i]); ++ if (!found_vol){ ++ refVol=seedsVol; ++ Sdims[0]=seedsVol.xdim(); ++ Sdims[1]=seedsVol.ydim(); ++ Sdims[2]=seedsVol.zdim(); ++ Ssizes[0]=seedsVol.xsize(); ++ Ssizes[1]=seedsVol.ysize(); ++ Ssizes[2]=seedsVol.zsize(); ++ set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); ++ if (initialize_m_prob){ ++ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(seedsVol,*m_prob); ++ *m_prob=0; ++ } ++ if (initialize_m_prob2){ ++ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(seedsVol,*m_prob2); ++ *m_prob2=0; ++ } ++ if(opts.opathdir.value()){ // OPATHDIR ++ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); ++ copybasicproperties(seedsVol,*m_localdir); ++ *m_localdir=0; ++ } ++ }else{ ++ if (Sdims[0]!=seedsVol.xdim()||Sdims[1]!=seedsVol.ydim()||Sdims[2]!=seedsVol.zdim()|| ++ Ssizes[0]!=seedsVol.xsize()||Ssizes[1]!=seedsVol.ysize()||Ssizes[2]!=seedsVol.zsize()){ ++ cerr<<"Seed volumes must have same dimensions"<reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(refVol,*m_prob); +- *m_prob=0; +- } +- if (initialize_m_prob2){ +- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(refVol,*m_prob2); +- *m_prob2=0; +- } +- if(opts.opathdir.value()){ // OPATHDIR +- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); +- copybasicproperties(refVol,*m_localdir); +- *m_localdir=0; +- } ++ read_volume(refVol,ref_filename); ++ Sdims[0]=refVol.xdim(); ++ Sdims[1]=refVol.ydim(); ++ Sdims[2]=refVol.zdim(); ++ Ssizes[0]=refVol.xsize(); ++ Ssizes[1]=refVol.ysize(); ++ Ssizes[2]=refVol.zsize(); ++ set_vox2mm(convention,Sdims,Ssizes,refVol,mm2vox,vox2mm); ++ if (initialize_m_prob){ ++ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(refVol,*m_prob); ++ *m_prob=0; ++ } ++ if (initialize_m_prob2){ ++ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(refVol,*m_prob2); ++ *m_prob2=0; ++ } ++ if(opts.opathdir.value()){ // OPATHDIR ++ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); ++ copybasicproperties(refVol,*m_localdir); ++ *m_localdir=0; ++ } + }else{ +- cerr<<"Reference volume "< locs; +- vector vertices; +- vector faces; +- load_mesh(fnames[i],vertices,faces,locs,nlocs,false,0,nullV); +- seedsV.resize(seedsV.size()+vertices.size()*3); +- int loc=0; +- float c1,c2,c3; +- float s1,s2,s3; +- for (unsigned int vertex=0;vertex=0 && s1=0 && s2=0 && s3 seedsVol; +- read_volume(seedsVol,fnames[i]); +- seedsV.resize(seedsV.size()+3*Ssizes[0]*Ssizes[1]*Ssizes[2]); //max +- for (int z=0;z locs; ++ vector vertices; ++ vector faces; ++ load_mesh(fnames[i],vertices,faces,locs,nlocs,false,0,nullV); ++ seedsV.resize(seedsV.size()+vertices.size()*3); ++ int loc=0; ++ float c1,c2,c3; ++ float s1,s2,s3; ++ for (unsigned int vertex=0;vertex=0 && s1=0 && s2=0 && s3 seedsVol; ++ read_volume(seedsVol,fnames[i]); ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; ++ seedsV.resize(seedsV.size()+3*sizeVol); //max ++ for (int z=0;z vol, +- Matrix& mm2vox, +- float* vox2mm) ++void tractographyInput::set_vox2mm(int convention, ++ float* Sdims, ++ int* Ssizes, ++ volume vol, ++ Matrix& mm2vox, ++ float* vox2mm) + { + // VOX2MM + Matrix Mvox2mm(4,4); +@@ -1315,9 +1253,9 @@ + // freesurfer + Matrix mat(4,4); + mat << -1/Sdims[0] << 0 << 0 << Ssizes[0]/2 +- << 0 << 0 << -1/Sdims[1] << Ssizes[2]/2 +- << 0 << 1/Sdims[2] << 0 << Ssizes[1]/2 +- << 0 << 0 << 0 << 1; ++ << 0 << 0 << -1/Sdims[1] << Ssizes[2]/2 ++ << 0 << 1/Sdims[2] << 0 << Ssizes[1]/2 ++ << 0 << 0 << 0 << 1; + mm2vox=mat; + Mvox2mm=mm2vox.i(); + }else if (convention==2){ +@@ -1349,25 +1287,26 @@ + vox2mm[12]=Mvox2mm(4,1); vox2mm[13]=Mvox2mm(4,2); vox2mm[14]=Mvox2mm(4,3); vox2mm[15]=Mvox2mm(4,4); + } + +-void tractographyInput::load_tractographyData( tractographyData& tData, +- volume*& m_prob, +- volume*& m_prob2, +- float**& ConNet, +- float**& ConNetb, +- int& nRowsNet, +- int& nColsNet, +- float**& ConMat1, +- float**& ConMat1b, +- int& nRowsMat1, +- int& nColsMat1, +- float**& ConMat3, +- float**& ConMat3b, +- int& nRowsMat3, +- int& nColsMat3, +- float*& m_s2targets, +- float*& m_s2targetsb, +- volume4D*& m_localdir) ++void tractographyInput::load_tractographyData(tractographyData& tData, ++ volume*& m_prob, ++ volume*& m_prob2, ++ float**& ConNet, ++ float**& ConNetb, ++ int& nRowsNet, ++ int& nColsNet, ++ float**& ConMat1, ++ float**& ConMat1b, ++ int& nRowsMat1, ++ int& nColsMat1, ++ float**& ConMat3, ++ float**& ConMat3b, ++ int& nRowsMat3, ++ int& nColsMat3, ++ float*& m_s2targets, ++ float*& m_s2targetsb, ++ volume4D*& m_localdir) + { ++ printf("Loading tractography data\n"); + probtrackxOptions& opts=probtrackxOptions::getInstance(); + Log& logger = LogSingleton::getInstance(); + +@@ -1427,7 +1366,7 @@ + for(int z=0;z0){ +- read_volume4D(tmpvol,basename+"_th"+num2str(f+1)+"samples"); +- tmpmat=tmpvol.matrix(mask3D); ++ read_volume4D(tmpvol,basename+"_th"+num2str(f+1)+"samples"); ++ tmpmat=tmpvol.matrix(mask3D); + } + for(int s=0;s Seeds transform needed" << endl; +- exit(1); ++ cerr << "TRACT::Streamliner:: DTI -> Seeds transform needed" << endl; ++ exit(1); + } + FnirtFileReader iffr(opts.dti_to_seeds.value()); + volume4D DTISeedwarp4D = iffr.FieldAsNewimageVolume4D(true); +@@ -1653,13 +1593,13 @@ + tData.Warp_D2S_sizes[2]=DTISeedwarp4D.zsize(); + tData.DTISeedwarp = new float[3*size]; + for(int v=0;v<3;v++){ +- for(int z=0;z + #include +@@ -83,84 +23,84 @@ + + /// Method load all the necessary data from the input files to perform GPU Tractography + void load_tractographyData( tractographyData& tData, +- volume*& m_prob, +- volume*& m_prob2, +- float**& ConNet, +- float**& ConNetb, +- int& nRowsNet, +- int& nColsNet, +- float**& ConMat1, +- float**& ConMat1b, +- int& nRowsMat1, +- int& nColsMat1, +- float**& ConMat3, +- float**& ConMat3b, +- int& nRowsMat3, +- int& nColsMat3, +- float*& m_s2targets, +- float*& m_s2targetsb, +- volume4D*& m_localdir); ++ volume*& m_prob, ++ volume*& m_prob2, ++ float**& ConNet, ++ float**& ConNetb, ++ int& nRowsNet, ++ int& nColsNet, ++ float**& ConMat1, ++ float**& ConMat1b, ++ int& nRowsMat1, ++ int& nColsMat1, ++ float**& ConMat3, ++ float**& ConMat3b, ++ int& nRowsMat3, ++ int& nColsMat3, ++ float*& m_s2targets, ++ float*& m_s2targetsb, ++ volume4D*& m_localdir); + + /// General Method to read a Surface file in ASCII, VTK or GIFTI format +- void load_mesh( string& filename, +- vector& vertices, // all the vertices, same order than file +- vector& faces, // all the faces, same order than file +- vector& locs, // used to store the id of a vertex in the Matrix. If -1, then vertex is non-activated +- int& nlocs, // number of ids(vertices) in the Matrix +- bool wcoords, // save coordinates of the vertices in a file ? +- int nroi, // number of ROI to identify coordinates +- vector& coords); // coordinates xyz of the vertices ++ void load_mesh( string& filename, ++ vector& vertices, // all the vertices, same order than file ++ vector& faces, // all the faces, same order than file ++ vector& locs, // used to store the id of a vertex in the Matrix. If -1, then vertex is non-activated ++ int& nlocs, // number of ids(vertices) in the Matrix ++ bool wcoords, // save coordinates of the vertices in a file ? ++ int nroi, // number of ROI to identify coordinates ++ vector& coords); // coordinates xyz of the vertices + + /// Method to read a surface file in ASCII format +- void load_mesh_ascii( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords); ++ void load_mesh_ascii( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords); + + /// Method to read a surface file in VTK format +- void load_mesh_vtk( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords); ++ void load_mesh_vtk( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords); + + /// Method to read a surface file in GIFTI format +- void load_mesh_gifti( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords); ++ void load_mesh_gifti( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords); + + /// Method to read a Volume + void load_volume( string& filename, +- int* Ssizes, +- float* Vout, +- int& nlocs, +- bool reset, +- bool wcoords, +- int nroi, +- vector& coords); ++ int* Ssizes, ++ float* Vout, ++ int& nlocs, ++ bool reset, ++ bool wcoords, ++ int nroi, ++ vector& coords); + + /// Method to initialise the realtionship between voxels and triangles for a Surface +- void init_surfvol( int* Ssizes, +- Matrix& mm2vox, +- vector& vertices, +- int* faces, +- int sizefaces, // number of faces this time (maybe there are several ROIs for the same mask) +- int initfaces, // number of faces in previos times +- vector& voxFaces, // list of faces of all the voxels +- int* voxFacesIndex, // starting point of each voxel in the list +- vector& locsV); ++ void init_surfvol( int* Ssizes, ++ Matrix& mm2vox, ++ vector& vertices, ++ int* faces, ++ int sizefaces, // number of faces this time (maybe there are several ROIs for the same mask) ++ int initfaces, // number of faces in previos times ++ vector& voxFaces, // list of faces of all the voxels ++ int* voxFacesIndex, // starting point of each voxel in the list ++ vector& locsV); + + /// Method to find out what voxels are crossed by a triangle + void csv_tri_crossed_voxels(float tri[3][3], +@@ -168,62 +108,62 @@ + + /// Method to read all the ROIs of a mask in the same structure: for stop and avoid masks + void load_rois_mixed(string filename, +- Matrix mm2vox, +- float* Sdims, +- int* Ssizes, +- // Output +- MaskData& matData); ++ Matrix mm2vox, ++ float* Sdims, ++ int* Ssizes, ++ // Output ++ MaskData& matData); + + /// Method to read the ROIs of a mask in concatenated structures: for wtstop and waypoints masks +- void load_rois(// Input +- string filename, +- Matrix mm2vox, +- float* Sdims, +- int* Ssizes, +- int wcoords, +- volume& refVol, +- // Output +- MaskData& matData, +- Matrix& coords); ++ void load_rois( // Input ++ string filename, ++ Matrix mm2vox, ++ float* Sdims, ++ int* Ssizes, ++ int wcoords, ++ volume& refVol, ++ // Output ++ MaskData& matData, ++ Matrix& coords); + + /// Same than load_rois but it includes the initialisation of the rows (including triangles) of Matrix1 + void load_rois_matrix1( tractographyData& tData, +- // Input +- string filename, +- Matrix mm2vox, +- float* Sdims, +- int* Ssizes, +- bool wcoords, +- volume& refVol, +- // Output +- MaskData& data, +- Matrix& coords); ++ // Input ++ string filename, ++ Matrix mm2vox, ++ float* Sdims, ++ int* Ssizes, ++ bool wcoords, ++ volume& refVol, ++ // Output ++ MaskData& data, ++ Matrix& coords); + + /// Method to load the seeds. Can be defined by volumes and/or by surfaces +- int load_seeds_rois(tractographyData& tData, +- string seeds_filename, +- string ref_filename, +- float* Sdims, +- int* Ssizes, +- int convention, +- float*& seeds, +- int*& seeds_ROI, +- Matrix& mm2vox, +- float* vox2mm, +- volume*& m_prob, +- bool initialize_m_prob, +- volume*& m_prob2, +- bool initialize_m_prob2, +- volume4D*& m_localdir, +- volume& refVol); ++ size_t load_seeds_rois(tractographyData& tData, ++ string seeds_filename, ++ string ref_filename, ++ float* Sdims, ++ int* Ssizes, ++ int convention, ++ float*& seeds, ++ int*& seeds_ROI, ++ Matrix& mm2vox, ++ float* vox2mm, ++ volume*& m_prob, ++ bool initialize_m_prob, ++ volume*& m_prob2, ++ bool initialize_m_prob2, ++ volume4D*& m_localdir, ++ volume& refVol); + + /// Method to set the transformation: voxel to milimeters +- void set_vox2mm(int convention, +- float* Sdims, +- int* Ssizes, +- volume vol, +- Matrix& mm2vox, // 4x4 +- float* vox2mm); // 4x4 ++ void set_vox2mm(int convention, ++ float* Sdims, ++ int* Ssizes, ++ volume vol, ++ Matrix& mm2vox, // 4x4 ++ float* vox2mm); // 4x4 + + }; + +diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tractographyKernels.cu +--- fsl.orig/src/ptx2/CUDA/tractographyKernels.cu 2019-11-15 10:47:30.371790061 +0100 ++++ fsl/src/ptx2/CUDA/tractographyKernels.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include + #include +@@ -77,17 +17,17 @@ + + template + __global__ void get_path_kernel( +- tractographyData* data_gpu, +- const int maxThread, ++ tractographyData* data_gpu, ++ const int maxThread, + //essential +- curandState* state, +- const long long offset, ++ curandState* state, ++ const long long offset, + //loopcheck +- int* loopcheckkeys, +- float3* loopcheckdirs, ++ int* loopcheckkeys, ++ float3* loopcheckdirs, + //OUTPUT +- float* path, +- int* lengths) ++ float* path, ++ int* lengths) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -124,13 +64,15 @@ + + // Use path to store my intial coordinates + // We want to start at the same exact point, even if sampvox is activated +- path[id*data_gpu->nsteps*3]= data_gpu->seeds[numseed*3]; +- path[id*data_gpu->nsteps*3+1]= data_gpu->seeds[numseed*3+1]; +- path[id*data_gpu->nsteps*3+2]= data_gpu->seeds[numseed*3+2]; +- +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]= data_gpu->seeds[numseed*3]; +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+1]= data_gpu->seeds[numseed*3+1]; +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+2]= data_gpu->seeds[numseed*3+2]; ++ uint offset_path_fw = id*data_gpu->nsteps*3; ++ uint offset_path_bw = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ path[offset_path_fw]= data_gpu->seeds[numseed*3]; ++ path[offset_path_fw+1]= data_gpu->seeds[numseed*3+1]; ++ path[offset_path_fw+2]= data_gpu->seeds[numseed*3+2]; ++ ++ path[offset_path_bw]= data_gpu->seeds[numseed*3]; ++ path[offset_path_bw+1]= data_gpu->seeds[numseed*3+1]; ++ path[offset_path_bw+2]= data_gpu->seeds[numseed*3+2]; + + + if(data_gpu->sampvox>0){ +@@ -145,13 +87,13 @@ + rej=false; + } + +- path[id*data_gpu->nsteps*3]+=dx/C_Sdims[0]; +- path[id*data_gpu->nsteps*3+1]+=dy/C_Sdims[1]; +- path[id*data_gpu->nsteps*3+2]+=dz/C_Sdims[2]; +- +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]+=dx/C_Sdims[0]; +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+1]+=dy/C_Sdims[1]; +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+2]+=dz/C_Sdims[2]; ++ path[offset_path_fw]+=dx/C_Sdims[0]; ++ path[offset_path_fw+1]+=dy/C_Sdims[1]; ++ path[offset_path_fw+2]+=dz/C_Sdims[2]; ++ ++ path[offset_path_bw]+=dx/C_Sdims[0]; ++ path[offset_path_bw+1]+=dy/C_Sdims[1]; ++ path[offset_path_bw+2]+=dz/C_Sdims[2]; + } + // track in one direction + lengths[id*2]=streamline(data_gpu, +@@ -161,7 +103,7 @@ + &partRx[threadIdx.x],&partRy[threadIdx.x],&partRz[threadIdx.x], + &memSH_a[threadIdx.x],&memSH_b[threadIdx.x],&memSH_c[threadIdx.x], + &memSH_d[threadIdx.x],&memSH_e[threadIdx.x],&memSH_f[threadIdx.x], +- &path[id*data_gpu->nsteps*3],part_init,part_has_jumped); ++ &path[offset_path_fw],part_init,part_has_jumped); + + // track in the other direction + lengths[id*2+1]=streamline(data_gpu, +@@ -171,7 +113,7 @@ + &partRx[threadIdx.x],&partRy[threadIdx.x],&partRz[threadIdx.x], + &memSH_a[threadIdx.x],&memSH_b[threadIdx.x],&memSH_c[threadIdx.x], + &memSH_d[threadIdx.x],&memSH_e[threadIdx.x],&memSH_f[threadIdx.x], +- &path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)],part_init,part_has_jumped); ++ &path[offset_path_bw],part_init,part_has_jumped); + + state[id]=localState; // save state, otherwise random numbers will be repeated (start at the same point) + } +@@ -180,11 +122,11 @@ + /////// AVOID MASK /////// + ///////////////////////// + template +-__global__ void avoid_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- //INPUT-OUTPUT +- float* paths, +- int* lengths) ++__global__ void avoid_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ //INPUT-OUTPUT ++ float* paths, ++ int* lengths) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -199,7 +141,8 @@ + /////////////////////// + ////// ONE WAY //////// + /////////////////////// +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + int2 rejflag; + +@@ -253,8 +196,9 @@ + /////////////////////// + ////// OTHER WAY ///// + /////////////////////// +- rejflag.y=0; +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ rejflag.y=0; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + segmentAx[threadIdx.x]=mypath[0]; +@@ -313,11 +257,11 @@ + /////// STOP MASK /////// + ///////////////////////// + template +-__global__ void stop_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- // INPUT-OUTPUT +- float* paths, +- int* lengths) // num of coordinates ++__global__ void stop_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ // INPUT-OUTPUT ++ float* paths, ++ int* lengths) // num of coordinates + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -333,7 +277,8 @@ + /////////////////////// + ////// ONE WAY //////// + /////////////////////// +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + segmentAx[threadIdx.x]=mypath[0]; + segmentAy[threadIdx.x]=mypath[1]; +@@ -387,8 +332,9 @@ + } + /////////////////////// + ////// OTHER WAY ///// +- /////////////////////// +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ /////////////////////// ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + segmentAx[threadIdx.x]=mypath[0]; +@@ -454,11 +400,11 @@ + // ignoring forcefirststep ... if seed is inside wtstop: is treated + + template +-__global__ void wtstop_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- // INPUT-OUTPUT +- float* paths, +- int* lengths) ++__global__ void wtstop_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ // INPUT-OUTPUT ++ float* paths, ++ int* lengths) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -480,7 +426,8 @@ + ///////////////// + //// ONE WAY //// + ///////////////// +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + bool wtstop=false; + // set flags to 1 (still not in roi) +@@ -546,7 +493,8 @@ + //////////////////// + //// OTHER WAY ///// + //////////////////// +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + wtstop=false; + // set flags to 1 (still not in roi) +@@ -615,11 +563,11 @@ + /////// WAYPOINTS MASK //////// + /////////////////////////////// + template +-__global__ void way_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- // INNPUT-OUTPUT +- float* paths, +- int* lengths) ++__global__ void way_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ // INNPUT-OUTPUT ++ float* paths, ++ int* lengths) + { + ///// DYNAMIC SHARED MEMORY ///// + extern __shared__ float shared[]; +@@ -634,7 +582,8 @@ + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; + +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + + int numpassed=0; +@@ -745,7 +694,8 @@ + numpassed=0; + order=true; + } +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + if(waySurf){ +@@ -841,18 +791,17 @@ + ///////////////////////////// + template + // savelength 0: no --pd, nor --ompl | 1: --pd | 2: --ompl (ConNet pathlengths, ConNetb binary hits, and later calculates mean) +-__global__ void net_masks_kernel( +- tractographyData* data_gpu, +- const int maxThread, +- const long long offset, +- // INNPUT-OUTPUT +- float* paths, +- int* lengths, +- float* ConNet, +- float* ConNetb, +- // To use in case too many Net ROIs +- float* net_flags_Global, +- float* net_values_Global) ++__global__ void net_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ const long long offset, ++ // INNPUT-OUTPUT ++ float* paths, ++ int* lengths, ++ float* ConNet, ++ float* ConNetb, ++ // To use in case too many Net ROIs ++ float* net_flags_Global, ++ float* net_values_Global) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -887,7 +836,8 @@ + int numseed = (offset+id)/data_gpu->nparticles; + int ROI = data_gpu->seeds_ROI[numseed]; + +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + int numpassed=1; // count my own ROI + +@@ -987,7 +937,8 @@ + net_flags[ROI]=1; // my own ROI + numpassed=1; // count my own ROI + +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + if(netSurf){ +@@ -1092,16 +1043,16 @@ + ///////////////////////////// + template + // savelength 0: no --pd or --ompl | 1: --pd | 2: --ompl +-__global__ void targets_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- const long long offset, +- // INNPUT-OUTPUT +- float* paths, +- int* lengths, +- float* s2targets_gpu, // a values for each Seed and for each target (Nseeds x NTragets) +- float* s2targetsb_gpu, +- // To use in case too many Net ROIs +- float* targ_flags_Global) ++__global__ void targets_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ const long long offset, ++ // INNPUT-OUTPUT ++ float* paths, ++ int* lengths, ++ float* s2targets_gpu, // (Nseeds x NTargets) ++ float* s2targetsb_gpu, ++ // To use in case too many Net ROIs ++ float* targ_flags_Global) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -1127,7 +1078,8 @@ + targ_flags = &targ_flags_Global[id*totalTargets]; + } + +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + + for(int i=0;isteplength; +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + if(targSurf){ +@@ -1289,16 +1242,16 @@ + /////// MATRIX MASKs ///////// + /////////////////////////////// + template // M2 is for Matrix2: it can be defined in a different space +-__global__ void matrix_kernel( tractographyData* data_gpu, +- const int maxThread, +- float* paths, +- int* lengths, +- bool pathdist, +- bool omeanpathlength, +- MaskData* matrixData, // info vols & surfs +- // OUTPUT +- float3* crossed, +- int* numcrossed) ++__global__ void matrix_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ float* paths, ++ int* lengths, ++ bool pathdist, ++ bool omeanpathlength, ++ MaskData* matrixData, // info vols & surfs ++ // OUTPUT ++ float3* crossed, ++ int* numcrossed) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -1331,7 +1284,8 @@ + ///////////////// + //// ONE WAY //// + ///////////////// +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + if(HSurfs){ + if(M2){ + vox_to_vox_S2M2(mypath,&segmentAx[threadIdx.x],&segmentAy[threadIdx.x],&segmentAz[threadIdx.x]); +@@ -1388,7 +1342,8 @@ + if(pathdist||omeanpathlength) pathlength=-data_gpu->steplength; // it starts with the second coordinate of the path + // reverse, m_tracksign !! . If different directions when crossing 2 nodes, then the path distance is longer. + +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + if(HSurfs){ + if(M2){ +@@ -1444,21 +1399,22 @@ + ///////// UPDATE PATHS VOLUME /////// + ///////////////////////////////////// + template +-__global__ void update_path_kernel( tractographyData* data_gpu, +- const int maxThread, +- float* path, +- int* lengths, +- int* beenhere, +- const int upper_limit, +- // OUTPUT +- float* m_prob, +- float* m_prob2, // for omeanpathlength +- float* m_localdir) // for opathdir ++__global__ void update_path_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ float* path, ++ int* lengths, ++ int* beenhere, ++ const int upper_limit, ++ // OUTPUT ++ float* m_prob, ++ float* m_prob2, // for omeanpathlength ++ float* m_localdir) // for opathdir + { + int id = threadIdx.x + blockIdx.x*blockDim.x; + if(id>=maxThread) return; + +- float* mypath = &path[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath = &path[offset_path]; + int mylength = lengths[id*2]; + int* m_beenhere = &beenhere[id*(data_gpu->nsteps)]; + int coordinatex,coordinatey,coordinatez; +@@ -1555,7 +1511,8 @@ + } + + // other way +- mypath = &path[id*data_gpu->nsteps*3+(data_gpu->nsteps/2)*3]; ++ offset_path = id*data_gpu->nsteps*3+(data_gpu->nsteps/2)*3; ++ mypath = &path[offset_path]; + mylength = lengths[id*2+1]; + pathlength=0.0f; + +diff -Nru fsl.orig/src/ptx2/CUDA/transformationsDevice.cu fsl/src/ptx2/CUDA/transformationsDevice.cu +--- fsl.orig/src/ptx2/CUDA/transformationsDevice.cu 2019-11-15 10:47:30.379790000 +0100 ++++ fsl/src/ptx2/CUDA/transformationsDevice.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2005 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + __constant__ float C_Sdims[3]; + __constant__ float C_Ddims[3]; +diff -Nru fsl.orig/src/ptx2/probtrackx_gpu.cc fsl/src/ptx2/probtrackx_gpu.cc +--- fsl.orig/src/ptx2/probtrackx_gpu.cc 2019-11-15 10:47:30.549788697 +0100 ++++ fsl/src/ptx2/probtrackx_gpu.cc 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include "probtrackx.h" + #include "saveResults_ptxGPU.h" +diff -Nru fsl.orig/src/ptx2/saveResults_ptxGPU.cc fsl/src/ptx2/saveResults_ptxGPU.cc +--- fsl.orig/src/ptx2/saveResults_ptxGPU.cc 2019-11-15 10:47:30.417789709 +0100 ++++ fsl/src/ptx2/saveResults_ptxGPU.cc 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include "probtrackx.h" + #include "CUDA/tractographyInput.h" +@@ -326,7 +266,7 @@ + ////// save seeds to targets ////// + /////////////////////////////////// + if(opts.s2tout.value()){ +- long pos=0; ++ size_t pos=0; + int ntargets=data_host.targets.NVols+data_host.targets.NSurfs; + if (fsl_imageexists(opts.seedfile.value())){ + volume tmp; +@@ -392,7 +332,7 @@ + int nfaces=data_host.seeds_mesh_info[1]; + + if(f.is_open()){ +- int pos2=0; ++ size_t pos2=0; + for(int i=0;i Date: Tue, 26 Nov 2019 16:54:17 +0100 Subject: [PATCH 025/468] adding easyconfigs: TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb --- ...ink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/t/TreeShrink/TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/t/TreeShrink/TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb b/easybuild/easyconfigs/t/TreeShrink/TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb new file mode 100644 index 00000000000..abe536acafa --- /dev/null +++ b/easybuild/easyconfigs/t/TreeShrink/TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'PythonPackage' + +name = 'TreeShrink' +version = '1.3.2' +versionsuffix = '-Python-%(pyver)s' +local_commit = '0b5fc31' + +homepage = 'https://github.com/uym2/TreeShrink' +description = """TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +github_account = 'uym2' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['94f987100f5ada99f47799336f51e47798a2bd1806cb188d66edb8135f5856d5'] + +skipsteps = ['build'] + +dependencies = [ + ('Python', '3.7.2'), + ('DendroPy', '4.4.0'), +] + +# buildininstalldir = True +download_dep_fail = True +use_pip = False + +sanity_check_commands = [('run_treeshrink.py', '--help')] + +sanity_check_paths = { + 'files': ['bin/run_treeshrink.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 9125ff3235596c931faaa3981421a182489d5169 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 26 Nov 2019 17:18:18 +0100 Subject: [PATCH 026/468] Add easyconfigs for missing deps --- .../libxml++/libxml++-2.40.1-GCCcore-7.3.0.eb | 31 +++++++++++++++++++ .../easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb | 29 +++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml++/libxml++-2.40.1-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb diff --git a/easybuild/easyconfigs/l/libxml++/libxml++-2.40.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libxml++/libxml++-2.40.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..7fd09ea7e1d --- /dev/null +++ b/easybuild/easyconfigs/l/libxml++/libxml++-2.40.1-GCCcore-7.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxml++' +version = '2.40.1' + +homepage = 'http://libxmlplusplus.sourceforge.net' +description = """libxml++ is a C++ wrapper for the libxml XML parser library.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(name)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['4ad4abdd3258874f61c2e2a41d08e9930677976d303653cd1670d3e9f35463e9'] + +builddependencies = [ + ('binutils', '2.30'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLibmm', '2.49.7'), + ('libxml2', '2.9.8'), +] + +sanity_check_paths = { + 'files': ['lib/libxml++-2.6.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/libxml++-2.6/libxml++'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb new file mode 100644 index 00000000000..bd5f39ebf7f --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.4' + +homepage = 'http://qwt.sourceforge.net/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qt5', '5.10.1'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@QWT_INSTALL_PREFIX[ ]*=.*@QWT_INSTALL_PREFIX = %(installdir)s@g' qwtconfig.pri && " +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' From 66c07168836218c5979ed6e21b9b61314d4d4ff8 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 26 Nov 2019 17:55:36 +0100 Subject: [PATCH 027/468] Changed to fosscuda toolchain, got rid of CUDA dep, simplified suffix based on new toolchain --- ....0.130.eb => FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb} | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/f/FSL/{FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb => FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb} (93%) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb similarity index 93% rename from easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb rename to easybuild/easyconfigs/f/FSL/FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb index 475d022425c..a0dd87f8589 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb @@ -10,14 +10,12 @@ name = 'FSL' version = '6.0.2' -local_python_suffix = '-Python-2.7.15' -local_CUDA_suffix = '-CUDA-10.0.130' -versionsuffix = '{0}{1}'.format(local_python_suffix, local_CUDA_suffix) +versionsuffix = '-Python-2.7.15' homepage = 'http://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'cstd': 'c++11'} source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] @@ -60,7 +58,6 @@ dependencies = [ ('VTK', '8.1.1', local_python_suffix), ('GSL', '2.5'), ('Qwt', '6.1.4'), - ('CUDA', '10.0.130'), ] # FSLDIR needs to be defined when running postinstall to get the correct shebang From 9fd81eb2338b032418826f103fa68126ed339b8a Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 09:58:37 +0100 Subject: [PATCH 028/468] Made this FSL without CUDA... Will make another one for fosscuda, for an FSL with GPU support --- .../FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..3ac7cfec986 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,77 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Some tools like icmp are missing since they are built with the fslpython_install.sh script +# which locally installs Miniconda and creates a virtual environment. This is too messy and +# an alternative solution is necessary to install them. +# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 +# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation + +name = 'FSL' +version = '6.0.2' +versionsuffix = '-Python-2.7.15' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-6.0.2_Makefile_fixes.patch', + 'FSL-6.0.2_Build_extras.patch', + 'FSL-6.0.1_Melodic-use-ifstream-good.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', +] +checksums = [ + 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz + '3a14d9c3ea75d90fa3e4beb5da3cd11a60c6859441acaece02b32ccab6aa278f', # FSL-6.0.2_Makefile_fixes.patch + '2b7ade2146fadbba6c983370bb030ac4e2b11d8bf5259eacc8f3054d3d11003f', # FSL-6.0.2_Build_extras.patch + 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch + '4479aa501a7e6e9f1a0063e4ddb680836147ba08673d3fccb9e1db3c4d910672', # FSL-6.0.1_Fix_fsl_exec_script.patch +] + +builddependencies = [ + ('Boost', '1.67.0'), +] + +dependencies = [ + ('libgd', '2.2.5'), + ('libxml2', '2.9.8'), + ('libxml++', '2.40.1'), + ('SQLite', '3.24.0'), + ('libpng', '1.6.34'), + ('Tk', '8.6.8'), + ('NLopt', '2.4.2'), + ('freeglut', '3.0.0'), + ('expat', '2.2.5'), + ('zlib', '1.2.11'), + ('VTK', '8.1.1', '-Python-%(pyver)s'), + ('GSL', '2.5'), + ('Qwt', '6.1.4'), +] + +# FSLDIR needs to be defined when running postinstall to get the correct shebang +# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 +postinstallcmds = [( + 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH' + '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' +)] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +# Adding the bin from the virtualenv was the only way to get things working... +modextrapaths = { + 'PATH': 'fsl/fslpython/bin', + 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', +} + +moduleclass = 'bio' From a237e4faf1f82f4b6f6787d4689f2273464c8b6e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 10:03:05 +0100 Subject: [PATCH 029/468] Added checksum for Qwt --- easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb index bd5f39ebf7f..a107e96b74c 100644 --- a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-foss-2018b.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1529215329e51fc562e0009505a838f427919a18b362afff441f035b2d9b5bd9'] dependencies = [ ('Qt5', '5.10.1'), From 9654d6bf82e1ca9d6b4b0cbc42acff3fdddcc4fa Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 10:05:12 +0100 Subject: [PATCH 030/468] Added GLibmm for GCCcore-7.3.0 because this was a missing dep for FSL --- .../g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..86c3ebd9520 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GLibmm' +version = '2.49.7' + +homepage = 'http://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +patches = ['GLibmm-2.49.7_Fix_gobject_type.patch'] +checksums = [ + '571d8ecd082a66fa7248f500063409c1f478edc36f553d0eb27cf6199dee0b25', # glibmm-2.49.7.tar.xz + '3ef7a95e80ab58ea9369a7842c4d2917c8bce828f2754eafd075cf82405c9564', # GLibmm-2.49.7_Fix_gobject_type.patch +] + +builddependencies = [ + ('binutils', '2.30'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.54.3'), + ('libsigc++', '2.10.1'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.4.%s' % SHLIB_EXT, 'lib/libgiomm-2.4.%s' % SHLIB_EXT, + 'include/glibmm-2.4/glibmm.h', 'include/giomm-2.4/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' From 76778eb4a5ac54ac6b594bd8372b2a6ac6443be0 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 10:21:36 +0100 Subject: [PATCH 031/468] Will do FSL with cuda support in separate PR, because it requires a hell of a lot of additional deps --- .../FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb | 83 ------------------- 1 file changed, 83 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb deleted file mode 100644 index a0dd87f8589..00000000000 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-fosscuda-2018b-Python-2.7.15.eb +++ /dev/null @@ -1,83 +0,0 @@ -# This build still relies on the following libraries (or part of them) shipped with FSL: -# GDCHART, libprob, libcprob, cprob, newran, newmat -# Attempts to use externally built libraries failed. Worth trying again in the future... -# -# Some tools like icmp are missing since they are built with the fslpython_install.sh script -# which locally installs Miniconda and creates a virtual environment. This is too messy and -# an alternative solution is necessary to install them. -# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 -# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation - -name = 'FSL' -version = '6.0.2' -versionsuffix = '-Python-2.7.15' - -homepage = 'http://www.fmrib.ox.ac.uk/fsl/' -description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] -sources = ['%(namelower)s-%(version)s-sources.tar.gz'] -patches = [ - 'FSL-6.0.2_Makefile_fixes.patch', - 'FSL-6.0.2_Build_extras.patch', - 'FSL-6.0.1_Melodic-use-ifstream-good.patch', - 'FSL-6.0.2_Enable_GPU_build.patch', - # Fixes https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1911&L=FSL&P=R2783 - 'FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch', - 'FSL-6.0.1_Fix_fsl_exec_script.patch', -] -checksums = [ - 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz - '3a14d9c3ea75d90fa3e4beb5da3cd11a60c6859441acaece02b32ccab6aa278f', # FSL-6.0.2_Makefile_fixes.patch - '2b7ade2146fadbba6c983370bb030ac4e2b11d8bf5259eacc8f3054d3d11003f', # FSL-6.0.2_Build_extras.patch - 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch - '4870f20e84c24331418ea9d5ee67d5ba9cf075bcc85b053d4d8b7a276a96a1a5', # FSL-6.0.2_Enable_GPU_build.patch - # FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch - '05f6ddf6b149e234ea7428bd5b510a72aa8f131a00fda0e369f854b722d88b19', - '4479aa501a7e6e9f1a0063e4ddb680836147ba08673d3fccb9e1db3c4d910672', # FSL-6.0.1_Fix_fsl_exec_script.patch -] - -builddependencies = [ - ('Boost', '1.67.0'), -] - -dependencies = [ - ('libgd', '2.2.5'), - ('libxml2', '2.9.8'), - ('libxml++', '2.40.1'), - ('SQLite', '3.24.0'), - ('libpng', '1.6.34'), - ('Tk', '8.6.8'), - ('NLopt', '2.4.2'), - ('freeglut', '3.0.0'), - ('expat', '2.2.5'), - ('zlib', '1.2.11'), - ('VTK', '8.1.1', local_python_suffix), - ('GSL', '2.5'), - ('Qwt', '6.1.4'), -] - -# FSLDIR needs to be defined when running postinstall to get the correct shebang -# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 -postinstallcmds = [( - 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH' - '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' -)] - -modextravars = { - 'FSLOUTPUTTYPE': 'NIFTI_GZ', - 'FSLMULTIFILEQUIT': 'TRUE', - 'FSLTCLSH': 'tclsh', - 'FSLWISH': 'wish8.6' -} - -# Adding the bin from the virtualenv was the only way to get things working... -modextrapaths = { - 'PATH': 'fsl/fslpython/bin', - 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', -} - -moduleclass = 'bio' From 1e8e270883dca2a215a53c2dea4f06cfe8a02b91 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 10:37:25 +0100 Subject: [PATCH 032/468] Define local pyver, since python is not a direct dep of FSL and the template pyver is not defined. --- .../easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb index 3ac7cfec986..8c378112714 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb @@ -10,7 +10,8 @@ name = 'FSL' version = '6.0.2' -versionsuffix = '-Python-2.7.15' +local_pyver = '2.7.15' +versionsuffix = '-Python-%s' % local_pyver homepage = 'http://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" @@ -49,7 +50,7 @@ dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.2.5'), ('zlib', '1.2.11'), - ('VTK', '8.1.1', '-Python-%(pyver)s'), + ('VTK', '8.1.1', '-Python-%s' % local_pyver), ('GSL', '2.5'), ('Qwt', '6.1.4'), ] From 04a93840db862fe6d8d01d802fc7b85d5ca8459a Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 10:48:11 +0100 Subject: [PATCH 033/468] [cart,lisa] [VTK-8.1.1-fosscuda-2018b-Python-2.7.15.eb] Added VTK for fosscuda, as a dep for FSL --- .../VTK-8.1.1-fosscuda-2018b-Python-2.7.15.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.1.1-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..02dd300e73e --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,68 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +checksums = [ + '71a09b4340f0a9c58559fe946dc745ab68a866cf20636a41d97b6046cb736324', # VTK-8.1.1.tar.gz + 'e16c2d665f052b6aeb981aea17f0309849e661a0038e18c9880bd6e6519c4fcc', # VTKData-8.1.1.tar.gz +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.6'), + ('HDF5', '1.10.2'), + ('libGLU', '9.0.0'), + ('X11', '20180604'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DVTK_WRAP_PYTHON=ON " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' From 0ac9c3e02902ecfb10640ff09fc6d68c22c36e99 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 10:50:36 +0100 Subject: [PATCH 034/468] Removed all GPU components of this PR... Will do that in separate PR --- .../f/FSL/FSL-6.0.2_Enable_GPU_build.patch | 16 - ....2_probtrackx2_gpu_large_mri_support.patch | 3883 ----------------- .../VTK-8.1.1-fosscuda-2018b-Python-2.7.15.eb | 68 - 3 files changed, 3967 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch delete mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch delete mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.1.1-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch deleted file mode 100644 index 8c908e9b7b0..00000000000 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -Nru fsl.orig/src/fdt/fslconfig fsl/src/fdt/fslconfig ---- fsl.orig/src/fdt/fslconfig 2019-10-11 13:50:36.336062960 +0200 -+++ fsl/src/fdt/fslconfig 2019-10-11 18:09:38.260806371 +0200 -@@ -1,3 +1 @@ --if [ `hostname` == "caper.fmrib.ox.ac.uk" -o `hostname` == "jalapeno19.fmrib.ox.ac.uk" ]; then -- export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; --fi -+export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; -diff -Nru fsl.orig/src/ptx2/fslconfig fsl/src/ptx2/fslconfig ---- fsl.orig/src/ptx2/fslconfig 2019-10-11 13:50:36.310062989 +0200 -+++ fsl/src/ptx2/fslconfig 2019-10-11 18:09:19.874825110 +0200 -@@ -1,3 +1 @@ --if [ `hostname` == "caper.fmrib.ox.ac.uk" -o `hostname` == "jalapeno19.fmrib.ox.ac.uk" ]; then -- export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; --fi -+export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch deleted file mode 100644 index 8d76f676392..00000000000 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch +++ /dev/null @@ -1,3883 +0,0 @@ -# This should fix what was described in this thread https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1911&L=FSL&O=D&X=C89E84F6301F100D81&Y=caspar.vanleeuwen%40surfsara.nl&P=96399 -# In addition, I included a change in tractographyInput.cc to explicitely call 'round' from the namespace 'MISCMATHS'. -diff -Nru fsl.orig/src/ptx2/CUDA/intersectionsDevice.cu fsl/src/ptx2/CUDA/intersectionsDevice.cu ---- fsl.orig/src/ptx2/CUDA/intersectionsDevice.cu 2019-11-15 10:47:30.358790161 +0100 -+++ fsl/src/ptx2/CUDA/intersectionsDevice.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include - -diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_gpu.cu ---- fsl.orig/src/ptx2/CUDA/memManager_gpu.cu 2019-11-15 10:47:30.376790024 +0100 -+++ fsl/src/ptx2/CUDA/memManager_gpu.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,70 +4,11 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - --cudaError_t checkCuda(cudaError_t result){ -+cudaError_t checkCuda(cudaError_t result, const char *msg=NULL){ - if (result != cudaSuccess) { -+ if (msg) fprintf(stderr, "Error: %s\n", msg); - fprintf(stderr, "CUDA Runtime Error: %s\n", - cudaGetErrorString(result)); - exit(1); -@@ -468,62 +409,155 @@ - } - } - -+size_t calculate_mem_required(tractographyData& data_host){ -+ probtrackxOptions& opts =probtrackxOptions::getInstance(); -+ size_t total_mem_required; -+ total_mem_required = sizeof(tractographyData); -+ total_mem_required += data_host.nseeds*3*sizeof(float); // seeds -+ if(opts.network.value()) total_mem_required += data_host.nseeds*sizeof(float); // network -+ total_mem_required += 2*data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float); //mask & lut_vol2mat -+ total_mem_required += 3*data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float); // samples -+ -+ size_t seedVolSize=data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]*sizeof(float); -+ size_t voxFacesIndexSize = (data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int); -+ if(data_host.avoid.NVols) total_mem_required += seedVolSize; -+ if(data_host.avoid.NSurfs){ -+ size_t surfSize = size_t(data_host.avoid.sizesStr[1]*sizeof(float)) + data_host.avoid.sizesStr[2]*sizeof(int) -+ + data_host.avoid.sizesStr[3]*sizeof(int) + voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.stop.NVols) total_mem_required += seedVolSize; -+ if(data_host.stop.NSurfs){ -+ size_t surfSize = size_t(data_host.stop.sizesStr[1]*sizeof(float)) + data_host.stop.sizesStr[2]*sizeof(int) -+ + data_host.stop.sizesStr[3]*sizeof(int) + voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.wtstop.NVols) total_mem_required += data_host.wtstop.NVols * seedVolSize; -+ if(data_host.wtstop.NSurfs){ -+ size_t surfSize = size_t(data_host.wtstop.sizesStr[1]*sizeof(float)) + data_host.wtstop.sizesStr[2]*sizeof(int) -+ + data_host.wtstop.sizesStr[3]*sizeof(int) + data_host.wtstop.NSurfs*voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.network.NVols) total_mem_required += data_host.network.NVols * seedVolSize; -+ if(data_host.network.NSurfs){ -+ size_t surfSize = size_t(data_host.network.sizesStr[1]*sizeof(float)) + data_host.network.sizesStr[2]*sizeof(int) -+ + data_host.network.sizesStr[3]*sizeof(int) + data_host.network.NSurfs*voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.network.NVols||data_host.network.NSurfs){ -+ total_mem_required += data_host.network.NVols+data_host.network.NSurfs*sizeof(int); -+ } -+ if(data_host.networkREF.NVols) total_mem_required += seedVolSize; -+ if(data_host.networkREF.NSurfs){ -+ size_t surfSize = size_t(data_host.networkREF.sizesStr[1]*sizeof(float)) + data_host.networkREF.sizesStr[2]*sizeof(int) -+ + data_host.networkREF.sizesStr[3]*sizeof(int) + voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.waypoint.NVols) total_mem_required += data_host.waypoint.NVols * seedVolSize; -+ if(data_host.waypoint.NSurfs){ -+ size_t surfSize = size_t(data_host.waypoint.sizesStr[1]*sizeof(float)) + data_host.waypoint.sizesStr[2]*sizeof(int) -+ + data_host.waypoint.sizesStr[3]*sizeof(int) + data_host.waypoint.NSurfs*voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.waypoint.NVols||data_host.waypoint.NSurfs){ -+ total_mem_required += data_host.waypoint.NVols+data_host.waypoint.NSurfs*sizeof(int); -+ } -+ if(data_host.targets.NVols) total_mem_required += data_host.targets.NVols * seedVolSize; -+ if(data_host.targets.NSurfs){ -+ size_t surfSize = size_t(data_host.targets.sizesStr[1]*sizeof(float)) + data_host.targets.sizesStr[2]*sizeof(int) -+ + data_host.targets.sizesStr[3]*sizeof(int) + data_host.targets.NSurfs*voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.targets.NVols||data_host.targets.NSurfs){ -+ total_mem_required += data_host.targets.NVols+data_host.targets.NSurfs*sizeof(int); -+ } -+ if(data_host.targetsREF.NVols) total_mem_required += seedVolSize; -+ if(data_host.targetsREF.NSurfs){ -+ size_t surfSize = size_t(data_host.targetsREF.sizesStr[1]*sizeof(float)) + data_host.targetsREF.sizesStr[2]*sizeof(int) -+ + data_host.targetsREF.sizesStr[3]*sizeof(int) + voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.lrmatrix1.NVols){ -+ if(opts.matrix2out.value()) -+ total_mem_required += data_host.lrmatrix1.NVols*data_host.M2sizes[0]*data_host.M2sizes[1]*data_host.M2sizes[2]*sizeof(float); -+ else -+ total_mem_required += data_host.lrmatrix1.NVols * seedVolSize; -+ } -+ if(data_host.lrmatrix1.NSurfs){ -+ size_t surfSize = size_t(data_host.lrmatrix1.sizesStr[0]*sizeof(int)) -+ + data_host.lrmatrix1.sizesStr[1]*sizeof(float) + data_host.lrmatrix1.sizesStr[2]*sizeof(int) -+ + data_host.lrmatrix1.sizesStr[3]*sizeof(int) + data_host.lrmatrix1.NSurfs*voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.matrix3.NVols) total_mem_required += data_host.matrix3.NVols * seedVolSize; -+ if(data_host.matrix3.NSurfs){ -+ size_t surfSize = size_t(data_host.matrix3.sizesStr[0]*sizeof(int)) -+ + data_host.matrix3.sizesStr[1]*sizeof(float) + data_host.matrix3.sizesStr[2]*sizeof(int) -+ + data_host.matrix3.sizesStr[3]*sizeof(int) + data_host.matrix3.NSurfs*voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ if(data_host.lrmatrix3.NVols) total_mem_required += data_host.lrmatrix3.NVols * seedVolSize; -+ if(data_host.lrmatrix3.NSurfs){ -+ size_t surfSize = size_t(data_host.lrmatrix3.sizesStr[0]*sizeof(int)) -+ + data_host.lrmatrix3.sizesStr[1]*sizeof(float) + data_host.lrmatrix3.sizesStr[2]*sizeof(int) -+ + data_host.lrmatrix3.sizesStr[3]*sizeof(int) + data_host.lrmatrix3.NSurfs*voxFacesIndexSize; -+ total_mem_required += surfSize; -+ } -+ return total_mem_required; -+} -+ - - void copy_to_gpu( tractographyData& data_host, -- tractographyData*& data_gpu) -+ tractographyData*& data_gpu) - { - probtrackxOptions& opts =probtrackxOptions::getInstance(); - -+ size_t total_mem_required = calculate_mem_required(data_host); -+ cout << "Memory required for allocating data (MB): "<< total_mem_required/1048576 << endl; -+ -+ size_t free,total; -+ cudaMemGetInfo(&free,&total); -+ if(total_mem_required > free){ -+ cout << "Not enough Memory available on device. Exiting ..." << endl; -+ terminate(); -+ } -+ - checkCuda(cudaMalloc((void**)&data_gpu,sizeof(tractographyData))); - checkCuda(cudaMemcpy(data_gpu,&data_host,sizeof(tractographyData),cudaMemcpyHostToDevice)); - - int* auxI; - float* auxF; -- -- // sizes and dims .... now in Constant memory -- -+ - // seeds -- checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*3*sizeof(float))); -+ checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*3*sizeof(float)), "Allocating seeds"); - checkCuda(cudaMemcpy(auxF,data_host.seeds,data_host.nseeds*3*sizeof(float),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->seeds,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - if(opts.network.value()){ -- checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*sizeof(float))); -+ checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*sizeof(float)), "Allocating Network ROIs"); - checkCuda(cudaMemcpy(auxF,data_host.seeds_ROI,data_host.nseeds*sizeof(float),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->seeds_ROI,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - } - // mask -- checkCuda(cudaMalloc((void**)&auxF,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float))); -+ checkCuda(cudaMalloc((void**)&auxF,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float)), "Allocating mask"); - checkCuda(cudaMemcpy(auxF,data_host.mask,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float),cudaMemcpyHostToDevice)); -- checkCuda(cudaMemcpy(&data_gpu->mask,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMemcpy(&data_gpu->mask,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - // th_samples -- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); -+ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating th_samples"); - checkCuda(cudaMemcpy(auxF,data_host.thsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); -- checkCuda(cudaMemcpy(&data_gpu->thsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMemcpy(&data_gpu->thsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - // ph_samples -- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); -+ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating ph_samples"); - checkCuda(cudaMemcpy(auxF,data_host.phsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); -- checkCuda(cudaMemcpy(&data_gpu->phsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMemcpy(&data_gpu->phsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - // f_samples -- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); -+ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating f_samples"); - checkCuda(cudaMemcpy(auxF,data_host.fsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); -- checkCuda(cudaMemcpy(&data_gpu->fsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMemcpy(&data_gpu->fsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - // lut_vol2mat -- checkCuda(cudaMalloc((void**)&auxI,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int))); -+ checkCuda(cudaMalloc((void**)&auxI,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int)), "Allocating lut_vol2mat"); - checkCuda(cudaMemcpy(auxI,data_host.lut_vol2mat,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->lut_vol2mat,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); - -- //Seeds_to_DTI...... now in Constant memory -- -- //DTI_to_Seeds...... now in Constant memory -- -- //VOX2MM...... now in Constant memory -- -- //NON-LINEAR ...... now in Constant memory and Texture Memory -- -- //Warp sizes.... now in constant memory -- -- //Sampling Inverse.... now in constant memory -- - //Avoid mask - if(data_host.avoid.NVols){ - checkCuda(cudaMalloc((void**)&auxF,data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]*sizeof(float))); -@@ -531,10 +565,6 @@ - checkCuda(cudaMemcpy(&data_gpu->avoid.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - } - if(data_host.avoid.NSurfs){ -- //cudaMalloc((void**)&auxI,data_host.avoid.sizesStr[0]*sizeof(int)); -- //cudaMemcpy(auxI,data_host.avoid.locs,data_host.avoid.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); -- //cudaMemcpy(&data_gpu->avoid.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); -- // no deed locs - checkCuda(cudaMalloc((void**)&auxF,data_host.avoid.sizesStr[1]*sizeof(float))); - checkCuda(cudaMemcpy(auxF,data_host.avoid.vertices,data_host.avoid.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->avoid.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -555,10 +585,6 @@ - checkCuda(cudaMemcpy(&data_gpu->stop.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - } - if(data_host.stop.NSurfs){ -- //cudaMalloc((void**)&auxI,data_host.stop.sizesStr[0]*sizeof(int)); -- //cudaMemcpy(auxI,data_host.stop.locs,data_host.stop.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); -- //cudaMemcpy(&data_gpu->stop.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); -- // no need locs - checkCuda(cudaMalloc((void**)&auxF,data_host.stop.sizesStr[1]*sizeof(float))); - checkCuda(cudaMemcpy(auxF,data_host.stop.vertices,data_host.stop.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->stop.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -579,10 +605,6 @@ - checkCuda(cudaMemcpy(&data_gpu->wtstop.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - } - if(data_host.wtstop.NSurfs){ -- //cudaMalloc((void**)&auxI,data_host.wtstop.sizesStr[0]*sizeof(int)); -- //cudaMemcpy(auxI,data_host.wtstop.locs,data_host.wtstop.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); -- //cudaMemcpy(&data_gpu->wtstop.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); -- // no need locs - checkCuda(cudaMalloc((void**)&auxF,data_host.wtstop.sizesStr[1]*sizeof(float))); - checkCuda(cudaMemcpy(auxF,data_host.wtstop.vertices,data_host.wtstop.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->wtstop.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -592,8 +614,8 @@ - checkCuda(cudaMalloc((void**)&auxI,data_host.wtstop.sizesStr[3]*sizeof(int))); - checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFaces,data_host.wtstop.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->wtstop.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); -- checkCuda(cudaMalloc((void**)&auxI,(data_host.wtstop.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); -- checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFacesIndex,(data_host.wtstop.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMalloc((void**)&auxI,(data_host.wtstop.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); -+ checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFacesIndex,(data_host.wtstop.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->wtstop.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); - } - // Network mask -@@ -603,10 +625,6 @@ - checkCuda(cudaMemcpy(&data_gpu->network.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - } - if(data_host.network.NSurfs){ -- //cudaMalloc((void**)&auxI,data_host.network.sizesStr[0]*sizeof(int)); -- //cudaMemcpy(auxI,data_host.network.locs,data_host.network.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); -- //cudaMemcpy(&data_gpu->network.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); -- // no locs - checkCuda(cudaMalloc((void**)&auxF,data_host.network.sizesStr[1]*sizeof(float))); - checkCuda(cudaMemcpy(auxF,data_host.network.vertices,data_host.network.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->network.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -616,8 +634,8 @@ - checkCuda(cudaMalloc((void**)&auxI,data_host.network.sizesStr[3]*sizeof(int))); - checkCuda(cudaMemcpy(auxI,data_host.network.VoxFaces,data_host.network.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->network.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); -- checkCuda(cudaMalloc((void**)&auxI,(data_host.network.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); -- checkCuda(cudaMemcpy(auxI,data_host.network.VoxFacesIndex,(data_host.network.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMalloc((void**)&auxI,(data_host.network.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); -+ checkCuda(cudaMemcpy(auxI,data_host.network.VoxFacesIndex,(data_host.network.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->network.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); - } - if(data_host.network.NVols||data_host.network.NSurfs){ -@@ -654,9 +672,6 @@ - checkCuda(cudaMemcpy(&data_gpu->waypoint.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); - } - if(data_host.waypoint.NSurfs){ -- //cudaMalloc((void**)&auxI,data_host.waypoint.sizesStr[0]*sizeof(int)); -- //cudaMemcpy(auxI,data_host.waypoint.locs,data_host.waypoint.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); -- //cudaMemcpy(&data_gpu->waypoint.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); - checkCuda(cudaMalloc((void**)&auxF,data_host.waypoint.sizesStr[1]*sizeof(float))); - checkCuda(cudaMemcpy(auxF,data_host.waypoint.vertices,data_host.waypoint.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->waypoint.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -666,8 +681,8 @@ - checkCuda(cudaMalloc((void**)&auxI,data_host.waypoint.sizesStr[3]*sizeof(int))); - checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFaces,data_host.waypoint.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->waypoint.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); -- checkCuda(cudaMalloc((void**)&auxI,(data_host.waypoint.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); -- checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFacesIndex,(data_host.waypoint.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMalloc((void**)&auxI,(data_host.waypoint.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); -+ checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFacesIndex,(data_host.waypoint.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->waypoint.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); - } - if(data_host.waypoint.NVols||data_host.waypoint.NSurfs){ -@@ -692,8 +707,8 @@ - checkCuda(cudaMalloc((void**)&auxI,data_host.targets.sizesStr[3]*sizeof(int))); - checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFaces,data_host.targets.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->targets.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); -- checkCuda(cudaMalloc((void**)&auxI,(data_host.targets.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); -- checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFacesIndex,(data_host.targets.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMalloc((void**)&auxI,(data_host.targets.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); -+ checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFacesIndex,(data_host.targets.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->targets.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); - } - if(data_host.targets.NVols||data_host.targets.NSurfs){ -@@ -748,8 +763,8 @@ - checkCuda(cudaMalloc((void**)&auxI,data_host.lrmatrix1.sizesStr[3]*sizeof(int))); - checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFaces,data_host.lrmatrix1.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->lrmatrix1.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); -- checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix1.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); -- checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFacesIndex,(data_host.lrmatrix1.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix1.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); -+ checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFacesIndex,(data_host.lrmatrix1.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->lrmatrix1.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); - //cudaMalloc((void**)&auxI,data_host.lrmatrix1.sizesStr[4]*sizeof(int)); - //cudaMemcpy(auxI,data_host.lrmatrix1.IndexRoi,data_host.lrmatrix1.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); -@@ -774,8 +789,8 @@ - checkCuda(cudaMalloc((void**)&auxI,data_host.matrix3.sizesStr[3]*sizeof(int))); - checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFaces,data_host.matrix3.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->matrix3.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); -- checkCuda(cudaMalloc((void**)&auxI,(data_host.matrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); -- checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFacesIndex,(data_host.matrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMalloc((void**)&auxI,(data_host.matrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); -+ checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFacesIndex,(data_host.matrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->matrix3.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); - //cudaMalloc((void**)&auxI,data_host.matrix3.sizesStr[4]*sizeof(int)); - //cudaMemcpy(auxI,data_host.matrix3.IndexRoi,data_host.matrix3.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); -@@ -800,8 +815,8 @@ - checkCuda(cudaMalloc((void**)&auxI,data_host.lrmatrix3.sizesStr[3]*sizeof(int))); - checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFaces,data_host.lrmatrix3.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->lrmatrix3.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); -- checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); -- checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFacesIndex,(data_host.lrmatrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); -+ checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); -+ checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFacesIndex,(data_host.lrmatrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); - checkCuda(cudaMemcpy(&data_gpu->lrmatrix3.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); - //cudaMalloc((void**)&auxI,data_host.lrmatrix3.sizesStr[4]*sizeof(int)); - //cudaMemcpy(auxI,data_host.lrmatrix3.IndexRoi,data_host.lrmatrix3.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); -diff -Nru fsl.orig/src/ptx2/CUDA/streamlinesDevice.cu fsl/src/ptx2/CUDA/streamlinesDevice.cu ---- fsl.orig/src/ptx2/CUDA/streamlinesDevice.cu 2019-11-15 10:47:30.363790122 +0100 -+++ fsl/src/ptx2/CUDA/streamlinesDevice.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2005 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #define DIVRND 1.00000001f - #define LCRAT 5.0f //box for loopcheck is five times smaller than brain mask -diff -Nru fsl.orig/src/ptx2/CUDA/tractography_CallKernels.cu fsl/src/ptx2/CUDA/tractography_CallKernels.cu ---- fsl.orig/src/ptx2/CUDA/tractography_CallKernels.cu 2019-11-15 10:47:30.381789984 +0100 -+++ fsl/src/ptx2/CUDA/tractography_CallKernels.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - void initialise_SeedsGPU( - curandState*& devStates, -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.cc fsl/src/ptx2/CUDA/tractographyData.cc ---- fsl.orig/src/ptx2/CUDA/tractographyData.cc 2019-11-15 10:47:30.365790108 +0100 -+++ fsl/src/ptx2/CUDA/tractographyData.cc 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #ifndef EXPOSE_TREACHEROUS - #define EXPOSE_TREACHEROUS 1 -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.h fsl/src/ptx2/CUDA/tractographyData.h ---- fsl.orig/src/ptx2/CUDA/tractographyData.h 2019-11-15 10:47:30.383789969 +0100 -+++ fsl/src/ptx2/CUDA/tractographyData.h 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - - #ifndef Data_gpu_ptx_H -@@ -99,7 +39,7 @@ - int nvoxels; - int nsamples; - int nfibres; -- int nseeds; -+ size_t nseeds; - int nparticles; - int nsteps; - -diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractography_gpu.cu ---- fsl.orig/src/ptx2/CUDA/tractography_gpu.cu 2019-11-15 10:47:30.374790038 +0100 -+++ fsl/src/ptx2/CUDA/tractography_gpu.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include - #include -@@ -92,7 +32,7 @@ - init_gpu(); - size_t free,total; - cudaMemGetInfo(&free,&total); -- cout << "Free memory at the beginning: "<< free << " ---- Total memory: " << total << "\n"; -+ cout << "Device memory available (MB): "<< free/1048576 << " ---- Total device memory(MB): " << total/1048576 << "\n"; - - probtrackxOptions& opts=probtrackxOptions::getInstance(); - -@@ -103,7 +43,7 @@ - copy_ToTextureMemory(data_host); // Set Texture memory - - cuMemGetInfo(&free,&total); -- cout << "Free memory after copying masks: "<< free << " ---- Total memory: " << total << "\n"; -+ cout << "Device memory available after copying data (MB): "<< free/1048576 << "\n"; - - int MAX_SLs; - int THREADS_STREAM; // MAX_Streamlines and NSTREAMS must be multiples -@@ -219,7 +159,6 @@ - - checkCuda(cudaDeviceSynchronize()); - cuMemGetInfo(&free,&total); -- cout << "Free memory before running iterations: "<< free << " ---- Total memory: " << total << "\n"; - - // run iterations - for(int iter=0;iter0||lengths_host[0][pos+1]>0){ - vector tmp; -- bool included_seed=false; - if(lengths_host[0][pos]>0){ - int posSEED=i*data_host.nsteps*3; - int posCURRENT=0; -@@ -365,12 +303,10 @@ - tmp.push_back(paths_host[0][posSEED+posCURRENT*3+1]); - tmp.push_back(paths_host[0][posSEED+posCURRENT*3+2]); - } -- included_seed=true; - } - if(lengths_host[0][pos+1]>0){ - int pos2=i*data_host.nsteps*3+((data_host.nsteps/2)*3); - int co=0; -- //if(included_seed) co=1; - for(;co0||lengths_host[0][pos+1]>0){ - vector tmp; -- bool included_seed=false; - if(lengths_host[0][pos]>0){ - int posSEED=i*data_host.nsteps*3; - int posCURRENT=0; -@@ -466,12 +401,10 @@ - tmp.push_back(paths_host[0][posSEED+posCURRENT*3+1]); - tmp.push_back(paths_host[0][posSEED+posCURRENT*3+2]); - } -- included_seed=true; - } - if(lengths_host[0][pos+1]>0){ - int pos2=i*data_host.nsteps*3+((data_host.nsteps/2)*3); - int co=0; -- //if(included_seed) co=1; - for(;co - #include -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractographyInput.cc ---- fsl.orig/src/ptx2/CUDA/tractographyInput.cc 2019-11-15 10:47:30.368790085 +0100 -+++ fsl/src/ptx2/CUDA/tractographyInput.cc 2019-11-15 15:03:45.388788544 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #ifndef EXPOSE_TREACHEROUS - #define EXPOSE_TREACHEROUS -@@ -85,26 +25,15 @@ - coords[1] = MISCMATHS::round(v(2)); - coords[2] = MISCMATHS::round(v(3)); - } --/*void applycoordchange(Matrix& coordvol, const Matrix& old2new_mat) --{ -- for (int n=1; n<=coordvol.Nrows(); n++) { -- ColumnVector v(4); -- v << coordvol(n,1) << coordvol(n,2) << coordvol(n,3) << 1.0; -- v = old2new_mat * v; -- coordvol(n,1) = MISCMATHS::round(v(1)); -- coordvol(n,2) = MISCMATHS::round(v(2)); -- coordvol(n,3) = MISCMATHS::round(v(3)); -- } -- }*/ -- --void tractographyInput::load_mesh( string& filename, -- vector& vertices, -- vector& faces, -- vector& locs, -- int& nlocs, -- bool wcoords, -- int nroi, -- vector& coords) -+ -+void tractographyInput::load_mesh( string& filename, -+ vector& vertices, -+ vector& faces, -+ vector& locs, -+ int& nlocs, -+ bool wcoords, -+ int nroi, -+ vector& coords) - { - int type=meshFileType(filename); - if (type==ASCII){ -@@ -119,14 +48,14 @@ - } - } - --void tractographyInput::load_mesh_ascii( string& filename, -- vector& vertices, -- vector& faces, -- vector& locs, -- int& nlocs, -- bool wcoords, -- int nroi, -- vector& coords) -+void tractographyInput::load_mesh_ascii( string& filename, -+ vector& vertices, -+ vector& faces, -+ vector& locs, -+ int& nlocs, -+ bool wcoords, -+ int nroi, -+ vector& coords) - { - // load a freesurfer ascii mesh - ifstream f(filename.c_str()); -@@ -139,10 +68,10 @@ - cerr<<"Loading ascii file: error in the header"<>NVertices>>NFaces; - -- int posV,posF,initV,posLV; -+ size_t posV,posF,initV,posLV; - posV=vertices.size(); // maybe there were some more vertices before - posLV=locs.size(); - initV=posV; -@@ -162,7 +91,7 @@ - values.resize(NVertices); - bool zeros=false; - bool nonzeros=false; -- for (int i=0; i>vertices[posV]>>vertices[posV+1]>>vertices[posV+2]>>values[i]; // write from file to vector - if(values[i]==0) zeros=true; - else nonzeros=true; -@@ -171,30 +100,30 @@ - if (zeros&&nonzeros) allMesh=false; // then some values should be ignored - - // storing locations: use same structure for active-nonactive vertex -- int auxCount=posV-NVertices*3; -- int local_loc=1; -- for (int i=0; i>p0>>p1>>p2>>val; -@@ -208,14 +137,14 @@ - }else {cout<<"Loading ascii file: error opening file: "<& vertices, -- vector& faces, -- vector& locs, -- int& nlocs, -- bool wcoords, -- int nroi, -- vector& coords) -+void tractographyInput::load_mesh_vtk(string& filename, -+ vector& vertices, -+ vector& faces, -+ vector& locs, -+ int& nlocs, -+ bool wcoords, -+ int nroi, -+ vector& coords) - { - ifstream f(filename.c_str()); - if (f.is_open()){ -@@ -229,9 +158,9 @@ - getline(f,header); - getline(f,header); - getline(f,header); -- int NVertices, NFaces; -+ size_t NVertices, NFaces; - f>>header>>NVertices>>header; -- int posV,posF,initV,posLV; -+ size_t posV,posF,initV,posLV; - posV=vertices.size(); - posLV=locs.size(); - initV=posV; -@@ -241,16 +170,16 @@ - // reading the points - // if is not possible to define values, then all vertices are activated - int local_loc=1; -- for (int i=0; i>vertices[posV]>>vertices[posV+1]>>vertices[posV+2]; - locs[posLV]=nlocs; - if (wcoords){ -- coords.push_back(MISCMATHS::round(vertices[posV])); -- coords.push_back(MISCMATHS::round(vertices[posV+1])); -- coords.push_back(MISCMATHS::round(vertices[posV+2])); -- coords.push_back(nroi); -- coords.push_back(local_loc); -- local_loc++; -+ coords.push_back(MISCMATHS::round(vertices[posV])); -+ coords.push_back(MISCMATHS::round(vertices[posV+1])); -+ coords.push_back(MISCMATHS::round(vertices[posV+2])); -+ coords.push_back(nroi); -+ coords.push_back(local_loc); -+ local_loc++; - } - posV=posV+3; - posLV++; -@@ -261,7 +190,7 @@ - faces.resize(posF+NFaces*3); - - // reading the triangles -- for (int i=0; i>j>>p0>>p1>>p2; -@@ -278,22 +207,22 @@ - } - } - --void tractographyInput::load_mesh_gifti( string& filename, -- vector& vertices, -- vector& faces, -- vector& locs, -- int& nlocs, -- bool wcoords, -- int nroi, -- vector& coords) -+void tractographyInput::load_mesh_gifti(string& filename, -+ vector& vertices, -+ vector& faces, -+ vector& locs, -+ int& nlocs, -+ bool wcoords, -+ int nroi, -+ vector& coords) - { - fslsurface_name::fslSurface surf; - read_surface(surf,filename); -- int posV,posF,initV,posLV; -+ size_t posV,posF,initV,posLV; - posV=vertices.size(); - posLV=locs.size(); - initV=posV; -- int count=0; -+ size_t count=0; - for (vector< fslsurface_name::vertex >::iterator i= surf.vbegin(); i!= surf.vend();++i){ - vertices.resize(posV+3); - vertices[posV]=i->x; -@@ -326,42 +255,42 @@ - } - if (zeros&&nonzeros) allMesh=false; - int local_loc=1; -- int auxCount=posV-count*3; -- for (int i=0; i& coords) -+ int* Ssizes, -+ float* Vout, -+ int& nlocs, -+ bool reset, -+ bool wcoords, -+ int nroi, -+ vector& coords) - { -+ //reset: if true, it sets -1 voxels not present in mask, -+ //reset must be false if mixed volume: stop / exclusion / targetREF, networkREF - int local_loc=1; - volume tmpvol; - read_volume(tmpvol,filename); - for (int z=0;z=0 && voxX=0 && voxY=0 && voxZ t(1); -- t[0]=j; // this position is relative to this portion of faces !!!!!! -- triangles.push_back(t); // add to set of triangles that cross voxels -- surfvol(voxX,voxY,voxZ)=triangles.size()-1; -- total++; -- }else{ // voxel already labeled as "crossed" -- triangles[val].push_back(j); // add this triangle to the set that cross this voxel -- total++; -- } -+ int val = surfvol(voxX,voxY,voxZ); -+ if (val==-1){ // this voxel hasn't been labeled yet -+ vector t(1); -+ t[0]=j; // this position is relative to this portion of faces !!!!!! -+ triangles.push_back(t); // add to set of triangles that cross voxels -+ surfvol(voxX,voxY,voxZ)=triangles.size()-1; -+ total++; -+ }else{ // voxel already labeled as "crossed" -+ triangles[val].push_back(j); // add this triangle to the set that cross this voxel -+ total++; -+ } - }else{ -- printf("Warning: Ignoring some vertices because they are defined outside the limits\n"); -- printf("Please check that your meshspace is defined correctly\n"); -+ printf("Warning: Ignoring some vertices because they are defined outside the limits\n"); -+ printf("Please check that your meshspace is defined correctly\n"); - } - } - } -@@ -471,41 +404,41 @@ - for (int z=0;z t; -- t.insert(t.end(),triangles[val].begin(),triangles[val].end()); // get position of the triangles (faces) crossed by this voxel -- for (unsigned int i=0;i add initfaces) -- count++; -- } -- voxFacesIndex[index+1]=voxFacesIndex[index]+t.size(); -- }else{ -- voxFacesIndex[index+1]=voxFacesIndex[index]; -- } -- index++; -+ int val = surfvol(x,y,z); -+ if (val!=-1){ -+ vector t; -+ t.insert(t.end(),triangles[val].begin(),triangles[val].end()); // get position of the triangles (faces) crossed by this voxel -+ for (unsigned int i=0;i add initfaces) -+ count++; -+ } -+ voxFacesIndex[index+1]=voxFacesIndex[index]+t.size(); -+ }else{ -+ voxFacesIndex[index+1]=voxFacesIndex[index]; -+ } -+ index++; - } - } - } - } - - void tractographyInput::csv_tri_crossed_voxels( float tri[3][3], -- vector& crossed) -+ vector& crossed) - { -- int minx=(int)round(tri[0][0]); -- int miny=(int)round(tri[0][1]); -- int minz=(int)round(tri[0][2]); -+ int minx=(int)MISCMATHS::round(tri[0][0]); -+ int miny=(int)MISCMATHS::round(tri[0][1]); -+ int minz=(int)MISCMATHS::round(tri[0][2]); - int maxx=minx,maxy=miny,maxz=minz; - crossed.clear(); - int i=0;int tmpi; - do{ -- tmpi=(int)round(tri[i][0]); -+ tmpi=(int)MISCMATHS::round(tri[i][0]); - minx=tmpimaxx?tmpi:maxx; -- tmpi=(int)round(tri[i][1]); -+ tmpi=(int)MISCMATHS::round(tri[i][1]); - miny=tmpimaxy?tmpi:maxy; -- tmpi=(int)round(tri[i][2]); -+ tmpi=(int)MISCMATHS::round(tri[i][2]); - minz=tmpimaxz?tmpi:maxz; - i++; -@@ -516,26 +449,26 @@ - for (int x=minx-s;x<=maxx+s;x+=1){ - for (int y=miny-s;y<=maxy+s;y+=1){ - for (int z=minz-s;z<=maxz+s;z+=1){ -- boxcentre[0]=(float)x; -- boxcentre[1]=(float)y; -- boxcentre[2]=(float)z; -- if (triBoxOverlap(boxcentre,boxhalfsize,tri)){ -- v< voxFacesVec; - vector nullV; - -+ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; -+ - if (fsl_imageexists(filename)){ - // filename is a volume -- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; -- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); -+ data.volume=new float[sizeVol]; -+ //memset(data.volume,-1,sizeVol*sizeof(float)); - load_volume(filename,Ssizes,data.volume,data.nlocs,true,false,0,nullV); - data.NVols=1; - }else if (meshExists(filename)){ -@@ -567,8 +502,8 @@ - if (fs){ - fs>>tmp; - do{ -- fnames.push_back(tmp); -- fs>>tmp; -+ fnames.push_back(tmp); -+ fs>>tmp; - }while (!fs.eof()); - }else{ - cerr<& refVol, -- // Output -- MaskData& data, -- Matrix& coords) -+void tractographyInput::load_rois( // Input -+ string filename, -+ Matrix mm2vox, -+ float* Sdims, // Or Matrix2 sizes -+ int* Ssizes, -+ int wcoords, -+ volume& refVol, -+ // Output -+ MaskData& data, -+ Matrix& coords) - { -+ //wcoords:0 do not write, 1 write only coords, 2 write also ROI-id and position -+ - data.sizesStr=new int[3]; - data.sizesStr[0]=0; - data.sizesStr[1]=0; -@@ -644,10 +579,12 @@ - vector voxFacesVec; - vector coordsV; - -+ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; -+ - if (fsl_imageexists(filename)){ - // filename is a volume -- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; -- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); -+ data.volume=new float[sizeVol]; -+ //memset(data.volume,-1,sizeSeed*sizeof(float)); - load_volume(filename,Ssizes,data.volume,data.nlocs,true,wcoords,0,coordsV); - data.NVols=1; - data.IndexRoi=new int[1]; -@@ -655,7 +592,8 @@ - data.sizesStr[4]=1; - }else if (meshExists(filename)){ - load_mesh(filename,verticesVec,facesVec,locsVec,data.nlocs,wcoords,0,coordsV); -- data.VoxFacesIndex=new int[Ssizes[0]*Ssizes[1]*Ssizes[2]+1]; -+ size_t sizeVox2Face = sizeVol+1; -+ data.VoxFacesIndex=new int[sizeVox2Face]; - init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[0],facesVec.size(), - 0,voxFacesVec,data.VoxFacesIndex,locsVec); - data.NSurfs=1; -@@ -670,20 +608,21 @@ - if (fs){ - fs>>tmp; - do{ -- fnames.push_back(tmp); -- if (fsl_imageexists(tmp)) data.NVols++; -- if (meshExists(tmp)) data.NSurfs++; -- fs>>tmp; -+ fnames.push_back(tmp); -+ if (fsl_imageexists(tmp)) data.NVols++; -+ if (meshExists(tmp)) data.NSurfs++; -+ fs>>tmp; - }while (!fs.eof()); - }else{ - cerr<(nv)*sizeVol; -+ load_volume(fnames[i],Ssizes,&data.volume[posSeedvol],data.nlocs,true,wcoords,nroi,coordsV); -+ data.IndexRoi[nv]=nroi; -+ nv++; -+ nroi++; - }else if (meshExists(fnames[i])){ -- load_mesh(fnames[i],verticesVec,facesVec,locsVec,data.nlocs,wcoords,nroi,coordsV); -- init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[lastfacesSize],facesVec.size()-lastfacesSize,lastfacesSize, -- voxFacesVec,&data.VoxFacesIndex[ns*(Ssizes[0]*Ssizes[1]*Ssizes[2]+1)],locsVec); -- data.IndexRoi[data.NVols+ns]=nroi; -- ns++; -- nroi++; -- lastfacesSize=facesVec.size(); -+ size_t posSeedsurf = size_t(ns)*(sizeVol+1); -+ load_mesh(fnames[i],verticesVec,facesVec,locsVec,data.nlocs,wcoords,nroi,coordsV); -+ init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[lastfacesSize],facesVec.size()-lastfacesSize,lastfacesSize, -+ voxFacesVec,&data.VoxFacesIndex[posSeedsurf],locsVec); -+ data.IndexRoi[data.NVols+ns]=nroi; -+ ns++; -+ nroi++; -+ lastfacesSize=facesVec.size(); - }else{ -- cerr<<"load_rois: Unknown file type: "< facesVec, -- // Output -- int* matrix1_locs, -- int* matrix1_idTri, -- int* matrix1_Ntri) -+ int id_vertex, -+ int id_search, -+ vector facesVec, -+ // Output -+ int* matrix1_locs, -+ int* matrix1_idTri, -+ int* matrix1_Ntri) - { - int id=id_search*3; - int num_triangles=0; -@@ -783,21 +721,19 @@ - matrix1_Ntri[id_vertex]=num_triangles; - } - -- -- - void tractographyInput::load_rois_matrix1( tractographyData& tData, -- // Input -- string filename, -- Matrix mm2vox, -- float* Sdims, -- int* Ssizes, -- bool wcoords, -- volume& refVol, -- // Output -- MaskData& data, -- Matrix& coords) -+ // Input -+ string filename, -+ Matrix mm2vox, -+ float* Sdims, -+ int* Ssizes, -+ bool wcoords, -+ volume& refVol, -+ // Output -+ MaskData& data, -+ Matrix& coords) - { -- // a maximum of 12 triangles per seed ? -+ // a maximum of 12 triangles per seed - tData.matrix1_locs=new int[12*tData.nseeds]; - tData.matrix1_idTri=new int[12*tData.nseeds]; - tData.matrix1_Ntri=new int[tData.nseeds]; -@@ -815,10 +751,12 @@ - vector voxFacesVec; - vector coordsV; - -+ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; -+ - if (fsl_imageexists(filename)){ - // filename is a volume -- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; -- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); -+ data.volume=new float[sizeVol]; -+ //memset(data.volume,-1,sizeVol*sizeof(float)); - load_volume(filename,Ssizes,data.volume,data.nlocs,true,wcoords,0,coordsV); - data.NVols=1; - data.IndexRoi=new int[1]; -@@ -832,7 +770,7 @@ - } - }else if (meshExists(filename)){ - load_mesh(filename,verticesVec,facesVec,locsVec,data.nlocs,wcoords,0,coordsV); -- data.VoxFacesIndex=new int[Ssizes[0]*Ssizes[1]*Ssizes[2]+1]; -+ data.VoxFacesIndex=new int[sizeVol+1]; - init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[0],facesVec.size(), - 0,voxFacesVec,data.VoxFacesIndex,locsVec); - data.NSurfs=1; -@@ -850,20 +788,19 @@ - if (fs){ - fs>>tmp; - do{ -- fnames.push_back(tmp); -- if (fsl_imageexists(tmp)) data.NVols++; -- if (meshExists(tmp)) data.NSurfs++; -- fs>>tmp; -+ fnames.push_back(tmp); -+ if (fsl_imageexists(tmp)) data.NVols++; -+ if (meshExists(tmp)) data.NSurfs++; -+ fs>>tmp; - }while (!fs.eof()); - }else{ - cerr<*& m_prob, -- bool initialize_m_prob, -- volume*& m_prob2, -- bool initialize_m_prob2, -- volume4D*& m_localdir, -- volume& refVol) // reference -+size_t tractographyInput::load_seeds_rois( tractographyData& tData, -+ string seeds_filename, -+ string ref_filename, -+ float* Sdims, -+ int* Ssizes, -+ int convention, -+ float*& seeds, -+ int*& seeds_ROI, -+ Matrix& mm2vox, -+ float* vox2mm, -+ volume*& m_prob, -+ bool initialize_m_prob, -+ volume*& m_prob2, -+ bool initialize_m_prob2, -+ volume4D*& m_localdir, -+ volume& refVol) // reference - { - Log& logger = LogSingleton::getInstance(); - probtrackxOptions& opts=probtrackxOptions::getInstance(); - vector nullV; -- int nseeds=0; -+ size_t nseeds=0; -+ - if (fsl_imageexists(seeds_filename)){ - // a volume file - if(opts.network.value()){ -@@ -981,19 +918,20 @@ - Ssizes[0]=seedsVol.xsize(); - Ssizes[1]=seedsVol.ysize(); - Ssizes[2]=seedsVol.zsize(); -+ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; - set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); - -- seeds=new float[3*Ssizes[0]*Ssizes[1]*Ssizes[2]]; //max -+ seeds=new float[3*sizeVol]; - for (int z=0;zreinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -- copybasicproperties(refVol,*m_prob); -- *m_prob=0; -- } -- if (initialize_m_prob2){ -- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -- copybasicproperties(refVol,*m_prob2); -- *m_prob2=0; -- } -- if(opts.opathdir.value()){ // OPATHDIR -- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); -- copybasicproperties(refVol,*m_localdir); -- *m_localdir=0; -- } -+ read_volume(refVol,ref_filename); -+ Sdims[0]=refVol.xdim(); -+ Sdims[1]=refVol.ydim(); -+ Sdims[2]=refVol.zdim(); -+ Ssizes[0]=refVol.xsize(); -+ Ssizes[1]=refVol.ysize(); -+ Ssizes[2]=refVol.zsize(); -+ set_vox2mm(convention,Sdims,Ssizes,refVol,mm2vox,vox2mm); -+ if (initialize_m_prob){ -+ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -+ copybasicproperties(refVol,*m_prob); -+ *m_prob=0; -+ } -+ if (initialize_m_prob2){ -+ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -+ copybasicproperties(refVol,*m_prob2); -+ *m_prob2=0; -+ } -+ if(opts.opathdir.value()){ // OPATHDIR -+ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); -+ copybasicproperties(refVol,*m_localdir); -+ *m_localdir=0; -+ } - }else{ -- cerr<<"Reference volume "< locs; -@@ -1059,38 +997,38 @@ - int loc=0; - float c1,c2,c3; - for (unsigned int vertex=0;vertex>tmp; - do{ -- fnames.push_back(tmp); -- fs>>tmp; -+ fnames.push_back(tmp); -+ fs>>tmp; - }while (!fs.eof()); - }else{ - cerr<<"Seed file "< seedsVol; -- read_volume(seedsVol,fnames[i]); -- if (!found_vol){ -- refVol=seedsVol; -- Sdims[0]=seedsVol.xdim(); -- Sdims[1]=seedsVol.ydim(); -- Sdims[2]=seedsVol.zdim(); -- Ssizes[0]=seedsVol.xsize(); -- Ssizes[1]=seedsVol.ysize(); -- Ssizes[2]=seedsVol.zsize(); -- set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); -- if (initialize_m_prob){ -- m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -- copybasicproperties(seedsVol,*m_prob); -- *m_prob=0; -- } -- if (initialize_m_prob2){ -- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -- copybasicproperties(seedsVol,*m_prob2); -- *m_prob2=0; -- } -- if(opts.opathdir.value()){ // OPATHDIR -- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); -- copybasicproperties(seedsVol,*m_localdir); -- *m_localdir=0; -- } -- }else{ -- if (Sdims[0]!=seedsVol.xdim()||Sdims[1]!=seedsVol.ydim()||Sdims[2]!=seedsVol.zdim()|| -- Ssizes[0]!=seedsVol.xsize()||Ssizes[1]!=seedsVol.ysize()||Ssizes[2]!=seedsVol.zsize()){ -- cerr<<"Seed volumes must have same dimensions"< seedsVol; -+ read_volume(seedsVol,fnames[i]); -+ if (!found_vol){ -+ refVol=seedsVol; -+ Sdims[0]=seedsVol.xdim(); -+ Sdims[1]=seedsVol.ydim(); -+ Sdims[2]=seedsVol.zdim(); -+ Ssizes[0]=seedsVol.xsize(); -+ Ssizes[1]=seedsVol.ysize(); -+ Ssizes[2]=seedsVol.zsize(); -+ set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); -+ if (initialize_m_prob){ -+ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -+ copybasicproperties(seedsVol,*m_prob); -+ *m_prob=0; -+ } -+ if (initialize_m_prob2){ -+ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -+ copybasicproperties(seedsVol,*m_prob2); -+ *m_prob2=0; -+ } -+ if(opts.opathdir.value()){ // OPATHDIR -+ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); -+ copybasicproperties(seedsVol,*m_localdir); -+ *m_localdir=0; -+ } -+ }else{ -+ if (Sdims[0]!=seedsVol.xdim()||Sdims[1]!=seedsVol.ydim()||Sdims[2]!=seedsVol.zdim()|| -+ Ssizes[0]!=seedsVol.xsize()||Ssizes[1]!=seedsVol.ysize()||Ssizes[2]!=seedsVol.zsize()){ -+ cerr<<"Seed volumes must have same dimensions"<reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -- copybasicproperties(refVol,*m_prob); -- *m_prob=0; -- } -- if (initialize_m_prob2){ -- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -- copybasicproperties(refVol,*m_prob2); -- *m_prob2=0; -- } -- if(opts.opathdir.value()){ // OPATHDIR -- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); -- copybasicproperties(refVol,*m_localdir); -- *m_localdir=0; -- } -+ read_volume(refVol,ref_filename); -+ Sdims[0]=refVol.xdim(); -+ Sdims[1]=refVol.ydim(); -+ Sdims[2]=refVol.zdim(); -+ Ssizes[0]=refVol.xsize(); -+ Ssizes[1]=refVol.ysize(); -+ Ssizes[2]=refVol.zsize(); -+ set_vox2mm(convention,Sdims,Ssizes,refVol,mm2vox,vox2mm); -+ if (initialize_m_prob){ -+ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -+ copybasicproperties(refVol,*m_prob); -+ *m_prob=0; -+ } -+ if (initialize_m_prob2){ -+ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); -+ copybasicproperties(refVol,*m_prob2); -+ *m_prob2=0; -+ } -+ if(opts.opathdir.value()){ // OPATHDIR -+ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); -+ copybasicproperties(refVol,*m_localdir); -+ *m_localdir=0; -+ } - }else{ -- cerr<<"Reference volume "< locs; -- vector vertices; -- vector faces; -- load_mesh(fnames[i],vertices,faces,locs,nlocs,false,0,nullV); -- seedsV.resize(seedsV.size()+vertices.size()*3); -- int loc=0; -- float c1,c2,c3; -- float s1,s2,s3; -- for (unsigned int vertex=0;vertex=0 && s1=0 && s2=0 && s3 seedsVol; -- read_volume(seedsVol,fnames[i]); -- seedsV.resize(seedsV.size()+3*Ssizes[0]*Ssizes[1]*Ssizes[2]); //max -- for (int z=0;z locs; -+ vector vertices; -+ vector faces; -+ load_mesh(fnames[i],vertices,faces,locs,nlocs,false,0,nullV); -+ seedsV.resize(seedsV.size()+vertices.size()*3); -+ int loc=0; -+ float c1,c2,c3; -+ float s1,s2,s3; -+ for (unsigned int vertex=0;vertex=0 && s1=0 && s2=0 && s3 seedsVol; -+ read_volume(seedsVol,fnames[i]); -+ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; -+ seedsV.resize(seedsV.size()+3*sizeVol); //max -+ for (int z=0;z vol, -- Matrix& mm2vox, -- float* vox2mm) -+void tractographyInput::set_vox2mm(int convention, -+ float* Sdims, -+ int* Ssizes, -+ volume vol, -+ Matrix& mm2vox, -+ float* vox2mm) - { - // VOX2MM - Matrix Mvox2mm(4,4); -@@ -1315,9 +1253,9 @@ - // freesurfer - Matrix mat(4,4); - mat << -1/Sdims[0] << 0 << 0 << Ssizes[0]/2 -- << 0 << 0 << -1/Sdims[1] << Ssizes[2]/2 -- << 0 << 1/Sdims[2] << 0 << Ssizes[1]/2 -- << 0 << 0 << 0 << 1; -+ << 0 << 0 << -1/Sdims[1] << Ssizes[2]/2 -+ << 0 << 1/Sdims[2] << 0 << Ssizes[1]/2 -+ << 0 << 0 << 0 << 1; - mm2vox=mat; - Mvox2mm=mm2vox.i(); - }else if (convention==2){ -@@ -1349,25 +1287,26 @@ - vox2mm[12]=Mvox2mm(4,1); vox2mm[13]=Mvox2mm(4,2); vox2mm[14]=Mvox2mm(4,3); vox2mm[15]=Mvox2mm(4,4); - } - --void tractographyInput::load_tractographyData( tractographyData& tData, -- volume*& m_prob, -- volume*& m_prob2, -- float**& ConNet, -- float**& ConNetb, -- int& nRowsNet, -- int& nColsNet, -- float**& ConMat1, -- float**& ConMat1b, -- int& nRowsMat1, -- int& nColsMat1, -- float**& ConMat3, -- float**& ConMat3b, -- int& nRowsMat3, -- int& nColsMat3, -- float*& m_s2targets, -- float*& m_s2targetsb, -- volume4D*& m_localdir) -+void tractographyInput::load_tractographyData(tractographyData& tData, -+ volume*& m_prob, -+ volume*& m_prob2, -+ float**& ConNet, -+ float**& ConNetb, -+ int& nRowsNet, -+ int& nColsNet, -+ float**& ConMat1, -+ float**& ConMat1b, -+ int& nRowsMat1, -+ int& nColsMat1, -+ float**& ConMat3, -+ float**& ConMat3b, -+ int& nRowsMat3, -+ int& nColsMat3, -+ float*& m_s2targets, -+ float*& m_s2targetsb, -+ volume4D*& m_localdir) - { -+ printf("Loading tractography data\n"); - probtrackxOptions& opts=probtrackxOptions::getInstance(); - Log& logger = LogSingleton::getInstance(); - -@@ -1427,7 +1366,7 @@ - for(int z=0;z0){ -- read_volume4D(tmpvol,basename+"_th"+num2str(f+1)+"samples"); -- tmpmat=tmpvol.matrix(mask3D); -+ read_volume4D(tmpvol,basename+"_th"+num2str(f+1)+"samples"); -+ tmpmat=tmpvol.matrix(mask3D); - } - for(int s=0;s Seeds transform needed" << endl; -- exit(1); -+ cerr << "TRACT::Streamliner:: DTI -> Seeds transform needed" << endl; -+ exit(1); - } - FnirtFileReader iffr(opts.dti_to_seeds.value()); - volume4D DTISeedwarp4D = iffr.FieldAsNewimageVolume4D(true); -@@ -1653,13 +1593,13 @@ - tData.Warp_D2S_sizes[2]=DTISeedwarp4D.zsize(); - tData.DTISeedwarp = new float[3*size]; - for(int v=0;v<3;v++){ -- for(int z=0;z - #include -@@ -83,84 +23,84 @@ - - /// Method load all the necessary data from the input files to perform GPU Tractography - void load_tractographyData( tractographyData& tData, -- volume*& m_prob, -- volume*& m_prob2, -- float**& ConNet, -- float**& ConNetb, -- int& nRowsNet, -- int& nColsNet, -- float**& ConMat1, -- float**& ConMat1b, -- int& nRowsMat1, -- int& nColsMat1, -- float**& ConMat3, -- float**& ConMat3b, -- int& nRowsMat3, -- int& nColsMat3, -- float*& m_s2targets, -- float*& m_s2targetsb, -- volume4D*& m_localdir); -+ volume*& m_prob, -+ volume*& m_prob2, -+ float**& ConNet, -+ float**& ConNetb, -+ int& nRowsNet, -+ int& nColsNet, -+ float**& ConMat1, -+ float**& ConMat1b, -+ int& nRowsMat1, -+ int& nColsMat1, -+ float**& ConMat3, -+ float**& ConMat3b, -+ int& nRowsMat3, -+ int& nColsMat3, -+ float*& m_s2targets, -+ float*& m_s2targetsb, -+ volume4D*& m_localdir); - - /// General Method to read a Surface file in ASCII, VTK or GIFTI format -- void load_mesh( string& filename, -- vector& vertices, // all the vertices, same order than file -- vector& faces, // all the faces, same order than file -- vector& locs, // used to store the id of a vertex in the Matrix. If -1, then vertex is non-activated -- int& nlocs, // number of ids(vertices) in the Matrix -- bool wcoords, // save coordinates of the vertices in a file ? -- int nroi, // number of ROI to identify coordinates -- vector& coords); // coordinates xyz of the vertices -+ void load_mesh( string& filename, -+ vector& vertices, // all the vertices, same order than file -+ vector& faces, // all the faces, same order than file -+ vector& locs, // used to store the id of a vertex in the Matrix. If -1, then vertex is non-activated -+ int& nlocs, // number of ids(vertices) in the Matrix -+ bool wcoords, // save coordinates of the vertices in a file ? -+ int nroi, // number of ROI to identify coordinates -+ vector& coords); // coordinates xyz of the vertices - - /// Method to read a surface file in ASCII format -- void load_mesh_ascii( string& filename, -- vector& vertices, -- vector& faces, -- vector& locs, -- int& nlocs, -- bool wcoords, -- int nroi, -- vector& coords); -+ void load_mesh_ascii( string& filename, -+ vector& vertices, -+ vector& faces, -+ vector& locs, -+ int& nlocs, -+ bool wcoords, -+ int nroi, -+ vector& coords); - - /// Method to read a surface file in VTK format -- void load_mesh_vtk( string& filename, -- vector& vertices, -- vector& faces, -- vector& locs, -- int& nlocs, -- bool wcoords, -- int nroi, -- vector& coords); -+ void load_mesh_vtk( string& filename, -+ vector& vertices, -+ vector& faces, -+ vector& locs, -+ int& nlocs, -+ bool wcoords, -+ int nroi, -+ vector& coords); - - /// Method to read a surface file in GIFTI format -- void load_mesh_gifti( string& filename, -- vector& vertices, -- vector& faces, -- vector& locs, -- int& nlocs, -- bool wcoords, -- int nroi, -- vector& coords); -+ void load_mesh_gifti( string& filename, -+ vector& vertices, -+ vector& faces, -+ vector& locs, -+ int& nlocs, -+ bool wcoords, -+ int nroi, -+ vector& coords); - - /// Method to read a Volume - void load_volume( string& filename, -- int* Ssizes, -- float* Vout, -- int& nlocs, -- bool reset, -- bool wcoords, -- int nroi, -- vector& coords); -+ int* Ssizes, -+ float* Vout, -+ int& nlocs, -+ bool reset, -+ bool wcoords, -+ int nroi, -+ vector& coords); - - /// Method to initialise the realtionship between voxels and triangles for a Surface -- void init_surfvol( int* Ssizes, -- Matrix& mm2vox, -- vector& vertices, -- int* faces, -- int sizefaces, // number of faces this time (maybe there are several ROIs for the same mask) -- int initfaces, // number of faces in previos times -- vector& voxFaces, // list of faces of all the voxels -- int* voxFacesIndex, // starting point of each voxel in the list -- vector& locsV); -+ void init_surfvol( int* Ssizes, -+ Matrix& mm2vox, -+ vector& vertices, -+ int* faces, -+ int sizefaces, // number of faces this time (maybe there are several ROIs for the same mask) -+ int initfaces, // number of faces in previos times -+ vector& voxFaces, // list of faces of all the voxels -+ int* voxFacesIndex, // starting point of each voxel in the list -+ vector& locsV); - - /// Method to find out what voxels are crossed by a triangle - void csv_tri_crossed_voxels(float tri[3][3], -@@ -168,62 +108,62 @@ - - /// Method to read all the ROIs of a mask in the same structure: for stop and avoid masks - void load_rois_mixed(string filename, -- Matrix mm2vox, -- float* Sdims, -- int* Ssizes, -- // Output -- MaskData& matData); -+ Matrix mm2vox, -+ float* Sdims, -+ int* Ssizes, -+ // Output -+ MaskData& matData); - - /// Method to read the ROIs of a mask in concatenated structures: for wtstop and waypoints masks -- void load_rois(// Input -- string filename, -- Matrix mm2vox, -- float* Sdims, -- int* Ssizes, -- int wcoords, -- volume& refVol, -- // Output -- MaskData& matData, -- Matrix& coords); -+ void load_rois( // Input -+ string filename, -+ Matrix mm2vox, -+ float* Sdims, -+ int* Ssizes, -+ int wcoords, -+ volume& refVol, -+ // Output -+ MaskData& matData, -+ Matrix& coords); - - /// Same than load_rois but it includes the initialisation of the rows (including triangles) of Matrix1 - void load_rois_matrix1( tractographyData& tData, -- // Input -- string filename, -- Matrix mm2vox, -- float* Sdims, -- int* Ssizes, -- bool wcoords, -- volume& refVol, -- // Output -- MaskData& data, -- Matrix& coords); -+ // Input -+ string filename, -+ Matrix mm2vox, -+ float* Sdims, -+ int* Ssizes, -+ bool wcoords, -+ volume& refVol, -+ // Output -+ MaskData& data, -+ Matrix& coords); - - /// Method to load the seeds. Can be defined by volumes and/or by surfaces -- int load_seeds_rois(tractographyData& tData, -- string seeds_filename, -- string ref_filename, -- float* Sdims, -- int* Ssizes, -- int convention, -- float*& seeds, -- int*& seeds_ROI, -- Matrix& mm2vox, -- float* vox2mm, -- volume*& m_prob, -- bool initialize_m_prob, -- volume*& m_prob2, -- bool initialize_m_prob2, -- volume4D*& m_localdir, -- volume& refVol); -+ size_t load_seeds_rois(tractographyData& tData, -+ string seeds_filename, -+ string ref_filename, -+ float* Sdims, -+ int* Ssizes, -+ int convention, -+ float*& seeds, -+ int*& seeds_ROI, -+ Matrix& mm2vox, -+ float* vox2mm, -+ volume*& m_prob, -+ bool initialize_m_prob, -+ volume*& m_prob2, -+ bool initialize_m_prob2, -+ volume4D*& m_localdir, -+ volume& refVol); - - /// Method to set the transformation: voxel to milimeters -- void set_vox2mm(int convention, -- float* Sdims, -- int* Ssizes, -- volume vol, -- Matrix& mm2vox, // 4x4 -- float* vox2mm); // 4x4 -+ void set_vox2mm(int convention, -+ float* Sdims, -+ int* Ssizes, -+ volume vol, -+ Matrix& mm2vox, // 4x4 -+ float* vox2mm); // 4x4 - - }; - -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tractographyKernels.cu ---- fsl.orig/src/ptx2/CUDA/tractographyKernels.cu 2019-11-15 10:47:30.371790061 +0100 -+++ fsl/src/ptx2/CUDA/tractographyKernels.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include - #include -@@ -77,17 +17,17 @@ - - template - __global__ void get_path_kernel( -- tractographyData* data_gpu, -- const int maxThread, -+ tractographyData* data_gpu, -+ const int maxThread, - //essential -- curandState* state, -- const long long offset, -+ curandState* state, -+ const long long offset, - //loopcheck -- int* loopcheckkeys, -- float3* loopcheckdirs, -+ int* loopcheckkeys, -+ float3* loopcheckdirs, - //OUTPUT -- float* path, -- int* lengths) -+ float* path, -+ int* lengths) - { - unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; - if(id>=maxThread) return; -@@ -124,13 +64,15 @@ - - // Use path to store my intial coordinates - // We want to start at the same exact point, even if sampvox is activated -- path[id*data_gpu->nsteps*3]= data_gpu->seeds[numseed*3]; -- path[id*data_gpu->nsteps*3+1]= data_gpu->seeds[numseed*3+1]; -- path[id*data_gpu->nsteps*3+2]= data_gpu->seeds[numseed*3+2]; -- -- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]= data_gpu->seeds[numseed*3]; -- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+1]= data_gpu->seeds[numseed*3+1]; -- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+2]= data_gpu->seeds[numseed*3+2]; -+ uint offset_path_fw = id*data_gpu->nsteps*3; -+ uint offset_path_bw = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); -+ path[offset_path_fw]= data_gpu->seeds[numseed*3]; -+ path[offset_path_fw+1]= data_gpu->seeds[numseed*3+1]; -+ path[offset_path_fw+2]= data_gpu->seeds[numseed*3+2]; -+ -+ path[offset_path_bw]= data_gpu->seeds[numseed*3]; -+ path[offset_path_bw+1]= data_gpu->seeds[numseed*3+1]; -+ path[offset_path_bw+2]= data_gpu->seeds[numseed*3+2]; - - - if(data_gpu->sampvox>0){ -@@ -145,13 +87,13 @@ - rej=false; - } - -- path[id*data_gpu->nsteps*3]+=dx/C_Sdims[0]; -- path[id*data_gpu->nsteps*3+1]+=dy/C_Sdims[1]; -- path[id*data_gpu->nsteps*3+2]+=dz/C_Sdims[2]; -- -- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]+=dx/C_Sdims[0]; -- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+1]+=dy/C_Sdims[1]; -- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+2]+=dz/C_Sdims[2]; -+ path[offset_path_fw]+=dx/C_Sdims[0]; -+ path[offset_path_fw+1]+=dy/C_Sdims[1]; -+ path[offset_path_fw+2]+=dz/C_Sdims[2]; -+ -+ path[offset_path_bw]+=dx/C_Sdims[0]; -+ path[offset_path_bw+1]+=dy/C_Sdims[1]; -+ path[offset_path_bw+2]+=dz/C_Sdims[2]; - } - // track in one direction - lengths[id*2]=streamline(data_gpu, -@@ -161,7 +103,7 @@ - &partRx[threadIdx.x],&partRy[threadIdx.x],&partRz[threadIdx.x], - &memSH_a[threadIdx.x],&memSH_b[threadIdx.x],&memSH_c[threadIdx.x], - &memSH_d[threadIdx.x],&memSH_e[threadIdx.x],&memSH_f[threadIdx.x], -- &path[id*data_gpu->nsteps*3],part_init,part_has_jumped); -+ &path[offset_path_fw],part_init,part_has_jumped); - - // track in the other direction - lengths[id*2+1]=streamline(data_gpu, -@@ -171,7 +113,7 @@ - &partRx[threadIdx.x],&partRy[threadIdx.x],&partRz[threadIdx.x], - &memSH_a[threadIdx.x],&memSH_b[threadIdx.x],&memSH_c[threadIdx.x], - &memSH_d[threadIdx.x],&memSH_e[threadIdx.x],&memSH_f[threadIdx.x], -- &path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)],part_init,part_has_jumped); -+ &path[offset_path_bw],part_init,part_has_jumped); - - state[id]=localState; // save state, otherwise random numbers will be repeated (start at the same point) - } -@@ -180,11 +122,11 @@ - /////// AVOID MASK /////// - ///////////////////////// - template --__global__ void avoid_masks_kernel( tractographyData* data_gpu, -- const int maxThread, -- //INPUT-OUTPUT -- float* paths, -- int* lengths) -+__global__ void avoid_masks_kernel( tractographyData* data_gpu, -+ const int maxThread, -+ //INPUT-OUTPUT -+ float* paths, -+ int* lengths) - { - unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; - if(id>=maxThread) return; -@@ -199,7 +141,8 @@ - /////////////////////// - ////// ONE WAY //////// - /////////////////////// -- float* mypath=&paths[id*data_gpu->nsteps*3]; -+ uint offset_path = id*data_gpu->nsteps*3; -+ float* mypath=&paths[offset_path]; - int mylength=lengths[id*2]; - int2 rejflag; - -@@ -253,8 +196,9 @@ - /////////////////////// - ////// OTHER WAY ///// - /////////////////////// -- rejflag.y=0; -- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; -+ rejflag.y=0; -+ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); -+ mypath=&paths[offset_path]; - mylength=lengths[id*2+1]; - - segmentAx[threadIdx.x]=mypath[0]; -@@ -313,11 +257,11 @@ - /////// STOP MASK /////// - ///////////////////////// - template --__global__ void stop_masks_kernel( tractographyData* data_gpu, -- const int maxThread, -- // INPUT-OUTPUT -- float* paths, -- int* lengths) // num of coordinates -+__global__ void stop_masks_kernel( tractographyData* data_gpu, -+ const int maxThread, -+ // INPUT-OUTPUT -+ float* paths, -+ int* lengths) // num of coordinates - { - unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; - if(id>=maxThread) return; -@@ -333,7 +277,8 @@ - /////////////////////// - ////// ONE WAY //////// - /////////////////////// -- float* mypath=&paths[id*data_gpu->nsteps*3]; -+ uint offset_path = id*data_gpu->nsteps*3; -+ float* mypath=&paths[offset_path]; - int mylength=lengths[id*2]; - segmentAx[threadIdx.x]=mypath[0]; - segmentAy[threadIdx.x]=mypath[1]; -@@ -387,8 +332,9 @@ - } - /////////////////////// - ////// OTHER WAY ///// -- /////////////////////// -- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; -+ /////////////////////// -+ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); -+ mypath=&paths[offset_path]; - mylength=lengths[id*2+1]; - - segmentAx[threadIdx.x]=mypath[0]; -@@ -454,11 +400,11 @@ - // ignoring forcefirststep ... if seed is inside wtstop: is treated - - template --__global__ void wtstop_masks_kernel( tractographyData* data_gpu, -- const int maxThread, -- // INPUT-OUTPUT -- float* paths, -- int* lengths) -+__global__ void wtstop_masks_kernel( tractographyData* data_gpu, -+ const int maxThread, -+ // INPUT-OUTPUT -+ float* paths, -+ int* lengths) - { - unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; - if(id>=maxThread) return; -@@ -480,7 +426,8 @@ - ///////////////// - //// ONE WAY //// - ///////////////// -- float* mypath=&paths[id*data_gpu->nsteps*3]; -+ uint offset_path = id*data_gpu->nsteps*3; -+ float* mypath=&paths[offset_path]; - int mylength=lengths[id*2]; - bool wtstop=false; - // set flags to 1 (still not in roi) -@@ -546,7 +493,8 @@ - //////////////////// - //// OTHER WAY ///// - //////////////////// -- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; -+ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); -+ mypath=&paths[offset_path]; - mylength=lengths[id*2+1]; - wtstop=false; - // set flags to 1 (still not in roi) -@@ -615,11 +563,11 @@ - /////// WAYPOINTS MASK //////// - /////////////////////////////// - template --__global__ void way_masks_kernel( tractographyData* data_gpu, -- const int maxThread, -- // INNPUT-OUTPUT -- float* paths, -- int* lengths) -+__global__ void way_masks_kernel( tractographyData* data_gpu, -+ const int maxThread, -+ // INNPUT-OUTPUT -+ float* paths, -+ int* lengths) - { - ///// DYNAMIC SHARED MEMORY ///// - extern __shared__ float shared[]; -@@ -634,7 +582,8 @@ - unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; - if(id>=maxThread) return; - -- float* mypath=&paths[id*data_gpu->nsteps*3]; -+ uint offset_path = id*data_gpu->nsteps*3; -+ float* mypath=&paths[offset_path]; - int mylength=lengths[id*2]; - - int numpassed=0; -@@ -745,7 +694,8 @@ - numpassed=0; - order=true; - } -- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; -+ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); -+ mypath=&paths[offset_path]; - mylength=lengths[id*2+1]; - - if(waySurf){ -@@ -841,18 +791,17 @@ - ///////////////////////////// - template - // savelength 0: no --pd, nor --ompl | 1: --pd | 2: --ompl (ConNet pathlengths, ConNetb binary hits, and later calculates mean) --__global__ void net_masks_kernel( -- tractographyData* data_gpu, -- const int maxThread, -- const long long offset, -- // INNPUT-OUTPUT -- float* paths, -- int* lengths, -- float* ConNet, -- float* ConNetb, -- // To use in case too many Net ROIs -- float* net_flags_Global, -- float* net_values_Global) -+__global__ void net_masks_kernel( tractographyData* data_gpu, -+ const int maxThread, -+ const long long offset, -+ // INNPUT-OUTPUT -+ float* paths, -+ int* lengths, -+ float* ConNet, -+ float* ConNetb, -+ // To use in case too many Net ROIs -+ float* net_flags_Global, -+ float* net_values_Global) - { - unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; - if(id>=maxThread) return; -@@ -887,7 +836,8 @@ - int numseed = (offset+id)/data_gpu->nparticles; - int ROI = data_gpu->seeds_ROI[numseed]; - -- float* mypath=&paths[id*data_gpu->nsteps*3]; -+ uint offset_path = id*data_gpu->nsteps*3; -+ float* mypath=&paths[offset_path]; - int mylength=lengths[id*2]; - int numpassed=1; // count my own ROI - -@@ -987,7 +937,8 @@ - net_flags[ROI]=1; // my own ROI - numpassed=1; // count my own ROI - -- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; -+ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); -+ mypath=&paths[offset_path]; - mylength=lengths[id*2+1]; - - if(netSurf){ -@@ -1092,16 +1043,16 @@ - ///////////////////////////// - template - // savelength 0: no --pd or --ompl | 1: --pd | 2: --ompl --__global__ void targets_masks_kernel( tractographyData* data_gpu, -- const int maxThread, -- const long long offset, -- // INNPUT-OUTPUT -- float* paths, -- int* lengths, -- float* s2targets_gpu, // a values for each Seed and for each target (Nseeds x NTragets) -- float* s2targetsb_gpu, -- // To use in case too many Net ROIs -- float* targ_flags_Global) -+__global__ void targets_masks_kernel( tractographyData* data_gpu, -+ const int maxThread, -+ const long long offset, -+ // INNPUT-OUTPUT -+ float* paths, -+ int* lengths, -+ float* s2targets_gpu, // (Nseeds x NTargets) -+ float* s2targetsb_gpu, -+ // To use in case too many Net ROIs -+ float* targ_flags_Global) - { - unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; - if(id>=maxThread) return; -@@ -1127,7 +1078,8 @@ - targ_flags = &targ_flags_Global[id*totalTargets]; - } - -- float* mypath=&paths[id*data_gpu->nsteps*3]; -+ uint offset_path = id*data_gpu->nsteps*3; -+ float* mypath=&paths[offset_path]; - int mylength=lengths[id*2]; - - for(int i=0;isteplength; -- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; -+ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); -+ mypath=&paths[offset_path]; - mylength=lengths[id*2+1]; - - if(targSurf){ -@@ -1289,16 +1242,16 @@ - /////// MATRIX MASKs ///////// - /////////////////////////////// - template // M2 is for Matrix2: it can be defined in a different space --__global__ void matrix_kernel( tractographyData* data_gpu, -- const int maxThread, -- float* paths, -- int* lengths, -- bool pathdist, -- bool omeanpathlength, -- MaskData* matrixData, // info vols & surfs -- // OUTPUT -- float3* crossed, -- int* numcrossed) -+__global__ void matrix_kernel( tractographyData* data_gpu, -+ const int maxThread, -+ float* paths, -+ int* lengths, -+ bool pathdist, -+ bool omeanpathlength, -+ MaskData* matrixData, // info vols & surfs -+ // OUTPUT -+ float3* crossed, -+ int* numcrossed) - { - unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; - if(id>=maxThread) return; -@@ -1331,7 +1284,8 @@ - ///////////////// - //// ONE WAY //// - ///////////////// -- float* mypath=&paths[id*data_gpu->nsteps*3]; -+ uint offset_path = id*data_gpu->nsteps*3; -+ float* mypath=&paths[offset_path]; - if(HSurfs){ - if(M2){ - vox_to_vox_S2M2(mypath,&segmentAx[threadIdx.x],&segmentAy[threadIdx.x],&segmentAz[threadIdx.x]); -@@ -1388,7 +1342,8 @@ - if(pathdist||omeanpathlength) pathlength=-data_gpu->steplength; // it starts with the second coordinate of the path - // reverse, m_tracksign !! . If different directions when crossing 2 nodes, then the path distance is longer. - -- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; -+ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); -+ mypath=&paths[offset_path]; - mylength=lengths[id*2+1]; - if(HSurfs){ - if(M2){ -@@ -1444,21 +1399,22 @@ - ///////// UPDATE PATHS VOLUME /////// - ///////////////////////////////////// - template --__global__ void update_path_kernel( tractographyData* data_gpu, -- const int maxThread, -- float* path, -- int* lengths, -- int* beenhere, -- const int upper_limit, -- // OUTPUT -- float* m_prob, -- float* m_prob2, // for omeanpathlength -- float* m_localdir) // for opathdir -+__global__ void update_path_kernel( tractographyData* data_gpu, -+ const int maxThread, -+ float* path, -+ int* lengths, -+ int* beenhere, -+ const int upper_limit, -+ // OUTPUT -+ float* m_prob, -+ float* m_prob2, // for omeanpathlength -+ float* m_localdir) // for opathdir - { - int id = threadIdx.x + blockIdx.x*blockDim.x; - if(id>=maxThread) return; - -- float* mypath = &path[id*data_gpu->nsteps*3]; -+ uint offset_path = id*data_gpu->nsteps*3; -+ float* mypath = &path[offset_path]; - int mylength = lengths[id*2]; - int* m_beenhere = &beenhere[id*(data_gpu->nsteps)]; - int coordinatex,coordinatey,coordinatez; -@@ -1555,7 +1511,8 @@ - } - - // other way -- mypath = &path[id*data_gpu->nsteps*3+(data_gpu->nsteps/2)*3]; -+ offset_path = id*data_gpu->nsteps*3+(data_gpu->nsteps/2)*3; -+ mypath = &path[offset_path]; - mylength = lengths[id*2+1]; - pathlength=0.0f; - -diff -Nru fsl.orig/src/ptx2/CUDA/transformationsDevice.cu fsl/src/ptx2/CUDA/transformationsDevice.cu ---- fsl.orig/src/ptx2/CUDA/transformationsDevice.cu 2019-11-15 10:47:30.379790000 +0100 -+++ fsl/src/ptx2/CUDA/transformationsDevice.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2005 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - __constant__ float C_Sdims[3]; - __constant__ float C_Ddims[3]; -diff -Nru fsl.orig/src/ptx2/probtrackx_gpu.cc fsl/src/ptx2/probtrackx_gpu.cc ---- fsl.orig/src/ptx2/probtrackx_gpu.cc 2019-11-15 10:47:30.549788697 +0100 -+++ fsl/src/ptx2/probtrackx_gpu.cc 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include "probtrackx.h" - #include "saveResults_ptxGPU.h" -diff -Nru fsl.orig/src/ptx2/saveResults_ptxGPU.cc fsl/src/ptx2/saveResults_ptxGPU.cc ---- fsl.orig/src/ptx2/saveResults_ptxGPU.cc 2019-11-15 10:47:30.417789709 +0100 -+++ fsl/src/ptx2/saveResults_ptxGPU.cc 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include "probtrackx.h" - #include "CUDA/tractographyInput.h" -@@ -326,7 +266,7 @@ - ////// save seeds to targets ////// - /////////////////////////////////// - if(opts.s2tout.value()){ -- long pos=0; -+ size_t pos=0; - int ntargets=data_host.targets.NVols+data_host.targets.NSurfs; - if (fsl_imageexists(opts.seedfile.value())){ - volume tmp; -@@ -392,7 +332,7 @@ - int nfaces=data_host.seeds_mesh_info[1]; - - if(f.is_open()){ -- int pos2=0; -+ size_t pos2=0; - for(int i=0;i -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html -## - -easyblock = 'CMakeMake' - -name = 'VTK' -version = '8.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.vtk.org' -description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for - 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several - interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization - algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques - such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} -toolchainopts = {'usempi': True} - -source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] -sources = [ - SOURCE_TAR_GZ, - '%(name)sData-%(version)s.tar.gz', -] -checksums = [ - '71a09b4340f0a9c58559fe946dc745ab68a866cf20636a41d97b6046cb736324', # VTK-8.1.1.tar.gz - 'e16c2d665f052b6aeb981aea17f0309849e661a0038e18c9880bd6e6519c4fcc', # VTKData-8.1.1.tar.gz -] - -builddependencies = [('CMake', '3.12.1')] - -dependencies = [ - ('Python', '3.6.6'), - ('HDF5', '1.10.2'), - ('libGLU', '9.0.0'), - ('X11', '20180604'), -] - -configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " -configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " -configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT -configopts += "-DVTK_Group_MPI:BOOL=ON " -configopts += "-DVTK_WRAP_PYTHON=ON " -preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " -preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -sanity_check_paths = { - 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource']], - 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], -} - -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - -moduleclass = 'vis' From 4bac4aad6e4f6b496d31ad3166a7e8dd0927045a Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 11:10:53 +0100 Subject: [PATCH 035/468] Changed reported http by Travis to https --- .../easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb | 4 ++-- easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb index 8c378112714..56b711bd3ea 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb @@ -13,13 +13,13 @@ version = '6.0.2' local_pyver = '2.7.15' versionsuffix = '-Python-%s' % local_pyver -homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +homepage = 'https://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'cstd': 'c++11'} -source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +source_urls = ["https://www.fmrib.ox.ac.uk/fsldownloads/"] sources = ['%(namelower)s-%(version)s-sources.tar.gz'] patches = [ 'FSL-6.0.2_Makefile_fixes.patch', diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb index 86c3ebd9520..265bdc85fff 100644 --- a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GLibmm' version = '2.49.7' -homepage = 'http://www.gtk.org/' +homepage = 'https://www.gtk.org/' description = """C++ bindings for Glib""" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} From 2efbd0c3eb682d49c20a619b2576bf50166aaa35 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 11:12:59 +0100 Subject: [PATCH 036/468] Added missing fix. Note that this fix also applied to FSL-6.0.1 - at least I needed it - hence the naming --- .../f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch new file mode 100644 index 00000000000..bc8cc68d796 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch @@ -0,0 +1,11 @@ +diff -Nru fsl.orig/src/misc_tcl/fsl_exec.tcl fsl/src/misc_tcl/fsl_exec.tcl +--- fsl.orig/src/misc_tcl/fsl_exec.tcl 2019-10-21 15:53:58.647058588 +0200 ++++ fsl/src/misc_tcl/fsl_exec.tcl 2019-10-21 16:28:52.811113241 +0200 +@@ -175,6 +175,7 @@ + set logout "" + } + ++ if { ! [ info exists ::errorCode ] } { set ::errorCode "NONE" } + # run and log the actual command + if { $do_logout } { + fsl:echo $logout "\n$thecommand" From 1d51bcb1f3ec2e35d8b3bc0ab668082e3006e25d Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 15:11:06 +0100 Subject: [PATCH 037/468] Fixes failing check for NCL-6.6.2-intel-2018b.eb when building with RPATH support --- .../easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb | 48 +++++++++++++++++++ .../n/NCL/NCL-6.6.2-intel-2018b.eb | 12 ++++- 2 files changed, 58 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb new file mode 100644 index 00000000000..e92d9f7c2d8 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb @@ -0,0 +1,48 @@ +name = 'NCL' +version = '6.6.2' + +homepage = 'http://www.ncl.ucar.edu' +description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True} + +source_urls = ['https://github.com/NCAR/ncl/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'NCL-6.4.0_fix-types.patch', +] +checksums = [ + 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz + 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch +] + +builddependencies = [ + ('makedepend', '1.0.6'), + ('Bison', '3.0.5'), +] + +dependencies = [ + ('cURL', '7.60.0'), + ('JasPer', '2.0.14'), + ('g2lib', '3.1.0'), + ('g2clib', '1.6.0'), + ('HDF', '4.2.14'), + ('HDF5', '1.10.2'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('Szip', '2.1.1'), + ('freetype', '2.9.1'), + ('zlib', '1.2.11'), + ('GDAL', '2.2.3', '-Python-3.6.6'), + ('UDUNITS', '2.2.26'), + ('ESMF', '7.1.0r'), + ('bzip2', '1.0.6'), + ('cairo', '1.14.12'), + ('libiconv', '1.15'), + ('GSL', '2.5'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb index 9e0124e0ac4..6d34056b226 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb @@ -9,12 +9,19 @@ toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True} source_urls = ['https://github.com/NCAR/ncl/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['NCL-6.4.0_fix-types.patch'] +patches = [ + 'NCL-6.4.0_fix-types.patch', +] checksums = [ 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch ] +builddependencies = [ + ('makedepend', '1.0.6'), + ('Bison', '3.0.5'), +] + dependencies = [ ('cURL', '7.60.0'), ('JasPer', '2.0.14'), @@ -34,7 +41,8 @@ dependencies = [ ('cairo', '1.14.12'), ('libiconv', '1.15'), ('GSL', '2.5'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), ] -builddependencies = [('makedepend', '1.0.6')] moduleclass = 'data' From 7bb0c919406d043c59116cd630620c18787011c6 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 27 Nov 2019 15:30:46 +0100 Subject: [PATCH 038/468] adding easyconfigs: OpenFOAM-7-foss-2019b.eb and patches: OpenFOAM-7-cleanup.patch --- .../o/OpenFOAM/OpenFOAM-7-cleanup.patch | 307 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-7-foss-2019b.eb | 33 ++ 2 files changed, 340 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch new file mode 100644 index 00000000000..8549fb184fa --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch @@ -0,0 +1,307 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# by Jiri Furst , based on patch for OpenFOAM 5.0 and 4.1 by +# Kennet Hoste (HPC-UGent) and Ward Poelmans +diff -ru OpenFOAM-7-version-7.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-7-version-7/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-7-version-7.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/applications/utilities/mesh/manipulation/setSet/Allwmake 2018-08-14 11:18:48.188975085 +0200 +@@ -7,19 +7,12 @@ + unset COMP_FLAGS LINK_FLAGS + + # Use readline if available +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo " found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" + +- # readline may require ncurses +- if [ -f /usr/include/ncurses/ncurses.h ] +- then +- echo " found -- maybe required by readline." +- export LINK_FLAGS="-lreadline -lncurses" +- else +- export LINK_FLAGS="-lreadline" +- fi ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake $targetType +diff -ru OpenFOAM-7-version-7.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-7-version-7/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-7-version-7.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2018-08-14 11:21:25.280419729 +0200 +@@ -14,8 +14,8 @@ + } + + # ensure CMake gets the correct C/C++ compilers +- [ -n "$WM_CC" ] && export CC="$WM_CC" +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CC" ] && export CC="$WM_CC" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-7-version-7.orig/etc/bashrc OpenFOAM-7-version-7/etc/bashrc +--- OpenFOAM-7-version-7.orig/etc/bashrc 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/etc/bashrc 2018-08-14 11:29:14.168761602 +0200 +@@ -43,8 +43,9 @@ + # Please set to the appropriate path if the default is not correct. + # + [ "$BASH" -o "$ZSH_NAME" ] && \ +-export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ ++#export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ru OpenFOAM-7-version-7.orig/etc/config.sh/CGAL OpenFOAM-7-version-7/etc/config.sh/CGAL +--- OpenFOAM-7-version-7.orig/etc/config.sh/CGAL 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/etc/config.sh/CGAL 2018-08-14 11:35:21.214457132 +0200 +@@ -35,33 +35,8 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=cgal-system +-#cgal_version=CGAL-4.10 +- +-thirdPartyPath=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-if [ "$boost_version" != "boost-system" ] +-then +- export BOOST_ARCH_PATH=$thirdPartyPath/$boost_version +- if [ -d "$BOOST_ARCH_PATH" ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +-else +- unset BOOST_ARCH_PATH +-fi +- +-if [ "$cgal_version" != "cgal-system" ] +-then +- export CGAL_ARCH_PATH=$thirdPartyPath/$cgal_version +- if [ -d "$CGAL_ARCH_PATH" ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH +- fi +-else +- unset CGAL_ARCH_PATH +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + if [ "$FOAM_VERBOSE" -a "$PS1" ] + then +@@ -70,6 +45,4 @@ + echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 + fi + +-unset thirdPartyPath +- + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-7-version-7.orig/etc/config.sh/gperftools OpenFOAM-7-version-7/etc/config.sh/gperftools +--- OpenFOAM-7-version-7.orig/etc/config.sh/gperftools 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/etc/config.sh/gperftools 2018-08-14 11:37:07.582078984 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-7-version-7.orig/etc/config.sh/metis OpenFOAM-7-version-7/etc/config.sh/metis +--- OpenFOAM-7-version-7.orig/etc/config.sh/metis 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/etc/config.sh/metis 2018-08-14 11:39:06.204657280 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-7-version-7.orig/etc/config.sh/mpi OpenFOAM-7-version-7/etc/config.sh/mpi +--- OpenFOAM-7-version-7.orig/etc/config.sh/mpi 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/etc/config.sh/mpi 2018-08-14 11:45:15.876343167 +0200 +@@ -257,6 +257,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-7-version-7.orig/etc/config.sh/paraview OpenFOAM-7-version-7/etc/config.sh/paraview +--- OpenFOAM-7-version-7.orig/etc/config.sh/paraview 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/etc/config.sh/paraview 2018-08-14 11:48:56.859557664 +0200 +@@ -41,21 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 cmake-3.9.0 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 +@@ -67,7 +52,8 @@ + #export ParaView_VERSION=5.0.1 + #export ParaView_VERSION=5.4.0 + #export ParaView_VERSION=5.5.0 +-export ParaView_VERSION=5.6.0 ++#export ParaView_VERSION=5.6.0 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + #export ParaView_GL=system +@@ -107,21 +93,15 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0 +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -136,18 +116,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- + [ "$ParaView_GL" = mesa ] && alias paraview="paraview --mesa" + else + unset PV_PLUGIN_PATH +diff -ru OpenFOAM-7-version-7.orig/etc/config.sh/scotch OpenFOAM-7-version-7/etc/config.sh/scotch +--- OpenFOAM-7-version-7.orig/etc/config.sh/scotch 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/etc/config.sh/scotch 2018-08-14 11:50:33.739213308 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.6 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-7-version-7.orig/etc/config.sh/settings OpenFOAM-7-version-7/etc/config.sh/settings +--- OpenFOAM-7-version-7.orig/etc/config.sh/settings 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/etc/config.sh/settings 2018-08-14 11:53:15.092639797 +0200 +@@ -61,11 +61,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-7-version-7.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-7-version-7/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-7-version-7.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/src/parallel/decompose/ptscotchDecomp/Make/options 2018-08-14 11:55:27.323169812 +0200 +@@ -5,14 +5,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-7-version-7.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-7-version-7/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-7-version-7.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2018-08-14 11:57:24.057754914 +0200 +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-7-version-7.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-7-version-7/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-7-version-7.orig/src/parallel/decompose/scotchDecomp/Make/options 2018-07-09 18:01:02.000000000 +0200 ++++ OpenFOAM-7-version-7/src/parallel/decompose/scotchDecomp/Make/options 2018-08-14 11:58:42.345476668 +0200 +@@ -8,7 +8,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb new file mode 100644 index 00000000000..fa351e2dd3a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb @@ -0,0 +1,33 @@ +name = 'OpenFOAM' +version = '7' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-%(version)s-cleanup.patch'] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.1'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.9'), + ('CGAL', '4.14.1', '-Python-3.7.4'), + ('ParaView', '5.6.2', '-Python-3.7.4-mpi'), +] + +builddependencies = [ + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' From 44651819d353621d1d30da8d98e491f88aa79d95 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 27 Nov 2019 15:45:43 +0100 Subject: [PATCH 039/468] Updates checksums --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb index fa351e2dd3a..dea35b091b5 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb @@ -13,6 +13,10 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] patches = ['OpenFOAM-%(version)s-cleanup.patch'] +checksums = [ + '12389cf092dc032372617785822a597aee434a50a62db2a520ab35ba5a7548b5', # version-7.tar.gz + '377734a328c75e8b2de8eadbc8a2f80ea8f740f4da790c48f7953db31bac598e', # OpenFOAM-7-cleanup.patch +] dependencies = [ ('libreadline', '8.0'), From 9efd52440e71027b3eed2d0452b1a3fc1eb7d955 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 27 Nov 2019 17:59:01 +0100 Subject: [PATCH 040/468] use template module_name_full and add patch --- .../s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb | 8 +++- .../SCOOP-0.7.1.1_fix-remote-launch.patch | 46 +++++++++++++++++++ 2 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1_fix-remote-launch.patch diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb index e89b49d0c60..794979ed9c3 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb @@ -30,15 +30,21 @@ exts_list = [ 'checksums': ['f1cc268a15ade58d9a0c04569fe6613e19b8b0345b64453064e2c3c6d79051af'], }), (name, version, { + 'patches': [ + '%(name)s-%(version)s_fix-localhost.patch', + '%(name)s-%(version)s_fix-remote-launch.patch', + ], 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'patches': ['%(name)s-%(version)s_fix-localhost.patch'], 'checksums': [ 'd8b6444c7bac901171e3327a97e241dde63f060354e162a65551fd8083ca62b4', # scoop-0.7.1.1.tar.gz '3299c905aefa1b53afa5887361ca6db3ddf31e35739453c7563fc0ecfe9ba97f', # SCOOP-0.7.1.1_fix-localhost.patch + 'c18e549a81717d99197d04d4b2976ae21100323c6da2f96dad70f5040ff0438b', # SCOOP-0.7.1.1_fix-remote-launch.patch ], }), ] +modextravars = {'SCOOP_LOAD_MODULE': 'module load %(module_name_full)s'} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1_fix-remote-launch.patch b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1_fix-remote-launch.patch new file mode 100644 index 00000000000..23620d0ce24 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1_fix-remote-launch.patch @@ -0,0 +1,46 @@ +Fix remote launch of broker and workers over ssh by starting login shell +Added environment variable SCOOP_MODULE_LOAD to load the SCOOP module +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) + +diff -ur scoop-0.7.1.1.orig/scoop/launch/brokerLaunch.py scoop-0.7.1.1/scoop/launch/brokerLaunch.py +--- scoop-0.7.1.1.orig/scoop/launch/brokerLaunch.py 2015-08-21 15:53:21.000000000 +0200 ++++ scoop-0.7.1.1/scoop/launch/brokerLaunch.py 2019-11-25 09:35:37.951797999 +0100 +@@ -110,10 +110,12 @@ + for i in range(5000, 10000, 2): + cmd = self.BASE_SSH + [ + hostname, ++ '""bash --login -c \'' + os.getenv('SCOOP_LOAD_MODULE', ':') + ' && ' + + brokerString.format(brokerPort=i, + infoPort=i + 1, + pythonExec=pythonExecutable, +- ) ++ ) + ++ '\'""' + ] + scoop.logger.debug("Launching remote broker: {cmd}" + "".format(cmd=" ".join(cmd))) +diff -ur scoop-0.7.1.1.orig/scoop/launch/workerLaunch.py scoop-0.7.1.1/scoop/launch/workerLaunch.py +--- scoop-0.7.1.1.orig/scoop/launch/workerLaunch.py 2015-08-21 15:53:21.000000000 +0200 ++++ scoop-0.7.1.1/scoop/launch/workerLaunch.py 2019-11-25 09:36:59.658799261 +0100 +@@ -17,6 +17,7 @@ + # Global imports + from collections import namedtuple + import logging ++import os + import sys + import subprocess + +@@ -205,7 +206,12 @@ + '-R {0}:127.0.0.1:{0}'.format(tunnelPorts[1]), + ] + self.subprocesses.append( +- subprocess.Popen(sshCmd + [self.hostname, self.getCommand()], ++ subprocess.Popen(sshCmd + [ ++ self.hostname, ++ '""bash --login -c \'' + os.getenv('SCOOP_LOAD_MODULE', ':') + ' && ' + ++ self.getCommand() + ++ '\'""' ++ ], + stdout=subprocess.PIPE if stdPipe else None, + stderr=subprocess.PIPE if stdPipe else None, + ) From c2aa7c5ab5c9cd5c462bee0676608049182f7038 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 27 Nov 2019 19:27:21 +0100 Subject: [PATCH 041/468] Inserted space that was missing after breaking the postinstallcmd in two lines... --- .../easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb index 56b711bd3ea..ef3b3dbba48 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb @@ -58,7 +58,7 @@ dependencies = [ # FSLDIR needs to be defined when running postinstall to get the correct shebang # https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 postinstallcmds = [( - 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH' + 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH ' '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' )] From 4e2241b0979dd5bd9534a834b3ce4cbeb203fd18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Nov 2019 11:30:29 +0100 Subject: [PATCH 042/468] adding easyconfigs: fastp-0.20.0-iccifort-2019.5.281.eb --- .../fastp/fastp-0.20.0-iccifort-2019.5.281.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.20.0-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.20.0-iccifort-2019.5.281.eb b/easybuild/easyconfigs/f/fastp/fastp-0.20.0-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..d8869c7f11d --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.20.0-iccifort-2019.5.281.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.20.0' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['https://github.com/OpenGene/fastp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8d751d2746db11ff233032fc49e3bcc8b53758dd4596fdcf4b4099a4d702ac22'] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'dirs': [], + 'files': ['bin/fastp'], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' From 4a5133c0e17771721de004529ab4dae022bcd4a8 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 28 Nov 2019 18:33:19 +0100 Subject: [PATCH 043/468] Patch for OpenFOAM bug 3303 --- .../o/OpenFOAM/OpenFOAM-7-cleanup.patch | 31 ++++++++++ .../o/OpenFOAM/OpenFOAM-7-foss-2019b.eb | 8 ++- .../OpenFOAM/OpenFOAM-7-mpi-compilation.patch | 57 +++++++++++++++++++ 3 files changed, 94 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-mpi-compilation.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch index 8549fb184fa..fd08f290afc 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch @@ -58,6 +58,37 @@ diff -ru OpenFOAM-7-version-7.orig/etc/bashrc OpenFOAM-7-version-7/etc/bashrc # export FOAM_INST_DIR=~$WM_PROJECT # export FOAM_INST_DIR=/opt/$WM_PROJECT # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +@@ -113,10 +113,30 @@ foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \ + export WM_PROJECT_INST_DIR=$FOAM_INST_DIR + export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION + ++if [ -d "$WM_PROJECT_DIR" ] ++then ++ WM_PROJECT_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P) ++ if [ -d "$WM_PROJECT_DIR_REAL" -a -e "$WM_PROJECT_DIR_REAL/etc/bashrc" ] ++ then ++ export WM_PROJECT_DIR=$WM_PROJECT_DIR_REAL ++ fi ++ unset WM_PROJECT_DIR_REAL ++fi ++ + # Location of third-party software + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION + ++if [ -d "$WM_THIRD_PARTY_DIR" ] ++then ++ WM_THIRD_PARTY_DIR_REAL=$(cd $WM_THIRD_PARTY_DIR && pwd -P) ++ if [ -d "$WM_THIRD_PARTY_DIR_REAL" -a -e "$WM_THIRD_PARTY_DIR_REAL/etc/tools" ] ++ then ++ export WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR_REAL ++ fi ++ unset WM_THIRD_PARTY_DIR_REAL ++fi ++ + # Location of site-specific templates etc + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + # unset is equivalent to $WM_PROJECT_INST_DIR/site diff -ru OpenFOAM-7-version-7.orig/etc/config.sh/CGAL OpenFOAM-7-version-7/etc/config.sh/CGAL --- OpenFOAM-7-version-7.orig/etc/config.sh/CGAL 2018-07-09 18:01:02.000000000 +0200 +++ OpenFOAM-7-version-7/etc/config.sh/CGAL 2018-08-14 11:35:21.214457132 +0200 diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb index dea35b091b5..129f4537a14 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb @@ -12,10 +12,14 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] -patches = ['OpenFOAM-%(version)s-cleanup.patch'] +patches = [ + 'OpenFOAM-%(version)s-cleanup.patch', + 'OpenFOAM-%(version)s-mpi-compilation.patch', +] checksums = [ '12389cf092dc032372617785822a597aee434a50a62db2a520ab35ba5a7548b5', # version-7.tar.gz - '377734a328c75e8b2de8eadbc8a2f80ea8f740f4da790c48f7953db31bac598e', # OpenFOAM-7-cleanup.patch + '64b8614e41f8e8a33d944cf5b91031fb10cec51784f4549e83dcd46985683ef3', # OpenFOAM-7-cleanup.patch + '9f2af8f67a57a187f68aadaa99bc99f1cfbfe41086e5839a57e1bb4e41b3762c', # OpenFOAM-7-mpi-compilation.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-mpi-compilation.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-mpi-compilation.patch new file mode 100644 index 00000000000..6cdbbe41ca0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-mpi-compilation.patch @@ -0,0 +1,57 @@ +# Resolves compilation bug https://bugs.openfoam.org/view.php?id=3303 +# +# authors: Henry Weller, Bruno Santos +--- OpenFOAM-7/wmake/wclean.orig 2019-11-28 16:10:41.511704188 +0100 ++++ OpenFOAM-7/wmake/wclean 2019-11-28 16:13:12.535866056 +0100 +@@ -3,7 +3,7 @@ + # ========= | + # \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + # \\ / O peration | Website: https://openfoam.org +-# \\ / A nd | Copyright (C) 2011-2018 OpenFOAM Foundation ++# \\ / A nd | Copyright (C) 2011-2019 OpenFOAM Foundation + # \\/ M anipulation | + #------------------------------------------------------------------------------ + # License +@@ -260,10 +260,11 @@ + if [ -d "$MakeDir" ] + then + objectsDir=$MakeDir/$WM_OPTIONS +- if [[ "$PWD" = *"$WM_PROJECT_DIR"* ]] ++ expandPath "$PWD" ++ if [[ "$exPath" = *"$WM_PROJECT_DIR"* ]] + then + platformPath=$WM_PROJECT_DIR/platforms/${WM_OPTIONS} +- objectsDir=$platformPath${PWD//$WM_PROJECT_DIR/} ++ objectsDir=$platformPath${exPath//$WM_PROJECT_DIR/} + fi + rm -rf "$objectsDir" 2>/dev/null + fi +--- OpenFOAM-7/wmake/wrmdep.orig 2019-11-28 16:13:30.359882390 +0100 ++++ OpenFOAM-7/wmake/wrmdep 2019-11-28 16:15:36.511999016 +0100 +@@ -3,7 +3,7 @@ + # ========= | + # \\ / F ield | OpenFOAM: The Open Source CFD Toolbox + # \\ / O peration | Website: https://openfoam.org +-# \\ / A nd | Copyright (C) 2015-2018 OpenFOAM Foundation ++# \\ / A nd | Copyright (C) 2015-2019 OpenFOAM Foundation + # \\/ M anipulation | + #------------------------------------------------------------------------------ + # License +@@ -227,12 +227,16 @@ + + updateMode) + +- if [ "$PWD" != "$WM_PROJECT_DIR" ] ++ expandPath "$PWD" ++ if [ "$exPath" != "$WM_PROJECT_DIR" ] + then + echo "Cannot 'update', not in the project top-level directory" + exit 1 + fi + ++ # Go into the real path ++ cd "$exPath" ++ + echo "Removing dep files corresponding to source files that no longer exist..." + fileNameList=$(find -L src applications -name '*.[CHL]' -type l) + From ac1b57e0126e3cc76fe7e519b079e6199241a693 Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Fri, 29 Nov 2019 10:21:32 +0100 Subject: [PATCH 044/468] adding easyconfigs: ncl-2.1.18-GCC-8.2.0-2.31.1.eb --- .../n/ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/n/ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/n/ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..51cd62e4229 --- /dev/null +++ b/easybuild/easyconfigs/n/ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'ncl' +version = '2.1.18' + +homepage = 'http://ncl.sourceforge.net/' +description = """The NEXUS Class Library is a C++ library for parsing NEXUS files.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6e792ede614f6969a0cd342fea1505b4ea3e3e4c0f50a1c0c16a3af67bfe9737'] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = 'CPPFLAGS=-DNCL_CONST_FUNCS ' + +sanity_check_paths = { + 'files': ["bin/%s" % local_binfile for local_binfile in ["NCLconverter", "NEXUSnormalizer", "NEXUSvalidator"]] + + ["lib/%(name)s/lib%(name)s.so"], + 'dirs': [], +} + +moduleclass = 'lib' From ddb9afea68941855db82ebf843653d9a1624fa2b Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Fri, 29 Nov 2019 10:24:25 +0100 Subject: [PATCH 045/468] adding easyconfigs: GARLI-2.01-gompi-2019a.eb --- .../g/GARLI/GARLI-2.01-gompi-2019a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb diff --git a/easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb b/easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb new file mode 100644 index 00000000000..16b75da45cb --- /dev/null +++ b/easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GARLI' +version = '2.01' + +homepage = 'https://code.google.com/archive/p/garli/' +description = """GARLI, Genetic Algorithm for Rapid Likelihood Inference is a + program for inferring phylogenetic trees. Using an approach similar to a + classical genetic algorithm, it rapidly searches the space of evolutionary + trees and model parameters to find the solution maximizing the likelihood + score. It implements nucleotide, amino acid and codon-based models of sequence + evolution, and runs on all platforms.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'pic': True, 'cstd': 'c++03'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e7fd4c115f9112fd9a019dcb6314e3a9d989f56daa0f833a28dc8249e50988ef'] + +builddependencies = [('Autotools', '20180311')] + +configopts = '--with-ncl=$EBROOTNCL' + +dependencies = [ + ('ncl', '2.1.18'), +] + +sanity_check_paths = { + 'files': ["bin/Garli"], + 'dirs': [], +} + +moduleclass = 'bio' From 7aa27c88f6b2d707ef3b86e277fa78602ad56c8a Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Fri, 29 Nov 2019 10:33:23 +0100 Subject: [PATCH 046/468] adding easyconfigs: HyPhy-2.5.1-gompi-2019a.eb --- .../h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb diff --git a/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb new file mode 100644 index 00000000000..e62eea9cb84 --- /dev/null +++ b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ + +easyblock = "CMakeMake" + +name = 'HyPhy' +version = '2.5.1' + +homepage = 'https://veg.github.io/hyphy-site/' +description = """HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package + for the analysis of genetic sequences (in particular the inference of natural selection) + using techniques in phylogenetics, molecular evolution, and machine learning""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/veg/hyphy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c402aab5eb483c1d3566cbbd620db95cba1d86f3bb60cc7f712d255c777a45e6'] + +builddependencies = [('CMake', '3.13.3')] + +buildopts = [ + 'hyphy', + 'HYPHYMPI', +] + +dependencies = [ + ('cURL', '7.63.0'), +] + +sanity_check_paths = { + 'files': ['bin/hyphy', 'bin/HYPHYMPI'], + 'dirs': [], +} + +moduleclass = 'bio' From 677dd79e378808d3f87a074afbc729a59271ba79 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Nov 2019 10:40:02 +0100 Subject: [PATCH 047/468] adding easyconfigs: QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb --- .../QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..09599abf99a --- /dev/null +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'QuickFF' +version = '2.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/QuickFF/' +description = """QuickFF is a Python package developed at the Center for +Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio +calculations.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = ['https://github.com/molmod/QuickFF/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3b37eef91a04621da86524e5dc1f81068217fe838e4ea4dd4c2409717b949d5e'] + +dependencies = [ + ('Python', '3.7.2'), + ('matplotlib', '3.0.3', versionsuffix), + ('molmod', '1.4.4', versionsuffix), + ('yaff', '1.6.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_pip_check = True + +moduleclass = 'chem' From ca1d963f18d25665a6c46a9a11bfbf95528f6e82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Nov 2019 11:20:47 +0100 Subject: [PATCH 048/468] stick to yaff 1.5.0 for QiuckFF 2.2.3 --- .../q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb index 09599abf99a..f43aad1f043 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '3.7.2'), ('matplotlib', '3.0.3', versionsuffix), ('molmod', '1.4.4', versionsuffix), - ('yaff', '1.6.0', versionsuffix), + ('yaff', '1.5.0', versionsuffix), ] download_dep_fail = True From 046b8a36b56d6d5e7cf0a0555a25681b29816a7f Mon Sep 17 00:00:00 2001 From: alozano Date: Fri, 29 Nov 2019 11:33:03 +0100 Subject: [PATCH 049/468] switch to get sources from PyPI --- .../m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb index 76b791b9366..5fa730a4a18 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.5-foss-2018b-Python-3.6.6.eb @@ -11,9 +11,9 @@ description = "Model Based Analysis for ChIP-Seq data" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https://github.com/taoliu/MACS/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['2434d5170facaeb7fd59c6a2040e000e49a77bd50767643e3b60996985d0a516'] +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a3d8c5885e3e2cb6ffd46fe292841f7d74fdbaaf549105c77e48a2b96e479741'] dependencies = [('Python', '3.6.6')] From 05d32168377a9e212d2ef76dbb28f3f2e220fbb8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Nov 2019 11:58:36 +0100 Subject: [PATCH 050/468] use https in homepage for QuickFF 2.2.3 --- .../q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb index f43aad1f043..7454de90561 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb @@ -4,7 +4,7 @@ name = 'QuickFF' version = '2.2.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://molmod.github.io/QuickFF/' +homepage = 'https://molmod.github.io/QuickFF/' description = """QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio calculations.""" From 903491144c89cdcb1c7d6a2318c6033b30df59f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Nov 2019 13:11:59 +0100 Subject: [PATCH 051/468] update to QuickFF 2.2.4 --- ...hon-3.7.2.eb => QuickFF-2.2.4-intel-2019a-Python-3.7.2.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/q/QuickFF/{QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb => QuickFF-2.2.4-intel-2019a-Python-3.7.2.eb} (89%) diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.4-intel-2019a-Python-3.7.2.eb similarity index 89% rename from easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.4-intel-2019a-Python-3.7.2.eb index 7454de90561..7ceef800f29 100644 --- a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.4-intel-2019a-Python-3.7.2.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'QuickFF' -version = '2.2.3' +version = '2.2.4' versionsuffix = '-Python-%(pyver)s' homepage = 'https://molmod.github.io/QuickFF/' @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2019a'} source_urls = ['https://github.com/molmod/QuickFF/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['3b37eef91a04621da86524e5dc1f81068217fe838e4ea4dd4c2409717b949d5e'] +checksums = ['9c916eab890eec865985bc3e11249b0b5fee28a049206b9755081adeaf13ff60'] dependencies = [ ('Python', '3.7.2'), From a655243274d8d2caa771d1cf94204cef43963c73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Nov 2019 16:01:22 +0100 Subject: [PATCH 052/468] adding easyconfigs: Qualimap-2.2.1-foss-2019a-R-3.6.0.eb --- .../Qualimap-2.2.1-foss-2019a-R-3.6.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb new file mode 100644 index 00000000000..90bf997ca5c --- /dev/null +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'Qualimap' +version = '2.2.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://qualimap.bioinfo.cipf.es/' +description = """Qualimap 2 is a platform-independent application written in Java and R that provides both + a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads/'] +sources = ['qualimap_v%(version)s.zip'] +checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] + +dependencies = [ + ('Java', '11', '', True), + ('R', '3.6.0'), + ('R-bundle-Bioconductor', '3.9', versionsuffix), +] + +sanity_check_paths = { + 'files': ['qualimap'], + 'dirs': [], +} + +sanity_check_commands = ["qualimap --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From a0069eaa7c81d3a5024466a884f5c284c8c35951 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 2 Dec 2019 13:37:31 +0100 Subject: [PATCH 053/468] adding easyconfigs: NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb --- ...CIPLOT-4.0-20190718-iccifort-2019.5.281.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..475de9510de --- /dev/null +++ b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'NCIPLOT' +local_ver = '4.0' +version = '%s-20190718' % local_ver +local_commit = '834af2e' + +homepage = 'https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html' +description = """ NCIPLOT is a program for revealing non covalent interactions + based on the reduced density gradient. """ + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/juliacontrerasgarcia/nciplot/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['d86943e7f4dff9098b87fdfb8ab3793478a9c8ed8b312c730cdbcb0cac4bef4d'] + +start_dir = 'src_%%(namelower)s_%s' % local_ver + +prebuildopts = "sed -i 's/include Makefile.inc//g' Makefile && " +buildopts = 'LDFLAGS="$LDFLAGS $LIBS"' + +files_to_copy = ['dat', 'LICENSE', (['nciplot'], 'bin')] + +modextrapaths = {'NCIPLOT_HOME': ''} + +sanity_check_paths = { + 'files': ['bin/nciplot'], + 'dirs': ['dat'], +} + +# site-specific: set OMP_NUM_THREADS equal to number of available cores +modluafooter = 'if os.getenv("PBS_NUM_PPN") ~= nil then pushenv("OMP_NUM_THREADS", os.getenv("PBS_NUM_PPN")) end' + +moduleclass = 'chem' From 23fbb8d8225ec9689ccbe576e4ba5c44d02d2f4d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 2 Dec 2019 15:33:43 +0200 Subject: [PATCH 054/468] adding easyconfigs: pyBigWig-0.3.17-GCCcore-8.2.0.eb --- .../pyBigWig/pyBigWig-0.3.17-GCCcore-8.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.17-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.17-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.17-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a4d931b2504 --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.17-GCCcore-8.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.17' + +github_account = 'deeptools' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A python extension, written in C, for quick access to bigBed + files and access to and creation of bigWig files.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a1ccd607db0ece1553471cab3763e318609171a8219a7e0625bc80b61479f8d7'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('binutils', '2.31.1'), + ('cURL', '7.63.0'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +moduleclass = 'bio' From 856aab620f26a083e4a1a8422a1faad8bad8210b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 2 Dec 2019 15:47:48 +0200 Subject: [PATCH 055/468] adding easyconfigs: bx-python-0.8.4-foss-2019a.eb --- .../b/bx-python/bx-python-0.8.4-foss-2019a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb new file mode 100644 index 00000000000..ec293b96726 --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'bx-python' +version = '0.8.4' + +github_account = 'bxlab' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('LZO', '2.10'), + ('SciPy-bundle', '2019.03'), +] + +prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " + +use_pip = True +exts_download_dep_fail = True + +exts_list = [ + ('python-lzo', '1.12', { + 'modulename': 'lzo', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], + 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], + }), + (name, version, { + 'modulename': 'bx', + 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s/'], + 'checksums': ['9698390a777a41d3b7f5e833ec1bacb8193fea847889a2092c848afd6b8a7b85'], + }), +] + +moduleclass = 'bio' From fc183ba990db405c2f4f59f0f11b280d842f9977 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 2 Dec 2019 16:16:07 +0200 Subject: [PATCH 056/468] bx-python-0.8.4: remove download_dep_fail --- easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb index ec293b96726..f102669b637 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb @@ -20,7 +20,6 @@ dependencies = [ prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " use_pip = True -exts_download_dep_fail = True exts_list = [ ('python-lzo', '1.12', { From 42935e47d42af8906ef271280c84cab8f80922b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2019 17:22:13 +0100 Subject: [PATCH 057/468] add missing 'wheel' extensions to Spark 2.4.0 easyconfig using intel/2018b toolchain --- ...-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb index 158c61b39d7..3c43a1d0e21 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb @@ -10,12 +10,12 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'intel', 'version': '2018b'} -sources = ['%%(namelower)s-%%(version)s-bin-hadoop%s.tgz' % local_hadoopver] source_urls = [ 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', ] +sources = ['%%(namelower)s-%%(version)s-bin-hadoop%s.tgz' % local_hadoopver] checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ @@ -31,9 +31,13 @@ exts_default_options = { } exts_list = [ + ('wheel', '0.33.6', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wheel'], + 'checksums': ['10c9da68765315ed98850f8e048347c3eb06dd81822dc2ab1d4fde9dc9702646'], + }), ('py4j', '0.10.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], }), ('pyspark', version, { From cd5881a58c94c0245209ffaf76022572fd821675 Mon Sep 17 00:00:00 2001 From: psakdhna Date: Tue, 3 Dec 2019 10:45:27 +0700 Subject: [PATCH 058/468] adding easyconfigs: cuDNN-7.6.4.38-CUDA-10.0.130.eb --- .../c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb new file mode 100644 index 00000000000..7a5dea11517 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '7.6.4.38' +local_cuda_version = '10.0.130' + +local_cuda_version_major_minor = '.'.join(local_cuda_version.split('.')[:2]) + +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = SYSTEM + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +# Download as cudnn-10.0-linux-x64-v7.6.5.32.tgz +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] +checksums = ['417bb5daf51377037eb2f5c87649000ca1b9cec0acb16cfe07cb1d3e9a961dbf'] + +dependencies = [('CUDA', local_cuda_version)] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From 2fbaff40d4f2effa82aa812d807c881d78a4b3d1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 3 Dec 2019 11:47:03 +0200 Subject: [PATCH 059/468] adding easyconfigs: Sambamba-0.7.1.eb --- .../easyconfigs/s/Sambamba/Sambamba-0.7.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb new file mode 100644 index 00000000000..8d3c5d978d1 --- /dev/null +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'Sambamba' +version = '0.7.1' +local_distbin = '%(namelower)s-%(version)s-linux-static' + +homepage = 'http://lomereiter.github.io/sambamba/' +description = """Sambamba is a high performance modern robust and fast tool + (and library), written in the D programming language, for working with SAM + and BAM files. Current functionality is an important subset of samtools + functionality, including view, index, sort, markdup, and depth.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/biod/%(namelower)s/releases/download/v%(version)s'] +sources = [{'download_filename': '%s.gz' % local_distbin, 'filename': '%(namelower)s-%(version)s.gz'}] +checksums = ['d6e3faaa4a5440067e65b396c9a23188765ea5acc6621485c48ac86158fa62f3'] + +postinstallcmds = [ + 'chmod 755 %(installdir)s/%(namelower)s-%(version)s', + 'cd %(installdir)s && ln -s %(namelower)s-%(version)s %(namelower)s', +] + +sanity_check_paths = { + 'files': ['%(namelower)s', '%(namelower)s-%(version)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 189cd9a55b1935594da33a7fb8acbd835e20de76 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 3 Dec 2019 12:04:31 +0200 Subject: [PATCH 060/468] Sambamba-0.7.1: fix homepage --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb index 8d3c5d978d1..83194e65344 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb @@ -4,7 +4,7 @@ name = 'Sambamba' version = '0.7.1' local_distbin = '%(namelower)s-%(version)s-linux-static' -homepage = 'http://lomereiter.github.io/sambamba/' +homepage = 'https://lomereiter.github.io/sambamba/' description = """Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools From b2e2327112998637db804d9a735015c587d24f93 Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Tue, 3 Dec 2019 15:46:38 +0100 Subject: [PATCH 061/468] Add openmp in toolchainopts, move buildopts after dependencies --- .../easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb index e62eea9cb84..06a1d1657cb 100644 --- a/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb +++ b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.1-gompi-2019a.eb @@ -11,7 +11,7 @@ description = """HyPhy (Hypothesis Testing using Phylogenies) is an open-source using techniques in phylogenetics, molecular evolution, and machine learning""" toolchain = {'name': 'gompi', 'version': '2019a'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['https://github.com/veg/hyphy/archive/'] sources = ['%(version)s.tar.gz'] @@ -19,15 +19,15 @@ checksums = ['c402aab5eb483c1d3566cbbd620db95cba1d86f3bb60cc7f712d255c777a45e6'] builddependencies = [('CMake', '3.13.3')] +dependencies = [ + ('cURL', '7.63.0'), +] + buildopts = [ 'hyphy', 'HYPHYMPI', ] -dependencies = [ - ('cURL', '7.63.0'), -] - sanity_check_paths = { 'files': ['bin/hyphy', 'bin/HYPHYMPI'], 'dirs': [], From b505c3210961dfeb5b509203d812cbe9a52f5d0d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 3 Dec 2019 15:37:04 +0000 Subject: [PATCH 062/468] adding easyconfigs: gffread-0.11.6-GCCcore-8.3.0.eb --- .../g/gffread/gffread-0.11.6-GCCcore-8.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/gffread/gffread-0.11.6-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.11.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.11.6-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..b0bd413bb67 --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.11.6-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.11.6' + +homepage = 'https://github.com/gpertea/%(name)s' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCE_TAR_GZ] +checksums = ['05841bfa0ad6eade333ee5fe153197ab74cf300e80d43c255e480f6b1d5da1ab'] + +builddependencies = [('binutils', '2.32')] + +buildopts = " release" + +files_to_copy = ['%(name)s', 'LICENSE'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s '] + +moduleclass = 'bio' From 0efd968f2846d7649cb686bf64c5baae8abc0434 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 3 Dec 2019 22:34:09 +0100 Subject: [PATCH 063/468] Updated patch for compilation without system-wide GL/gl.h --- .../o/OpenFOAM/OpenFOAM-7-cleanup.patch | 18 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-7-foss-2019b.eb | 2 +- 2 files changed, 19 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch index fd08f290afc..a1a97a78f81 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch @@ -43,6 +43,24 @@ diff -ru OpenFOAM-7-version-7.orig/applications/utilities/postProcessing/graphic wmake $targetType vtkPVblockMesh wmake $targetType vtkPVFoam +@@ -26,7 +26,7 @@ + cd PVblockMeshReader + mkdir -p Make/$WM_OPTIONS > /dev/null 2>&1 + cd Make/$WM_OPTIONS +- cmake ../.. ++ cmake -D_qt5gui_OPENGL_INCLUDE_DIR=$EBROOTMESA/include ../.. + make + ) + +@@ -34,7 +34,7 @@ + cd PVFoamReader + mkdir -p Make/$WM_OPTIONS > /dev/null 2>&1 + cd Make/$WM_OPTIONS +- cmake ../.. ++ cmake -D_qt5gui_OPENGL_INCLUDE_DIR=$EBROOTMESA/include ../.. + make + ) + fi diff -ru OpenFOAM-7-version-7.orig/etc/bashrc OpenFOAM-7-version-7/etc/bashrc --- OpenFOAM-7-version-7.orig/etc/bashrc 2018-07-09 18:01:02.000000000 +0200 +++ OpenFOAM-7-version-7/etc/bashrc 2018-08-14 11:29:14.168761602 +0200 diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb index 129f4537a14..6bcf5936ff2 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb @@ -18,7 +18,7 @@ patches = [ ] checksums = [ '12389cf092dc032372617785822a597aee434a50a62db2a520ab35ba5a7548b5', # version-7.tar.gz - '64b8614e41f8e8a33d944cf5b91031fb10cec51784f4549e83dcd46985683ef3', # OpenFOAM-7-cleanup.patch + '8b2f6bcd396e7779de2c03561d4a004014ab250274b1fc82444845c074dcf6a3', # OpenFOAM-7-cleanup.patch '9f2af8f67a57a187f68aadaa99bc99f1cfbfe41086e5839a57e1bb4e41b3762c', # OpenFOAM-7-mpi-compilation.patch ] From 0e53eaa4884e38a96c38f79d34454b6c5447dccd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Dec 2019 22:39:00 +0100 Subject: [PATCH 064/468] adding easyconfigs: GROMACS-2019.4-foss-2019b.eb --- .../g/GROMACS/GROMACS-2019.4-foss-2019b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb new file mode 100644 index 00000000000..f7b9ece4ad0 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +# 2019.3 version +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# + +name = 'GROMACS' +version = '2019.4' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch', +] +checksums = [ + 'ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867', # gromacs-2019.4.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch + '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +moduleclass = 'bio' From 54d31aac5410f69fa3bc5bab747df23850df17ad Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Tue, 3 Dec 2019 22:40:46 +0100 Subject: [PATCH 065/468] adding easyconfigs: GROMACS-2019.3-foss-2019b.eb, GROMACS-2019.3-fosscuda-2019b.eb --- .../g/GROMACS/GROMACS-2019.3-foss-2019b.eb | 53 +++++++++++++++++++ .../GROMACS/GROMACS-2019.3-fosscuda-2019b.eb | 53 +++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb new file mode 100644 index 00000000000..41bfe8d5061 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +# 2019.3 version +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# + +name = 'GROMACS' +version = '2019.3' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch', +] +checksums = [ + '4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573', # gromacs-2019.3.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch + '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06' +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb new file mode 100644 index 00000000000..e7c29a6de9b --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +# 2019.3 version +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# + +name = 'GROMACS' +version = '2019.3' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', +] +checksums = [ + '4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573', # gromacs-2019.3.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +moduleclass = 'bio' From 00e8f7848926e6857dec853e94c11b75c02cf0ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Dec 2019 11:04:41 +0100 Subject: [PATCH 066/468] remove incorrect version from header in GROMACS 2019.4 easyconfig --- easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb index f7b9ece4ad0..986323cee9a 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b.eb @@ -9,10 +9,8 @@ # * George Tsouloupas # * Kenneth Hoste # * Adam Huffman +# * J. Sassmannshausen (Crick HPC team) # License:: MIT/GPL -# 2019.3 version -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen # name = 'GROMACS' From c9ec9a8aba9ece4f84b3c3afc703e41d0e964798 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 4 Dec 2019 13:18:12 +0200 Subject: [PATCH 067/468] adding easyconfigs: Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb, Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb --- .../Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb | 24 +++++++++++++++++++ .../Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..979e0afb22a --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,24 @@ +name = 'Gurobi' +version = '9.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +# registration is required +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +checksums = ['07c48fe0f18097ddca6ddc6f5a276e1548a37b31016d0b8575bb12ec8f44546e'] + +dependencies = [ + ('Python', '3.6.6'), +] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..27261c4c57a --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,24 @@ +name = 'Gurobi' +version = '9.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +# registration is required +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +checksums = ['07c48fe0f18097ddca6ddc6f5a276e1548a37b31016d0b8575bb12ec8f44546e'] + +dependencies = [ + ('Python', '3.6.6'), +] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +moduleclass = 'math' From 62e1282536c034a58fb9ef7710654a09c7d5f593 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 4 Dec 2019 13:33:40 +0200 Subject: [PATCH 068/468] Use https in homepage url. --- .../g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb | 2 +- .../g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb index 979e0afb22a..6978ea2cca2 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb @@ -2,7 +2,7 @@ name = 'Gurobi' version = '9.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.gurobi.com' +homepage = 'https://www.gurobi.com' description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb index 27261c4c57a..b638eb73fa5 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb @@ -2,7 +2,7 @@ name = 'Gurobi' version = '9.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.gurobi.com' +homepage = 'https://www.gurobi.com' description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the From 583507dd38d9a1dfb3322daab2e92452a66c222c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Dec 2019 14:38:46 +0100 Subject: [PATCH 069/468] adding easyconfigs: IGMPlot-2.4.2-iccifort-2019.5.281.eb, IGMPlot-2.4.2-GCC-8.3.0-2.32.eb --- .../i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0-2.32.eb | 30 +++++++++++++++++++ .../IGMPlot-2.4.2-iccifort-2019.5.281.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0-2.32.eb create mode 100644 easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0-2.32.eb new file mode 100644 index 00000000000..6a3a6ca75e7 --- /dev/null +++ b/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0-2.32.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'IGMPlot' +version = '2.4.2' + +homepage = 'http://igmplot.univ-reims.fr' +description = """IGMPlot is a free open-source program developed to identify molecular interactions and + prepare data to build 2D and 3D representations of them in the molecular environment.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} +toolchainopts = {'openmp': True} + +source_urls = ['http://igmplot.univ-reims.fr/download/'] +sources = ['IGMPLOT-%(version)s.tbz2'] +checksums = ['532a8e4041c8e2eca0a01a6796da37ebb4115eb408300a45a224f761d6546ae5'] + +start_dir = 'source' + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS -I src/include" ' + +files_to_copy = [(['source/IGMPLOT'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IGMPLOT'], + 'dirs': [], +} + +sanity_check_commands = ["cd %(builddir)s/IGMPLOT-%(version)s/tests/01test/ && IGMPLOT param.igm"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..afa94a4eb7d --- /dev/null +++ b/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-iccifort-2019.5.281.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'IGMPlot' +version = '2.4.2' + +homepage = 'http://igmplot.univ-reims.fr' +description = """IGMPlot is a free open-source program developed to identify molecular interactions and + prepare data to build 2D and 3D representations of them in the molecular environment.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} +toolchainopts = {'openmp': True} + +source_urls = ['http://igmplot.univ-reims.fr/download/'] +sources = ['IGMPLOT-%(version)s.tbz2'] +checksums = ['532a8e4041c8e2eca0a01a6796da37ebb4115eb408300a45a224f761d6546ae5'] + +start_dir = 'source' + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS -I src/include" ' + +files_to_copy = [(['source/IGMPLOT'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IGMPLOT'], + 'dirs': [], +} + +sanity_check_commands = ["cd %(builddir)s/IGMPLOT-%(version)s/tests/01test/ && IGMPLOT param.igm"] + +moduleclass = 'chem' From 430227e496cd40a59f3b431c135201b89fcd0fb6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 4 Dec 2019 22:49:30 +0800 Subject: [PATCH 070/468] adding easyconfigs: EasyBuild-4.1.0.eb --- .../e/EasyBuild/EasyBuild-4.1.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb new file mode 100644 index 00000000000..65b2ca298a7 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.1.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/75/70/0f4c795c8c16257f35ec677fb171c968f0bd10d4c144862d045d8b869ee0/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/af/b5/627da5604c960ec688b64be6ac0ba09439865c9c2a45d40ed065f67132ab/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/0e/03/1cf77cda33026d51e86df1092ced461ee51ab56cbfdd1d4633eddd9a36ec/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '336b1adc3ea410aabf900a07f6a55dcf316dc55658afc1d665d3565040be0641', # easybuild-framework-4.1.0.tar.gz + 'f6e017d703334e6008acfb9d28e97aecddef4bf04b24890f3e98b6d5cacc08bd', # easybuild-easyblocks-4.1.0.tar.gz + 'bfe1f630e2494eca6cbe72d1218f54e10a863c869bce34962d0c79e0b3003716', # easybuild-easyconfigs-4.1.0.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From d3fd9c4574d6adc06670bd659191c4a6e96eca63 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Dec 2019 17:00:11 +0200 Subject: [PATCH 071/468] Sambamba-0.7.1: use upstream binary name --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb index 83194e65344..95acb07d326 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb @@ -13,16 +13,16 @@ description = """Sambamba is a high performance modern robust and fast tool toolchain = SYSTEM source_urls = ['https://github.com/biod/%(namelower)s/releases/download/v%(version)s'] -sources = [{'download_filename': '%s.gz' % local_distbin, 'filename': '%(namelower)s-%(version)s.gz'}] +sources = ['%s.gz' % local_distbin] checksums = ['d6e3faaa4a5440067e65b396c9a23188765ea5acc6621485c48ac86158fa62f3'] postinstallcmds = [ - 'chmod 755 %(installdir)s/%(namelower)s-%(version)s', - 'cd %(installdir)s && ln -s %(namelower)s-%(version)s %(namelower)s', + 'chmod 755 %%(installdir)s/%s' % local_distbin, + 'cd %%(installdir)s && ln -s %s %%(namelower)s' % local_distbin, ] sanity_check_paths = { - 'files': ['%(namelower)s', '%(namelower)s-%(version)s'], + 'files': ['%(namelower)s', '%s' % local_distbin], 'dirs': [], } From 39e72fbc4d1b6504125395de16fc7ee26f203e8a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Dec 2019 17:09:49 +0200 Subject: [PATCH 072/468] bx-python-0.8.4: use PYPI_SOURCE --- .../easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb index f102669b637..383a112a1eb 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.4-foss-2019a.eb @@ -3,8 +3,7 @@ easyblock = 'PythonBundle' name = 'bx-python' version = '0.8.4' -github_account = 'bxlab' -homepage = 'https://github.com/%(github_account)s/%(name)s' +homepage = 'https://github.com/bxlab/bx-python' description = """The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.""" @@ -21,15 +20,15 @@ prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + exts_list = [ ('python-lzo', '1.12', { 'modulename': 'lzo', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], }), (name, version, { 'modulename': 'bx', - 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s/'], 'checksums': ['9698390a777a41d3b7f5e833ec1bacb8193fea847889a2092c848afd6b8a7b85'], }), ] From 30df37c252ce55c3635cf7cd5970b4560d91d552 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Dec 2019 17:19:32 +0200 Subject: [PATCH 073/468] adding easyconfigs: OpenFOAM-6-foss-2019b.eb --- .../o/OpenFOAM/OpenFOAM-6-foss-2019b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb new file mode 100644 index 00000000000..02c430de214 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb @@ -0,0 +1,37 @@ +name = 'OpenFOAM' +version = '6' + +homepage = 'http://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-%(version)s-cleanup.patch'] +checksums = [ + '32a6af4120e691ca2df29c5b9bd7bc7a3e11208947f9bccf6087cfff5492f025', # version-6.tar.gz + '5accbde6bde116691ea6a4666348f85487b5d5503a9761435c2cb1412b036c28', # OpenFOAM-6-cleanup.patch +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.1'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.9'), + ('CGAL', '4.14.1', '-Python-3.7.4'), + ('ParaView', '5.6.2', '-Python-3.7.4-mpi'), +] + +builddependencies = [ + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' From 6e291c348e81a9d279f5755fb36614b5dbd2e375 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Wed, 4 Dec 2019 17:23:04 +0200 Subject: [PATCH 074/468] adding easyconfigs: CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb --- .../CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..bf8fa364933 --- /dev/null +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'CRPropa' +version = '3.1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://crpropa.desy.de' +description = """CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron + on their voyage through an extra galactic environment.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/CRPropa/CRPropa3/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ee394b42967fabe93b83205751a38b70cc67a126bce5968d49656a556ff022d5'] + +dependencies = [ + ('Python', '3.7.2'), + ('HDF5','1.10.5'), + ('SciPy-bundle','2019.03'), +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('SWIG','3.0.12'), + ('pkg-config','0.29.2'), + ('Doxygen','1.8.15'), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages' +} + +sanity_check_commands = [ + """python -c "import crpropa; 'initTurbulence' in dir(crpropa)" """ +] + +sanity_check_paths = { + 'files': ["lib/libcrpropa.so"], + 'dirs': [ + "lib/python%(pyshortver)s/site-packages", + "share" + ], +} + +moduleclass = 'astro' From a539f71a3b2851bc2fc0dfef7360b69aaeefa628 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Wed, 4 Dec 2019 17:35:21 +0200 Subject: [PATCH 075/468] CRPropa: codestyle improvement --- .../c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb index bf8fa364933..a8df525ab72 100644 --- a/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb @@ -16,15 +16,15 @@ checksums = ['ee394b42967fabe93b83205751a38b70cc67a126bce5968d49656a556ff022d5'] dependencies = [ ('Python', '3.7.2'), - ('HDF5','1.10.5'), - ('SciPy-bundle','2019.03'), + ('HDF5', '1.10.5'), + ('SciPy-bundle', '2019.03'), ] builddependencies = [ ('CMake', '3.13.3'), - ('SWIG','3.0.12'), - ('pkg-config','0.29.2'), - ('Doxygen','1.8.15'), + ('SWIG', '3.0.12'), + ('pkg-config', '0.29.2'), + ('Doxygen', '1.8.15'), ] modextrapaths = { From ba554984af74110d5415db6676fa05d1a22357aa Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Wed, 4 Dec 2019 16:49:22 +0100 Subject: [PATCH 076/468] Release available in source repository, removed local_commit --- .../TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TreeShrink/TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb b/easybuild/easyconfigs/t/TreeShrink/TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb index abe536acafa..00f20179218 100644 --- a/easybuild/easyconfigs/t/TreeShrink/TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TreeShrink/TreeShrink-1.3.2-GCC-8.2.0-2.31.1-Python-3.7.2.eb @@ -4,7 +4,6 @@ easyblock = 'PythonPackage' name = 'TreeShrink' version = '1.3.2' versionsuffix = '-Python-%(pyver)s' -local_commit = '0b5fc31' homepage = 'https://github.com/uym2/TreeShrink' description = """TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees.""" @@ -13,8 +12,8 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} github_account = 'uym2' source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['94f987100f5ada99f47799336f51e47798a2bd1806cb188d66edb8135f5856d5'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4ba64b16c4376ea3023bb3bfa8e6d32e8334b254ce2cf084d640e7efdcfc3a4c'] skipsteps = ['build'] From 2471e6bf99f17ad8716fa525de2e661c8cb5493b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Dec 2019 18:14:48 +0200 Subject: [PATCH 077/468] fiji-20170530: remove comments about other releases --- easybuild/easyconfigs/f/fiji/fiji-20170530.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb index 080fb56b339..8262909fbac 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb +++ b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb @@ -6,14 +6,10 @@ version = '20170530' homepage = 'https://fiji.sc/' description = """Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. -This release is based on ImageJ-1.51n""" + This release is based on ImageJ 2.0.0-rc-69/1.52p.""" toolchain = SYSTEM -# More recent releases of fiji can be found in the non-versioned tarballs available at -# source_urls = ['https://downloads.imagej.net/fiji/latest/'] -# Manually download the 'nojre' version and check the versions of ImageJ and fiji in the folder 'jars' -# sources = ['%(name)s-nojre.tar.gz'] source_urls = ['https://downloads.imagej.net/fiji/Life-Line/'] sources = ['%(name)s-nojre-%(version)s.zip'] checksums = ['cf9fb45c48b22a7888b479968477f1f7a300a9c833e47244cbe0d1e93890bd20'] From 72a5dd2e8db4a39e751d73278e1f487e40290e95 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Dec 2019 18:15:41 +0200 Subject: [PATCH 078/468] fiji: update to archive version 20191119-2057 --- .../easyconfigs/f/fiji/fiji-20191119-2057.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb diff --git a/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb b/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb new file mode 100644 index 00000000000..63e8e333d3d --- /dev/null +++ b/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'fiji' +version = '20191119-2057' + +homepage = 'https://fiji.sc/' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. + This release is based on ImageJ 2.0.0-rc-69/1.52p.""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.imagej.net/fiji/archive/%(version)s'] +sources = [{ + 'download_filename': '%(name)s-nojre.tar.gz', + 'filename': '%(name)s-nojre-%(version)s.tar.gz', +}] +checksums = ['7fad8e8f8676edbcfe7eb979421ab163e8d48bb7950a815f7821cbe58b8bb051'] + +dependencies = [('Java', '1.8', '', True)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe,ImageJ-linux32}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' http://sites.imagej.net/Tboudier/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' http://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modextrapaths = {'MATLABPATH': 'scripts'} + +modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64. + Plugins can be installed in your $HOME/.plugins folder. + If you need any other update sites to be enabled, please contact support.""" + +moduleclass = 'vis' From 4026776c58d902104d00874ef1b3e445be7b400a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Dec 2019 18:23:30 +0200 Subject: [PATCH 079/468] OpenFOAM-6: fix homepage --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb index 02c430de214..063b50689c4 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2019b.eb @@ -1,7 +1,7 @@ name = 'OpenFOAM' version = '6' -homepage = 'http://www.openfoam.org/' +homepage = 'https://www.openfoam.org/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, From b2aaae1aac658723e0f777a74f7394b5de926335 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Dec 2019 18:33:37 +0200 Subject: [PATCH 080/468] fiji: fix unsecured URLs --- easybuild/easyconfigs/f/fiji/fiji-20170530.eb | 4 ++-- easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb index 8262909fbac..5f5475c9b95 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb +++ b/easybuild/easyconfigs/f/fiji/fiji-20170530.eb @@ -24,10 +24,10 @@ postinstallcmds = [ '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' ' https://sites.imagej.net/ImageScience/', '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' - ' http://sites.imagej.net/Tboudier/', + ' https://sites.imagej.net/Tboudier/', # Add a new update site # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' - # ' http://site.url/NewName/', + # ' https://site.url/NewName/', # Update the installation '%(installdir)s/ImageJ-linux64 --headless --update update', ] diff --git a/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb b/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb index 63e8e333d3d..09b9ba4f632 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb +++ b/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb @@ -27,10 +27,10 @@ postinstallcmds = [ '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' ' https://sites.imagej.net/ImageScience/', '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' - ' http://sites.imagej.net/Tboudier/', + ' https://sites.imagej.net/Tboudier/', # Add a new update site # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' - # ' http://site.url/NewName/', + # ' https://site.url/NewName/', # Update the installation '%(installdir)s/ImageJ-linux64 --headless --update update', ] From 1f6d0392e2857138c5e1c3d310421480b5754eb8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 4 Dec 2019 20:14:47 +0200 Subject: [PATCH 081/468] Removed outdated comment. --- .../easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb | 1 - .../g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb index 6978ea2cca2..3f29c9cdf51 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-foss-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ latest algorithms.""" toolchain = {'name': 'foss', 'version': '2018b'} -# registration is required source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] sources = ['%(namelower)s%(version)s_linux64.tar.gz'] checksums = ['07c48fe0f18097ddca6ddc6f5a276e1548a37b31016d0b8575bb12ec8f44546e'] diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb index b638eb73fa5..bacf7ca408c 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0-intel-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ latest algorithms.""" toolchain = {'name': 'intel', 'version': '2018b'} -# registration is required source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] sources = ['%(namelower)s%(version)s_linux64.tar.gz'] checksums = ['07c48fe0f18097ddca6ddc6f5a276e1548a37b31016d0b8575bb12ec8f44546e'] From 213f92fe7289a208e8bfde8b398a7e3a9c78616d Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Wed, 4 Dec 2019 20:37:02 +0200 Subject: [PATCH 082/468] CRPropa: migrated to CMakePythonPackage g.eb., code style impr. --- .../CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb index a8df525ab72..c3e6c9033a4 100644 --- a/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-3.1.5-foss-2019a-Python-3.7.2.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'CRPropa' version = '3.1.5' @@ -14,12 +14,6 @@ source_urls = ['https://github.com/CRPropa/CRPropa3/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['ee394b42967fabe93b83205751a38b70cc67a126bce5968d49656a556ff022d5'] -dependencies = [ - ('Python', '3.7.2'), - ('HDF5', '1.10.5'), - ('SciPy-bundle', '2019.03'), -] - builddependencies = [ ('CMake', '3.13.3'), ('SWIG', '3.0.12'), @@ -27,9 +21,13 @@ builddependencies = [ ('Doxygen', '1.8.15'), ] -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages' -} +dependencies = [ + ('Python', '3.7.2'), + ('HDF5', '1.10.5'), + ('SciPy-bundle', '2019.03'), +] + +runtest = False sanity_check_commands = [ """python -c "import crpropa; 'initTurbulence' in dir(crpropa)" """ From d2a277c0ab3deb1f2f46777d29bdaa46b047bc01 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 5 Dec 2019 10:34:17 +0800 Subject: [PATCH 083/468] bump version to 4.1.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 3d26829ae6b..669fd196b9e 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.1.0' +VERSION = '4.1.1.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 9d4dd1e309ed99a6d0d7b051ca9cfb67bed18f36 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 5 Dec 2019 08:53:34 +0100 Subject: [PATCH 084/468] Removed -D_qt5gui_.. patch --- .../o/OpenFOAM/OpenFOAM-7-cleanup.patch | 18 ------------------ .../o/OpenFOAM/OpenFOAM-7-foss-2019b.eb | 2 +- 2 files changed, 1 insertion(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch index a1a97a78f81..fd08f290afc 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-cleanup.patch @@ -43,24 +43,6 @@ diff -ru OpenFOAM-7-version-7.orig/applications/utilities/postProcessing/graphic wmake $targetType vtkPVblockMesh wmake $targetType vtkPVFoam -@@ -26,7 +26,7 @@ - cd PVblockMeshReader - mkdir -p Make/$WM_OPTIONS > /dev/null 2>&1 - cd Make/$WM_OPTIONS -- cmake ../.. -+ cmake -D_qt5gui_OPENGL_INCLUDE_DIR=$EBROOTMESA/include ../.. - make - ) - -@@ -34,7 +34,7 @@ - cd PVFoamReader - mkdir -p Make/$WM_OPTIONS > /dev/null 2>&1 - cd Make/$WM_OPTIONS -- cmake ../.. -+ cmake -D_qt5gui_OPENGL_INCLUDE_DIR=$EBROOTMESA/include ../.. - make - ) - fi diff -ru OpenFOAM-7-version-7.orig/etc/bashrc OpenFOAM-7-version-7/etc/bashrc --- OpenFOAM-7-version-7.orig/etc/bashrc 2018-07-09 18:01:02.000000000 +0200 +++ OpenFOAM-7-version-7/etc/bashrc 2018-08-14 11:29:14.168761602 +0200 diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb index 6bcf5936ff2..129f4537a14 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2019b.eb @@ -18,7 +18,7 @@ patches = [ ] checksums = [ '12389cf092dc032372617785822a597aee434a50a62db2a520ab35ba5a7548b5', # version-7.tar.gz - '8b2f6bcd396e7779de2c03561d4a004014ab250274b1fc82444845c074dcf6a3', # OpenFOAM-7-cleanup.patch + '64b8614e41f8e8a33d944cf5b91031fb10cec51784f4549e83dcd46985683ef3', # OpenFOAM-7-cleanup.patch '9f2af8f67a57a187f68aadaa99bc99f1cfbfe41086e5839a57e1bb4e41b3762c', # OpenFOAM-7-mpi-compilation.patch ] From 1215e711baa1b798820c4f85324bbccea37f8c11 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 4 Dec 2019 17:49:19 +0100 Subject: [PATCH 085/468] [CUDA] Add power9 support to CUDA 10.1 ECs --- .../c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb | 5 ++--- easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb | 4 ++-- easybuild/easyconfigs/c/CUDA/CUDA-10.1.168.eb | 12 ++++++++++-- .../easyconfigs/c/CUDA/CUDA-10.1.243-GCC-8.3.0.eb | 12 ++++++++++-- easybuild/easyconfigs/c/CUDA/CUDA-10.1.243.eb | 12 ++++++++++-- 5 files changed, 34 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb index 4a1a840c70c..3d95d57b058 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb @@ -14,12 +14,11 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] sources = ['%%(namelower)s_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] - checksums = [ { - '%(namelower)s_%(version)s_418.39_linux.run': + '%%(namelower)s_%%(version)s_%s_linux.run' % local_nv_version: '33ac60685a3e29538db5094259ea85c15906cbd0f74368733f4111eab6187c8f', - '%(namelower)s_%(version)s_418.39_linux_ppc64le.run': + '%%(namelower)s_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: 'b81290b834483847e317ff4eafacc14d96bae8ad873aa9b1adddf2567318d658', } ] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb index 95afcc93891..fd253dedae4 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb @@ -18,9 +18,9 @@ source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_maj sources = ['%%(namelower)s_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] checksums = [ { - '%(namelower)s_%(version)s_418.39_linux.run': + '%%(namelower)s_%%(version)s_%s_linux.run' % local_nv_version: '33ac60685a3e29538db5094259ea85c15906cbd0f74368733f4111eab6187c8f', - '%(namelower)s_%(version)s_418.39_linux_ppc64le.run': + '%%(namelower)s_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: 'b81290b834483847e317ff4eafacc14d96bae8ad873aa9b1adddf2567318d658', } ] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.168.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.168.eb index bb9e734f21f..a596c39f88d 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.168.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.168.eb @@ -3,6 +3,7 @@ name = 'CUDA' version = '10.1.168' +local_nv_version = '418.67' homepage = 'https://developer.nvidia.com/cuda-toolkit' description = """CUDA (formerly Compute Unified Device Architecture) is a parallel @@ -13,7 +14,14 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] -sources = ['%(namelower)s_%(version)s_418.67_linux.run'] -checksums = ['4fcad1d2af35495ff57b8ea5851f6031c3d350d14e88f5db12c40a4074ddf43f'] +sources = ['%%(namelower)s_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + '%%(namelower)s_%%(version)s_%s_linux.run' % local_nv_version: + '4fcad1d2af35495ff57b8ea5851f6031c3d350d14e88f5db12c40a4074ddf43f', + '%%(namelower)s_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '0545d3bbf2ec29635b7f5668a9186b5875a95a79d66b78c47544fba046078f4c', + } +] moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.243-GCC-8.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.243-GCC-8.3.0.eb index 2bc8a66cbbf..951baab5cbb 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.243-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.243-GCC-8.3.0.eb @@ -3,6 +3,7 @@ name = 'CUDA' version = '10.1.243' +local_nv_version = '418.87.00' homepage = 'https://developer.nvidia.com/cuda-toolkit' description = """CUDA (formerly Compute Unified Device Architecture) is a parallel @@ -13,7 +14,14 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] -sources = ['%(namelower)s_%(version)s_418.87.00_linux.run'] -checksums = ['e7c22dc21278eb1b82f34a60ad7640b41ad3943d929bebda3008b72536855d31'] +sources = ['%%(namelower)s_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + '%%(namelower)s_%%(version)s_%s_linux.run' % local_nv_version: + 'e7c22dc21278eb1b82f34a60ad7640b41ad3943d929bebda3008b72536855d31', + '%%(namelower)s_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'b198002eef010bab9e745ae98e47567c955d00cf34cc8f8d2f0a6feb810523bf', + } +] moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.243.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.243.eb index c75aad6a2ae..2d154c30366 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.243.eb @@ -3,6 +3,7 @@ name = 'CUDA' version = '10.1.243' +local_nv_version = '418.87.00' homepage = 'https://developer.nvidia.com/cuda-toolkit' description = """CUDA (formerly Compute Unified Device Architecture) is a parallel @@ -13,7 +14,14 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = SYSTEM source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] -sources = ['%(namelower)s_%(version)s_418.87.00_linux.run'] -checksums = ['e7c22dc21278eb1b82f34a60ad7640b41ad3943d929bebda3008b72536855d31'] +sources = ['%%(namelower)s_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + '%%(namelower)s_%%(version)s_%s_linux.run' % local_nv_version: + 'e7c22dc21278eb1b82f34a60ad7640b41ad3943d929bebda3008b72536855d31', + '%%(namelower)s_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'b198002eef010bab9e745ae98e47567c955d00cf34cc8f8d2f0a6feb810523bf', + } +] moduleclass = 'system' From 460fe222b11d8c4e6c2a2c336121b053264564d5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 5 Dec 2019 11:36:40 +0200 Subject: [PATCH 086/468] OpenFOAM-6: add warning about OF bug 3071 in build with foss/2018b --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb index 77809ff5e69..9032b2d8e5f 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb @@ -7,6 +7,8 @@ description = """OpenFOAM is a free, open source CFD software package. involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.""" +# Warning: this build of OpenFOAM-6 with OpenMPI-3.1.1 (foss/2018b) is subject +# to OF bug 3071 - https://bugs.openfoam.org/view.php?id=3071 toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'cstd': 'c++11'} From 6e833d8648a70d3d583a0bf91a87c5036cd851a1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 5 Dec 2019 11:39:15 +0200 Subject: [PATCH 087/468] OpenFOAM-6: fix unsecure URLs --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb index 9032b2d8e5f..ca8cd436873 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-6-foss-2018b.eb @@ -1,7 +1,7 @@ name = 'OpenFOAM' version = '6' -homepage = 'http://www.openfoam.org/' +homepage = 'https://www.openfoam.org/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, From 02426f6e66c0271834e1d258bec6b1ad668ff495 Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Thu, 5 Dec 2019 14:59:50 +0100 Subject: [PATCH 088/468] remove modluafooter, add modloadmsg --- .../n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb index 475de9510de..a1f1884327a 100644 --- a/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb @@ -30,7 +30,8 @@ sanity_check_paths = { 'dirs': ['dat'], } -# site-specific: set OMP_NUM_THREADS equal to number of available cores -modluafooter = 'if os.getenv("PBS_NUM_PPN") ~= nil then pushenv("OMP_NUM_THREADS", os.getenv("PBS_NUM_PPN")) end' +modloadmsg = """ +set environment variable OMP_NUM_THREADS equal to the number of available cores before running +""" moduleclass = 'chem' From 6af2b88538a85dd7d6ca24b56d9bcb404ed0ccf6 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Thu, 5 Dec 2019 15:53:12 +0100 Subject: [PATCH 089/468] Easyconfigs for Anaconda2/3 version 2019.10 --- .../a/Anaconda2/Anaconda2-2019.10.eb | 21 ++++++++++++++++++ .../a/Anaconda3/Anaconda3-2019.10.eb | 22 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.10.eb create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.10.eb diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.10.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.10.eb new file mode 100644 index 00000000000..6976f7e3657 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.10.eb @@ -0,0 +1,21 @@ +# author: Jillian Rowe +# config upgrade to 5.0.1, 5.1.0, 5.3.0, 2018.12, 2019.07, 2019.10 by Joachim Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda2' +version = '2019.10' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['8b2e7dea2da7d8cc18e822e8ec1804052102f4eefb94c1b3d0e586e126e8cd2f'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.10.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.10.eb new file mode 100644 index 00000000000..9b4241b60fd --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.10.eb @@ -0,0 +1,22 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, 2019.10 by Joachim Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2019.10' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['46d762284d252e51cd58a8ca6c8adc9da2eadc82c342927b2f66ed011d1d8b53'] + +moduleclass = 'lang' From b8199fb60fdc1e2fb7e49e47dc47765993534671 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 5 Dec 2019 17:11:56 +0100 Subject: [PATCH 090/468] fix modloadmsg --- .../n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb index a1f1884327a..6c7d444b9d5 100644 --- a/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20190718-iccifort-2019.5.281.eb @@ -31,7 +31,7 @@ sanity_check_paths = { } modloadmsg = """ -set environment variable OMP_NUM_THREADS equal to the number of available cores before running +Set environment variable OMP_NUM_THREADS equal to the number of available cores before running this program. """ moduleclass = 'chem' From f60535b6f6e3b417fdafeffabea136d34c12321c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 5 Dec 2019 20:26:30 +0000 Subject: [PATCH 091/468] adding easyconfigs: libxslt-1.1.34-GCCcore-8.3.0.eb, lxml-4.4.2-GCCcore-8.3.0.eb --- .../l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb | 26 +++++++++++++++ .../l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb | 32 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..7ab9151b5ba --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.34' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.9'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..92272c2d52a --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.4.2' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] +checksums = ['eff69ddbf3ad86375c344339371168640951c302450c5d3e9936e98d6459db06'] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('libxml2', '2.9.9'), + ('libxslt', '1.1.34'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From d4435fb427838b5022f8b11cc673790139e4fde8 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 5 Dec 2019 20:29:59 +0000 Subject: [PATCH 092/468] https urls in lxml --- easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb index 92272c2d52a..4611e381e8a 100644 --- a/easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/lxml/lxml-4.4.2-GCCcore-8.3.0.eb @@ -3,12 +3,12 @@ easyblock = 'PythonPackage' name = 'lxml' version = '4.4.2' -homepage = 'http://lxml.de/' +homepage = 'https://lxml.de/' description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['http://lxml.de/files/'] +source_urls = ['https://lxml.de/files/'] sources = [SOURCE_TGZ] checksums = ['eff69ddbf3ad86375c344339371168640951c302450c5d3e9936e98d6459db06'] From 4a775edae878a2590aa5ee3fb7ec410cbf7375f2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 5 Dec 2019 20:45:30 +0000 Subject: [PATCH 093/468] add sanity paths check to libxslt --- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb index 7ab9151b5ba..f3c2326d6f8 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb @@ -23,4 +23,9 @@ dependencies = [ ('libxml2', '2.9.9'), ] +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + moduleclass = 'lib' From b3990ae5900adda0eec5b09b6149fcd0599ba4ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 14:10:18 +0100 Subject: [PATCH 094/468] adding easyconfigs: cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb --- ...toolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..711e79ca048 --- /dev/null +++ b/easybuild/easyconfigs/c/cytoolz/cytoolz-0.10.1-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'cytoolz' +version = '0.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pytoolz/cytoolz' +description = """Cython implementation of the toolz package, which provides high performance utility functions + for iterables, functions, and dictionaries.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('Python', '3.7.2'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('toolz', '0.10.0', { + 'checksums': ['08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560'], + }), + (name, version, { + 'checksums': ['82f5bba81d73a5a6b06f2a3553ff9003d865952fcb32e1df192378dd944d8a5c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 4f014fd905dd9be189a7e5f85aacf4634fadf3ad Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Dec 2019 16:30:51 +0100 Subject: [PATCH 095/468] Stay with JDK8 (Java 1.8) as stated by Bazel docus --- easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb index e757c2e2f28..0716751362a 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb @@ -15,6 +15,6 @@ builddependencies = [ ('binutils', '2.32'), ('Python', '3.7.4'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '1.8', '', True)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb index ae409699bec..31b40be4150 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb @@ -19,6 +19,6 @@ builddependencies = [ ('binutils', '2.32'), ('Python', '3.7.4'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '1.8', '', True)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb index e8195054ab9..02b10ad1651 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb @@ -19,6 +19,6 @@ builddependencies = [ ('binutils', '2.32'), ('Python', '3.7.4'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '1.8', '', True)] moduleclass = 'devel' From 0092dfc96002eea451b9e1fc251b6a570428360d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 19:24:11 +0100 Subject: [PATCH 096/468] adding easyconfigs: barrnap-0.9-GCC-8.2.0-2.31.1.eb --- .../b/barrnap/barrnap-0.9-GCC-8.2.0-2.31.1.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/barrnap/barrnap-0.9-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/b/barrnap/barrnap-0.9-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..6a55f15c1a6 --- /dev/null +++ b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'barrnap' +version = '0.9' + +homepage = 'https://github.com/tseemann/barrnap' +description = "Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes." + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/tseemann/barrnap/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15'] + +dependencies = [ + ('Perl', '5.28.1'), + ('HMMER', '3.2.1'), + ('BEDTools', '2.28.0'), +] + +sanity_check_paths = { + 'files': ['bin/barrnap'], + 'dirs': [], +} + +sanity_check_commands = ["barrnap --help"] + +moduleclass = 'bio' From 47a5b1287666c4f7f2a032a7c990edeec2ca8fc9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 19:28:21 +0100 Subject: [PATCH 097/468] adding easyconfigs: seqtk-1.3-GCC-8.2.0-2.31.1.eb --- .../s/seqtk/seqtk-1.3-GCC-8.2.0-2.31.1.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..f1f4f99403c --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.3' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/lh3/seqtk/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] + +dependencies = [('zlib', '1.2.11')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +moduleclass = 'bio' From a7dc2cc5bd324b720da65dd985fdd386f5154d6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 19:38:08 +0100 Subject: [PATCH 098/468] adding easyconfigs: KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb --- ...KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb b/easybuild/easyconfigs/k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb new file mode 100644 index 00000000000..0169f657e83 --- /dev/null +++ b/easybuild/easyconfigs/k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'KMC' +version = '3.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sun.aei.polsl.pl/kmc' +description = "KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files." + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/refresh-bio/KMC/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d7cdf37d90a07d1a432b7427436f962914b5f63a1b6dbb9a116609a1c64d1324'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '3.7.2'), +] + +# Makefile does static linking with libc.a, libpthread.a, libm.a +osdependencies = ['glibc-static'] + +prebuildopts = "sed -i 's@[^ ]*/libz.a@${EBROOTZLIB}/lib/libz.a@g' makefile && " +prebuildopts += "sed -i 's@[^ ]*/libbz2.a@${EBROOTBZIP2}/lib/libbz2.a@g' makefile && " + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/kmc', 'bin/kmc_dump'], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import py_kmc_api'"] + +# Python bindings are also located in bin/ +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'bio' From 6694f74027b5cf605001e917381e93ee3203dd87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 19:45:02 +0100 Subject: [PATCH 099/468] adding easyconfigs: fastp-0.20.0-GCC-8.2.0-2.31.1.eb --- .../f/fastp/fastp-0.20.0-GCC-8.2.0-2.31.1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.20.0-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.20.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/f/fastp/fastp-0.20.0-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..bef580d5803 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.20.0-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.20.0' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/OpenGene/fastp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8d751d2746db11ff233032fc49e3bcc8b53758dd4596fdcf4b4099a4d702ac22'] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'dirs': [], + 'files': ['bin/fastp'], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' From fd349e5d79dae89f0df232fbd68032aa9378b968 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 19:49:24 +0100 Subject: [PATCH 100/468] adding easyconfigs: EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb --- .../e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..a4cabd71a43 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,59 @@ +# authors: Kenneth Hoste (Ghent University) +# George Tsouloupas +# Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component +# of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute +# +# Updated: Pavel Grochal (INUITS) +# +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' + +homepage = 'https://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite' +. EMBOSS is a free Open Source software analysis package specially developed + for the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +github_account = 'kimrutherford' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_disable-embossupdate.patch'] +checksums = [ + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz + '7e0a7deffd76f60093be9c5253605f2d6d2e3b0c2d3c9365035cc6bda43eb46c', # EMBOSS-6.6.0_disable-embossupdate.patch +] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('X11', '20190311'), + ('libharu', '2.3.0'), + ('Java', '11', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} +sanity_check_commands = [ + 'embossdata -h' +] + +moduleclass = 'bio' From 94b89589f52631661ef2e54b424ef8ffbd15ae96 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 20:57:40 +0100 Subject: [PATCH 101/468] adding easyconfigs: QUAST-5.0.2-foss-2019a-Python-3.7.2.eb --- .../QUAST-5.0.2-foss-2019a-Python-3.7.2.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..af6c0aea139 --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,57 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ablab/%(namelower)s' +description = """QUAST evaluates genome assemblies by computing various metrics. + It works both with and without reference genomes. The tool accepts multiple + assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.7.2'), + ('Perl', '5.28.1'), + ('matplotlib', '3.0.3', versionsuffix), + ('Java', '11', '', True), + ('Boost', '1.70.0'), +] + +use_pip = True + +exts_list = [ + ('simplejson', '3.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], + 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], + }), + (name, version, { + 'source_tmpl': 'quast_%(version)s.tar.gz', + 'source_urls': ['https://github.com/ablab/quast/archive/'], + 'checksums': ['9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d'], + 'install_target': 'install_full', + 'modulename': 'quast_libs', + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "wget quast.sf.net/test_data.tar.gz && " + "tar xzf test_data.tar.gz && " + "%(namelower)s.py --test && " + "rm ./test_data.tar.gz ./test_data -rf" +] + +sanity_pip_check = True + +moduleclass = 'bio' From c0e96f72a56c46a249cb45978ba7a859c234814e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 21:00:17 +0100 Subject: [PATCH 102/468] use GCC/8.3.0 toolchain for IGMPlot --- ...MPlot-2.4.2-GCC-8.3.0-2.32.eb => IGMPlot-2.4.2-GCC-8.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/i/IGMPlot/{IGMPlot-2.4.2-GCC-8.3.0-2.32.eb => IGMPlot-2.4.2-GCC-8.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0.eb similarity index 93% rename from easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0-2.32.eb rename to easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0.eb index 6a3a6ca75e7..d2d59b1e439 100644 --- a/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.4.2-GCC-8.3.0.eb @@ -7,7 +7,7 @@ homepage = 'http://igmplot.univ-reims.fr' description = """IGMPlot is a free open-source program developed to identify molecular interactions and prepare data to build 2D and 3D representations of them in the molecular environment.""" -toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} +toolchain = {'name': 'GCC', 'version': '8.3.0'} toolchainopts = {'openmp': True} source_urls = ['http://igmplot.univ-reims.fr/download/'] From 6d044dcc907c5993bc30375aa882a6669b74c1e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 21:02:43 +0100 Subject: [PATCH 103/468] symlink quast.py to quast in QUAST easyconfig --- .../q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb index af6c0aea139..5ff4f1c58e1 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb @@ -40,8 +40,10 @@ exts_list = [ }), ] +postinstallcmds = ["cd %(installdir)s/bin && ln -s quast.py quast"] + sanity_check_paths = { - 'files': ['bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } @@ -49,7 +51,8 @@ sanity_check_commands = [ "wget quast.sf.net/test_data.tar.gz && " "tar xzf test_data.tar.gz && " "%(namelower)s.py --test && " - "rm ./test_data.tar.gz ./test_data -rf" + "rm ./test_data.tar.gz ./test_data -rf", + "%(namelower)s -h", ] sanity_pip_check = True From b329338fed1d2486c6eff072527d01ef3db1d02b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 22:38:57 +0100 Subject: [PATCH 104/468] adding easyconfigs: ReFrame-2.20.eb --- .../easyconfigs/r/ReFrame/ReFrame-2.20.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-2.20.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-2.20.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-2.20.eb new file mode 100644 index 00000000000..5cdee77f23d --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-2.20.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'ReFrame' +version = '2.20' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +source_urls = ['https://pypi.python.org/packages/source/R/ReFrame-HPC'] +sources = ['ReFrame-HPC-%(version)s.tar.gz'] +checksums = ['34c333015c90c1137ff0fbc93f211c41e210c8e0a3d73f44fdac7a13e052721b'] + +dependencies = [('setuptools', '41.0.1', '-py3')] + +download_dep_fail = True +use_pip = False + +# ReFrame requires Python 3.5, may only be available via 'python3' +req_py_majver = 3 +req_py_minver = 5 + +sanity_check_paths = { + 'files': ['bin/reframe'], + 'dirs': [] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' From ea54df5f38b5b5015e3e17608f87299bcc1161cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Dec 2019 09:55:39 +0100 Subject: [PATCH 105/468] add libc6-dev (Debian/Ubuntu) for libc.a & co in KMC easyconfig --- .../k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb b/easybuild/easyconfigs/k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb index 0169f657e83..753f60bb4b5 100644 --- a/easybuild/easyconfigs/k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb +++ b/easybuild/easyconfigs/k/KMC/KMC-3.1.1-GCC-8.2.0-2.31.1-Python-3.7.2.eb @@ -20,7 +20,7 @@ dependencies = [ ] # Makefile does static linking with libc.a, libpthread.a, libm.a -osdependencies = ['glibc-static'] +osdependencies = [('glibc-static', 'libc6-dev')] prebuildopts = "sed -i 's@[^ ]*/libz.a@${EBROOTZLIB}/lib/libz.a@g' makefile && " prebuildopts += "sed -i 's@[^ ]*/libbz2.a@${EBROOTBZIP2}/lib/libbz2.a@g' makefile && " From f18f896b892f59eb014adce1dc5c5a1f7147f0d2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Sat, 7 Dec 2019 15:12:55 +0100 Subject: [PATCH 106/468] Fix build on Power9 (include zip -d patch) --- .../b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb | 6 ++- .../b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb | 6 ++- .../Bazel-0.29.1_fix-zip-d-on-power.patch | 43 +++++++++++++++++++ 3 files changed, 53 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-0.29.1_fix-zip-d-on-power.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb index 1b1f8939fb2..f39c220e1a9 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb @@ -9,10 +9,14 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -patches = ['Bazel-%(version)s_fix-gold-flag.patch'] +patches = [ + 'Bazel-%(version)s_fix-gold-flag.patch', + 'Bazel-%(version)s_fix-zip-d-on-power.patch', +] checksums = [ '872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5', # bazel-0.29.1-dist.zip '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch + '0089567af6a991084d5628a8b6fa92b68402ff4b7a0ef8fa944e629e7be63b93', # Bazel-0.29.1_fix-zip-d-on-power.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb index 31b40be4150..ea9845b83a9 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb @@ -9,10 +9,14 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -patches = ['Bazel-%(version)s_fix-gold-flag.patch'] +patches = [ + 'Bazel-%(version)s_fix-gold-flag.patch', + 'Bazel-%(version)s_fix-zip-d-on-power.patch', +] checksums = [ '872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5', # bazel-0.29.1-dist.zip '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch + '0089567af6a991084d5628a8b6fa92b68402ff4b7a0ef8fa944e629e7be63b93', # Bazel-0.29.1_fix-zip-d-on-power.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1_fix-zip-d-on-power.patch b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1_fix-zip-d-on-power.patch new file mode 100644 index 00000000000..0dbc7a3817b --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1_fix-zip-d-on-power.patch @@ -0,0 +1,43 @@ +From 99775df8356ab6c7dd77493b35e59de5f6a773f8 Mon Sep 17 00:00:00 2001 +From: Christy Norman +Date: Wed, 4 Sep 2019 18:41:37 -0400 +Subject: [PATCH] fix build for Power + +The zip -d flag will error if it doesn't find that extension. +This is a fix for Power, but doesn't fix the default case. + +Signed-off-by: Christy Norman +--- + src/conditions/BUILD | 6 ++++++ + third_party/BUILD | 1 + + 2 files changed, 7 insertions(+) + +diff --git a/src/conditions/BUILD b/src/conditions/BUILD +index 2b28e280576..faa41a439d4 100644 +--- a/src/conditions/BUILD ++++ b/src/conditions/BUILD +@@ -10,6 +10,12 @@ filegroup( + visibility = ["//src:__pkg__"], + ) + ++config_setting( ++ name = "linux_ppc", ++ values = {"cpu": "ppc"}, ++ visibility = ["//visibility:public"], ++) ++ + config_setting( + name = "linux_x86_64", + values = {"cpu": "k8"}, +diff --git a/third_party/BUILD b/third_party/BUILD +index 7545b3df33a..b4115b2988c 100644 +--- a/third_party/BUILD ++++ b/third_party/BUILD +@@ -528,6 +528,7 @@ UNNECESSARY_DYNAMIC_LIBRARIES = select({ + # The .so file is an x86 one, so we can just remove it if the CPU is not x86 + "//src/conditions:arm": "*.so *.jnilib *.dll", + "//src/conditions:linux_aarch64": "*.so *.jnilib *.dll", ++ "//src/conditions:linux_ppc": "*.so *.jnilib *.dll", + # Play it safe -- better have a big binary than a slow binary + # zip -d does require an argument. Supply something bogus. + "//conditions:default": "*.bogusextension", From 7ed1f2809ef4a581cd2f78b8c28d68358510781b Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Sat, 7 Dec 2019 18:18:05 +0100 Subject: [PATCH 107/468] adding easyconfigs: SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb --- ...uiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb new file mode 100644 index 00000000000..d6575e478cc --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb @@ -0,0 +1,26 @@ +name = 'SuiteSparse' +version = '5.6.0' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['76d34d9f6dafc592b69af14f58c1dc59e24853dcd7c2e8f4c98ffa223f6a1adb'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [('METIS', local_metis_ver)] + +parallel = 1 + +#prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From 25eb5ddb6ddd4e6aaa6396e8b67397690b8153dc Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Sat, 7 Dec 2019 18:23:51 +0100 Subject: [PATCH 108/468] adding easyconfigs: arpack-ng-3.7.0-foss-2019b.eb --- .../a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb new file mode 100644 index 00000000000..be0c9d7dedd --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = "3.7.0" + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6'] + +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Eigen', '3.3.7', '', True) +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'numlib' From b5a80d77f0b30950e5287c7fdc2f4fd1e4b026f0 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Sat, 7 Dec 2019 19:03:28 +0100 Subject: [PATCH 109/468] Corrected coding style --- .../s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb index d6575e478cc..e6bbce45c81 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.6.0-foss-2019b-METIS-5.1.0.eb @@ -19,7 +19,6 @@ dependencies = [('METIS', local_metis_ver)] parallel = 1 -#prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " # make sure that bin/demo can find libsuitesparseconfig.so.5 during build prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " From 8673b3f6b846510611855cf0d48921806f0f6349 Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Sun, 8 Dec 2019 22:00:16 +0100 Subject: [PATCH 110/468] define module load command in easyconfig --- .../easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb index 794979ed9c3..5510c1583b8 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb @@ -43,7 +43,11 @@ exts_list = [ }), ] -modextravars = {'SCOOP_LOAD_MODULE': 'module load %(module_name_full)s'} +# site-specific: this is for the (default) EB module naming scheme +# if necesarry, change to the command(s) necessary to loads this module +modextravars = { + 'SCOOP_LOAD_MODULE': 'module load %(name)s/%(version)s-%(toolchain_name)s-%(toolchain_version)s%(versionsuffix)s', +} sanity_check_paths = { 'files': [], From 919d455c1f0d34b9078e0989b17d53047c6a42d5 Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Mon, 9 Dec 2019 10:55:27 +0100 Subject: [PATCH 111/468] typo --- easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb index 5510c1583b8..45b05158e7e 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.7.1.1-GCCcore-8.2.0.eb @@ -43,8 +43,8 @@ exts_list = [ }), ] -# site-specific: this is for the (default) EB module naming scheme -# if necesarry, change to the command(s) necessary to loads this module +# site-specific: the line below is the command for loading this module with the (default) EB module naming scheme +# if necesary, change this command to match your cluster setup modextravars = { 'SCOOP_LOAD_MODULE': 'module load %(name)s/%(version)s-%(toolchain_name)s-%(toolchain_version)s%(versionsuffix)s', } From 3cbf007e6049ab5919c8d5e298fbef4057bdb0f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Dec 2019 11:50:44 +0100 Subject: [PATCH 112/468] adding easyconfigs: Gurobi-9.0.0.eb --- .../easyconfigs/g/Gurobi/Gurobi-9.0.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb new file mode 100644 index 00000000000..605a8fd65bf --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb @@ -0,0 +1,20 @@ +name = 'Gurobi' +version = '9.0.0' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = SYSTEM + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +checksums = ['07c48fe0f18097ddca6ddc6f5a276e1548a37b31016d0b8575bb12ec8f44546e'] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +sanity_check_commands = ["gurobi_cl --help"] + +moduleclass = 'math' From 4771bf388c248840117cace31b786d3b85c6ab4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Dec 2019 12:01:58 +0100 Subject: [PATCH 113/468] adding easyconfigs: worker-1.6.11-intel-2019b.eb --- .../w/worker/worker-1.6.11-intel-2019b.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb new file mode 100644 index 00000000000..39fdb66f7a2 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb @@ -0,0 +1,87 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.11' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['680a852586a712f82c4f1fc17d166b789b374d52a3c8a8ed30b8dc67ff38daf2'] + +osdependencies = ['perl'] + +local_tcname = 'intel' +local_tcver = '2019b' +builddependencies = [(local_tcname, local_tcver)] +versionsuffix = '-%s-%s' % (local_tcname, local_tcver) + +exts_defaultclass = 'PerlModule' + +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + 'checksums': ['8c67fd6608c3c4e74f7324f1404a856c331dbf48d9deda6aaa8296ea41bf199d'], + }), + ('Text::CSV', '2.00', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['8ccbd9195805222d995844114d0e595bb24ce188f85284dbf256080311cbb2c2'], + }), + ('DBI', '1.642', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': ['3f2025023a56286cebd15cb495e36ccd9b456c3cc229bf2ce1f69e9ebfc27f5d'], + }), + ('DBD::SQLite', '1.64', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['f4ae8f7b50842305566aadd90f7bfd12a9e32b6c603a9b1c1529e73eb82aff01'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': ['75bd254871cb5853a6aa0403ac0be270cdd75c9d1b6639f18ecba63c15298e86'], + }), + ('Template', '2.29', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['2bddd71cf41fb805fd5234780daf53226b8e7004c623e1647ba2658113614779'], + }), +] + +modextrapaths = { + 'PERL5LIB': ['share/perl5', 'lib64/perl5'], +} + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['dbilogstrip', 'dbiprof', 'dbiproxy', 'tpage', 'ttree', 'wcat', 'wconvert', + 'wload', 'worker', 'wreduce', 'wresume', 'wsub', 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt', 'lib64/perl5'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' From 3e6fda10a4bc63aacadbf68170b83ad628edbb1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Dec 2019 12:02:24 +0100 Subject: [PATCH 114/468] adding easyconfigs: yaff-1.6.0-intel-2019b-Python-3.7.4.eb, molmod-1.4.5-intel-2019b-Python-3.7.4.eb --- .../molmod-1.4.5-intel-2019b-Python-3.7.4.eb | 35 ++++++++++++++ .../yaff-1.6.0-intel-2019b-Python-3.7.4.eb | 46 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..42000037157 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['69c625fe081ea498371642d6237a8958cfc89608908fa8daa475f5d9dc5dc47c'] + +dependencies = [ + ('Python', '3.7.4'), + ('matplotlib', '3.1.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..4f4578abca6 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,46 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this at non-interactive job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] + +dependencies = [ + ('Python', '3.7.4'), + ('h5py', '2.10.0', versionsuffix), + ('molmod', '1.4.5', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From d7b5f4637052f64753f34002da18702af3cba5bf Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 9 Dec 2019 13:24:56 +0100 Subject: [PATCH 115/468] Fix CMake build on Power --- .../c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb | 9 +- .../c/CMake/CMake-3.15.3-fix-toc-flag.patch | 103 ++++++++++++++++++ 2 files changed, 110 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb index 0f633c737f7..620dbef46e0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5'] +patches = ['CMake-%(version)s-fix-toc-flag.patch'] +checksums = [ + '13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5', # cmake-3.15.3.tar.gz + '2c23aa7556e545ee8fd9df2df4f49fe5f983875162bff77d67fb7dd2a7867eb7', # CMake-3.15.3-fix-toc-flag.patch +] builddependencies = [ ('binutils', '2.32'), @@ -34,7 +38,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 ' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 ' configopts += '-DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include ' configopts += '-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.%s ' % SHLIB_EXT configopts += '-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch new file mode 100644 index 00000000000..0e8d1e58728 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch @@ -0,0 +1,103 @@ +diff -Naurd cmake-3.15.3/bootstrap cmake-3.15.3-patched/bootstrap +--- cmake-3.15.3/bootstrap 2019-09-04 15:58:03.000000000 +0200 ++++ cmake-3.15.3-patched/bootstrap 2019-12-09 13:13:29.004220868 +0100 +@@ -419,6 +419,7 @@ + cmTargetCompileOptionsCommand \ + cmTargetIncludeDirectoriesCommand \ + cmTargetLinkLibrariesCommand \ ++ cmTargetLinkOptionsCommand \ + cmTargetPropCommandBase \ + cmTargetPropertyComputer \ + cmTargetSourcesCommand \ +diff -Naurd cmake-3.15.3/CompileFlags.cmake cmake-3.15.3-patched/CompileFlags.cmake +--- cmake-3.15.3/CompileFlags.cmake 2019-09-04 15:58:00.000000000 +0200 ++++ cmake-3.15.3-patched/CompileFlags.cmake 2019-12-09 13:13:29.004220868 +0100 +@@ -54,12 +54,20 @@ + endif() + + # Workaround for TOC Overflow on ppc64 ++set(bigTocFlag "") + if(CMAKE_SYSTEM_NAME STREQUAL "AIX" AND + CMAKE_SYSTEM_PROCESSOR MATCHES "powerpc") +- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-bbigtoc") ++ set(bigTocFlag "-Wl,-bbigtoc") + elseif(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND + CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64") +- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--no-multi-toc") ++ set(bigTocFlag "-Wl,--no-multi-toc") ++endif() ++if(bigTocFlag) ++ include(CheckCXXLinkerFlag) ++ check_cxx_linker_flag(${bigTocFlag} BIG_TOC_FLAG_SUPPORTED) ++ if(BIG_TOC_FLAG_SUPPORTED) ++ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${bigTocFlag}") ++ endif() + endif() + + if (CMAKE_CXX_COMPILER_ID STREQUAL SunPro AND +diff -Naurd cmake-3.15.3/Source/cmCommands.cxx cmake-3.15.3-patched/Source/cmCommands.cxx +--- cmake-3.15.3/Source/cmCommands.cxx 2019-09-04 15:58:01.000000000 +0200 ++++ cmake-3.15.3-patched/Source/cmCommands.cxx 2019-12-09 13:13:29.043221389 +0100 +@@ -74,6 +74,7 @@ + #include "cmTargetCompileOptionsCommand.h" + #include "cmTargetIncludeDirectoriesCommand.h" + #include "cmTargetLinkLibrariesCommand.h" ++#include "cmTargetLinkOptionsCommand.h" + #include "cmTargetSourcesCommand.h" + #include "cmTryCompileCommand.h" + #include "cmTryRunCommand.h" +@@ -102,7 +103,6 @@ + # include "cmSourceGroupCommand.h" + # include "cmSubdirDependsCommand.h" + # include "cmTargetLinkDirectoriesCommand.h" +-# include "cmTargetLinkOptionsCommand.h" + # include "cmUseMangledMesaCommand.h" + # include "cmUtilitySourceCommand.h" + # include "cmVariableRequiresCommand.h" +@@ -259,6 +259,8 @@ + new cmTargetIncludeDirectoriesCommand); + state->AddBuiltinCommand("target_link_libraries", + new cmTargetLinkLibrariesCommand); ++ state->AddBuiltinCommand("target_link_options", ++ new cmTargetLinkOptionsCommand); + state->AddBuiltinCommand("target_sources", new cmTargetSourcesCommand); + state->AddBuiltinCommand("try_compile", new cmTryCompileCommand); + state->AddBuiltinCommand("try_run", new cmTryRunCommand); +@@ -277,8 +279,6 @@ + state->AddBuiltinCommand("install_programs", new cmInstallProgramsCommand); + state->AddBuiltinCommand("add_link_options", new cmAddLinkOptionsCommand); + state->AddBuiltinCommand("link_libraries", new cmLinkLibrariesCommand); +- state->AddBuiltinCommand("target_link_options", +- new cmTargetLinkOptionsCommand); + state->AddBuiltinCommand("target_link_directories", + new cmTargetLinkDirectoriesCommand); + state->AddBuiltinCommand("load_cache", new cmLoadCacheCommand); +diff -Naurd cmake-3.15.3/Source/Modules/CheckCXXLinkerFlag.cmake cmake-3.15.3-patched/Source/Modules/CheckCXXLinkerFlag.cmake +--- cmake-3.15.3/Source/Modules/CheckCXXLinkerFlag.cmake 1970-01-01 01:00:00.000000000 +0100 ++++ cmake-3.15.3-patched/Source/Modules/CheckCXXLinkerFlag.cmake 2019-12-09 13:13:29.024221135 +0100 +@@ -0,0 +1,25 @@ ++include(CheckCXXSourceCompiles) ++include(CMakeCheckCompilerFlagCommonPatterns) ++ ++function(check_cxx_linker_flag _flag _var) ++ if(CMAKE_VERSION VERSION_LESS "3.14") ++ set(CMAKE_REQUIRED_LIBRARIES "${_flag}") ++ else() ++ set(CMAKE_REQUIRED_LINK_OPTIONS "${_flag}") ++ endif() ++ ++ # Normalize locale during test compilation. ++ set(_locale_vars LC_ALL LC_MESSAGES LANG) ++ foreach(v ${_locale_vars}) ++ set(_locale_vars${v} "$ENV{${v}}") ++ set(ENV{${v}} C) ++ endforeach() ++ check_compiler_flag_common_patterns(_common_patterns) ++ check_cxx_source_compiles("int main() { return 0; }" ${_var} ++ ${_CheckCXXCompilerFlag_COMMON_PATTERNS} ++ ) ++ foreach(v ${_locale_vars}) ++ set(ENV{${v}} ${_locale_vars${v}}) ++ endforeach() ++ set(${_var} "${${_var}}" PARENT_SCOPE) ++endfunction() From 9a35caac11e74d34443c39446b2cac07d0bc0f20 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 9 Dec 2019 13:28:36 +0100 Subject: [PATCH 116/468] Add link to upstream issue --- .../easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch | 7 +++++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb index 620dbef46e0..582c9d66bda 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['CMake-%(version)s-fix-toc-flag.patch'] checksums = [ '13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5', # cmake-3.15.3.tar.gz - '2c23aa7556e545ee8fd9df2df4f49fe5f983875162bff77d67fb7dd2a7867eb7', # CMake-3.15.3-fix-toc-flag.patch + '580e0b5df7543b998ecbe524c21afd3940df672784757d957012e604baa219fa', # CMake-3.15.3-fix-toc-flag.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch index 0e8d1e58728..08b75db1ccc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch +++ b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch @@ -1,3 +1,6 @@ +Fix --no-multi-toc: unknown option on gold linker +See https://gitlab.kitware.com/cmake/cmake/issues/20076 + diff -Naurd cmake-3.15.3/bootstrap cmake-3.15.3-patched/bootstrap --- cmake-3.15.3/bootstrap 2019-09-04 15:58:03.000000000 +0200 +++ cmake-3.15.3-patched/bootstrap 2019-12-09 13:13:29.004220868 +0100 @@ -14,7 +17,7 @@ diff -Naurd cmake-3.15.3/CompileFlags.cmake cmake-3.15.3-patched/CompileFlags.cm +++ cmake-3.15.3-patched/CompileFlags.cmake 2019-12-09 13:13:29.004220868 +0100 @@ -54,12 +54,20 @@ endif() - + # Workaround for TOC Overflow on ppc64 +set(bigTocFlag "") if(CMAKE_SYSTEM_NAME STREQUAL "AIX" AND @@ -33,7 +36,7 @@ diff -Naurd cmake-3.15.3/CompileFlags.cmake cmake-3.15.3-patched/CompileFlags.cm + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${bigTocFlag}") + endif() endif() - + if (CMAKE_CXX_COMPILER_ID STREQUAL SunPro AND diff -Naurd cmake-3.15.3/Source/cmCommands.cxx cmake-3.15.3-patched/Source/cmCommands.cxx --- cmake-3.15.3/Source/cmCommands.cxx 2019-09-04 15:58:01.000000000 +0200 From 46a7b0c68fd5b9ac4a0092a2ab6deb92fad836b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Dec 2019 14:14:09 +0100 Subject: [PATCH 117/468] use https for Gurobi 9.0.0 homepage --- easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb index 605a8fd65bf..2a8400c71a3 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.0.eb @@ -1,7 +1,7 @@ name = 'Gurobi' version = '9.0.0' -homepage = 'http://www.gurobi.com' +homepage = 'https://www.gurobi.com' description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the From a7c6097de7d356e7978decbde0dc06fa1941caf1 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 9 Dec 2019 14:14:12 +0100 Subject: [PATCH 118/468] adding easyconfigs: ICU-65.1-GCCcore-8.3.0.eb --- .../i/ICU/ICU-65.1-GCCcore-8.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/ICU/ICU-65.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/i/ICU/ICU-65.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-65.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..84d18a2664c --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-65.1-GCCcore-8.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '65.1' + +homepage = 'https://site.icu-project.org/home' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['53e37466b3d6d6d01ead029e3567d873a43a5d1c668ed2278e253b683136d948'] + +builddependencies = [ + ('binutils', '2.32'), + ('Python', '3.7.4'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' From 89bb79b51a9e72373c9092d9eab798d4de9f40a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Dec 2019 14:16:24 +0100 Subject: [PATCH 119/468] fix source URL for Text::CSV extension in worker 1.6.11 easyconfig --- easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb index 39fdb66f7a2..ea77925899b 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb @@ -36,7 +36,7 @@ exts_list = [ }), ('Text::CSV', '2.00', { 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], 'checksums': ['8ccbd9195805222d995844114d0e595bb24ce188f85284dbf256080311cbb2c2'], }), ('DBI', '1.642', { From 564e31adb854c844de45cce8f9e6ab80e2c1a3d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Dec 2019 14:17:16 +0100 Subject: [PATCH 120/468] use https for molmod 1.4.5 homepage --- .../m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb index 42000037157..6b1d9fb8ff1 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2019b-Python-3.7.4.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.4.5' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://molmod.github.io/molmod/' +homepage = 'https://molmod.github.io/molmod/' description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2019b'} From c8c1d12680997c8cf6b0a36956d6f54f839dc0a9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 9 Dec 2019 14:17:41 +0100 Subject: [PATCH 121/468] Fix style --- easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb index 582c9d66bda..02b2a7e14aa 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb @@ -16,8 +16,8 @@ source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] patches = ['CMake-%(version)s-fix-toc-flag.patch'] checksums = [ - '13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5', # cmake-3.15.3.tar.gz - '580e0b5df7543b998ecbe524c21afd3940df672784757d957012e604baa219fa', # CMake-3.15.3-fix-toc-flag.patch + '13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5', # cmake-3.15.3.tar.gz + '580e0b5df7543b998ecbe524c21afd3940df672784757d957012e604baa219fa', # CMake-3.15.3-fix-toc-flag.patch ] builddependencies = [ From 487574d47ca0b0ba864c94459983dd1dcdacde31 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 9 Dec 2019 14:19:12 +0100 Subject: [PATCH 122/468] adding easyconfigs: LibTIFF-4.1.0-GCCcore-8.3.0.eb --- .../l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..0af1d12af09 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.1.0' + +homepage = 'https://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [ + 'https://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['5d29f32517dadb6dbcd1255ea5bbc93a2b54b94fbf83653b4d65c7d6775b8634'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.3') +] + +configopts = " --enable-ld-version-script " + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' From 681a682a55da70aa14626e55f73253dbb38323b2 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 9 Dec 2019 14:20:22 +0100 Subject: [PATCH 123/468] adding easyconfigs: texinfo-6.7-GCCcore-8.3.0.eb --- .../t/texinfo/texinfo-6.7-GCCcore-8.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..6741827f753 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-6.7-GCCcore-8.3.0.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '6.7' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [('binutils', '2.32')] + +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': [ + 'texmf/tex/texinfo/texinfo.tex', + 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' + ], + 'dirs': ['bin', 'share', 'texmf'], +} + +moduleclass = 'devel' From fd02c96ed14ef4348b7f805f4da2adec85083f98 Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Mon, 9 Dec 2019 14:50:33 +0100 Subject: [PATCH 124/468] adding easyconfigs: snakemake-5.7.1-foss-2019a-Python-3.7.2.eb, GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb and patches: snakemake-5.7.1_fix_jobs.patch --- ...Python-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb | 42 +++++++++++ ...snakemake-5.7.1-foss-2019a-Python-3.7.2.eb | 72 +++++++++++++++++++ .../snakemake/snakemake-5.7.1_fix_jobs.patch | 17 +++++ 3 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-5.7.1-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-5.7.1_fix_jobs.patch diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..9928e8f891c --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.0.3-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/gitpython-developers/GitPython' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('Python', '3.7.2'), +] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('smmap2', '2.0.5', { + 'modulename': 'smmap', + 'checksums': ['29a9ffa0497e7f2be94ca0ed1ca1aa3cd4cf25a1f6b4f5f87f74b46ed91d609a'], + }), + ('gitdb2', '2.0.6', { + 'modulename': 'gitdb', + 'checksums': ['1b6df1433567a51a4a9c1a5a0de977aa351a405cc56d7d35f3388bad1f630350'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['631263cc670aa56ce3d3c414cf0fe2e840f2e913514b138ea28d88a477bbcd21'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/git'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..23bc59ed412 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '5.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('PyYAML', '5.1'), + ('GitPython', '3.0.3', versionsuffix), +] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('zipp', '0.6.0', { + 'checksums': ['3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e'], + }), + ('importlib_metadata', '0.23', { + 'checksums': ['aa18d7378b00b40847790e7c27e11673d7fed219354109d0e7b9e5b25dc3ad26'], + }), + ('pyrsistent', '0.15.4', { + 'checksums': ['34b47fa169d6006b32e99d4b3c4031f155e6e68ebcc107d6454852e8e0ee6533'], + }), + ('jsonschema', '3.1.1', { + 'checksums': ['2fa0684276b6333ff3c0b1b27081f4b2305f0a36cf702a23db50edb141893c3f'], + }), + ('datrie', '0.8', { + 'checksums': ['bdd5da6ba6a97e7cd96eef2e7441c8d2ef890d04ba42694a41c7dffa3aca680c'], + }), + ('appdirs', '1.4.3', { + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('ConfigArgParse', '0.15.1', { + 'checksums': ['baaf0fd2c1c108d007f402dab5481ac5f12d77d034825bf5a27f8224757bd0ac'], + }), + ('ratelimiter', '1.2.0.post0', { + 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], + }), + ('wrapt', '1.11.2', { + 'checksums': ['565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1'], + }), + (name, version, { + 'patches': ['snakemake-5.7.1_fix_jobs.patch'], + 'checksums': [ + '5ab5ee0cd7d6a538776d8081f8b9a83ae35b1b1d9f03331e4347098becded7de', # snakemake-5.7.1.tar.gz + 'e3d0e25adee35314ea20b0511acbd11d0b4c8badd7f7e9d78275f5ec11721ecc', # snakemake-5.7.1_fix_jobs.patch + ], + }), +] + +# site-specific: the line below is the command for loading this module with the (default) EB module naming scheme +# if necessary, change this command to match your cluster setup +local_snakemake_load = 'module load %(name)s/%(version)s-%(toolchain_name)s-%(toolchain_version)s%(versionsuffix)s' +modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1_fix_jobs.patch b/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1_fix_jobs.patch new file mode 100644 index 00000000000..2a8205cc127 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-5.7.1_fix_jobs.patch @@ -0,0 +1,17 @@ +Load the snakemake module before running in job script, with added environment variable SNAKEMAKE_LOAD_MODULE +Always use the python executable defined by the environment +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur snakemake-5.7.1.orig/snakemake/executors.py snakemake-5.7.1/snakemake/executors.py +--- snakemake-5.7.1.orig/snakemake/executors.py 2019-10-16 12:04:28.000000000 +0200 ++++ snakemake-5.7.1/snakemake/executors.py 2019-11-03 16:45:49.435118155 +0100 +@@ -505,8 +505,9 @@ + if exec_job is None: + self.exec_job = "\\\n".join( + ( ++ os.getenv('SNAKEMAKE_LOAD_MODULE', ':') + ' && ', + "cd {workflow.workdir_init} && " if assume_shared_fs else "", +- "{sys.executable} " if assume_shared_fs else "python ", ++ "python ", + "-m snakemake {target} --snakefile {snakefile} ", + "--force -j{cores} --keep-target-files --keep-remote ", + "--wait-for-files {wait_for_files} --latency-wait {latency_wait} ", From 8b11390b39d90b42ff8d1bb24763b3084432d60e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 9 Dec 2019 16:11:41 +0100 Subject: [PATCH 125/468] Update patch to latest revision --- .../c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb | 2 +- .../c/CMake/CMake-3.15.3-fix-toc-flag.patch | 16 ++++++++++------ 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb index 02b2a7e14aa..05a04a8030b 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-GCCcore-8.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['CMake-%(version)s-fix-toc-flag.patch'] checksums = [ '13958243a01365b05652fa01b21d40fa834f70a9e30efa69c02604e64f58b8f5', # cmake-3.15.3.tar.gz - '580e0b5df7543b998ecbe524c21afd3940df672784757d957012e604baa219fa', # CMake-3.15.3-fix-toc-flag.patch + '4c424bfe3a5476ec1017ad2518a178658b7f2d43a076384f0da81f38d063c8f2', # CMake-3.15.3-fix-toc-flag.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch index 08b75db1ccc..35bea6be688 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch +++ b/easybuild/easyconfigs/c/CMake/CMake-3.15.3-fix-toc-flag.patch @@ -78,7 +78,11 @@ diff -Naurd cmake-3.15.3/Source/cmCommands.cxx cmake-3.15.3-patched/Source/cmCom diff -Naurd cmake-3.15.3/Source/Modules/CheckCXXLinkerFlag.cmake cmake-3.15.3-patched/Source/Modules/CheckCXXLinkerFlag.cmake --- cmake-3.15.3/Source/Modules/CheckCXXLinkerFlag.cmake 1970-01-01 01:00:00.000000000 +0100 +++ cmake-3.15.3-patched/Source/Modules/CheckCXXLinkerFlag.cmake 2019-12-09 13:13:29.024221135 +0100 -@@ -0,0 +1,25 @@ +@@ -0,0 +1,29 @@ ++# Distributed under the OSI-approved BSD 3-Clause License. See accompanying ++# file Copyright.txt or https://cmake.org/licensing for details. ++ ++include_guard(GLOBAL) +include(CheckCXXSourceCompiles) +include(CMakeCheckCompilerFlagCommonPatterns) + @@ -91,16 +95,16 @@ diff -Naurd cmake-3.15.3/Source/Modules/CheckCXXLinkerFlag.cmake cmake-3.15.3-pa + + # Normalize locale during test compilation. + set(_locale_vars LC_ALL LC_MESSAGES LANG) -+ foreach(v ${_locale_vars}) -+ set(_locale_vars${v} "$ENV{${v}}") ++ foreach(v IN LISTS _locale_vars) ++ set(_locale_vars_saved_${v} "$ENV{${v}}") + set(ENV{${v}} C) + endforeach() + check_compiler_flag_common_patterns(_common_patterns) + check_cxx_source_compiles("int main() { return 0; }" ${_var} -+ ${_CheckCXXCompilerFlag_COMMON_PATTERNS} ++ ${_common_patterns} + ) -+ foreach(v ${_locale_vars}) -+ set(ENV{${v}} ${_locale_vars${v}}) ++ foreach(v IN LISTS _locale_vars) ++ set(ENV{${v}} ${_locale_vars_saved_${v}}) + endforeach() + set(${_var} "${${_var}}" PARENT_SCOPE) +endfunction() From f0e6d6104f3147ee2647a1bb71875e592afe6998 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Dec 2019 16:44:53 +0100 Subject: [PATCH 126/468] adding easyconfigs: MDTraj-1.9.3-intel-2019b-Python-3.7.4.eb --- .../MDTraj-1.9.3-intel-2019b-Python-3.7.4.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.3-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.3-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.3-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..ca0f8a6860f --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.3-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'MDTraj' +version = '1.9.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mdtraj/mdtraj/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['15997a9c2bbe8a5148316a30ae420f9c345797a586369ad064b7fca9bd302bb3'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('zlib', '1.2.11'), +] + +download_dep_fail = True +use_pip = True + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From 4ab91261b89e41d6579bd9662390b28ef071cf90 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 9 Dec 2019 19:26:47 +0200 Subject: [PATCH 127/468] Sambamba-0.7.1: add author information --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb index 95acb07d326..e3a9a7aabb0 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb @@ -1,3 +1,10 @@ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Alex Domingo +# SISC - Vrije Universiteit Brussel + easyblock = 'PackedBinary' name = 'Sambamba' From 43da0c544d2fe444e923af7003ab20a541815e94 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 10 Dec 2019 09:04:49 +0200 Subject: [PATCH 128/468] adding easyconfigs: mayavi-4.7.1-foss-2019a-Python-3.7.2.eb --- .../libevent/libevent-2.1.11-GCCcore-8.2.0.eb | 37 +++++++++++++ .../mayavi-4.7.1-foss-2019a-Python-3.7.2.eb | 55 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..cbed70e0519 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.11' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['a65bac6202ea8c5609fd5c7e480e6d25de467ea1917c08290c521752f147283d'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..5b35f6f3f9d --- /dev/null +++ b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'mayavi' +version = '4.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.enthought.com/projects/mayavi/' +description = """The Mayavi scientific data 3-dimensional visualizer""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('VTK', '8.2.0', versionsuffix), + ('PyQt5', '5.12.1', versionsuffix), +] + +use_pip = True + +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('traits', '5.2.0', { + 'checksums': ['8194696df87ec93815204f29e119dd88ce9a0def2801ae9020431442c1dde1ac'], + }), + ('pyface', '6.1.2', { + 'checksums': ['7c2ac3d5cbec85e8504b3b0b63e9307be12c6d710b46bae372ce6562d41f4fbc'], + }), + ('traitsui', '6.1.3', { + 'checksums': ['48381763b181efc58eaf288431d1d92d028d0d97dfdd33eba7809aae8aef814f'], + }), + ('apptools', '4.5.0', { + 'checksums': ['260ae0e2a86cb2df2fede631ab6ac8ece694a58a1def78cd015c890c57140582'], + }), + ('envisage', '4.9.0', { + 'checksums': ['2cec48e4de6e0052a3bbb58baeb993025a6960229301d549bf323067cbc5e74b'], + }), + (name, version, { + 'source_tmpl': 'mayavi-%(version)s.tar.bz2', + 'checksums': ['be51fb6f886f304f7c593c907e6a2e88d7919f8f446cdccfcd184fa35b3db724'], + }), +] + +sanity_check_paths = { + 'files': ['bin/mayavi2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 4fe81b07b072c5fe96ee6267db1d3b6ce7ed7a83 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 10 Dec 2019 09:21:02 +0200 Subject: [PATCH 129/468] libevent doesnt belong in this PR. --- .../libevent/libevent-2.1.11-GCCcore-8.2.0.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb deleted file mode 100644 index cbed70e0519..00000000000 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libevent' -version = '2.1.11' - -homepage = 'https://libevent.org/' - -description = """ - The libevent API provides a mechanism to execute a callback function when - a specific event occurs on a file descriptor or after a timeout has been - reached. Furthermore, libevent also support callbacks due to signals or - regular timeouts. -""" - -toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] -sources = ['%(name)s-%(version)s-stable.tar.gz'] -checksums = ['a65bac6202ea8c5609fd5c7e480e6d25de467ea1917c08290c521752f147283d'] - -builddependencies = [ - ('binutils', '2.31.1'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', - 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], - 'dirs': [], -} - -moduleclass = 'lib' From 2f09df6db79bb8ab31c34f58d35a10a304799564 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 10 Dec 2019 11:58:12 +0200 Subject: [PATCH 130/468] Add comment about the requirement for connecting to X server during pip install. --- .../libevent/libevent-2.1.11-GCCcore-8.2.0.eb | 37 +++++++++++++++++++ .../mayavi-4.7.1-foss-2019a-Python-3.7.2.eb | 2 + 2 files changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..cbed70e0519 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.11' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['a65bac6202ea8c5609fd5c7e480e6d25de467ea1917c08290c521752f147283d'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb index 5b35f6f3f9d..fd681c43573 100644 --- a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb @@ -7,6 +7,8 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://code.enthought.com/projects/mayavi/' description = """The Mayavi scientific data 3-dimensional visualizer""" +# mayavi must have be able to connect to X server during pip install + toolchain = {'name': 'foss', 'version': '2019a'} dependencies = [ From bb73d2b0ab26607263c8b194316b5e6166af0cce Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 10 Dec 2019 12:03:03 +0200 Subject: [PATCH 131/468] libevent still doesnt belong in this PR. Must have a --robot flag turned on in some config... --- .../libevent/libevent-2.1.11-GCCcore-8.2.0.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb deleted file mode 100644 index cbed70e0519..00000000000 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-8.2.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libevent' -version = '2.1.11' - -homepage = 'https://libevent.org/' - -description = """ - The libevent API provides a mechanism to execute a callback function when - a specific event occurs on a file descriptor or after a timeout has been - reached. Furthermore, libevent also support callbacks due to signals or - regular timeouts. -""" - -toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] -sources = ['%(name)s-%(version)s-stable.tar.gz'] -checksums = ['a65bac6202ea8c5609fd5c7e480e6d25de467ea1917c08290c521752f147283d'] - -builddependencies = [ - ('binutils', '2.31.1'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', - 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], - 'dirs': [], -} - -moduleclass = 'lib' From f29f7abc6eb94ce74f638db9f0546dcbccc8adf0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Dec 2019 12:15:04 +0100 Subject: [PATCH 132/468] use PYPI_SOURCE in exts_default_options in Spark 2.4.0 easyconfig --- ...Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb index 3c43a1d0e21..8fc9c0cab45 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb @@ -27,17 +27,16 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'download_dep_fail': True, + 'source_urls': [PYPI_SOURCE], 'use_pip': True, } exts_list = [ ('wheel', '0.33.6', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wheel'], 'checksums': ['10c9da68765315ed98850f8e048347c3eb06dd81822dc2ab1d4fde9dc9702646'], }), ('py4j', '0.10.8.1', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], }), ('pyspark', version, { From efd157f47d35bf2e35229afe3fb8e61ce93dfbcb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 10 Dec 2019 14:15:54 +0200 Subject: [PATCH 133/468] Use offscreen mode for Qt while installing mayavi. Also see #7345 , this does not affect actually running mayavi. --- .../m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb index fd681c43573..7b97300ef57 100644 --- a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.1-foss-2019a-Python-3.7.2.eb @@ -7,8 +7,6 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://code.enthought.com/projects/mayavi/' description = """The Mayavi scientific data 3-dimensional visualizer""" -# mayavi must have be able to connect to X server during pip install - toolchain = {'name': 'foss', 'version': '2019a'} dependencies = [ @@ -46,6 +44,7 @@ exts_list = [ (name, version, { 'source_tmpl': 'mayavi-%(version)s.tar.bz2', 'checksums': ['be51fb6f886f304f7c593c907e6a2e88d7919f8f446cdccfcd184fa35b3db724'], + 'preinstallopts': 'export QT_QPA_PLATFORM=offscreen && ', }), ] From d30c3b97ad54fd5cf8015eb3925055765ec33770 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 10 Dec 2019 14:42:30 +0200 Subject: [PATCH 134/468] Sambamba-0.7.1: add version information in author list --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb index e3a9a7aabb0..b45a9d3630b 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb @@ -1,7 +1,9 @@ +# Version: 0.6.6 # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics # +# Version: 0.7.1 # Author: Alex Domingo # SISC - Vrije Universiteit Brussel From 9ffbe7935fdd243eefb190aa3a44e72322749782 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 11 Dec 2019 11:37:00 +1030 Subject: [PATCH 135/468] xorg-macros-1.19.2 url update --- .../x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb index 146f1a3338a..5ed165a8015 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb @@ -8,9 +8,9 @@ description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'] +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] # no slash ('/') at the end! +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] builddependencies = [ ('binutils', '2.31.1'), From 024ab7b0cf7d5683f949b264722a422f97989054 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 11 Dec 2019 11:52:55 +1030 Subject: [PATCH 136/468] xorg-macros-1.19.2 url update --- .../x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb index 5ed165a8015..d71a302d1bb 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb @@ -1,3 +1,13 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' From 960cef8ee6bcaee62a96ede8151fcc6de4b11a3c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 11 Dec 2019 13:33:04 +1030 Subject: [PATCH 137/468] xorg-macros-1.19.2 syntax fix --- .../x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb index d71a302d1bb..b8771d27e4e 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] # no slash ('/') at the end! +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] sources = ['macros-util-macros-%(version)s.tar.gz'] checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] From e0aa72d99fda5b4c6d573d37d9f247482d635604 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 11 Dec 2019 14:13:38 +1030 Subject: [PATCH 138/468] xorg-macros-1.19.2 https fix --- .../x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb index b8771d27e4e..eb7e409a24a 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.2' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} From 5d02fc3be7984deb1e5e56b7e1a3efdfa07e9454 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2019 14:21:39 +0100 Subject: [PATCH 139/468] add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs (required by pytest) + enable 'pip check' in sanity check --- .../p/Python/Python-2.7.15-GCCcore-8.2.0.eb | 74 ++----------------- .../p/Python/Python-2.7.16-GCCcore-8.3.0.eb | 4 + 2 files changed, 9 insertions(+), 69 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb index 160d5740a4a..c6a55fca047 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb @@ -30,7 +30,9 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] exts_default_options = { 'download_dep_fail': True, + 'source_urls': [PYPI_SOURCE], 'use_pip': True, + 'sanity_pip_check': True, } # order is important! @@ -38,289 +40,223 @@ exts_default_options = { exts_list = [ ('setuptools', '40.8.0', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'use_pip': False, 'checksums': ['6e4eec90337e849ade7103723b9a99631c1f0d19990d6e8412dc42f5ae8b304d'], }), ('pip', '19.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], 'use_pip': False, 'checksums': ['6e6f197a1abfb45118dbb878b5c859a0edbdd33fd250100bc015b67fded4b9f2'], }), ('wheel', '0.33.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wheel'], 'checksums': ['66a8fd76f28977bb664b098372daef2b27f60dc4d1688cfab7b37a09448f0e9d'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), ('pbr', '5.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], 'checksums': ['8c361cc353d988e4f5b998555c88098b9d5964c2e11acf7b0d21925a66bb5824'], }), ('Cython', '0.29.6', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], 'checksums': ['6c5d33f1b5c864382fbce810a8fd9e015447869ae42e98e6301e977b8165e7ae'], }), ('six', '1.12.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], 'checksums': ['c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e'], 'modulename': 'dateutil', }), ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], }), ('decorator', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 'checksums': ['33cd704aea07b4c28b3eb2c97d288a06918275dac0ecebdaf1bc8a48d98adb9e'], }), ('liac-arff', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], 'modulename': 'arff', }), ('pycrypto', '2.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], 'modulename': 'Crypto', }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('enum34', '1.1.6', { - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], 'modulename': 'enum', }), ('ipaddress', '1.0.22', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], }), ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], }), ('idna', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], }), ('pycparser', '2.19', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), ('cffi', '1.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e113878a446c6228669144ae8a56e268c91b7f1fafae927adc4879d9849e0ea7'], }), ('cryptography', '2.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], 'checksums': ['26c821cbeb683facb966045e2064303029d572a87ee69ca5a1bf54bf55f93ca6'], }), ('pyasn1', '0.4.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], 'checksums': ['da2420fe13a9452d8ae97a0e478adde1dee153b11ba832a95b223a2ba01c10f7'], }), ('PyNaCl', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], 'modulename': 'nacl', }), ('bcrypt', '3.1.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], 'checksums': ['44636759d222baa62806bbceb20e96f75a015a6381690d1bc2eda91c01ec02ea'], }), ('paramiko', '2.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], 'checksums': ['a8975a7df3560c9f1e2b43dc54ebd40fd00a7017392ca5445ce7df409f900fcb'], }), ('pyparsing', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], 'checksums': ['66c9268862641abcac4a96ba74506e594c884e3f57690a696d21ad8210ed667a'], }), ('netifaces', '0.10.9', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], }), ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], }), ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], }), ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], }), ('pytz', '2018.9', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], 'checksums': ['d5f05e487007e29e03409f9398d074e158d920d36eb82eaf66fb1136b0c5374c'], }), ('bitstring', '3.1.5', { 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], 'checksums': ['984d7e607b0a5d1329425dd8845bd971b957424b5ba664729fab51ab8c11bc39'], }), ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), ('joblib', '0.13.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], 'checksums': ['315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524'], }), ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), ('certifi', '2019.3.9', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], 'checksums': ['b26104d6835d1f5e49452a26eb2ff87fe7090b89dfcaee5ea2212697e1e1d7ae'], }), ('urllib3', '1.24.1', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], }), ('requests', '2.21.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], }), ('xlrd', '1.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], }), ('py_expression_eval', '0.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['0907cef96a7c370b2a58ea2179f88e48f421f5a41821b32f7defb81ca4e5247e'], }), ('tabulate', '0.8.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['8af07a39377cee1103a5c8b3330a421c2d99b9141e9cc5ddd2e3263fea416943'], }), ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], }), ('atomicwrites', '1.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites'], 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('py', '1.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('scandir', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir'], 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2'], 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), ('pluggy', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy'], 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('more-itertools', '5.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools'], 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('attrs', '19.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], 'modulename': 'attr', }), + ('wcwidth', '0.1.7', { + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), ('pytest', '4.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytest'], 'checksums': ['592eaa2c33fae68c7d75aacf042efc9f77b27c08a6224a4f59beab8d9a420523'], }), ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('packaging', '19.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], }), ('sphinxcontrib-websupport', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], 'modulename': 'sphinxcontrib.websupport', }), ('Pygments', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], }), ('imagesize', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], }), ('docutils', '0.14', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docutils/'], 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], }), ('snowballstemmer', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], }), ('Babel', '2.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], }), ('alabaster', '0.7.12', { - 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], }), ('Sphinx', '1.8.5', { - 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], }), ('Click', '7.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), ('psutil', '5.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], }), ('future', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb index 3352bac9316..d76321fc7e8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb @@ -32,6 +32,7 @@ exts_default_options = { 'download_dep_fail': True, 'source_urls': [PYPI_SOURCE], 'use_pip': True, + 'sanity_pip_check': True, } # order is important! @@ -215,6 +216,9 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), + ('wcwidth', '0.1.7', { + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), # pytest 4.6.x is the most recent version still supporting Python 2.x ('pytest', '4.6.5', { 'checksums': ['8fc39199bdda3d9d025d3b1f4eb99a192c20828030ea7c9a0d2840721de7d347'], From 4013c34575d38b2d982b42ab8a17dfc8e4682088 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2019 14:46:57 +0100 Subject: [PATCH 140/468] adding easyconfigs: deepTools-3.3.1-intel-2019b-Python-3.7.4.eb, plotly.py-4.4.1-intel-2019b.eb --- ...eepTools-3.3.1-intel-2019b-Python-3.7.4.eb | 52 +++++++++++++++++++ .../plotly.py/plotly.py-4.4.1-intel-2019b.eb | 28 ++++++++++ 2 files changed, 80 insertions(+) create mode 100755 easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-intel-2019b-Python-3.7.4.eb new file mode 100755 index 00000000000..ce3518f3fcf --- /dev/null +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.3.1-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'deepTools' +version = '3.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://deeptools.readthedocs.io/' +description = """deepTools is a suite of python tools particularly developed for the efficient analysis of + high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('Pysam', '0.15.3'), + ('matplotlib', '3.1.1', versionsuffix), + ('plotly.py', '4.4.1'), +] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('py2bit', '0.3.0', { + 'checksums': ['450555c40cba66957ac8c9a4b6afb625fb34c4bb41638de78c87661ff8b682ef'], + }), + ('pyBigWig', '0.3.17', { + 'modulename': 'pyBigWig', + 'checksums': ['41f64f802689ed72e15296a21a4b7abd3904780b2e4f8146fd29098fc836fd94'], + }), + ('deeptoolsintervals', '0.1.9', { + 'checksums': ['7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6'], + }), + ('numpydoc', '0.9.1', { + 'checksums': ['e08f8ee92933e324ff347771da15e498dbf0bc6295ed15003872b34654a0a627'], + }), + (name, version, { + 'checksums': ['514240f97e58bcfbf8c8b69ae9071d26569b491f089e1c1c46ba4866d335e322'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bamCompare', 'bin/bamCoverage', 'bin/bamPEFragmentSize', 'bin/computeGCBias', 'bin/computeMatrix', + 'bin/correctGCBias', 'bin/multiBamSummary', 'bin/plotCorrelation', 'bin/plotCoverage', + 'bin/plotHeatmap', 'bin/plotProfile'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb new file mode 100644 index 00000000000..bc4a11ccdf6 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '4.4.1' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'intel', 'version': '2019b'} + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('retrying', '1.3.3', { + 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], + }), + ('plotly', version, { + 'checksums': ['acc94f17452471ca3446c2ce491c4d1affb99b9ddd9eac4e05614ac4318f8780'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 6961e6a65353ff04a0a5e96028b6874f4a0cbf9a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 11 Dec 2019 17:47:59 +0200 Subject: [PATCH 141/468] adding easyconfigs: CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb --- .../CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..036ac9462e8 --- /dev/null +++ b/easybuild/easyconfigs/c/CrossMap/CrossMap-0.3.9-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'CrossMap' +version = '0.3.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://crossmap.sourceforge.net' +description = """CrossMap is a program for genome coordinates conversion + between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). + It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, + BigWig, BED, GFF, GTF and VCF.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e20a4653e9fc313ac0f5a6cfc37b42e83c3cf2b42f9483706cfb9ec9ff72c74c'] + +dependencies = [ + ('Python', '3.7.2'), + ('bx-python', '0.8.4'), + ('pyBigWig', '0.3.17'), + ('Pysam', '0.15.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_commands = [('CrossMap.py', '')] + +sanity_check_paths = { + 'files': ['bin/CrossMap.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'cmmodule'} + +moduleclass = 'bio' From 36398a130608d2bf4e3dc4e4c74831d85dc60be5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 11 Dec 2019 18:26:42 +0200 Subject: [PATCH 142/468] fiji: rename to Fiji --- .../f/{fiji/fiji-20170530.eb => Fiji/Fiji-20170530.eb} | 6 +++--- .../fiji-20191119-2057.eb => Fiji/Fiji-20191119-2057.eb} | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/f/{fiji/fiji-20170530.eb => Fiji/Fiji-20170530.eb} (92%) rename easybuild/easyconfigs/f/{fiji/fiji-20191119-2057.eb => Fiji/Fiji-20191119-2057.eb} (89%) diff --git a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb similarity index 92% rename from easybuild/easyconfigs/f/fiji/fiji-20170530.eb rename to easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb index 5f5475c9b95..b1a1a6b217b 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20170530.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb @@ -1,6 +1,6 @@ easyblock = 'PackedBinary' -name = 'fiji' +name = 'Fiji' version = '20170530' homepage = 'https://fiji.sc/' @@ -11,7 +11,7 @@ description = """Fiji is an image processing package—a 'batteries-included' di toolchain = SYSTEM source_urls = ['https://downloads.imagej.net/fiji/Life-Line/'] -sources = ['%(name)s-nojre-%(version)s.zip'] +sources = ['%(namelower)s-nojre-%(version)s.zip'] checksums = ['cf9fb45c48b22a7888b479968477f1f7a300a9c833e47244cbe0d1e93890bd20'] dependencies = [('Java', '1.8', '', True)] @@ -39,7 +39,7 @@ sanity_check_paths = { modextrapaths = {'MATLABPATH': 'scripts'} -modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64 +modloadmsg = """ ImageJ/Fiji can be started with the command: ImageJ-linux64 Plugins can be installed in your $HOME/.plugins folder. If you need any other update sites to be enabled, please contact support.""" diff --git a/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb similarity index 89% rename from easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb rename to easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb index 09b9ba4f632..3309bd66a45 100644 --- a/easybuild/easyconfigs/f/fiji/fiji-20191119-2057.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb @@ -1,6 +1,6 @@ easyblock = 'PackedBinary' -name = 'fiji' +name = 'Fiji' version = '20191119-2057' homepage = 'https://fiji.sc/' @@ -12,8 +12,8 @@ toolchain = SYSTEM source_urls = ['https://downloads.imagej.net/fiji/archive/%(version)s'] sources = [{ - 'download_filename': '%(name)s-nojre.tar.gz', - 'filename': '%(name)s-nojre-%(version)s.tar.gz', + 'download_filename': '%(namelower)s-nojre.tar.gz', + 'filename': '%(namelower)s-nojre-%(version)s.tar.gz', }] checksums = ['7fad8e8f8676edbcfe7eb979421ab163e8d48bb7950a815f7821cbe58b8bb051'] @@ -42,7 +42,7 @@ sanity_check_paths = { modextrapaths = {'MATLABPATH': 'scripts'} -modloadmsg = """ ImageJ/fiji can be started with the command: ImageJ-linux64. +modloadmsg = """ ImageJ/Fiji can be started with the command: ImageJ-linux64. Plugins can be installed in your $HOME/.plugins folder. If you need any other update sites to be enabled, please contact support.""" From e95b00ecdb2817878ae191c27edb98652662572e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Dec 2019 10:12:50 +0100 Subject: [PATCH 143/468] adding easyconfigs: prokka-1.14.5-gompi-2019a.eb --- .../p/prokka/prokka-1.14.5-gompi-2019a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb new file mode 100644 index 00000000000..d6d0512712d --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb @@ -0,0 +1,46 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = """Prokka is a software tool for the rapid annotation of prokaryotic genomes.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.2', '-Perl-5.28.1'), + ('BLAST+', '2.9.0'), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' From 76dc9bec76773e2ed7fdc167e56969c236a95d6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Dec 2019 10:35:27 +0100 Subject: [PATCH 144/468] adding easyconfigs: tbl2asn-25.8-linux64.eb --- .../t/tbl2asn/tbl2asn-25.8-linux64.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-25.8-linux64.eb diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-25.8-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-25.8-linux64.eb new file mode 100644 index 00000000000..d767d61a910 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-25.8-linux64.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'tbl2asn' +# see first output of 'tbl2asl --help' to determine version +version = '25.8' +versionsuffix = '-linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = SYSTEM + +source_urls = ['ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/'] +sources = [{'download_filename': 'linux64.tbl2asn.gz', 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] +checksums = ['05b4cec586fab9f07926413e61bed718ab401242859ebd5e8b9b11fbd6e6c203'] + +cmds_map = [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")] + +files_to_copy = [ + (['tbl2asn'], 'bin'), +] + +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + +sanity_check_paths = { + 'files': ['bin/tbl2asn'], + 'dirs': [], +} + +sanity_check_commands = ["tbl2asn --help"] + +moduleclass = 'bio' From 73d4b0eeac1fe9127166d30d409861ba61590f94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Dec 2019 11:40:10 +0100 Subject: [PATCH 145/468] adding easyconfigs: glibc-2.30-GCCcore-8.3.0.eb, make-4.2.1-GCCcore-8.3.0.eb --- .../g/glibc/glibc-2.30-GCCcore-8.3.0.eb | 31 ++++++++++++++ .../m/make/make-4.2.1-GCCcore-8.3.0.eb | 40 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..37e6bd4fdc5 --- /dev/null +++ b/easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'glibc' +version = '2.30' + +homepage = 'https://www.gnu.org/software/libc/' +description = """The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, + as well as many other systems that use Linux as the kernel.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/glibc/'] +sources = ['glibc-%(version)s.tar.xz'] +checksums = ['e2c4114e569afbe7edbc29131a43be833850ab9a459d81beb2588016d2bbb8af'] + +builddependencies = [ + ('binutils', '2.32'), + ('make', '4.2.1'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/ldd', 'lib/libc.a', 'lib/libc.%s' % SHLIB_EXT], + 'dirs': ['etc', 'libexec', 'include', 'sbin', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..64a440b6a73 --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.2.1' + +homepage = 'http://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['d6e262bf3601b42d2b1e4ef8310029e1dcf20083c5446b4b7aa67081fdffc589'] + +builddependencies = [('binutils', '2.32')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' From 26b3a6223fd61ff15bf2248706dbd6d59d72701d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Dec 2019 12:36:50 +0100 Subject: [PATCH 146/468] use https for make 4.2.1 homepage --- easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb index 64a440b6a73..0ee7c0b4033 100644 --- a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'make' version = '4.2.1' -homepage = 'http://www.gnu.org/software/make/make.html' +homepage = 'https://www.gnu.org/software/make/make.html' description = "GNU version of make utility" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} From e955fd01adb7f78e8b6a3678712b47a7954c3524 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Dec 2019 15:08:03 +0100 Subject: [PATCH 147/468] allow multiple WRF dependency variants as long as they're deps for WPS with matching version --- test/easyconfigs/easyconfigs.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1a9bd430c39..74fbcb6cc9a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -182,14 +182,16 @@ def check_dep_vars(self, dep, dep_vars): if len(empty_vsuff_vars) == 1: dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) - # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools - if dep == 'HTSlib' and len(dep_vars) > 1: - for key in list(dep_vars): - ecs = dep_vars[key] - # filter out HTSlib variants that are only used as dependency for BCFtools with same version - htslib_ver = re.search('^version: (?P[^;]+);', key).group('ver') - if all(ec.startswith('BCFtools-%s-' % htslib_ver) for ec in ecs): - dep_vars.pop(key) + # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; + # same goes for WRF and WPS + for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS')]: + if dep == dep_name and len(dep_vars) > 1: + for key in list(dep_vars): + ecs = dep_vars[key] + # filter out dep variants that are only used as dependency for parent with same version + dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs): + dep_vars.pop(key) # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python if dep == 'Boost' and len(dep_vars) > 1: From 1146547381be5061d6a2900097eb5f03c0f66dcf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Dec 2019 15:16:18 +0100 Subject: [PATCH 148/468] fix checksum for WRF 4.x patch --- easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 2 +- easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index da0969fb160..9f9f1115682 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -18,7 +18,7 @@ patches = [ checksums = [ 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch - '3b9b1334b4611f924961008181d0202d2e3160af67d67b2ab5869d0db968cac9', # WRFv4_netCDF-Fortran_separate_path.patch + 'a431159180757a895c07fc193fe93bb69c4c9d25d31adcc7c2adfa7c1edb04ad', # WRFv4_netCDF-Fortran_separate_path.patch ] # csh is used by WRF install scripts diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb index 984cd3a1abe..3c3a15ff808 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb @@ -18,7 +18,7 @@ patches = [ checksums = [ '161637aded4c1b30105cee66d3dee5d0f5bd57a78a4a8704d1dde1734f83a17e', # v4.0.2.tar.gz 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch - '3b9b1334b4611f924961008181d0202d2e3160af67d67b2ab5869d0db968cac9', # WRFv4_netCDF-Fortran_separate_path.patch + 'a431159180757a895c07fc193fe93bb69c4c9d25d31adcc7c2adfa7c1edb04ad', # WRFv4_netCDF-Fortran_separate_path.patch ] # csh is used by WRF install scripts From 3b431d29f74fc0d1928585bacc601d90b57cd402 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Dec 2019 15:16:32 +0100 Subject: [PATCH 149/468] add missing patch description in patch file for WPS 4.0.2 --- easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb | 2 +- easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch | 8 ++++++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb index 24257a43d60..5b0b782a73f 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb @@ -18,7 +18,7 @@ patches = [ checksums = [ 'e053b3348d942288d04aca642ec700d97ec6895d6ef96ffa6168581c127dac00', # v4.0.2.tar.gz '495341f7ae883ba4eb1fbeb41f336745d55d6b63e79360d35680c3f7f29f01ec', # WPSv4_netCDF-Fortran_seperate_path.patch - '4c8ac67526c3600a5252f2fe8efbe706a556af1b3f58e206a734f31899fbeee9', # WPS-4.0.2_find-wrfdir.patch + '4d4dafe93cce05b6a455626f5e0c98bb2c31e25ab77239e5e726db12d3a76027', # WPS-4.0.2_find-wrfdir.patch ] buildtype = "dmpar" diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch index fc1a67d5426..7b32ff868f3 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch @@ -1,3 +1,11 @@ +# Allow WRF source code directory to be located in EasyBuild module tree +# ============================================================================ +# Since WPS v4.0, the WPS build system seems to make strong assumptions on +# where to find the WRF source code. This patch allows the WRF source code to +# be found also when WRF is located in the EasyBuild module tree. $WRF_DIR_PRE +# is being set from the wps EasyBlock. +# Patch written by @andreas-h (Oct 2018) + diff -uNr WPS-4.0.2.orig/arch/preamble WPS-4.0.2/arch/preamble --- WPS-4.0.2.orig/arch/preamble 2018-11-10 01:13:04.000000000 +0100 +++ WPS-4.0.2/arch/preamble 2018-11-21 16:42:38.066848290 +0100 From 219570709d69744c4c54cf6d18fe62217563e87d Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Thu, 12 Dec 2019 15:59:33 +0100 Subject: [PATCH 150/468] adding easyconfigs: pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb --- ...ran-0.9.4.post1-foss-2019b-Python-3.7.4.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..db39a88d3cb --- /dev/null +++ b/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'pythran' +version = '0.9.4.post1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pythran.readthedocs.io' +description = """ Pythran is an ahead of time compiler for a subset of the Python language, +with a focus on scientific computing. It takes a Python module annotated with a few interface description +and turns it into a native Python module with the same interface, but (hopefully) faster. """ + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('networkx', '2.4', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.3.2', { + 'checksums': ['5c7617f1f6c8b8b426819642b16b9016727ddaecd16af9a07753e537eba8a3a5'], + }), + ('beniget', '0.2.0', { + 'checksums': ['4495fb8ef0e99f9291c751856e3cc0695115e7936acc54717a3f620ab331b247'], + }), + (name, version, { + 'checksums': ['3842fefbb2374a28f8bb3e1ca9403513299438deb07608a5d76b1ae7b4fd24c0'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +modloadmsg = """ +To use the OpenBLAS library, run: +pythran --config=compiler.blas=openblas +""" + +moduleclass = 'compiler' From e3e61f08ea2acf780818b831a363c0d4bb0d50f6 Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Thu, 12 Dec 2019 16:02:22 +0100 Subject: [PATCH 151/468] add networkx dep --- .../networkx-2.4-foss-2019b-Python-3.7.4.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..416da59ab61 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True + +moduleclass = 'tools' From b61f728c3d3c667dc80a6919c1cb73eac31a06b4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 12 Dec 2019 17:21:55 +0200 Subject: [PATCH 152/468] adding easyconfigs: OpenSlide-3.4.1-GCCcore-8.2.0.eb --- .../OpenSlide-3.4.1-GCCcore-8.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..093f79a5b57 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' + +github_account = 'openslide' +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c'] + +builddependencies = [ + ('Autoconf', '2.69'), + ('Automake', '1.16.1'), + ('libtool', '2.4.6'), + ('M4', '1.4.18'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.36'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('OpenJPEG', '2.3.1'), + ('libxml2', '2.9.8'), + ('SQLite', '3.27.2'), + ('cairo', '1.16.0'), + ('Gdk-Pixbuf', '2.38.1'), +] + +preconfigopts = 'libtoolize && ' +preconfigopts += 'aclocal && ' +preconfigopts += 'autoheader && ' +preconfigopts += 'automake --add-missing && ' +preconfigopts += 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/openslide-quickhash1sum', 'bin/openslide-show-properties', 'bin/openslide-write-png', + 'lib/libopenslide.la', 'lib/libopenslide.%s' % SHLIB_EXT], + 'dirs': ['include/openslide'] +} + +moduleclass = 'vis' From 077362bad780f38acd5e9623f0163dfe8101515a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 12 Dec 2019 17:41:42 +0200 Subject: [PATCH 153/468] OpenSlide-3.4.1: add build dependency on binutils --- .../easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb index 093f79a5b57..db4733a3155 100644 --- a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-8.2.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ('libtool', '2.4.6'), ('M4', '1.4.18'), ('pkg-config', '0.29.2'), + ('binutils', '2.31.1'), ] dependencies = [ From e39fa83cc158a17b9b17adb1f41927326bc328de Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 12 Dec 2019 18:12:48 +0200 Subject: [PATCH 154/468] adding easyconfigs: pydicom-1.2.2-GCCcore-8.2.0.eb --- .../p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..5558f6a6dbe --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '1.2.2' + +github_account = 'pydicom' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f3080249aea2243ded81c3019f0af6e06b7b187d624d06ec89d9e3fac58a204c'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +use_pip = True +download_dep_fail = True + +moduleclass = 'vis' From 4018dc0db336d29ff42254d334fd5035dea95e27 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 12 Dec 2019 18:37:29 +0200 Subject: [PATCH 155/468] pydicom-1.2.2: add build dependency on binutils --- easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb index 5558f6a6dbe..a8553f2effe 100644 --- a/easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/pydicom/pydicom-1.2.2-GCCcore-8.2.0.eb @@ -15,6 +15,8 @@ checksums = ['f3080249aea2243ded81c3019f0af6e06b7b187d624d06ec89d9e3fac58a204c'] multi_deps = {'Python': ['3.7.2', '2.7.15']} +builddependencies = [('binutils', '2.31.1')] + use_pip = True download_dep_fail = True From 28201be5603ee6b0c1ea5db013b73cf23753fddb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 07:34:16 +0100 Subject: [PATCH 156/468] make sure one dependency variant is retained when filtering WRF as dep for WPS --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 74fbcb6cc9a..48fa2abf4a6 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -190,7 +190,7 @@ def check_dep_vars(self, dep, dep_vars): ecs = dep_vars[key] # filter out dep variants that are only used as dependency for parent with same version dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') - if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs): + if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: dep_vars.pop(key) # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python From 42b21784b50d924e1ed3ebbdbd413e092e647de5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 11:16:55 +0100 Subject: [PATCH 157/468] disable running of 'sudo apt-get update' in GitHub CI config, since it's failing (and we don't really need it) --- .github/workflows/unit_tests.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 918d45c8d28..6babd8c5a9a 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -30,7 +30,10 @@ jobs: - name: install OS & Python packages run: | - sudo apt-get update + # apt-get update is disabled for now, because it was failing in GitHub since Fri Dec 13th 2019, + # due to 'Conflicting distribution' issue + # sudo apt-get update + # # for modules tool sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082 From f02b6dd3a69d7903bbc69ec0ccbcfde8c0365ce7 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 13 Dec 2019 12:34:21 +0100 Subject: [PATCH 158/468] Pillow for 2019b with same deps and gcc 8.3.0 A version for 2019b --- .../Pillow-SIMD-6.0.x.post0-GCCcore-8.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-6.0.x.post0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-6.0.x.post0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-6.0.x.post0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..bee79a5fc25 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-6.0.x.post0-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '6.0.x.post0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7bccd59fa8b47f63591a993691de550a21e7ace4b92b3cd38dad9472b01fb008'] + +builddependencies = [('binutils', '2.32')] + +multi_deps = {'Python': ['3.7.4']} + +dependencies = [ + ('libjpeg-turbo', '2.0.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.10'), + ('freetype', '2.10.1') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +moduleclass = 'vis' From 47bb50b63c97df41cf9296bb1d31810eb92c7e54 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 13 Dec 2019 14:09:50 +0200 Subject: [PATCH 159/468] adding easyconfigs: netCDF-4.7.1-gompic-2019b.eb, netCDF-4.7.1-iimpic-2019b.eb, netCDF-4.7.1-iimpi-2019b.eb, HDF5-1.10.5-iimpic-2019b.eb --- .../h/HDF5/HDF5-1.10.5-iimpic-2019b.eb | 21 ++++++++++++ .../n/netCDF/netCDF-4.7.1-gompic-2019b.eb | 34 +++++++++++++++++++ .../n/netCDF/netCDF-4.7.1-iimpi-2019b.eb | 34 +++++++++++++++++++ .../n/netCDF/netCDF-4.7.1-iimpic-2019b.eb | 34 +++++++++++++++++++ 4 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpic-2019b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-gompic-2019b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpi-2019b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpic-2019b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpic-2019b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpic-2019b.eb new file mode 100644 index 00000000000..c1444c78a88 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpic-2019b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpic', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-gompic-2019b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-gompic-2019b.eb new file mode 100644 index 00000000000..e5d68159138 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-gompic-2019b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.7.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompic', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['583e6b89c57037293fc3878c9181bb89151da8c6015ecea404dd426fea219b2c'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.15.3'), + ('Doxygen', '1.8.16'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('cURL', '7.66.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpi-2019b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpi-2019b.eb new file mode 100644 index 00000000000..b450b97976f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpi-2019b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.7.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['583e6b89c57037293fc3878c9181bb89151da8c6015ecea404dd426fea219b2c'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.15.3'), + ('Doxygen', '1.8.16'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('cURL', '7.66.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpic-2019b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpic-2019b.eb new file mode 100644 index 00000000000..f7087d634cf --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpic-2019b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.7.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpic', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['583e6b89c57037293fc3878c9181bb89151da8c6015ecea404dd426fea219b2c'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.15.3'), + ('Doxygen', '1.8.16'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('cURL', '7.66.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From 7ed241e60d3e9bea422704cb608ba7d329453cbb Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 13 Dec 2019 14:08:57 +0100 Subject: [PATCH 160/468] torchvision 0.4.2 for fosscuda --- ...ision-0.4.2-fosscuda-2019a-Python-3.7.4.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019a-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019a-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019a-Python-3.7.4.eb new file mode 100644 index 00000000000..2c22505bfcf --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019a-Python-3.7.4.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'torchvision' +version = '0.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('Python', '3.7.4'), + ('Pillow-SIMD', '6.0.x.post0'), + ('PyTorch', '1.3.1', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/torchvision'], +} + +moduleclass = 'vis' From 6fb11db947aa95489699672a6d47121e594049b2 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 13 Dec 2019 14:46:34 +0100 Subject: [PATCH 161/468] Renamed to 2019b to make the CI happy --- ...-3.7.4.eb => torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/t/torchvision/{torchvision-0.4.2-fosscuda-2019a-Python-3.7.4.eb => torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb} (100%) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019a-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb similarity index 100% rename from easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019a-Python-3.7.4.eb rename to easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb From 1194153fbe6625793ae33717e5d2a991e6d9ec6f Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 13 Dec 2019 14:52:14 +0100 Subject: [PATCH 162/468] added torchvision checksum --- .../torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb index 2c22505bfcf..fff03c08a58 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.4.2-fosscuda-2019b-Python-3.7.4.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'fosscuda', 'version': '2019b'} source_urls = ['https://github.com/pytorch/vision/archive'] sources = ['v%(version)s.tar.gz'] +checksums = ['1184a27eab85c9e784bacc6f9d6fec99e168ab4eda6047ef9f709e7fdb22d8f9'] builddependencies = [('CMake', '3.15.3')] From bfcb17083de092a98e9813fb78b1fa64f03798e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 14:55:29 +0100 Subject: [PATCH 163/468] adding easyconfigs: tcsh-6.22.02-GCCcore-8.3.0.eb --- .../t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..7a95d27e3fc --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.22.02' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ed287158ca1b00ba477e8ea57bac53609838ebcfd05fcb05ca95021b7ebe885b'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('ncurses', '6.1')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' From 2c9d52d16acea126f95040cb5ead5078c3b4b61e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 14:59:33 +0100 Subject: [PATCH 164/468] adding easyconfigs: netCDF-Fortran-4.5.2-iimpi-2019b.eb, netCDF-4.7.1-iimpi-2019b.eb --- .../netCDF-Fortran-4.5.2-iimpi-2019b.eb | 18 ++++++++++ .../n/netCDF/netCDF-4.7.1-iimpi-2019b.eb | 34 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpi-2019b.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb new file mode 100644 index 00000000000..177985f30a2 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.5.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b05c629c70d6d224a3be28699c066bfdfeae477aea211fbf034d973a8309b49'] + +dependencies = [('netCDF', '4.7.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpi-2019b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpi-2019b.eb new file mode 100644 index 00000000000..466f6c63b95 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.1-iimpi-2019b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.7.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['583e6b89c57037293fc3878c9181bb89151da8c6015ecea404dd426fea219b2c'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.15.3'), + ('Doxygen', '1.8.16'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('cURL', '7.66.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From 6b040f58177bdb261cc69e06e03595be975b09a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 15:56:04 +0100 Subject: [PATCH 165/468] use 'name' rather in exts_list in plotly.py easyconfig --- .../easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb index bc4a11ccdf6..807fabdbf56 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb @@ -18,7 +18,7 @@ exts_list = [ ('retrying', '1.3.3', { 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], }), - ('plotly', version, { + (name, version, { 'checksums': ['acc94f17452471ca3446c2ce491c4d1affb99b9ddd9eac4e05614ac4318f8780'], }), ] From 9664c60f241b3a694fc6393ec64c089867e3be6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 15:58:07 +0100 Subject: [PATCH 166/468] build netCDF-Fortran single-core, since parallel build tends to fail due to missing Fortran module --- .../n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb index 177985f30a2..d3363ceba7b 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb @@ -15,4 +15,7 @@ checksums = ['0b05c629c70d6d224a3be28699c066bfdfeae477aea211fbf034d973a8309b49'] dependencies = [('netCDF', '4.7.1')] +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + moduleclass = 'data' From 2fb87f6c498cffed33f2095e56b764e86d37dfec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 16:45:29 +0100 Subject: [PATCH 167/468] use https for netCDF-Fortran 4.5.2 homepage --- .../n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb index d3363ceba7b..1921d8350d8 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2019b.eb @@ -1,7 +1,7 @@ name = 'netCDF-Fortran' version = '4.5.2' -homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' description = """NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" From 99ac2479faa0daf6656830f677368f5fee7b1098 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 13 Dec 2019 17:51:10 +0200 Subject: [PATCH 168/468] adding easyconfigs: openslide-python-1.1.1-GCCcore-8.2.0.eb --- .../openslide-python-1.1.1-GCCcore-8.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..e405937df07 --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.1.1' + +github_account = 'openslide' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['33c390fe43e3d7d443fafdd66969392d3e9efd2ecd5d4af73c3dbac374485ed5'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('OpenSlide', '3.4.1'), + ('Pillow', '6.0.0'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' From 35399599ae152b7d879eb38eaf371bd98cf6929d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 18:43:16 +0100 Subject: [PATCH 169/468] use https for tcsh 6.22.02 homepage --- easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb index 7a95d27e3fc..5703fe5fafb 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'tcsh' version = '6.22.02' -homepage = 'http://www.tcsh.org' +homepage = 'https://www.tcsh.org' description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history From bd9e8a062470ecc1caef5acdeffa6db3b6628f46 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 20:08:54 +0100 Subject: [PATCH 170/468] {cae}[intel/2019b] OpenFOAM-Extend v4.0 (+ deps) --- .../Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb | 21 ++++++++ .../OpenFOAM-Extend-4.0-intel-2019b.eb | 53 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2019b.eb | 23 ++++++++ .../ParMGridGen-1.0-iimpi-2019b.eb | 30 +++++++++++ .../s/SCOTCH/SCOTCH-6.0.9-iimpi-2019b.eb | 19 +++++++ 5 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2019b.eb create mode 100644 easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-iimpi-2019b.eb diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..bfdf546db12 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'Mesquite' +version = '2.3.0' + +homepage = 'https://software.sandia.gov/mesquite/' + +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://software.sandia.gov/mesquite/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4ab4ceadfa596e16c00dbb0e8b830a9112fa1b73291ca07633ec379a39b8bb28'] + +builddependencies = [ + ('binutils', '2.32'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b.eb new file mode 100644 index 00000000000..bd6c3496c15 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b.eb @@ -0,0 +1,53 @@ +easyblock = 'EB_OpenFOAM' + +name = 'OpenFOAM-Extend' +version = '4.0' + +homepage = 'http://www.extend-project.de/' +description = """OpenFOAM is a free, open source CFD software package. +OpenFOAM has an extensive range of features to solve anything from complex fluid flows +involving chemical reactions, turbulence and heat transfer, +to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-%(version)s/archive'] +sources = [{'download_filename': '268bb07.tar.gz', 'filename': 'v%(version)s-20181028.tar.gz'}] +patches = [ + 'OpenFOAM-Extend-3.2-ParMGridGen.patch', + 'OpenFOAM-Extend-3.1_build-qa.patch', + 'OpenFOAM-Extend-3.1_comp-mpi.patch', + 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', +] +checksums = [ + 'cbdae138b9b1bd1c3056e22c13845f91e32d193af3e06df9a92cbc8561016a35', # v4.0-20181028.tar.gz + 'f7676a7a12ced7c74caea64c62826a28449fdb2beb8b5be2c4ae7528ffece16e', # OpenFOAM-Extend-3.2-ParMGridGen.patch + '14dcc12ea7191ba42a9c297fcb2f4fbc2c55bf57226029489aa116e2d060b4bf', # OpenFOAM-Extend-3.1_build-qa.patch + '89fe47abec4cd9dbe863887140421e803e16801655bb2c7fb7bb1ac8532861ca', # OpenFOAM-Extend-3.1_comp-mpi.patch + # OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch + 'c88b23cd2f5dcf3bd86e02d7ea5dc6719c2049cf4b20e39f1b3262381dee3c50', +] + +dependencies = [ + ('hwloc', '2.0.3'), + ('ParMETIS', '4.0.3'), + ('METIS', '5.1.0'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right + ('SCOTCH', '6.0.9'), + ('Mesquite', '2.3.0'), + ('ParMGridGen', '1.0'), + ('Python', '2.7.16'), + # Libccmio v2.6.1, zoltan v3.5 +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + ('M4', '1.4.18'), + ('CMake', '3.15.3'), +] + +# too many builds in parallel actually slows down the build +maxparallel = 4 + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2019b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2019b.eb new file mode 100644 index 00000000000..3f1926dab6c --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2019b.eb @@ -0,0 +1,23 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.15.3')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb new file mode 100644 index 00000000000..4123d6d983a --- /dev/null +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'ParMGridGen' +version = '1.0' + +homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' +description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, + that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited + for geometric multigrid methods.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://www-users.cs.umn.edu/~moulitsa/download/'] +sources = [SOURCE_TAR_GZ] +patches = ['ParMGridGen-%(version)s_malloc_include.patch'] +checksums = [ + '62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395', # ParMGridGen-1.0.tar.gz + '3e0d72f82b3b56cbfcb1e3c9afc6594eb25316a0faeb49237faa8d969b4daeaa', # ParMGridGen-1.0_malloc_include.patch +] + +buildopts = 'parallel make=make CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' + +files_to_copy = [ + (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), + (['mgridgen.h', 'parmgridgen.h'], 'include'), + (['libmgrid.a', 'libparmgrid.a'], 'lib'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-iimpi-2019b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-iimpi-2019b.eb new file mode 100644 index 00000000000..11113aad205 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-iimpi-2019b.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.0.9' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/file/38187/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['622b4143cf01c480bb15708b3651b29c25e4aeb00c8c6447ff196aca2eca5c93'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' From b365fedec1070590a5f6a2156ac72801ca8c913c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 20:49:12 +0100 Subject: [PATCH 171/468] adding easyconfigs: WRF-4.1.3-intel-2019b-dmpar.eb --- .../w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb new file mode 100644 index 00000000000..a0a67a78575 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '4.1.3' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRFv4_netCDF-Fortran_separate_path.patch', +] +checksums = [ + 'a020e83e8a7a927fb080075031630e2af592e9fa802293ad72caa7ee50d6968d', # v4.1.3.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + 'a431159180757a895c07fc193fe93bb69c4c9d25d31adcc7c2adfa7c1edb04ad', # WRFv4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.22.02')] + +dependencies = [ + ('JasPer', '2.0.14'), + ('netCDF', '4.7.1'), + ('netCDF-Fortran', '4.5.2'), +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' From f91eb090c5130455f46dfd2205ab6ebfe128158f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Dec 2019 20:45:41 +0100 Subject: [PATCH 172/468] stick to hwloc 1.11.12 as dep for OpenFOAM-Extend 4.0 w/ intel/2019b + add Python versionsuffix --- ...19b.eb => OpenFOAM-Extend-4.0-intel-2019b-Python-2.7.16.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/o/OpenFOAM-Extend/{OpenFOAM-Extend-4.0-intel-2019b.eb => OpenFOAM-Extend-4.0-intel-2019b-Python-2.7.16.eb} (96%) diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b-Python-2.7.16.eb similarity index 96% rename from easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b.eb rename to easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b-Python-2.7.16.eb index bd6c3496c15..0862e32f1f0 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2019b-Python-2.7.16.eb @@ -2,6 +2,7 @@ easyblock = 'EB_OpenFOAM' name = 'OpenFOAM-Extend' version = '4.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.extend-project.de/' description = """OpenFOAM is a free, open source CFD software package. @@ -30,7 +31,7 @@ checksums = [ ] dependencies = [ - ('hwloc', '2.0.3'), + ('hwloc', '1.11.12'), ('ParMETIS', '4.0.3'), ('METIS', '5.1.0'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right ('SCOTCH', '6.0.9'), From aecb48bd5ba2e29b2dc65f843d7795ab05aed93e Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Sat, 14 Dec 2019 10:34:28 +0100 Subject: [PATCH 173/468] Updated homepage source url --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb index 0af1d12af09..0e11b9bdee7 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb @@ -14,14 +14,13 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.1.0' -homepage = 'https://www.remotesensing.org/libtiff/' +homepage = 'https://libtiff.maptools.org/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [ 'https://download.osgeo.org/libtiff/', - 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] checksums = ['5d29f32517dadb6dbcd1255ea5bbc93a2b54b94fbf83653b4d65c7d6775b8634'] From e97faac6aa03270a1cb679dd03d50047f90e7692 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Dec 2019 13:52:16 +0100 Subject: [PATCH 174/468] add custom sanity check paths for ParMGridGen --- .../p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb index 4123d6d983a..8ac5f07d1d5 100644 --- a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-iimpi-2019b.eb @@ -27,4 +27,10 @@ files_to_copy = [ (['libmgrid.a', 'libparmgrid.a'], 'lib'), ] +sanity_check_paths = { + 'files': ['bin/mgridgen', 'bin/parmgridgen', 'include/mgridgen.h', 'include/parmgridgen.h', + 'lib/libmgrid.a', 'lib/libparmgrid.a'], + 'dirs': [], +} + moduleclass = 'math' From 1effac8962804202123af10cb3e2b3b677dc720a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Dec 2019 14:39:24 +0100 Subject: [PATCH 175/468] add custom sanity check paths for Mesquite --- .../easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb index bfdf546db12..b1b1a3aeb62 100644 --- a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-8.3.0.eb @@ -18,4 +18,9 @@ builddependencies = [ ('binutils', '2.32'), ] +sanity_check_paths = { + 'files': ['bin/msqquality', 'bin/msqshape', 'lib/libmesquite.a'], + 'dirs': ['include'], +} + moduleclass = 'math' From bba3d1918b7f4248b73ca459e89fa28244895412 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Dec 2019 15:48:27 +0100 Subject: [PATCH 176/468] add easyconfig for WPS 4.1 on top of WRF 4.1.3 with intel/2019b --- .../w/WPS/WPS-4.1-intel-2019b-dmpar.eb | 32 +++++++ ...WPS-4.1_netCDF-Fortran_seperate_path.patch | 85 +++++++++++++++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.1-intel-2019b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.1_netCDF-Fortran_seperate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.1-intel-2019b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.1-intel-2019b-dmpar.eb new file mode 100644 index 00000000000..6c18bc7ec01 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.1-intel-2019b-dmpar.eb @@ -0,0 +1,32 @@ +name = 'WPS' +version = '4.1' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['WPS-%(version)s_netCDF-Fortran_seperate_path.patch'] +checksums = [ + '3a7785268f991824f5a812a0322aa7f1f4491417d6a325f8c733281015fd3c3d', # v4.1.tar.gz + '1f2edd2e6c28f94391237cd3cf27a83fd9f7ff3ece7df38ae792123dabe0a8bb', # WPS-4.1_netCDF-Fortran_seperate_path.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', '4.1.3', versionsuffix), + ('JasPer', '2.0.14'), + ('netCDF', '4.7.1'), + ('netCDF-Fortran', '4.5.2'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.1_netCDF-Fortran_seperate_path.patch new file mode 100644 index 00000000000..5ae74aa977d --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.1_netCDF-Fortran_seperate_path.patch @@ -0,0 +1,85 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# +# updated for WPS v4.1 yby Kenneth Hoste (HPC-UGent) + +--- WPS-4.1/arch/Config.pl.orig 2019-04-12 23:48:41.000000000 +0200 ++++ WPS-4.1/arch/Config.pl 2019-12-14 15:27:30.931325333 +0100 +@@ -41,6 +41,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +--- WPS-4.1/arch/preamble.orig 2019-04-12 23:48:41.000000000 +0200 ++++ WPS-4.1/arch/preamble 2019-12-14 15:27:30.933363000 +0100 +@@ -39,7 +39,7 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include -I$(NETCDFF)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ +--- WPS-4.1/configure.orig 2019-04-12 23:48:41.000000000 +0200 ++++ WPS-4.1/configure 2019-12-14 15:28:37.173438862 +0100 +@@ -119,9 +119,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -190,7 +195,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir + + + #Checking cross-compiling capability for some particular environment +@@ -356,9 +361,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +--- WPS-4.1/util/src/Makefile.orig 2019-04-12 23:48:41.000000000 +0200 ++++ WPS-4.1/util/src/Makefile 2019-12-14 15:27:30.937981000 +0100 +@@ -41,11 +41,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o odule_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o From 4ae19d1c07cf9d269e18fb42bbcfc4478eb65f93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Dec 2019 17:26:53 +0100 Subject: [PATCH 177/468] add missing 'time' build dep for WRF --- .../t/time/time-1.9-GCCcore-8.3.0.eb | 26 +++++++++++++++++++ .../w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb | 5 +++- 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..362b1b0d447 --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'http://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('binutils', '2.32')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb index a0a67a78575..ca1b5d4a5dd 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dmpar.eb @@ -22,7 +22,10 @@ checksums = [ ] # csh is used by WRF install scripts -builddependencies = [('tcsh', '6.22.02')] +builddependencies = [ + ('tcsh', '6.22.02'), + ('time', '1.9'), +] dependencies = [ ('JasPer', '2.0.14'), From 3cf30aea3a0d07a326d29d16305291bc564c1451 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Dec 2019 17:57:33 +0100 Subject: [PATCH 178/468] add missing checksum in time 1.9 easyconfig --- easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb index 362b1b0d447..c024be73282 100644 --- a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] builddependencies = [('binutils', '2.32')] From 1085a641c735d9fb843ee9defe210f04749159aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Dec 2019 19:03:33 +0100 Subject: [PATCH 179/468] use https for time 1.9 homepage --- easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb index c024be73282..dfcdb33c8f5 100644 --- a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'time' version = '1.9' -homepage = 'http://www.gnu.org/software/time/' +homepage = 'https://www.gnu.org/software/time/' description = """The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running.""" From 6c78c8108793d1b5e0430c8c6400090e6678f4b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Dec 2019 19:57:12 +0100 Subject: [PATCH 180/468] adding easyconfigs: GSL-2.6-GCC-8.3.0.eb, GSL-2.6-iccifort-2019.5.281.eb --- .../easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb | 25 +++++++++++++++++++ .../g/GSL/GSL-2.6-iccifort-2019.5.281.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb new file mode 100644 index 00000000000..37f070d0534 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.6' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..44c79b68d0c --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.6' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 727612393f712e8f8d19a4fda6d985a09df5796c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:46:56 +0100 Subject: [PATCH 181/468] use https for GSL 2.6 homepage --- easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb | 2 +- easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb index 37f070d0534..868a3b9ea2b 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GSL' version = '2.6' -homepage = 'http://www.gnu.org/software/gsl/' +homepage = 'https://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb index 44c79b68d0c..12fda91aa6a 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2019.5.281.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GSL' version = '2.6' -homepage = 'http://www.gnu.org/software/gsl/' +homepage = 'https://www.gnu.org/software/gsl/' description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" From 1125ceb3d964612df80c2ddd89bc2942ca3af27f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:48:22 +0100 Subject: [PATCH 182/468] adding easyconfigs: HDF-4.2.14-GCCcore-8.3.0.eb --- .../h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..d157c789b73 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.14' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] + +builddependencies = [ + ('binutils', '2.32'), + ('Bison', '3.3.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.3'), + ('Szip', '2.1.1'), + ('zlib', '1.2.11'), +] + +configopts = '' +configopts += '--with-szlib=$EBROOTSZIP ' +configopts += '--includedir=%(installdir)s/include/%(namelower)s ' + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' From e991e0b3619254a2002331e7a69a10ebe5fc3163 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:48:37 +0100 Subject: [PATCH 183/468] adding easyconfigs: g2clib-1.6.0-GCCcore-8.3.0.eb, g2lib-3.1.0-GCCcore-8.3.0.eb --- .../g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb | 27 +++++++++++++++ .../g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb | 33 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..6bb52f7bddd --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb @@ -0,0 +1,27 @@ +name = 'g2clib' +version = '1.6.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = ['g2clib-%(version)s-with-JasPer-2.x.patch'] +checksums = [ + 'afec1ea29979b84369d0f46f305ed12f73f1450ec2db737664ec7f75c1163add', # g2clib-1.6.0.tar + '2e62502d7823be5407ea023029dd206930a1034421d141dd346b468e177a7fce', # g2clib-1.6.0-with-JasPer-2.x.patch +] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('JasPer', '2.0.14'), + ('libpng', '1.6.37'), +] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..fb082f5a5cc --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +name = 'g2lib' +version = '3.1.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + 'g2lib-3.1.0_makefile.patch', + 'g2lib-1.4.0-with-JasPer-2.x.patch', +] +checksums = [ + '8a2de259de82094c5867f8d7945359f211592a4a503f9ed65dc60469337414e7', # g2lib-3.1.0.tar + '702f76c77638fb36b662caf96890a69f19c507778c92aa1e163898b150cc8282', # g2lib-3.1.0_makefile.patch + 'cd4c668dab76ef3b61fa902c2eed24747517d4cbc3ec0aaffab37e6b80946170', # g2lib-1.4.0-with-JasPer-2.x.patch +] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('JasPer', '2.0.14'), + ('libpng', '1.6.37'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -fno-range-check -I." FC=$FC CC=$CC' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From 6e142dd94ad616ef32b93237644e3ec257ff5eb4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:49:37 +0100 Subject: [PATCH 184/468] adding easyconfigs: UDUNITS-2.2.26-GCCcore-8.3.0.eb --- .../u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..fdfcbdce65b --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.26' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('expat', '2.2.7')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 3096869d2ece1d2f173a81f0d7c356e379744822 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:50:14 +0100 Subject: [PATCH 185/468] adding easyconfigs: makedepend-1.0.6-GCCcore-8.3.0.eb, xproto-7.0.31-GCCcore-8.3.0.eb --- .../makedepend-1.0.6-GCCcore-8.3.0.eb | 26 +++++++++++++++++ .../x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb | 29 +++++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..537c8054072 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.6' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] + +builddependencies = [ + ('binutils', '2.32'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..4d20bbbad64 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.32'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 56fea280671956a14d8dba79c1acd585abbc2143 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:51:55 +0100 Subject: [PATCH 186/468] adding easyconfigs: ncview-2.1.7-intel-2019b.eb --- .../n/ncview/ncview-2.1.7-intel-2019b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2019b.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2019b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2019b.eb new file mode 100644 index 00000000000..edcfbd45337 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2019b.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.7' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(command -v $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.7.1'), + ('netCDF-Fortran', '4.5.2'), + ('UDUNITS', '2.2.26'), + ('X11', '20190717'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' From c8e2826eb274afda848dfd418d6ce4fff7ca609d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:54:04 +0100 Subject: [PATCH 187/468] adding easyconfigs: PROJ-6.2.1-GCCcore-8.3.0.eb --- .../p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..9ae47303c11 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '6.2.1' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7f2e0fe63312f1e766057cceb53dc9585c4a335ff6641de45696dbd40d17c340'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.32'), +] + +dependencies = [('SQLite', '3.29.0')] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 652b10f7c8c4262f24f17476825570701ff87728 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:54:09 +0100 Subject: [PATCH 188/468] adding easyconfigs: SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb --- .../SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..24a66a0e9cf --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a00b4d0d53ad97a14316135e2d702091cd5f193bb58bcfcd8bc59d41e7887a9'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Python', '3.7.4'), + ('PCRE', '8.43'), +] + +moduleclass = 'devel' + From da5940cbcd1e8c4d3b0280278ab20448be547e81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:56:12 +0100 Subject: [PATCH 189/468] adding easyconfigs: GDAL-3.0.2-intel-2019b-Python-3.7.4.eb, GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb, libgeotiff-1.5.1-GCCcore-8.3.0.eb --- .../GDAL-3.0.2-intel-2019b-Python-3.7.4.eb | 59 +++++++++++++++++++ ...-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb | 33 +++++++++++ .../libgeotiff-1.5.1-GCCcore-8.3.0.eb | 34 +++++++++++ 3 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..9b64239497c --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + 'c3765371ce391715c8f28bd6defbc70b57aa43341f6e94605f04fe3c92468983', # gdal-3.0.2.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +dependencies = [ + ('Python', '3.7.4'), + ('netCDF', '4.7.1'), + ('expat', '2.2.7'), + ('GEOS', '3.8.0', versionsuffix), + ('SQLite', '3.29.0'), + ('libxml2', '2.9.9'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.3'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.0.10'), + ('zlib', '1.2.11'), + ('cURL', '7.66.0'), + ('PCRE', '8.43'), + ('PROJ', '6.2.1'), + ('libgeotiff', '1.5.1'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +prebuildopts = "export LDSHARED='icc -shared' && " + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb new file mode 100644 index 00000000000..e307f9dbf96 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-3.7.2_fix-Python3.patch'] +checksums = [ + '99114c3dc95df31757f44d2afde73e61b9f742f0b683fd1894cbbee05dda62d5', # geos-3.8.0.tar.bz2 + 'e14b54796d9d41261caae64b5a106b4bd8a77f37a51aa9b8ada30d87d208e2e0', # GEOS-3.7.2_fix-Python3.patch +] + +dependencies = [('Python', '3.7.4')] + +builddependencies = [('SWIG', '4.0.1', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..8eb97cf8820 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.5.1' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['f9e99733c170d11052f562bcd2c7cb4de53ed405f7acdde4f16195cd3ead612c'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.10'), + ('PROJ', '6.2.1'), + ('libjpeg-turbo', '2.0.3'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 325d6d50c110f0ced99766d70d74548a315f9e62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:56:29 +0100 Subject: [PATCH 190/468] adding easyconfigs: ESMF-8.0.0-intel-2019b.eb, netCDF-C++4-4.3.1-iimpi-2019b.eb --- .../e/ESMF/ESMF-8.0.0-intel-2019b.eb | 31 +++++++++++++++++++ .../netCDF-C++4-4.3.1-iimpi-2019b.eb | 25 +++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb new file mode 100644 index 00000000000..755830ac660 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb @@ -0,0 +1,31 @@ +name = 'ESMF' +version = '8.0.0' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '75c34c41806e703551b6b79566edf34c23f1eebcf821749e5320e860e565d94f', # esmf_8_0_0_src.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +dependencies = [ + ('netCDF', '4.7.1'), + ('netCDF-Fortran', '4.5.2'), + ('netCDF-C++4', '4.3.1'), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb new file mode 100644 index 00000000000..eef160af75c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.7.1')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From c64349f61ddf41ccb472d887ce58a7bb12cc0787 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 09:58:12 +0100 Subject: [PATCH 191/468] adding easyconfigs: cairo-1.16.0-GCCcore-8.3.0.eb, pixman-0.38.4-GCCcore-8.3.0.eb --- .../c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb | 47 +++++++++++++++++++ .../p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb | 29 ++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..65b25f4a08d --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.16.0' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] + +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('pixman', '0.38.4'), + ('expat', '2.2.7'), + ('GLib', '2.62.0'), + ('X11', '20190717'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..fcacf43063d --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.38.4' + +homepage = 'http://www.pixman.org/' + +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['da66d6fd6e40aee70f7bd02e4f8f76fc3f006ec879d346bae6a723025cfbdde7'] + +builddependencies = [ + ('binutils', '2.32'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' From 9dfadef11bda0fd1e5741949b35b12fda40796fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 10:00:29 +0100 Subject: [PATCH 192/468] adding easyconfigs: NCL-6.6.2-intel-2019b.eb, libiconv-1.16-GCCcore-8.3.0.eb --- .../l/libiconv/libiconv-1.16-GCCcore-8.3.0.eb | 23 ++++++++++ .../n/NCL/NCL-6.6.2-intel-2019b.eb | 46 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..9aa08c8c1b2 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.16' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04'] + +builddependencies = [('binutils', '2.32')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb new file mode 100644 index 00000000000..700d1c17437 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb @@ -0,0 +1,46 @@ +name = 'NCL' +version = '6.6.2' + +homepage = 'http://www.ncl.ucar.edu' +description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True} + +source_urls = ['https://github.com/NCAR/ncl/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['NCL-6.4.0_fix-types.patch'] +checksums = [ + 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz + 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch +] + +builddependencies = [ + ('makedepend', '1.0.6'), + ('Bison', '3.3.2'), + ('flex', '2.6.4'), +] +dependencies = [ + ('cURL', '7.66.0'), + ('JasPer', '2.0.14'), + ('g2lib', '3.1.0'), + ('g2clib', '1.6.0'), + ('HDF', '4.2.14'), + ('HDF5', '1.10.5'), + ('netCDF', '4.7.1'), + ('netCDF-Fortran', '4.5.2'), + ('Szip', '2.1.1'), + ('freetype', '2.10.1'), + ('zlib', '1.2.11'), + ('GDAL', '3.0.2', '-Python-3.7.4'), + ('UDUNITS', '2.2.26'), + ('ESMF', '8.0.0'), + ('bzip2', '1.0.8'), + ('cairo', '1.16.0'), + ('libiconv', '1.16'), + ('GSL', '2.6'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.3'), +] + +moduleclass = 'data' From ec4bfa001099b5d9a22f6ee85b80356018b0bc60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 10:05:03 +0100 Subject: [PATCH 193/468] use https for g2lib/g2clib homepage --- easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb index 6bb52f7bddd..662a091752b 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-GCCcore-8.3.0.eb @@ -1,7 +1,7 @@ name = 'g2clib' version = '1.6.0' -homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb index fb082f5a5cc..e5175e58ec8 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-GCCcore-8.3.0.eb @@ -1,7 +1,7 @@ name = 'g2lib' version = '3.1.0' -homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} From 092c7420d11c497d3d12b87cb9396aab938bf917 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 10:07:24 +0100 Subject: [PATCH 194/468] use https for UDUNITS homepage --- easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb index fdfcbdce65b..f02517cc319 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'UDUNITS' version = '2.2.26' -homepage = 'http://www.unidata.ucar.edu/software/udunits/' +homepage = 'https://www.unidata.ucar.edu/software/udunits/' description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" From 3a8e17036ad2b05bee2be981229ab0fbe6850925 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 10:08:16 +0100 Subject: [PATCH 195/468] use https for xproto homepage --- easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb index 4d20bbbad64..6d0f45d86e1 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'xproto' version = '7.0.31' -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' description = "X protocol and ancillary headers" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} From 87b7136f93f8b7fb8ed559f65f28e6c7f27e942f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 10:09:53 +0100 Subject: [PATCH 196/468] use https for PROJ homepage & source URLs --- easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb index 9ae47303c11..fbf999ac44c 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb @@ -11,14 +11,14 @@ easyblock = 'ConfigureMake' name = 'PROJ' version = '6.2.1' -homepage = 'http://trac.osgeo.org/proj/' +homepage = 'https://proj.org' description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://download.osgeo.org/proj/'] +source_urls = ['https://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7f2e0fe63312f1e766057cceb53dc9585c4a335ff6641de45696dbd40d17c340'] From 5bd59faa46662cbe69e019d1d5d13a1916776081 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 10:16:27 +0100 Subject: [PATCH 197/468] remove trailing empty line in SWIG easyconfig --- .../easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb index 24a66a0e9cf..ee1ac33527f 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -21,4 +21,3 @@ dependencies = [ ] moduleclass = 'devel' - From 5737506436f77f75e9648ed9ea72e333f0d47a24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 10:20:19 +0100 Subject: [PATCH 198/468] use https for netCDF-C++4 homepage --- .../n/netCDF-C++4/netCDF-C++4-4.3.0-iimpi-2019a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-iimpi-2019a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-iimpi-2019a.eb index 7b3e08702ac..f413ebd23a4 100644 --- a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-iimpi-2019a.eb +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-iimpi-2019a.eb @@ -3,9 +3,9 @@ easyblock = 'ConfigureMake' name = 'netCDF-C++4' version = '4.3.0' -homepage = 'http://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" toolchain = {'name': 'iimpi', 'version': '2019a'} From 96ef7cd22227190c4430428e7828b5546c023db0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 10:23:05 +0100 Subject: [PATCH 199/468] use https for pixman/cairo homepage & source URLs --- easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb | 4 ++-- easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb index 65b25f4a08d..3d1fc418f00 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'cairo' version = '1.16.0' -homepage = 'http://cairographics.org' +homepage = 'https://cairographics.org' description = """Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['http://cairographics.org/releases/'] +source_urls = ['https://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb index fcacf43063d..644a1d671ca 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['http://cairographics.org/releases/'] +source_urls = ['https://cairographics.org/releases/'] sources = [SOURCE_TAR_GZ] checksums = ['da66d6fd6e40aee70f7bd02e4f8f76fc3f006ec879d346bae6a723025cfbdde7'] From 63439adb5c6ce5d78db3a36bef2613ca23ce5fab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 11:02:16 +0100 Subject: [PATCH 200/468] use https for ESMF/netCDF-C++4 homepage --- easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb | 2 +- .../easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb index 755830ac660..ea0f932b061 100644 --- a/easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.0.0-intel-2019b.eb @@ -1,7 +1,7 @@ name = 'ESMF' version = '8.0.0' -homepage = 'http://sourceforge.net/projects/esmf' +homepage = 'https://sourceforge.net/projects/esmf' description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.""" diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb index eef160af75c..b6f56dc4b6e 100644 --- a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2019b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'netCDF-C++4' version = '4.3.1' -homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' description = """NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" From 039fe2472bf7a1d4366cb7775cfa2ce84eccebca Mon Sep 17 00:00:00 2001 From: guacke Date: Mon, 16 Dec 2019 11:47:49 +0200 Subject: [PATCH 201/468] adding easyconfigs: ORCA-4.2.1-OpenMPI-3.1.4.eb --- .../o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb new file mode 100644 index 00000000000..65745271904 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb @@ -0,0 +1,36 @@ +easyblock = "PackedBinary" + +name = "ORCA" +version = '4.2.1' + +local_ompi_ver = '3.1.4' +versionsuffix = '-OpenMPI-%s' % local_ompi_ver + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry + with specific emphasis on spectroscopic properties of open-shell molecules. + It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- + and multireference correlated ab initio methods. + It can also treat environmental and relativistic effects.""" + +toolchain = SYSTEM + +# Download from https://orcaforum.kofo.mpg.de +sources = ['%%(namelower)s_%s_linux_x86-64_openmpi314.tar.xz' % version.replace('.', '_')] +checksums = ['470c7362293ebc2fb14bfce5b6652ff8'] + +dependencies = [('OpenMPI', local_ompi_ver, '-GCC-8.3.0')] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca'], + 'dirs': [], +} + +moduleclass = 'chem' From a59a5a17bbe4f16bd75d3ba50eef9e78c0a61cc6 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 16 Dec 2019 09:51:32 +0000 Subject: [PATCH 202/468] adding easyconfigs: R-3.6.2-fosscuda-2019b.eb --- .../easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 2365 +++++++++++++++++ 1 file changed, 2365 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb new file mode 100644 index 00000000000..28e049be24e --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -0,0 +1,2365 @@ +name = 'R' +version = '3.6.2' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', '20190717'), + ('Mesa', '19.1.7'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.4'), + ('zlib', '1.2.11'), + ('SQLite', '3.29.0'), + ('PCRE', '8.43'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.3'), # for plottting in R + ('LibTIFF', '4.0.10'), + ('Java', '11', '', True), + ('Tk', '8.6.9'), # for tcltk + ('cURL', '7.66.0'), # for RCurl + ('libxml2', '2.9.9'), # for XML + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.6.1'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '64.2'), # for rJava & gdsfmt + ('HDF5', '1.10.5'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.9-5'), # for animation + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1b'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on June 7, 2019 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9', { + 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.3', { + 'checksums': ['2b3500dd3aca16f7b3cb5442625e76dcf4f7c974b4249d33041e9184a5ff030e'], + }), + ('RcppProgress', '0.4.1', { + 'checksums': ['11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a'], + }), + ('lpSolve', '5.6.13.3', { + 'checksums': ['e64165428c40d730f7686d233c22936bf4b3b91a618a600bdf87acaa905f5ff5'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '1.1-14', { + 'checksums': ['5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '2.2-14', { + 'checksums': ['1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0'], + }), + ('bnlearn', '4.5', { + 'checksums': ['a8047625533260a855d309b3c0785cbeec0f9ec13f284b6664a1f61638138578'], + 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['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.7', { + 'checksums': ['11083ee44c92569aadbb9baf60a2e079ab7a721c849b74d102694975cc8d778b'], + }), + ('xfun', '0.11', { + 'checksums': ['3cc24b5a67a11204255b71e5fadbb4c303dfb34a32e79c95b787aa8997e1cc36'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-1', { + 'checksums': ['748141d56531a39dc4d37cf0a5165a40b653a04c507e916854053ed77119e0e6'], + }), + ('NLP', 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('RCircos', '1.2.1', { + 'checksums': ['3b9489ab05ea83ead99ca6e4a1e6830467a2064779834aff1317b42bd41bb8fd'], + }), + ('lambda.r', '1.2.4', { + 'checksums': ['d252fee39065326c6d9f45ad798076522cec05e73b8905c1b30f95a61f7801d6'], + }), + ('futile.options', '1.0.1', { + 'checksums': ['7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570'], + }), + ('futile.logger', '1.4.3', { + 'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'], + }), + ('VennDiagram', '1.6.20', { + 'checksums': ['e51cb3fff23c6ec8191966490bf875a7415f8725d4054bae881a25febb9281c5'], + }), + ('xlsxjars', '0.6.1', { + 'checksums': ['37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6'], + }), + ('xlsx', '0.6.1', { + 'checksums': ['a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4'], + }), + ('uroot', '2.1-0', { + 'patches': ['uroot-2.0-9.1_CUDA.patch'], + 'checksums': [ + '3c02a9dadd22aa67a59e99007ab6f576dc428859fa746d3a8f3ffa2bb43d18c2', # uroot_2.1-0.tar.gz + '5de954038020d1d0c42eb0cb6b51950228ccc900c401dff6fbae43e4bc8fb936', # uroot-2.0-9.1_CUDA.patch + ], + }), + ('forecast', '8.10', { + 'checksums': ['798e15d15be9af0b8f505e826db83d5f09d7a7434567ec291a31eaf3b8c88c49'], + }), + ('fma', '2.3', { + 'checksums': ['f516eff79e14d4ffefcdc2db06d97ae57f998e37e871264457078f671384fafc'], + }), + ('expsmooth', '2.3', { + 'checksums': ['ac7da36347f983d6ec71715daefd2797fe2fc505c019f4965cff9f77ce79982a'], + }), + ('fpp', '0.5', { + 'checksums': ['9c87dd8591b8a87327cae7a03fd362a5492495a96609e5845ccbeefb96e916cb'], + }), + ('tensor', '1.5', { + 'checksums': ['e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6'], + }), + ('polyclip', '1.10-0', { + 'checksums': ['74dabc0dfe5a527114f0bb8f3d22f5d1ae694e6ea9345912909bae885525d34b'], + }), + ('goftest', '1.2-2', { + 'checksums': ['e497992666b002b6c6bed73bf05047ad7aa69eb58898da0ad8f1f5b2219e7647'], + }), + ('spatstat.utils', '1.15-0', { + 'checksums': ['90e07d730b6939f47f93c939afae10874b2c82bd402960ede4133de67dca2a0c'], + }), + ('spatstat.data', '1.4-0', { + 'checksums': ['121e5bb92beb7ccac920f921e760f429fd71bcfe11cb9b07a7e7326c7a72ec8c'], + }), + ('spatstat', '1.62-2', { + 'checksums': ['57cc1dc51b3d74fb4e3edfa30e6441db98c99e354ff65ffc82d5419a49a8353b'], + }), + ('pracma', '2.2.9', { + 'checksums': ['0cea0ff5e88643df121e07b9aebfe57084c61e11801680039752f371fe87bf1e'], + }), + ('RCurl', '1.95-4.12', { + 'checksums': ['393779efafdf40823dac942a1e028905d65c34f3d41cfd21bcd225e411385ff4'], + }), + ('bio3d', '2.4-0', { + 'checksums': ['9ab86e299adee14e9a87ec87284f4c52a0114d303f21d166aaa0dc766f987746'], + }), + ('AUC', '0.3.0', { + 'checksums': ['e705f2c63d336249d19187f3401120d738d42d323fce905f3e157c2c56643766'], + }), + ('interpretR', '0.2.4', { + 'checksums': ['4c08a6dffd6fd5764f27812f3a085c53e6a21d59ae82d903c9c0da93fd1dd059'], + }), + ('cvAUC', '1.1.0', { + 'checksums': ['c4d8ed53b93869650aa2f666cf6d1076980cbfea7fa41f0b8227595be849738d'], + }), + ('SuperLearner', '2.0-26', { + 'checksums': ['4462922c8daae2773f79ecdea7ca3cc4ea51bfd101c5e6c1ad22f9190e746081'], + }), + ('mediation', '4.5.0', { + 'checksums': ['210206618787c395a67689be268283df044deec7199d9860ed95218ef1e60845'], + }), + ('ModelMetrics', '1.2.2', { + 'checksums': ['66d6fc75658287fdbae4d437b51d26781e138b8baa558345fb9e5a2df86a0d95'], + }), + ('CVST', '0.2-2', { + 'checksums': ['854b8c983427ecf9f2f7798c4fd1c1d06762b5b0bcb1045502baadece6f78316'], + }), + ('DRR', '0.0.3', { + 'checksums': ['7493389c1fb9ddc4d4261e15bf2d4198603227275688b1d3e3994d47e976a1f9'], + }), + ('dimRed', '0.2.3', { + 'checksums': ['e6e56e3f6999ebdc326e64ead5269f3aaf61dd587beefafb7536ac3890370d84'], + }), + ('lubridate', '1.7.4', { + 'checksums': ['510ca87bd91631c395655ee5029b291e948b33df09e56f6be5839f43e3104891'], + }), + ('ddalpha', '1.3.10', { + 'checksums': ['5f52e0aae9917476078daf031f2213b0b6b83d225530394bdb759e86fc79c480'], + }), + ('gower', '0.2.1', { + 'checksums': ['af3fbe91cf818c0841b2c0ec4ddf282c182a588031228c8d88f7291b2cdff100'], + }), + ('RcppRoll', '0.3.0', { + 'checksums': ['cbff2096443a8a38a6f1dabf8c90b9e14a43d2196b412b5bfe5390393f743f6b'], + }), + ('recipes', '0.1.7', { + 'checksums': ['28e96953355749dd1deb6786b22ec825a6fdb9f336e2785d45611e89f7e988bf'], + }), + ('caret', '6.0-84', { + 'checksums': ['a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d'], + }), + ('adabag', '4.2', { + 'checksums': ['47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81'], + }), + ('parallelMap', '1.4', { + 'checksums': ['fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b'], + }), + ('ParamHelpers', '1.13', { + 'checksums': ['b9b5212a485f441504716fcddf4fd7376bf3b909aae049c7394245e853424e79'], + }), + ('ggvis', '0.4.5', { + 'checksums': ['82373c3565c299279f6849f798cc39127b2b3f7ff2deee1946528474824b3124'], + }), + ('mlr', '2.16.0', { + 'checksums': ['3db8141d9cbb71139c9bf3a3ea995524322512221b56e6bcf44338d24f84e76a'], + }), + ('unbalanced', '2.0', { + 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], + }), + ('RSNNS', '0.4-12', { + 'checksums': ['b18dfeda71573bc92c6888af72da407651bff7571967965fd3008f0d331743b9'], + }), + ('abc.data', '1.0', { + 'checksums': ['b242f43c3d05de2e8962d25181c6b1bb6ca1852d4838868ae6241ca890b161af'], + }), + ('abc', '2.1', { + 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], + }), + ('lhs', '1.0.1', { + 'checksums': ['a4d5ac0c6f585f2880364c867fa94e6554698beb65d3678ba5938dd84fc6ea53'], + }), + ('tensorA', '0.36.1', { + 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], + }), + ('EasyABC', '1.5', { + 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + }), + ('whisker', '0.4', { + 'checksums': ['7a86595be4f1029ec5d7152472d11b16175737e2777134e296ae97341bf8fba8'], + }), + ('commonmark', '1.7', { + 'checksums': ['d14a767a3ea9778d6165f44f980dd257423ca6043926e3cd8f664f7171f89108'], + }), + ('roxygen2', '7.0.2', { + 'checksums': ['5823937df68ea558e5e85771b8b6e090775b82f7f797ca5d539e7378c4535d98'], + }), + ('git2r', '0.26.1', { + 'checksums': ['13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435'], + }), + ('rversions', '2.0.1', { + 'checksums': ['51ec1f64e7d628e88d716a020d5d521eba71d472e3c9ae7b694428ef6dd786c5'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('sessioninfo', '1.1.1', { + 'checksums': ['166b04678448a7decd50f24afabe5e2ad613e3c55b180ef6e8dd7a870a1dae48'], + }), + ('rcmdcheck', '1.3.3', { + 'checksums': ['1ab679eb1976d74cd3be5bcad0af7fcc673dbdfd4406bbce32591c8fddfb93b4'], + }), + ('remotes', '2.1.0', { + 'checksums': ['8944c8f6fc9f0cd0ca04d6cf1221b716eee08facef9f4b4c4d91d0346d6d68a7'], + }), + ('fs', '1.3.1', { + 'checksums': ['d6934dca8f835d8173e3fb9fd4d5e2740c8c04348dd2bcc57df1b711facb46bc'], + }), + ('clisymbols', '1.2.0', { + 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gh', '1.0.1', { + 'checksums': ['f3c02b16637ae390c3599265852d94b3de3ef585818b260d00e7812595b391d2'], + }), + ('usethis', '1.5.1', { + 'checksums': ['9e3920a04b0df82adf59eef2c1b2b4d835c4a757a51b3c163b8fc619172f561d'], + }), + ('DT', '0.10', { + 'checksums': ['3cc6dfc9697b52aef21d30dcfd355831c6216edcc6dd6bfb9a106cce6ab0906f'], + }), + ('rex', '1.1.2', { + 'checksums': ['bd3c74ceaf335336f5dd04314d0a791f6311e421a2158f321f5aab275f539a2a'], + }), + ('covr', '3.4.0', { + 'checksums': ['e57d9c656b4ab50a7f9557dee422d8777efaf08ecde0fd8bfa5897ef4d9e845c'], + }), + ('devtools', '2.2.1', { + 'checksums': ['2e988fb56b068ba958ea471224d2462427868ce7706e157a90c0ce0e13294e44'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-10', { + 'checksums': ['7837f0c384cd49bb3342cb39a916d7a80b02fffbf123913a58014e597f69b5d5'], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.0-6', { + 'checksums': ['4910e2952f767c1062d7cbe648c90a97009e2b3da316c6b33f6d022cd38b23d6'], + }), + ('extRemes', '2.0-11', { + 'checksums': ['75fbdeef677c81cf5661b8df3df4090c55f53e9bb96bb138b498eb0fbbf5af42'], + }), + ('pixmap', '0.4-11', { + 'checksums': ['6fa010749a59cdf56aad9f81271473b7d55697036203f2cd5d81372bcded7412'], + }), + ('tkrplot', '0.0-24', { + 'checksums': ['2873630a37d7ae1e09a5803d9a89ca0494edd83526c7b1860d9246543722f311'], + }), + ('misc3d', '0.8-4', { + 'checksums': ['75de3d2237f67f9e58a36e80a6bbf7e796d43eb46789f2dd1311270007bf5f62'], + }), + ('multicool', '0.1-11', { + 'checksums': ['1c907e64af2ac39facdf431a5691e69649f64af1f50e198ae39da5bf30026476'], + }), + ('plot3D', '1.1.1', { + 'checksums': ['f6fe4a001387132626fc553ed1d5720d448b8064eb5a6917458a798e1d381632'], + }), + ('plot3Drgl', '1.0.1', { + 'checksums': ['466d428d25c066c9c96d892f24da930513d42b1bdf76d3b53628c3ba13c3e48a'], + }), + ('OceanView', '1.0.4', { + 'checksums': ['e67f6f376737e1e5cf22fdfe2769a8f674e90c886b0e43942e97d9a3e6924f1c'], + }), + ('ks', '1.11.6', { + 'checksums': ['d8f1ccb99281eed092b8f950cfbf422330e88f2a0ce1ef6c9dbd7d8b9d648c41'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-18', { + 'checksums': ['2d7e8c4452653364ee086d95cea620c50378e30acfcff129b7261e1756a99504'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('randomForestSRC', '2.9.2', { + 'checksums': ['780fbc07ca0b2676fadf576d4d278887672b431ba42cd49b769ed8ccbc4e6d74'], + }), + ('sm', '2.2-5.6', { + 'checksums': ['b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-5', { + 'checksums': ['feeb6e1b419aa1d54fd5af1d67260b5d13ff251c19de8136a4df565305d47b12'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.10-1', { + 'checksums': ['6f1158c9295e65bd649139224497d3356189b931ff143f9b374daae72548776f'], + }), + ('mi', '1.0', { + 'checksums': 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['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '2.1', { + 'checksums': ['d21959ce5b1ee20efd1483f6020b57e5f6616bd525af77a7bd325501cc670606'], + }), + ('bbmle', '1.0.20', { + 'checksums': ['6c0fe8df7243f8a039e62d14014065df2002b9329c0e8a3c2df4e7ccf591f1f7'], + }), + ('emdbook', '1.3.11', { + 'checksums': ['f848d4c0a2da50dc8a5af76429d8f9d4960dee3fad1e98f7b507bdfd9b2ca128'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.47', { + 'checksums': ['123ebe870895c2ba3a4b64d8a18bccab5287c831fa14bb0fe07f0d7de61e51d3'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2019.04.22', { + 'checksums': ['2386440c3bed8391ee3a029aab86c107d435d0dd6a970236512d7c105d146b6e'], + }), + ('stopwords', '1.0', { + 'checksums': ['9b727a5d827ac8dcfa6329140d294dcf964a06d80132b4ca434330d0ee02b1da'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.6.0', { + 'checksums': ['61617d344444235940f5b9ac1cd6b86938e74a8c76791235724b16b755c3f72c'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0', { + 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], + }), + ('topicmodels', '0.2-9', { + 'checksums': ['40770fb7de6ab6bd6e3ef6a0c777fa6db65d0322e67503c26c84ea857ac9a79c'], + }), + ('tidytext', '0.2.2', { + 'checksums': ['188f294cf3177fe6fc85e9b7e16a05211cebeab0e0f7b05a9443416790bf2ec0'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('OpenCL', '0.1-3.1', { + 'checksums': ['daff23d777a27cd9d2e67ca8f5db1d29940cf0422708c1ea7e2d9661e3d6ae6f'], + }), + ('assertive.base', '0.0-7', { + 'checksums': ['f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-2', { + 'checksums': ['e8d4b1af89cc8b544f32092a7e8c0ee067526baf1c41af261bf98e8bba434901'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-4', { + 'checksums': ['123672e1a99fc79e7e9e91566ee21bba1fb45fd13e353e41c52e3300ecd2f5a7'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-5', { + 'checksums': ['23ff6c8893e9c0b5b6bf4009a10de42a4a3a86eec2c48e7b73ae2cd6295c8b2e'], + }), + ('RViennaCL', '1.7.1.8', { + 'checksums': ['adcc74537337582153d5b11d281e391e91a7f3afae116aa1b9a034ffd11b0252'], + }), + ('gpuR', '2.0.3', { + 'checksums': ['1e6f0082c9fc89bb2094979b78dbc1aa06db793202bea3f0683a43306db6cba9'], + }), +] + +moduleclass = 'lang' From 39de813d2356f24d4db5501ff3a2ae38558185cb Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 16 Dec 2019 10:06:15 +0000 Subject: [PATCH 203/468] Adding missing dependencies - copied from https://github.com/easybuilders/easybuild-easyconfigs/pull/9365 --- .../g/GSL/GSL-2.6-GCCcore-8.3.0.eb | 27 ++++++++++++ .../ImageMagick-7.0.9-5-GCCcore-8.3.0.eb | 44 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..a466491e697 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCCcore-8.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.6' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] + +builddependencies = [('binutils', '2.32')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..91f9c48f1bd --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.9-5' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d15abd31e7e18f7edec47df156773a23e5100386e55c6ce50f5353e9572d3413'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20190717'), + ('Ghostscript', '9.50'), + ('JasPer', '2.0.14'), + ('libjpeg-turbo', '2.0.3'), + ('LibTIFF', '4.0.10'), + ('LittleCMS', '2.9'), +] + +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' From d454cdf2b905d96649c42ff65e5ddd3106d945a4 Mon Sep 17 00:00:00 2001 From: guacke Date: Mon, 16 Dec 2019 12:08:51 +0200 Subject: [PATCH 204/468] Add SHA256 checksum. --- easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb index 65745271904..0bf451a7b42 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb @@ -17,7 +17,7 @@ toolchain = SYSTEM # Download from https://orcaforum.kofo.mpg.de sources = ['%%(namelower)s_%s_linux_x86-64_openmpi314.tar.xz' % version.replace('.', '_')] -checksums = ['470c7362293ebc2fb14bfce5b6652ff8'] +checksums = ['a1ff07bb01ac81ce9a4d6637fef77c12d0ec45354cebc72245c4e0d1620af956'] dependencies = [('OpenMPI', local_ompi_ver, '-GCC-8.3.0')] From 546a14f7ba2b628f12ad7b152267c2dd538676fc Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 16 Dec 2019 10:13:51 +0000 Subject: [PATCH 205/468] Adding missing dependencies - copied from https://github.com/easybuilders/easybuild-easyconfigs/pull/9365 --- .../c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb | 47 + .../Ghostscript-9.50-GCCcore-8.3.0.eb | 46 + .../i/ICU/ICU-64.2-GCCcore-8.3.0.eb | 29 + .../LittleCMS/LittleCMS-2.9-GCCcore-8.3.0.eb | 29 + .../libsndfile-1.0.28-GCCcore-8.3.0.eb | 23 + .../n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb | 38 + .../p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb | 29 + .../easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 2309 +++++++++++++++++ .../u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb | 41 + 9 files changed, 2591 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..65b25f4a08d --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.16.0' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] + +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('pixman', '0.38.4'), + ('expat', '2.2.7'), + ('GLib', '2.62.0'), + ('X11', '20190717'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..0936a47c70a --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.50' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0f53e89fd647815828fc5171613e860e8535b68f7afbc91bf89aee886769ce89'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('libjpeg-turbo', '2.0.3'), + ('expat', '2.2.7'), + ('GLib', '2.62.0'), + ('cairo', '1.16.0'), + ('LibTIFF', '4.0.10'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.32'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +sanity_check_paths = { + 'files': ['bin/gs'], + 'dirs': ['lib/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..9b42d14795b --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '64.2' + +homepage = 'http://site.icu-project.org/home' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.icu-project.org/files/icu4c/%(version)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['627d5d8478e6d96fc8c90fed4851239079a561a6a8b9e48b0892f24e82d31d6c'] + +builddependencies = [ + ('binutils', '2.32'), + ('Python', '2.7.16'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..6a67315b996 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-8.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.9' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['48c6fdf98396fa245ed86e622028caf49b96fa22f3e5734f853f806fbc8e7d20'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.32'), +] + +dependencies = [('libjpeg-turbo', '2.0.3')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..695966b278a --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-8.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libsndfile' +version = '1.0.28' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://www.mega-nerd.com/libsndfile/files/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1ff33929f042fa333aed1e8923aa628c3ee9e1eb85512686c55092d1e5a9dfa9'] + +builddependencies = [('binutils', '2.32')] + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..f6215c30b67 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2019-06-05 John Dey jfdey@fredhutch.org fizwit@github.com - updated for CMake +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.6.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['66d63a505187fb6f98642703bd0ef006fedcae2f9a6d1efa4f362ea919a02650'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('binutils', '2.32'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..aed47325cd6 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.38.4' + +homepage = 'http://www.pixman.org/' + +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['da66d6fd6e40aee70f7bd02e4f8f76fc3f006ec879d346bae6a723025cfbdde7'] + +builddependencies = [ + ('binutils', '2.32'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb new file mode 100644 index 00000000000..7d3aed301bd --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -0,0 +1,2309 @@ +name = 'R' +version = '3.6.2' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', '20190717'), + ('Mesa', '19.1.7'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.4'), + ('zlib', '1.2.11'), + ('SQLite', '3.29.0'), + ('PCRE', '8.43'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.3'), # for plottting in R + ('LibTIFF', '4.0.10'), + ('Java', '11', '', True), + ('Tk', '8.6.9'), # for tcltk + ('cURL', '7.66.0'), # for RCurl + ('libxml2', '2.9.9'), # for XML + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.6.1'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '64.2'), # for rJava & gdsfmt + ('HDF5', '1.10.5'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.9-5'), # for animation + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1b'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on June 7, 2019 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9', { + 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.3', { + 'checksums': ['2b3500dd3aca16f7b3cb5442625e76dcf4f7c974b4249d33041e9184a5ff030e'], + }), + ('RcppProgress', '0.4.1', { + 'checksums': ['11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a'], + }), + ('lpSolve', '5.6.13.3', { + 'checksums': ['e64165428c40d730f7686d233c22936bf4b3b91a618a600bdf87acaa905f5ff5'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '1.1-14', { + 'checksums': ['5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '2.2-14', { + 'checksums': ['1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0'], + }), + ('bnlearn', '4.5', { + 'checksums': ['a8047625533260a855d309b3c0785cbeec0f9ec13f284b6664a1f61638138578'], + 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}), + ('openxlsx', '4.1.4', { + 'checksums': ['07a38b21f6ce6e92d58d7a51ea9f4b5fd77db49b019a18ba9ecea69878a39dd7'], + }), + ('rematch', '1.0.1', { + 'checksums': ['a409dec978cd02914cdddfedc974d9b45bd2975a124d8870d52cfd7d37d47578'], + }), + ('cellranger', '1.1.0', { + 'checksums': ['5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99'], + }), + ('readxl', '1.3.1', { + 'checksums': ['24b441713e2f46a3e7c6813230ad6ea4d4ddf7e0816ad76614f33094fbaaaa96'], + }), + ('rio', '0.5.16', { + 'checksums': ['d3eb8d5a11e0a3d26169bb9d08f834a51a6516a349854250629072d59c29d465'], + }), + ('car', '3.0-5', { + 'checksums': ['7ed4f7e79b39089796ca07ca78de560f517967b6ad79b93ecf98037b03aaee70'], + }), + ('flashClust', '1.01-2', { + 'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'], + }), + ('ggrepel', '0.8.1', { + 'checksums': ['d5d03a77ab6d8c831934bc46e840cc4e3df487272ab591fa72767ad42bcb7283'], + }), + ('FactoMineR', '2.0', { + 'checksums': ['48828a7491a9210aa908f77e8aaacc774b1205a269898f752f6e0d773d303c62'], + }), + ('flexclust', '1.4-0', { + 'checksums': ['82fe445075a795c724644864c7ee803c5dd332a89ea9e6ccf7cd1ae2d1ecfc74'], + }), + ('flexmix', '2.3-15', { + 'checksums': ['ba444c0bfe33ab87d440ab590c06b03605710acd75811c1622253171bb123f43'], + }), + ('prabclus', '2.3-1', { + 'checksums': ['ef3294767d43bc3f72478fdaf0d1f13c8de18881bf9040c9f1add68af808b3c0'], + }), + ('diptest', '0.75-7', { + 'checksums': ['462900100ca598ef21dbe566bf1ab2ce7c49cdeab6b7a600a50489b05f61b61b'], + }), + ('trimcluster', '0.1-2.1', { + 'checksums': ['b64a872a6c2ad677dfeecc776c9fe5aff3e8bab6bc6a8c86957b5683fd5d2300'], + }), + ('fpc', '2.2-3', { + 'checksums': ['8100a74e6ff96b1cd65fd22494f2d200e54ea5ea533cfca321fa494914bdc3b7'], + }), + ('BiasedUrn', '1.07', { + 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], + }), + ('TeachingDemos', '2.10', { + 'checksums': ['2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704'], + }), + ('kohonen', '3.0.10', { + 'checksums': ['996956ea46a827c9f214e4f940a19304a0ff35bda707d4d7312f80d3479067b2'], + }), + ('base64', '2.0', { + 'checksums': ['8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1'], + }), + ('doRNG', '1.7.1', { + 'checksums': ['27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9'], + }), + ('nleqslv', '3.3.2', { + 'checksums': ['f54956cf67f9970bb3c6803684c84a27ac78165055745e444efc45cfecb63fed'], + }), + ('Deriv', '4.0', { + 'checksums': ['76788764177b24dc27f4e27046fa563ad97014e0d53e14a880ebff2f9177b40e'], + }), + ('RGCCA', '2.1.2', { + 'checksums': ['20f341fca8f616c556699790814debdf2ac7aa4dd9ace2071100c66af1549d7d'], + }), + ('pheatmap', '1.0.12', { + 'checksums': ['579d96ee0417203b85417780eca921969cda3acc210c859bf9dfeff11539b0c1'], + }), + ('pvclust', '2.2-0', { + 'checksums': ['7892853bacd413b5a921006429641ad308a344ca171b3081c15e4c522a8b0201'], + }), + ('RCircos', '1.2.1', { + 'checksums': ['3b9489ab05ea83ead99ca6e4a1e6830467a2064779834aff1317b42bd41bb8fd'], + }), + ('lambda.r', '1.2.4', { + 'checksums': ['d252fee39065326c6d9f45ad798076522cec05e73b8905c1b30f95a61f7801d6'], + }), + ('futile.options', '1.0.1', { + 'checksums': ['7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570'], + }), + ('futile.logger', '1.4.3', { + 'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'], + }), + ('VennDiagram', '1.6.20', { + 'checksums': ['e51cb3fff23c6ec8191966490bf875a7415f8725d4054bae881a25febb9281c5'], + }), + ('xlsxjars', '0.6.1', { + 'checksums': ['37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6'], + }), + ('xlsx', '0.6.1', { + 'checksums': ['a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4'], + }), + ('uroot', '2.1-0', { + 'patches': ['uroot-2.0-9.1_CUDA.patch'], + 'checksums': [ + '3c02a9dadd22aa67a59e99007ab6f576dc428859fa746d3a8f3ffa2bb43d18c2', # uroot_2.1-0.tar.gz + '5de954038020d1d0c42eb0cb6b51950228ccc900c401dff6fbae43e4bc8fb936', # uroot-2.0-9.1_CUDA.patch + ], + }), + ('forecast', '8.10', { + 'checksums': ['798e15d15be9af0b8f505e826db83d5f09d7a7434567ec291a31eaf3b8c88c49'], + }), + ('fma', '2.3', { + 'checksums': ['f516eff79e14d4ffefcdc2db06d97ae57f998e37e871264457078f671384fafc'], + }), + ('expsmooth', '2.3', { + 'checksums': ['ac7da36347f983d6ec71715daefd2797fe2fc505c019f4965cff9f77ce79982a'], + }), + ('fpp', '0.5', { + 'checksums': ['9c87dd8591b8a87327cae7a03fd362a5492495a96609e5845ccbeefb96e916cb'], + }), + ('tensor', '1.5', { + 'checksums': ['e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6'], + }), + ('polyclip', '1.10-0', { + 'checksums': ['74dabc0dfe5a527114f0bb8f3d22f5d1ae694e6ea9345912909bae885525d34b'], + }), + ('goftest', '1.2-2', { + 'checksums': ['e497992666b002b6c6bed73bf05047ad7aa69eb58898da0ad8f1f5b2219e7647'], + }), + ('spatstat.utils', '1.15-0', { + 'checksums': ['90e07d730b6939f47f93c939afae10874b2c82bd402960ede4133de67dca2a0c'], + }), + ('spatstat.data', '1.4-0', { + 'checksums': ['121e5bb92beb7ccac920f921e760f429fd71bcfe11cb9b07a7e7326c7a72ec8c'], + }), + ('spatstat', '1.62-2', { + 'checksums': ['57cc1dc51b3d74fb4e3edfa30e6441db98c99e354ff65ffc82d5419a49a8353b'], + }), + ('pracma', '2.2.9', { + 'checksums': ['0cea0ff5e88643df121e07b9aebfe57084c61e11801680039752f371fe87bf1e'], + }), + ('RCurl', '1.95-4.12', { + 'checksums': ['393779efafdf40823dac942a1e028905d65c34f3d41cfd21bcd225e411385ff4'], + }), + ('bio3d', '2.4-0', { + 'checksums': ['9ab86e299adee14e9a87ec87284f4c52a0114d303f21d166aaa0dc766f987746'], + }), + ('AUC', '0.3.0', { + 'checksums': ['e705f2c63d336249d19187f3401120d738d42d323fce905f3e157c2c56643766'], + }), + ('interpretR', '0.2.4', { + 'checksums': ['4c08a6dffd6fd5764f27812f3a085c53e6a21d59ae82d903c9c0da93fd1dd059'], + }), + ('cvAUC', '1.1.0', { + 'checksums': ['c4d8ed53b93869650aa2f666cf6d1076980cbfea7fa41f0b8227595be849738d'], + }), + ('SuperLearner', '2.0-26', { + 'checksums': ['4462922c8daae2773f79ecdea7ca3cc4ea51bfd101c5e6c1ad22f9190e746081'], + }), + ('mediation', '4.5.0', { + 'checksums': ['210206618787c395a67689be268283df044deec7199d9860ed95218ef1e60845'], + }), + ('ModelMetrics', '1.2.2', { + 'checksums': ['66d6fc75658287fdbae4d437b51d26781e138b8baa558345fb9e5a2df86a0d95'], + }), + ('CVST', '0.2-2', { + 'checksums': ['854b8c983427ecf9f2f7798c4fd1c1d06762b5b0bcb1045502baadece6f78316'], + }), + ('DRR', '0.0.3', { + 'checksums': ['7493389c1fb9ddc4d4261e15bf2d4198603227275688b1d3e3994d47e976a1f9'], + }), + ('dimRed', '0.2.3', { + 'checksums': ['e6e56e3f6999ebdc326e64ead5269f3aaf61dd587beefafb7536ac3890370d84'], + }), + ('lubridate', '1.7.4', { + 'checksums': ['510ca87bd91631c395655ee5029b291e948b33df09e56f6be5839f43e3104891'], + }), + ('ddalpha', '1.3.10', { + 'checksums': ['5f52e0aae9917476078daf031f2213b0b6b83d225530394bdb759e86fc79c480'], + }), + ('gower', '0.2.1', { + 'checksums': ['af3fbe91cf818c0841b2c0ec4ddf282c182a588031228c8d88f7291b2cdff100'], + }), + ('RcppRoll', '0.3.0', { + 'checksums': ['cbff2096443a8a38a6f1dabf8c90b9e14a43d2196b412b5bfe5390393f743f6b'], + }), + ('recipes', '0.1.7', { + 'checksums': ['28e96953355749dd1deb6786b22ec825a6fdb9f336e2785d45611e89f7e988bf'], + }), + ('caret', '6.0-84', { + 'checksums': ['a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d'], + }), + ('adabag', '4.2', { + 'checksums': ['47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81'], + }), + ('parallelMap', '1.4', { + 'checksums': ['fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b'], + }), + ('ParamHelpers', '1.13', { + 'checksums': ['b9b5212a485f441504716fcddf4fd7376bf3b909aae049c7394245e853424e79'], + }), + ('ggvis', '0.4.5', { + 'checksums': ['82373c3565c299279f6849f798cc39127b2b3f7ff2deee1946528474824b3124'], + }), + ('mlr', '2.16.0', { + 'checksums': ['3db8141d9cbb71139c9bf3a3ea995524322512221b56e6bcf44338d24f84e76a'], + }), + ('unbalanced', '2.0', { + 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], + }), + ('RSNNS', '0.4-12', { + 'checksums': ['b18dfeda71573bc92c6888af72da407651bff7571967965fd3008f0d331743b9'], + }), + ('abc.data', '1.0', { + 'checksums': ['b242f43c3d05de2e8962d25181c6b1bb6ca1852d4838868ae6241ca890b161af'], + }), + ('abc', '2.1', { + 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], + }), + ('lhs', '1.0.1', { + 'checksums': ['a4d5ac0c6f585f2880364c867fa94e6554698beb65d3678ba5938dd84fc6ea53'], + }), + ('tensorA', '0.36.1', { + 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], + }), + ('EasyABC', '1.5', { + 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + }), + ('whisker', '0.4', { + 'checksums': ['7a86595be4f1029ec5d7152472d11b16175737e2777134e296ae97341bf8fba8'], + }), + ('commonmark', '1.7', { + 'checksums': ['d14a767a3ea9778d6165f44f980dd257423ca6043926e3cd8f664f7171f89108'], + }), + ('roxygen2', '7.0.2', { + 'checksums': ['5823937df68ea558e5e85771b8b6e090775b82f7f797ca5d539e7378c4535d98'], + }), + ('git2r', '0.26.1', { + 'checksums': ['13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435'], + }), + ('rversions', '2.0.1', { + 'checksums': ['51ec1f64e7d628e88d716a020d5d521eba71d472e3c9ae7b694428ef6dd786c5'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('sessioninfo', '1.1.1', { + 'checksums': ['166b04678448a7decd50f24afabe5e2ad613e3c55b180ef6e8dd7a870a1dae48'], + }), + ('rcmdcheck', '1.3.3', { + 'checksums': ['1ab679eb1976d74cd3be5bcad0af7fcc673dbdfd4406bbce32591c8fddfb93b4'], + }), + ('remotes', '2.1.0', { + 'checksums': ['8944c8f6fc9f0cd0ca04d6cf1221b716eee08facef9f4b4c4d91d0346d6d68a7'], + }), + ('fs', '1.3.1', { + 'checksums': ['d6934dca8f835d8173e3fb9fd4d5e2740c8c04348dd2bcc57df1b711facb46bc'], + }), + ('clisymbols', '1.2.0', { + 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gh', '1.0.1', { + 'checksums': ['f3c02b16637ae390c3599265852d94b3de3ef585818b260d00e7812595b391d2'], + }), + ('usethis', '1.5.1', { + 'checksums': ['9e3920a04b0df82adf59eef2c1b2b4d835c4a757a51b3c163b8fc619172f561d'], + }), + ('DT', '0.10', { + 'checksums': ['3cc6dfc9697b52aef21d30dcfd355831c6216edcc6dd6bfb9a106cce6ab0906f'], + }), + ('rex', '1.1.2', { + 'checksums': ['bd3c74ceaf335336f5dd04314d0a791f6311e421a2158f321f5aab275f539a2a'], + }), + ('covr', '3.4.0', { + 'checksums': ['e57d9c656b4ab50a7f9557dee422d8777efaf08ecde0fd8bfa5897ef4d9e845c'], + }), + ('devtools', 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['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], + }), + ('bdsmatrix', '1.3-3', { + 'checksums': ['70ea81708c97dedd483a5d3866d2e906fa0e9098ff854c41cf0746fbc8dfad9d'], + }), + ('fftwtools', '0.9-8', { + 'checksums': ['4641c8cd70938c2a8bde0b6da6cf7f83e96175ef52f1ca42ec3920a1dabf1bdb'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.1', { + 'checksums': ['71750b741672a435ecf749b69c72f0681aa8bb795e317f4e3056d5e33f6d79e8'], + }), + ('LaplacesDemon', '16.1.1', { + 'checksums': ['779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': ['6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8'], + }), + ('sampling', '2.8', { + 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '2.1', { + 'checksums': ['d21959ce5b1ee20efd1483f6020b57e5f6616bd525af77a7bd325501cc670606'], + }), + ('bbmle', '1.0.20', { + 'checksums': ['6c0fe8df7243f8a039e62d14014065df2002b9329c0e8a3c2df4e7ccf591f1f7'], + }), + ('emdbook', '1.3.11', { + 'checksums': ['f848d4c0a2da50dc8a5af76429d8f9d4960dee3fad1e98f7b507bdfd9b2ca128'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.47', { + 'checksums': ['123ebe870895c2ba3a4b64d8a18bccab5287c831fa14bb0fe07f0d7de61e51d3'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2019.04.22', { + 'checksums': ['2386440c3bed8391ee3a029aab86c107d435d0dd6a970236512d7c105d146b6e'], + }), + ('stopwords', '1.0', { + 'checksums': ['9b727a5d827ac8dcfa6329140d294dcf964a06d80132b4ca434330d0ee02b1da'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.6.0', { + 'checksums': ['61617d344444235940f5b9ac1cd6b86938e74a8c76791235724b16b755c3f72c'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0', { + 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], + }), + ('topicmodels', '0.2-9', { + 'checksums': ['40770fb7de6ab6bd6e3ef6a0c777fa6db65d0322e67503c26c84ea857ac9a79c'], + }), + ('tidytext', '0.2.2', { + 'checksums': ['188f294cf3177fe6fc85e9b7e16a05211cebeab0e0f7b05a9443416790bf2ec0'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..fdfcbdce65b --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.26' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('expat', '2.2.7')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 5194b88806d60ab0277ed9a6a5088ad83c32d192 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 16 Dec 2019 10:22:12 +0000 Subject: [PATCH 206/468] Setting updated date on R extensions --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 7d3aed301bd..1521af66a3d 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -69,7 +69,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on June 7, 2019 +# packages updated on 16 December 2019 exts_list = [ 'base', 'datasets', diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 28e049be24e..4f6a4484142 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -69,7 +69,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on June 7, 2019 +# packages updated on 16 December 2019 exts_list = [ 'base', 'datasets', From f716cb9c3f66723d3727584c5db669a8bb8da2b9 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 16 Dec 2019 10:45:49 +0000 Subject: [PATCH 207/468] Changing http to https --- easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb | 4 ++-- .../g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb | 2 +- .../i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb | 4 ++-- .../easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb | 2 +- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb index 65b25f4a08d..3d1fc418f00 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.3.0.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'cairo' version = '1.16.0' -homepage = 'http://cairographics.org' +homepage = 'https://cairographics.org' description = """Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['http://cairographics.org/releases/'] +source_urls = ['https://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb index 0936a47c70a..40ca1c0e4c0 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Ghostscript' version = '9.50' -homepage = 'http://ghostscript.com' +homepage = 'https://ghostscript.com' description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.""" diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb index 91f9c48f1bd..86774a66a7a 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb @@ -7,7 +7,7 @@ easyblock = 'ConfigureMake' name = 'ImageMagick' version = '7.0.9-5' -homepage = 'http://www.imagemagick.org/' +homepage = 'https://www.imagemagick.org/' description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb index aed47325cd6..01e75e6fab2 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = "pixman" version = '0.38.4' -homepage = 'http://www.pixman.org/' +homepage = 'https://www.pixman.org/' description = """ Pixman is a low-level software library for pixel manipulation, providing @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['http://cairographics.org/releases/'] +source_urls = ['https://cairographics.org/releases/'] sources = [SOURCE_TAR_GZ] checksums = ['da66d6fd6e40aee70f7bd02e4f8f76fc3f006ec879d346bae6a723025cfbdde7'] diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb index fdfcbdce65b..f02517cc319 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'UDUNITS' version = '2.2.26' -homepage = 'http://www.unidata.ucar.edu/software/udunits/' +homepage = 'https://www.unidata.ucar.edu/software/udunits/' description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" From 2065b87fe3dd8b9c370a0b2bbf4f62d40886314c Mon Sep 17 00:00:00 2001 From: guacke Date: Mon, 16 Dec 2019 12:54:38 +0200 Subject: [PATCH 208/468] Change toolchain to gompi. --- .../o/ORCA/ORCA-4.2.1-gompi-2019b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb new file mode 100644 index 00000000000..49892b30f36 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb @@ -0,0 +1,31 @@ +easyblock = "PackedBinary" + +name = "ORCA" +version = '4.2.1' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry + with specific emphasis on spectroscopic properties of open-shell molecules. + It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- + and multireference correlated ab initio methods. + It can also treat environmental and relativistic effects.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} + +# Download from https://orcaforum.kofo.mpg.de +sources = ['%%(namelower)s_%s_linux_x86-64_openmpi314.tar.xz' % version.replace('.', '_')] +checksums = ['a1ff07bb01ac81ce9a4d6637fef77c12d0ec45354cebc72245c4e0d1620af956'] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca'], + 'dirs': [], +} + +moduleclass = 'chem' From a57faa8f26491f2a4e6f87a7dcfcacd83e04c6e3 Mon Sep 17 00:00:00 2001 From: guacke Date: Mon, 16 Dec 2019 12:07:22 +0100 Subject: [PATCH 209/468] Remove outdated file. --- .../o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb deleted file mode 100644 index 0bf451a7b42..00000000000 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-OpenMPI-3.1.4.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = "PackedBinary" - -name = "ORCA" -version = '4.2.1' - -local_ompi_ver = '3.1.4' -versionsuffix = '-OpenMPI-%s' % local_ompi_ver - -homepage = 'https://orcaforum.kofo.mpg.de' -description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry - with specific emphasis on spectroscopic properties of open-shell molecules. - It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- - and multireference correlated ab initio methods. - It can also treat environmental and relativistic effects.""" - -toolchain = SYSTEM - -# Download from https://orcaforum.kofo.mpg.de -sources = ['%%(namelower)s_%s_linux_x86-64_openmpi314.tar.xz' % version.replace('.', '_')] -checksums = ['a1ff07bb01ac81ce9a4d6637fef77c12d0ec45354cebc72245c4e0d1620af956'] - -dependencies = [('OpenMPI', local_ompi_ver, '-GCC-8.3.0')] - -sanity_check_paths = { - 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + - ['orca'], - 'dirs': [], -} - -moduleclass = 'chem' From cf7ee80504a0b6a77cb86397781218157c8d9a85 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 16 Dec 2019 12:22:28 +0100 Subject: [PATCH 210/468] Added easyconfigs for missing deps, put https instead of http link --- .../g/g2clib/g2clib-1.6.0-foss-2018b.eb | 25 +++++++++++++++ .../g/g2lib/g2lib-3.1.0-foss-2018b.eb | 31 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb new file mode 100644 index 00000000000..de7da799051 --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb @@ -0,0 +1,25 @@ +name = 'g2clib' +version = '1.6.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = ['g2clib-1.6.0-with-JasPer-2.x.patch'] +checksums = [ + 'afec1ea29979b84369d0f46f305ed12f73f1450ec2db737664ec7f75c1163add', # g2clib-1.6.0.tar + '2e62502d7823be5407ea023029dd206930a1034421d141dd346b468e177a7fce', # g2clib-1.6.0-with-JasPer-2.x.patch +] + +dependencies = [ + ('JasPer', '2.0.14'), + ('libpng', '1.6.34'), +] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb new file mode 100644 index 00000000000..e93c5d6cca6 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb @@ -0,0 +1,31 @@ +name = 'g2lib' +version = '3.1.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + 'g2lib-3.1.0_makefile.patch', + 'g2lib-1.4.0-with-JasPer-2.x.patch', +] +checksums = [ + '8a2de259de82094c5867f8d7945359f211592a4a503f9ed65dc60469337414e7', # g2lib-3.1.0.tar + '702f76c77638fb36b662caf96890a69f19c507778c92aa1e163898b150cc8282', # g2lib-3.1.0_makefile.patch + 'cd4c668dab76ef3b61fa902c2eed24747517d4cbc3ec0aaffab37e6b80946170', # g2lib-1.4.0-with-JasPer-2.x.patch +] + +dependencies = [ + ('JasPer', '2.0.14'), + ('libpng', '1.6.34'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -cpp -I. -fno-range-check" FC=$FC CC=$CC ' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From 46bcaea6cbf9c6e11079bfe28ec76806bfb09323 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 16 Dec 2019 13:23:40 +0100 Subject: [PATCH 211/468] Ok, now really put https instead of http link... --- easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb | 2 +- easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb | 3 ++- easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb index e93c5d6cca6..918e0d90b1a 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-foss-2018b.eb @@ -1,7 +1,7 @@ name = 'g2lib' version = '3.1.0' -homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" toolchain = {'name': 'foss', 'version': '2018b'} diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb index e92d9f7c2d8..3094670a488 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2018b.eb @@ -1,7 +1,7 @@ name = 'NCL' version = '6.6.2' -homepage = 'http://www.ncl.ucar.edu' +homepage = 'https://www.ncl.ucar.edu' description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." toolchain = {'name': 'foss', 'version': '2018b'} @@ -20,6 +20,7 @@ checksums = [ builddependencies = [ ('makedepend', '1.0.6'), ('Bison', '3.0.5'), + ('flex', '2.6.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb index 6d34056b226..526f30c100c 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb @@ -1,7 +1,7 @@ name = 'NCL' version = '6.6.2' -homepage = 'http://www.ncl.ucar.edu' +homepage = 'https://www.ncl.ucar.edu' description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." toolchain = {'name': 'intel', 'version': '2018b'} @@ -20,6 +20,7 @@ checksums = [ builddependencies = [ ('makedepend', '1.0.6'), ('Bison', '3.0.5'), + ('flex', '2.6.4'), ] dependencies = [ From 7511ea366fd01c79d140e2969ce5eff42fb79d3b Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 16 Dec 2019 13:04:48 +0000 Subject: [PATCH 212/468] Removing patch we don't need anymore --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 6 +----- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 6 +----- 2 files changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 1521af66a3d..0a0238825f5 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -1323,11 +1323,7 @@ exts_list = [ 'checksums': ['a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4'], }), ('uroot', '2.1-0', { - 'patches': ['uroot-2.0-9.1_CUDA.patch'], - 'checksums': [ - '3c02a9dadd22aa67a59e99007ab6f576dc428859fa746d3a8f3ffa2bb43d18c2', # uroot_2.1-0.tar.gz - '5de954038020d1d0c42eb0cb6b51950228ccc900c401dff6fbae43e4bc8fb936', # uroot-2.0-9.1_CUDA.patch - ], + 'checksums': ['3c02a9dadd22aa67a59e99007ab6f576dc428859fa746d3a8f3ffa2bb43d18c2'], }), ('forecast', '8.10', { 'checksums': ['798e15d15be9af0b8f505e826db83d5f09d7a7434567ec291a31eaf3b8c88c49'], diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 4f6a4484142..7276c0ae8fb 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -1322,11 +1322,7 @@ exts_list = [ 'checksums': ['a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4'], }), ('uroot', '2.1-0', { - 'patches': ['uroot-2.0-9.1_CUDA.patch'], - 'checksums': [ - '3c02a9dadd22aa67a59e99007ab6f576dc428859fa746d3a8f3ffa2bb43d18c2', # uroot_2.1-0.tar.gz - '5de954038020d1d0c42eb0cb6b51950228ccc900c401dff6fbae43e4bc8fb936', # uroot-2.0-9.1_CUDA.patch - ], + 'checksums': ['3c02a9dadd22aa67a59e99007ab6f576dc428859fa746d3a8f3ffa2bb43d18c2'], }), ('forecast', '8.10', { 'checksums': ['798e15d15be9af0b8f505e826db83d5f09d7a7434567ec291a31eaf3b8c88c49'], From f24b8f06534927be64c2c666406903641f1bd0b0 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 16 Dec 2019 13:18:08 +0000 Subject: [PATCH 213/468] Including cairo and pixman from #9514 --- easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb index 01e75e6fab2..644a1d671ca 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-8.3.0.eb @@ -1,9 +1,9 @@ easyblock = 'ConfigureMake' -name = "pixman" +name = 'pixman' version = '0.38.4' -homepage = 'https://www.pixman.org/' +homepage = 'http://www.pixman.org/' description = """ Pixman is a low-level software library for pixel manipulation, providing From abda90d4161ca455ea1ff770cbe46c6338d49118 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Dec 2019 16:21:23 +0100 Subject: [PATCH 214/468] Fix missing dependencies on Java 1.8 --- .../easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb b/easybuild/easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb index b1a661c26f1..fb57f27e39f 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb @@ -42,7 +42,15 @@ checksums = [ '5b897f75739bf14c702ae4cbf2b4afeeb160791ca0a6e06f4e1d5324db443429', # a53a027482b0.tar.gz ] -osdependencies = ['java-1.8.0-openjdk-devel', 'cups-devel', 'alsa-lib-devel'] +osdependencies = [ + ('java-1.8.0-openjdk-devel', 'openjdk-8-jdk'), + ('cups-devel', 'libcups2-dev'), + ('alsa-lib-devel', 'libasound2-dev'), + ('freetype-devel', 'libfreetype6-dev'), + ('libXtst-devel', 'libxtst-dev'), + ('libXt-devel', 'libxt-dev'), + ('libXrender-devel', 'libxrender-dev'), +] preconfigopts = 'mv ../corba-* corba && ' preconfigopts += 'mv ../jaxp-* jaxp && ' From 81f4918ba2de4876af01af951f082051206bb1e6 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 16 Dec 2019 15:46:22 +0100 Subject: [PATCH 215/468] And another link fix... --- easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb index de7da799051..7091764c0ab 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-foss-2018b.eb @@ -1,7 +1,7 @@ name = 'g2clib' version = '1.6.0' -homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'foss', 'version': '2018b'} From 3078b3679869a5b101eda1cd175760a9a87dbc54 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Dec 2019 09:03:04 +0100 Subject: [PATCH 216/468] adding easyconfigs: PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb --- ...Cairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..6cb57952d29 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cairographics.org/pycairo/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abd42a4c9c2069febb4c38fe74bfc4b4a9d3a89fea3bc2e4ba7baff7a20f783f'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('cairo', '1.16.0'), +] + +# PyGTK needs PyCairo installed by pip +use_pip = True +sanity_pip_check = True + +# Don't build a wheel or the pkg-cfg file won't be installed +installopts = '--no-cache-dir' + +sanity_check_paths = { + 'files': ['include/pycairo/py3cairo.h', 'lib/pkgconfig/py3cairo.pc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' From 9ad0e9b4cf762057733064ab0c5c6e7e276e9f5d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Dec 2019 10:20:26 +0100 Subject: [PATCH 217/468] Add download_dep_fail --- .../p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb index 6cb57952d29..24c964afe10 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb @@ -26,6 +26,7 @@ dependencies = [ # PyGTK needs PyCairo installed by pip use_pip = True sanity_pip_check = True +download_dep_fail = True # Don't build a wheel or the pkg-cfg file won't be installed installopts = '--no-cache-dir' From d5cb7e5f01cbdadc2adce1a96cc175751f0f8d53 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Dec 2019 10:55:06 +0100 Subject: [PATCH 218/468] Use https --- .../p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb index 24c964afe10..d47b6f39603 100644 --- a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-GCCcore-8.2.0-Python-3.7.2.eb @@ -4,7 +4,7 @@ name = 'PyCairo' version = '1.18.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cairographics.org/pycairo/' +homepage = 'https://cairographics.org/pycairo/' description = """Python bindings for the cairo library""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} From 69bcbeb9cbe2577eee0b908af8e930e2c233111a Mon Sep 17 00:00:00 2001 From: Ed Date: Tue, 17 Dec 2019 10:26:08 +0000 Subject: [PATCH 219/468] Delete GSL-2.6-GCCcore-8.3.0.eb --- .../g/GSL/GSL-2.6-GCCcore-8.3.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCCcore-8.3.0.eb deleted file mode 100644 index a466491e697..00000000000 --- a/easybuild/easyconfigs/g/GSL/GSL-2.6-GCCcore-8.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '2.6' - -homepage = 'https://www.gnu.org/software/gsl/' -description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions - and least-squares fitting.""" - -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] - -builddependencies = [('binutils', '2.32')] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + - ['include/gsl/gsl_types.h'] + - ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], - 'dirs': [], -} - -moduleclass = 'numlib' From f3e7533a95becf1409325b4ce726e71cafef06a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2019 15:01:06 +0100 Subject: [PATCH 220/468] adding easyconfigs: FFTW-3.3.8-intel-2019b.eb --- .../f/FFTW/FFTW-3.3.8-intel-2019b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2019b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2019b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2019b.eb new file mode 100644 index 00000000000..2b6696418ec --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2019b.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' From 665a028f0db57ae6cdad350ac14d97f1f0fc3835 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Dec 2019 15:38:42 +0100 Subject: [PATCH 221/468] adding easyconfigs: GtkSourceView-3.24.11-GCCcore-8.2.0.eb, GtkSourceView-4.4.0-GCCcore-8.2.0.eb --- .../GtkSourceView-3.24.11-GCCcore-8.2.0.eb | 40 +++++++++++++++++ .../GtkSourceView-4.4.0-GCCcore-8.2.0.eb | 44 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-4.4.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..bb6cbb86f4c --- /dev/null +++ b/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-8.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GtkSourceView' +version = '3.24.11' + +homepage = 'https://wiki.gnome.org/Projects/GtkSourceView' +description = """ + GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ + widget for multiline text editing. GtkSourceView adds support for syntax + highlighting, undo/redo, file loading and saving, search and replace, a + completion system, printing, displaying line numbers, and other features + typical of a source code editor. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['691b074a37b2a307f7f48edc5b8c7afa7301709be56378ccf9cc9735909077fd'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), +] + +dependencies = [ + ('GLib', '2.60.1'), + ('GTK+', '3.24.8'), + ('libxml2', '2.9.8'), +] + +configopts = "--disable-silent-rules --enable-introspection=yes " + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['include/%(namelower)s-%(version_major)s.0', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-4.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-4.4.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..3e9cb196722 --- /dev/null +++ b/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-4.4.0-GCCcore-8.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GtkSourceView' +version = '4.4.0' + +homepage = 'https://wiki.gnome.org/Projects/GtkSourceView' +description = """ + GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ + widget for multiline text editing. GtkSourceView adds support for syntax + highlighting, undo/redo, file loading and saving, search and replace, a + completion system, printing, displaying line numbers, and other features + typical of a source code editor. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9ddb914aef70a29a66acd93b4f762d5681202e44094d2d6370e51c9e389e689a'] + +builddependencies = [ + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), +] + +dependencies = [ + ('GLib', '2.60.1'), + ('GTK+', '3.24.8'), + ('libxml2', '2.9.8'), + ('FriBidi', '1.0.5'), +] + +configopts = "--buildtype=release " +configopts += "-Dgir=true -Dvapi=false " + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s-%%(version_major)s.%s' % SHLIB_EXT], + 'dirs': ['include/%(namelower)s-%(version_major)s', 'share'], +} + +moduleclass = 'vis' From ae65dbeed85fb285e03727abd7cd2273e285a0fc Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Tue, 17 Dec 2019 15:58:22 +0000 Subject: [PATCH 222/468] Removing multtest which has a Biobase dep, which is from Bioconductor --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 3 --- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 3 --- 2 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 0a0238825f5..4ab0d04d08d 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -1988,9 +1988,6 @@ exts_list = [ ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), - ('multtest', '2.8.0', { - 'checksums': ['e41181f8a58fe09a48acc5165057209cd3ba24a6343333dd3c881e9ddd475431'], - }), ('mutoss', '0.1-12', { 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], }), diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 7276c0ae8fb..64053d30e8d 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -1987,9 +1987,6 @@ exts_list = [ ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), - ('multtest', '2.8.0', { - 'checksums': ['e41181f8a58fe09a48acc5165057209cd3ba24a6343333dd3c881e9ddd475431'], - }), ('mutoss', '0.1-12', { 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], }), From a097e747bb29fc5548a732e8b88e1bb4c66d800b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2019 20:34:24 +0100 Subject: [PATCH 223/468] adding easyconfigs: NLopt-2.6.1-GCCcore-8.3.0.eb --- .../n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..406e8e66c09 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2019-06-05 John Dey jfdey@fredhutch.org fizwit@github.com - updated for CMake +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.6.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['66d63a505187fb6f98642703bd0ef006fedcae2f9a6d1efa4f362ea919a02650'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('binutils', '2.32'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' From a960085c1963ed51722f64f0357fbd6647643fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2019 20:34:49 +0100 Subject: [PATCH 224/468] adding easyconfigs: freeglut-3.2.1-GCCcore-8.3.0.eb --- .../freeglut/freeglut-3.2.1-GCCcore-8.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..1aefe3a18df --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-8.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.2.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['d4000e02102acaf259998c870e25214739d1f16f67f99cb35e4f46841399da68'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3'), +] + +dependencies = [ + ('X11', '20190717'), + ('Mesa', '19.1.7'), + ('libGLU', '9.0.1'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' From f1ced8074b052cd5bb55da14c1b92c6ecb90a9bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2019 20:35:13 +0100 Subject: [PATCH 225/468] adding easyconfigs: libgd-2.2.5-GCCcore-8.3.0.eb --- .../l/libgd/libgd-2.2.5-GCCcore-8.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.2.5-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.5-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..16d1d2c9547 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.5-GCCcore-8.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.2.5' + +homepage = 'https://libgd.github.io/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a66111c9b4a04e818e9e2a37d7ae8d4aae0939a100a36b0ffb52c706a09074b5'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('fontconfig', '2.13.1'), + ('libjpeg-turbo', '2.0.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' From a33a124bcbbe3f95ef34973e9406c43f437c935b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2019 20:35:41 +0100 Subject: [PATCH 226/468] adding easyconfigs: Qwt-6.1.4-GCCcore-8.3.0.eb --- .../q/Qwt/Qwt-6.1.4-GCCcore-8.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..4e313324c4b --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.4-GCCcore-8.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.4' + +homepage = 'https://qwt.sourceforge.net/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-%(version)s_Fix_prefix_and_pkgconfig.patch'] +checksums = [ + '1529215329e51fc562e0009505a838f427919a18b362afff441f035b2d9b5bd9', # qwt-6.1.4.tar.bz2 + '82788aaa23e4bc764ab1f2769e9260d154976c7d7f043ba4e288330d6984b6a9', # Qwt-6.1.4_Fix_prefix_and_pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Qt5', '5.13.1'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += 'qmake qwt.pro && ' + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' From 864d6d16e39d1d9eaf06cd9016483477cd8f732d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2019 21:02:48 +0100 Subject: [PATCH 227/468] adding easyconfigs: MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb --- ...MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..a125848089a --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb @@ -0,0 +1,28 @@ +name = 'MRtrix' +version = '3.0_RC4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4f246e4cc6ddd5d2480d368342bcbeb9c5d21c04a3a4b5e6e2adb8c036611426'] + +builddependencies = [ + ('Eigen', '3.3.7', '', True), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.16'), + ('Mesa', '19.1.7'), + ('Qt5', '5.13.1'), + ('LibTIFF', '4.0.10'), +] + +moduleclass = 'bio' From 55ac2f781c26db43c28883dcaaa42c207a622c4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2019 18:14:44 +0100 Subject: [PATCH 228/468] require that sanity_pip_check is enabled in new/changed easyconfigs --- test/easyconfigs/easyconfigs.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 48fa2abf4a6..d0d240a0193 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -542,6 +542,7 @@ def check_python_packages(self, changed_ecs): ec_fn = os.path.basename(ec.path) easyblock = ec.get('easyblock') exts_defaultclass = ec.get('exts_defaultclass') + exts_default_options = ec.get('exts_default_options', {}) download_dep_fail = ec.get('download_dep_fail') exts_download_dep_fail = ec.get('exts_download_dep_fail') @@ -571,7 +572,6 @@ def check_python_packages(self, changed_ecs): else: # both download_dep_fail and use_pip should be set via exts_default_options # when installing Python packages as extensions - exts_default_options = ec.get('exts_default_options', {}) for key in ['download_dep_fail', 'use_pip']: if exts_default_options.get(key) is None: failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn)) @@ -582,6 +582,12 @@ def check_python_packages(self, changed_ecs): if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): failing_checks.append("'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn) + # require that running of "pip check" during sanity check is enabled via sanity_pip_check + if easyblock in ['PythonBundle', 'PythonPackage']: + sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') + if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip): + failing_checks.append("sanity_pip_check is enabled in %s" % ec_fn) + self.assertFalse(failing_checks, '\n'.join(failing_checks)) def check_sanity_check_paths(self, changed_ecs): From 7e3b4a5e039c50109a8702c0aa6fd3b291f49b75 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 18 Dec 2019 13:37:27 +1030 Subject: [PATCH 229/468] xorg-macros-1.19.2 URL fix --- .../xorg-macros-1.19.2-GCCcore-7.2.0.eb | 16 +++++++++++++--- .../xorg-macros-1.19.2-GCCcore-7.3.0.eb | 18 ++++++++++++++---- .../xorg-macros-1.19.2-GCCcore-8.2.0.eb | 2 +- .../xorg-macros-1.19.2-GCCcore-8.3.0.eb | 18 ++++++++++++++---- 4 files changed, 42 insertions(+), 12 deletions(-) mode change 100644 => 100755 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb index 4f708ab8e6b..1eb874b93b0 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb @@ -1,16 +1,26 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.2' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '7.2.0'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'] +checksums = ['aae54a5b4556f35a85d6808e8d9a467156697c71f66b4142e42330e3a79f80c6'] builddependencies = [ ('binutils', '2.29'), diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.3.0.eb index 1eb46361cc8..d2394a9852b 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.3.0.eb @@ -1,16 +1,26 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.2' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'] +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] builddependencies = [ ('binutils', '2.30'), diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb index eb7e409a24a..2235fec9138 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ # Homepage: https://staff.flinders.edu.au/research/deep-thought # # Authors:: Robert Qiao -# License:: +# License:: Custom # # Notes:: ## diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb old mode 100644 new mode 100755 index fec1d50a969..a93ab006e04 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb @@ -1,16 +1,26 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.2' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'] +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] builddependencies = [ ('binutils', '2.32'), From 7e229374f9474417b05b0867038f4f2848d63d55 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 18 Dec 2019 15:02:28 +1030 Subject: [PATCH 230/468] xorg-macros-1.19.1 URL fix --- .../xorg-macros-1.19.1-GCCcore-6.3.0.eb | 13 ++++++++++++- .../xorg-macros-1.19.1-GCCcore-6.4.0.eb | 16 +++++++++++++--- 2 files changed, 25 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb index 6f48acb1542..34661508544 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb @@ -1,3 +1,13 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' @@ -8,8 +18,9 @@ description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] sources = ['util-macros-%(version)s.tar.gz'] +checksums = ['52f6e8c86a40cff3fd840783d338da6430e1441ce4d0546179c0f74ea90591ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb index a6e30ced56b..0ae501fd71a 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb @@ -1,3 +1,13 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' @@ -8,9 +18,9 @@ description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['f056411c49a9955f141cad4d7b258a1a5e5bcc0f2a197ee00c63ac3bbe9f347a'] +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['0bb70872f45d9973db645123fe9fae9c587d1cc0ad1b3bfa67864c3f99adbd2a'] builddependencies = [ ('binutils', '2.28'), From d59406c70b7c2f6119dea91f85f02f61f837a487 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 18 Dec 2019 15:03:54 +1030 Subject: [PATCH 231/468] xorg-macros-1.19.1 https fix --- .../x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb | 2 +- .../x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb index 34661508544..ef5b29b65ee 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.1' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb index 0ae501fd71a..2ab17936d96 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.4.0.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.1' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} From 179c42bd5a6d5b6213969d96b4fbc1f978c192f0 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 18 Dec 2019 15:12:40 +1030 Subject: [PATCH 232/468] xorg-macros-1.19.0 https fix --- .../xorg-macros/xorg-macros-1.19.0-foss-2016a.eb | 15 +++++++++++++-- .../xorg-macros/xorg-macros-1.19.0-foss-2016b.eb | 13 ++++++++++++- .../xorg-macros-1.19.0-gimkl-2.11.5.eb | 14 ++++++++++++-- .../xorg-macros/xorg-macros-1.19.0-intel-2016b.eb | 15 +++++++++++++-- 4 files changed, 50 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb index 3965c120785..efb13236f60 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -1,14 +1,25 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.0' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] sources = ['util-macros-%(version)s.tar.gz'] +checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb index 2e98d1a81eb..8485551fd7a 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb @@ -1,3 +1,13 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' @@ -7,8 +17,9 @@ homepage = 'http://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] sources = ['util-macros-%(version)s.tar.gz'] +checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb index 536fa8c6ffb..376e86d42e2 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb @@ -1,14 +1,24 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.0' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! sources = ['util-macros-%(version)s.tar.gz'] +checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb index 52e3d066e82..76ade227e31 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb @@ -1,14 +1,25 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.0' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] sources = ['util-macros-%(version)s.tar.gz'] +checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] builddependencies = [('Autotools', '20150215')] From 970b907f534ce7d8034d80e19d4b8f62dbec7c82 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 18 Dec 2019 15:13:00 +1030 Subject: [PATCH 233/468] xorg-macros-1.19.1 https fix --- .../easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb index 8485551fd7a..f73239877bc 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.0' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'foss', 'version': '2016b'} From c8e744bb278dfb09d8cea3399bec3c0d378cfab6 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 18 Dec 2019 15:15:13 +1030 Subject: [PATCH 234/468] xorg-macros-1.19.0 URL fix --- .../xorg-macros/xorg-macros-1.19.0-intel-2016a.eb | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb index 0697bb42ab9..433f59d5532 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb @@ -1,14 +1,25 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + easyblock = 'ConfigureMake' name = 'xorg-macros' version = '1.19.0' -homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] sources = ['util-macros-%(version)s.tar.gz'] +checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] builddependencies = [('Autotools', '20150215')] From 518ca0a5746899dd8b46ffcd87b2a47b1322c038 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 18 Dec 2019 17:34:47 +1030 Subject: [PATCH 235/468] Jellyfish-2.3.0-foss-2019a --- .../j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb new file mode 100644 index 00000000000..874e6dc0509 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb @@ -0,0 +1,31 @@ +## # This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia # Homepage: https://staff.flinders.edu.au/research/deep-thought # # Authors:: Robert Qiao # License:: Custom # # Notes:: ## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.0' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3d5b68bdf741acdb119546bfaf52219834f83cea1f47b0caa135fc649d0d6faf'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' From 5458e92bd753f1675dad709e37fc96c9eb0c4a08 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 18 Dec 2019 10:03:23 +0200 Subject: [PATCH 236/468] adding easyconfigs: jemalloc-5.2.1-GCCcore-8.3.0.eb --- .../jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..19d9c427384 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.2.1' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ed51b0b37098af4ca6ed31c22324635263f8ad6471889e0592a9c0dba9136aea'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.32'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# Why did someone set this?? LD_PRELOAD should NEVER be set automatically +#modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' From 1510914ff78dc64589f710233122be2bf37aac7c Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Wed, 18 Dec 2019 08:20:14 +0000 Subject: [PATCH 237/468] Removing mutoss and metap as they depend ultimately on Biobase (via multtest) --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 6 ------ easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 6 ------ 2 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 4ab0d04d08d..ec8b3565370 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -1988,12 +1988,6 @@ exts_list = [ ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), - ('mutoss', '0.1-12', { - 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], - }), - ('metap', '1.2', { - 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], - }), ('lsei', '1.2-0', { 'checksums': ['4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6'], }), diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 64053d30e8d..5b046a7b3de 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -1987,12 +1987,6 @@ exts_list = [ ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), - ('mutoss', '0.1-12', { - 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], - }), - ('metap', '1.2', { - 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], - }), ('lsei', '1.2-0', { 'checksums': ['4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6'], }), From dbd956e4ae227dfa1d72077f6c18c6d3cdaeb387 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 18 Dec 2019 10:22:31 +0200 Subject: [PATCH 238/468] Fix block comment --- .../easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb index 19d9c427384..7f92bfde3eb 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb @@ -31,6 +31,6 @@ sanity_check_paths = { } # Why did someone set this?? LD_PRELOAD should NEVER be set automatically -#modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} moduleclass = 'lib' From b5f21f58e9178326ea941e0512fabcbf6f48ff0b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Dec 2019 11:01:20 +0100 Subject: [PATCH 239/468] adding easyconfigs: libiconv-1.16-GCCcore-8.2.0.eb --- .../l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..99b6f411cb6 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.16' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' From b7125115386e3b7967d8ec60199b076296c9b0ec Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 18 Dec 2019 11:51:56 +0100 Subject: [PATCH 240/468] Added comments in patches, removed separate local var for python version --- .../f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch | 5 +++++ .../f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb | 11 +++++------ .../easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch | 5 +++++ .../easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch | 4 ++++ 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch index bc8cc68d796..ed7ddbde309 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.1_Fix_fsl_exec_script.patch @@ -1,3 +1,8 @@ +Solves an issue where running 'feat' produces the error +"can't read "::errorCode": no such variable" +See issue and solution at +https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1412&L=FSL&D=0&P=300830 +Author: Caspar van Leeuwen (SURFsara) diff -Nru fsl.orig/src/misc_tcl/fsl_exec.tcl fsl/src/misc_tcl/fsl_exec.tcl --- fsl.orig/src/misc_tcl/fsl_exec.tcl 2019-10-21 15:53:58.647058588 +0200 +++ fsl/src/misc_tcl/fsl_exec.tcl 2019-10-21 16:28:52.811113241 +0200 diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb index ef3b3dbba48..e19de0ecdaf 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15.eb @@ -10,8 +10,7 @@ name = 'FSL' version = '6.0.2' -local_pyver = '2.7.15' -versionsuffix = '-Python-%s' % local_pyver +versionsuffix = '-Python-2.7.15' homepage = 'https://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" @@ -29,10 +28,10 @@ patches = [ ] checksums = [ 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz - '3a14d9c3ea75d90fa3e4beb5da3cd11a60c6859441acaece02b32ccab6aa278f', # FSL-6.0.2_Makefile_fixes.patch - '2b7ade2146fadbba6c983370bb030ac4e2b11d8bf5259eacc8f3054d3d11003f', # FSL-6.0.2_Build_extras.patch + '4212478ef24be4bce7a9ce513aa9c45fcf67eccfe064331a2e8e52be41d3513c', # FSL-6.0.2_Makefile_fixes.patch + '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch - '4479aa501a7e6e9f1a0063e4ddb680836147ba08673d3fccb9e1db3c4d910672', # FSL-6.0.1_Fix_fsl_exec_script.patch + 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch ] builddependencies = [ @@ -50,7 +49,7 @@ dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.2.5'), ('zlib', '1.2.11'), - ('VTK', '8.1.1', '-Python-%s' % local_pyver), + ('VTK', '8.1.1', versionsuffix), ('GSL', '2.5'), ('Qwt', '6.1.4'), ] diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch index 9f133c9daca..1bb8a354fe2 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Build_extras.patch @@ -1,3 +1,8 @@ +Define which internal dependencies should be built. +Building them with EB and linking them didn't work. +Author: Caspar van Leeuwen (SURFsara) +Adapted from: FSL-6.0.1_Build_extras.patch +Original author: Davide Vanzo (Vanderbilt University) --- fsl.orig/extras/build 2019-11-15 10:48:52.249162071 +0100 +++ fsl/extras/build 2019-11-15 17:19:51.859063451 +0100 @@ -106,6 +106,8 @@ diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch index 43f133d60ab..eb23cf54f41 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Makefile_fixes.patch @@ -1,3 +1,7 @@ +Fix the Makefile to use libraries built with EB instead of the ones +shipped with the code. +Also: invoke the system's tclsh, instead of the one shipped with fsl +Author: Caspar van Leeuwen (SURFsara) diff -Nru fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk --- fsl.orig/config/buildSettings.mk 2019-03-20 15:06:00.000000000 +0100 +++ fsl/config/buildSettings.mk 2019-11-18 18:23:47.688894797 +0100 From 2fc41c2a502161cd5cf047d1e73c4424a36234af Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Wed, 18 Dec 2019 11:36:16 +0000 Subject: [PATCH 241/468] Removing libdrm_intel check as that's platform specific --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb index 35e34a785b9..cce837c3ccf 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb @@ -19,8 +19,8 @@ builddependencies = [ dependencies = [('X11', '20190717')] sanity_check_paths = { - 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, - 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_radeon.%s' % SHLIB_EXT, + 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } From be6fc55981c3654c3cd39a62681b285874877810 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Dec 2019 12:57:12 +0100 Subject: [PATCH 242/468] Use correct binutils --- easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb index 99b6f411cb6..2ce580f345a 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-8.2.0.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04'] -builddependencies = [('binutils', '2.30')] +builddependencies = [('binutils', '2.31.1')] sanity_check_paths = { 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', From 87c1d4f1855f77a2321abb9c7c3d385dca110cf3 Mon Sep 17 00:00:00 2001 From: Ed Date: Wed, 18 Dec 2019 12:28:46 +0000 Subject: [PATCH 243/468] Update libdrm-2.4.99-GCCcore-8.3.0.eb Actually - let's do POWER9 support in a new PR - there looks like there's a few bits here and there --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb index cce837c3ccf..35e34a785b9 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.99-GCCcore-8.3.0.eb @@ -19,8 +19,8 @@ builddependencies = [ dependencies = [('X11', '20190717')] sanity_check_paths = { - 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_radeon.%s' % SHLIB_EXT, - 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } From 971d12464d05220ec7ef77df7c7d159502ac67e3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Dec 2019 15:26:07 +0100 Subject: [PATCH 244/468] Bootstrap CMake in parallel --- easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb | 2 ++ easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb | 2 ++ easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb | 3 ++- 29 files changed, 58 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb index 0897dc0c562..94041e9052f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb @@ -14,6 +14,8 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('ncurses', '5.9')] +configopts = '--parallel=%(parallel)s ' + sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], 'dirs': [], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb index 971067f85f1..40594025cf0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb @@ -16,7 +16,8 @@ source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['b3345c17609ea0f039960ef470aa099de9942135990930a57c14575aae884987'] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb index 79f6b252b57..3f49a38b03e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb @@ -16,7 +16,8 @@ source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7be36ee24b0f5928251b644d29f5ff268330a916944ef4a75e23ba01e7573284'] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb index ea98e5ab5bf..49df2d11d66 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb index 0c3d025bdd0..8a99c66cd8f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb index 7d54349de7f..431138146fd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb index 39669e75605..adcb76ac169 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb index 526960767cd..5ab278555cc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb index 399992b88b3..5e2cc31d69f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb index 05e88ad7767..bb4705aa9d1 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb index 6726195396b..a27344cdd3f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb @@ -34,7 +34,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 ' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 ' configopts += '-DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include ' configopts += '-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.%s ' % SHLIB_EXT configopts += '-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb index 287f3d6348a..ba6af00d35c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb @@ -34,7 +34,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 ' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 ' configopts += '-DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include ' configopts += '-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.%s ' % SHLIB_EXT configopts += '-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb index 652ac940ab2..a510584d01d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb @@ -34,7 +34,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 ' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 ' configopts += '-DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include ' configopts += '-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.%s ' % SHLIB_EXT configopts += '-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb index d122346d10b..48bb3d03240 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb @@ -22,7 +22,8 @@ builddependencies = [('ncurses', '6.1')] # Use OS dependencies in order to ensure that CMake can build software that depends on them osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -configopts = "-- -DCMAKE_USE_OPENSSL=1 " +configopts = '--parallel=%(parallel)s ' +configopts += "-- -DCMAKE_USE_OPENSSL=1 " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include " diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb index a66b36e9a78..70b737eae24 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb @@ -34,7 +34,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 ' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 ' configopts += '-DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include ' configopts += '-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.%s ' % SHLIB_EXT configopts += '-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb index 151b1f33306..6742e50ba87 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb @@ -14,6 +14,8 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('ncurses', '5.9')] +configopts = '--parallel=%(parallel)s ' + sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], 'dirs': [], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb index 0d0b35f0b3e..2d723b83500 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -12,7 +12,8 @@ toolchain = SYSTEM source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb index 5808143c4e5..853429f8e7c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -19,7 +19,8 @@ builddependencies = [('ncurses', '5.9')] # depends on them osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -configopts = "-- -DCMAKE_USE_OPENSSL=1 " +configopts = '--parallel=%(parallel)s ' +configopts += "-- -DCMAKE_USE_OPENSSL=1 " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include " diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb index 99526d7cb2d..65a86a5bc77 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb @@ -11,7 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.2.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb index 29e1e466f95..ef0d66967c8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb @@ -11,7 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb index 522448447cd..469fd59d3af 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb @@ -12,7 +12,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb index 4eddbf2181c..b9dec85256e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb @@ -12,7 +12,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb index 23aa365a15d..65e4170b400 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb @@ -12,7 +12,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb index 4b9208d0886..a2929e49241 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb @@ -17,7 +17,8 @@ builddependencies = [ ('binutils', '2.27'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb index 3fbbcb5eaaa..481190cff13 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb @@ -16,7 +16,8 @@ source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb index f6d16d18754..14b52efe84e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb @@ -19,7 +19,8 @@ builddependencies = [('ncurses', '5.9')] # depends on them osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -configopts = "-- -DCMAKE_USE_OPENSSL=1 " +configopts = '--parallel=%(parallel)s ' +configopts += "-- -DCMAKE_USE_OPENSSL=1 " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include " diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb index 24fa6e41440..1f8753304e1 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb index 424c924ba95..062c522c968 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb @@ -31,7 +31,8 @@ osdependencies = [ ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' +configopts = '--parallel=%(parallel)s ' +configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb index 0f1e52cc09a..1ce0480139b 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb @@ -18,7 +18,8 @@ builddependencies = [('ncurses', '5.9')] # Use OS dependencies in order to ensure that CMake can build software that depends on them osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -configopts = "-- -DCMAKE_USE_OPENSSL=1 " +configopts = '--parallel=%(parallel)s ' +configopts += "-- -DCMAKE_USE_OPENSSL=1 " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include " From 0a519c89839c9e78b1ca0da777505dabce55c8fe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Dec 2019 16:10:47 +0100 Subject: [PATCH 245/468] Add checksums and https --- easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb | 5 +++-- easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb | 5 +++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb | 5 +++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb | 5 +++-- easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb | 5 +++-- easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb | 5 +++-- easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb | 5 +++-- easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb | 5 +++-- easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb | 4 ++-- 29 files changed, 66 insertions(+), 58 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb index 94041e9052f..8fa94116078 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb @@ -3,14 +3,15 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.1.3' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = SYSTEM -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['45f4d3fa8a2f61cc092ae461aac4cac1bab4ac6706f98274ea7f314dd315c6d0'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb index 40594025cf0..a1909b5fcd8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.0-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.10.0' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['b3345c17609ea0f039960ef470aa099de9942135990930a57c14575aae884987'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb index 3f49a38b03e..323ac6d3a25 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.1-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.10.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7be36ee24b0f5928251b644d29f5ff268330a916944ef4a75e23ba01e7573284'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb index 49df2d11d66..eeb92e4f930 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.10.2' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['80d0faad4ab56de07aa21a7fc692c88c4ce6156d42b0579c6962004a70a3218b'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb index 8a99c66cd8f..c7199eff497 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.2-GCCcore-7.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.10.2' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['80d0faad4ab56de07aa21a7fc692c88c4ce6156d42b0579c6962004a70a3218b'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb index 431138146fd..64abde81ec0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.10.3' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['0c3a1dcf0be03e40cf4f341dda79c96ffb6c35ae35f2f911845b72dab3559cf8'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb index adcb76ac169..f63384fc09e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.10.3-GCCcore-7.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.10.3' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['0c3a1dcf0be03e40cf4f341dda79c96ffb6c35ae35f2f911845b72dab3559cf8'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb index 5ab278555cc..f068578364a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.11.1-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.11.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['57bebc6ca4d1d42c6385249d148d9216087e0fda57a47dc5c858790a70217d0c'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb index 5e2cc31d69f..d797079b903 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.11.4' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8f864e9f78917de3e1483e256270daabc4a321741592c5b36af028e72bff87f5'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb index bb4705aa9d1..23106be4cdf 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.11.4' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8f864e9f78917de3e1483e256270daabc4a321741592c5b36af028e72bff87f5'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb index a27344cdd3f..43d922f3976 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.12.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c53d5c2ce81d7a957ee83e3e635c8cda5dfe20c9d501a4828ee28e1615e57ab2'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb index ba6af00d35c..72afab95b57 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.12.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c53d5c2ce81d7a957ee83e3e635c8cda5dfe20c9d501a4828ee28e1615e57ab2'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb index a510584d01d..992c963d316 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.12.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c53d5c2ce81d7a957ee83e3e635c8cda5dfe20c9d501a4828ee28e1615e57ab2'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb index 48bb3d03240..7542ee26ca2 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.12.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -13,7 +13,7 @@ description = """ # note: requires C++ compiler that supports C++11, which is not the case in older OSs like CentOS 6... toolchain = SYSTEM -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c53d5c2ce81d7a957ee83e3e635c8cda5dfe20c9d501a4828ee28e1615e57ab2'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb index 70b737eae24..93ed194d89f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.13.3-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.13.3' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['665f905036b1f731a2a16f83fb298b1fb9d0f98c382625d023097151ad016b25'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb index 6742e50ba87..06fc7e6c4a5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb @@ -3,14 +3,15 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.3.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = SYSTEM -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['cd65022c6a0707f1c7112f99e9c981677fdd5518f7ddfa0f778d4cee7113e3d6'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb index 2d723b83500..3759b3236da 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -3,14 +3,15 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.5.2' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = SYSTEM -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['92d8410d3d981bb881dfff2aed466da55a58d34c7390d50449aa59b32bb5e62a'] configopts = '--parallel=%(parallel)s ' configopts += '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb index 853429f8e7c..c46d3b2c483 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.6.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = SYSTEM -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['28ee98ec40427d41a45673847db7a905b59ce9243bb866eaf59dce0f58aaef11'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb index 65a86a5bc77..37488ce2c9e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb @@ -2,14 +2,15 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.7.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'GCCcore', 'version': '6.2.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['449a5bce64dbd4d5b9517ebd1a1248ed197add6ad27934478976fd5f1f9330e1'] configopts = '--parallel=%(parallel)s ' configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb index ef0d66967c8..402f2da3096 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb @@ -2,14 +2,15 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.7.2' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['dc1246c4e6d168ea4d6e042cfba577c1acd65feea27e56f5ff37df920c30cae0'] configopts = '--parallel=%(parallel)s ' configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb index 469fd59d3af..b35433d8f02 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb @@ -3,14 +3,15 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.8.0' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['cab99162e648257343a20f61bcd0b287f5e88e36fcb2f1d77959da60b7f35969'] configopts = '--parallel=%(parallel)s ' configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb index b9dec85256e..2f5247be5d1 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb @@ -3,14 +3,15 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.8.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['ce5d9161396e06501b00e52933783150a87c33080d4bdcef461b5b7fd24ac228'] configopts = '--parallel=%(parallel)s ' configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb index 65e4170b400..6a4517e4f29 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb @@ -3,14 +3,15 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.8.2' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['da3072794eb4c09f2d782fcee043847b99bb4cf8d4573978d9b2024214d6e92d'] configopts = '--parallel=%(parallel)s ' configopts += '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb index a2929e49241..2f4d3177684 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.9.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb index 481190cff13..0aed3192124 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.9.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb index 14b52efe84e..72f40704a04 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.9.1' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = SYSTEM -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb index 1f8753304e1..e07d04e10dc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.4-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.9.4' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['b5d86f12ae0072db520fdbdad67405f799eb728b610ed66043c20a92b4906ca1'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb index 062c522c968..236aac2cd35 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.5-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.9.5' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """ CMake, the cross-platform, open-source build system. CMake is a family of @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['6220c1683b4e6bb8f38688fa3ffb17a7cf39f36317c2ddfdc3f12f09d086c166'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb index 1ce0480139b..489bdc9c639 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'CMake' version = '3.9.6' -homepage = 'http://www.cmake.org' +homepage = 'https://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" toolchain = SYSTEM -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7410851a783a41b521214ad987bb534a7e4a65e059651a2514e6ebfc8f46b218'] From 786834311c00318c3f592473ffa23d99aeab1045 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Dec 2019 11:03:12 +0100 Subject: [PATCH 246/468] adding easyconfigs: libxml2-python-2.9.8-GCCcore-8.2.0-Python-3.7.2.eb --- ...python-2.9.8-GCCcore-8.2.0-Python-3.7.2.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.8-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.8-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.8-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..996b46893ab --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.8-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonPackage' + +name = 'libxml2-python' +version = '2.9.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://xmlsoft.org/' +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). This is the Python binding.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = ['libxml2-%(version)s.tar.gz'] +patches = ['libxml2-2.9.7_fix-hardcoded-paths.patch'] +checksums = [ + '0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732', # libxml2-2.9.8.tar.gz + '3d5651c015fd375d855421983b7d33ffd4af797b7411f46e05cd8c57b210e542', # libxml2-2.9.7_fix-hardcoded-paths.patch +] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), + ('Python', '3.7.2'), + ('libxml2', version), + ('libiconv', '1.16'), +] + +start_dir = 'python' + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'libxml2'} + +moduleclass = 'lib' From 0385fd1efb18a9ad63efafb41f40e9b1061ee003 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Dec 2019 18:09:10 +0100 Subject: [PATCH 247/468] Use xorg-macros ECs to fix URL errors --- .../easyconfigs/x/X11/X11-20160819-foss-2016b.eb | 13 ++++--------- .../easyconfigs/x/X11/X11-20160819-intel-2016b.eb | 13 ++++--------- .../easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb | 13 ++++--------- .../easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb | 13 ++++--------- .../easyconfigs/x/X11/X11-20171023-GCCcore-6.4.0.eb | 13 ++++--------- .../easyconfigs/x/X11/X11-20180131-GCCcore-6.4.0.eb | 11 +++-------- .../easyconfigs/x/X11/X11-20180604-GCCcore-7.3.0.eb | 11 +++-------- .../easyconfigs/x/X11/X11-20190311-GCCcore-8.2.0.eb | 11 +++-------- .../easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb | 11 +++-------- 9 files changed, 32 insertions(+), 77 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb index 0dd2a979f87..065732c7e27 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', ] @@ -22,7 +21,8 @@ builddependencies = [ ('Bison', '3.0.4'), ('gettext', '0.19.8'), ('pkg-config', '0.29.1'), - ('intltool', '0.51.0', '-Perl-5.24.0') + ('intltool', '0.51.0', '-Perl-5.24.0'), + ('xorg-macros', '1.19.0'), ] dependencies = [ ('freetype', '2.6.5'), @@ -38,11 +38,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.0', { # 2014-03-27 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['9cca766593cc0ce6bffe1e503127e047aafce61891e4de26b591c86f603af623'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.3', { # 2009-10-14 'checksums': ['3031f466cf0b06de6b3ccbf2019d15c4fcf75229b7d226a711bc1885b3a82cde'], }), diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index 5b7f365ec57..a18479c11ff 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', ] @@ -22,7 +21,8 @@ builddependencies = [ ('Bison', '3.0.4'), ('gettext', '0.19.8'), ('pkg-config', '0.29.1'), - ('intltool', '0.51.0', '-Perl-5.24.0') + ('intltool', '0.51.0', '-Perl-5.24.0'), + ('xorg-macros', '1.19.0'), ] dependencies = [ ('freetype', '2.6.5'), @@ -38,11 +38,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.0', { # 2014-03-27 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['9cca766593cc0ce6bffe1e503127e047aafce61891e4de26b591c86f603af623'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.3', { # 2009-10-14 'checksums': ['3031f466cf0b06de6b3ccbf2019d15c4fcf75229b7d226a711bc1885b3a82cde'], }), diff --git a/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb index 231e4d58506..f7fe477cb1b 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] @@ -23,6 +22,7 @@ dependencies = [ ('fontconfig', '2.12.1'), ('freetype', '2.7.1'), ('zlib', '1.2.11'), + ('xorg-macros', '1.19.1'), ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain @@ -31,7 +31,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('gettext', '0.19.8.1'), ('pkg-config', '0.29.1'), - ('intltool', '0.51.0', '-Perl-5.24.1') + ('intltool', '0.51.0', '-Perl-5.24.1'), ] default_easyblock = 'ConfigureMake' @@ -41,11 +41,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.1', { # 2017-01-29 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['f056411c49a9955f141cad4d7b258a1a5e5bcc0f2a197ee00c63ac3bbe9f347a'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.3', { # 2009-10-14 'checksums': ['3031f466cf0b06de6b3ccbf2019d15c4fcf75229b7d226a711bc1885b3a82cde'], }), diff --git a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb index 1cdca9418c0..e36cb012947 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] @@ -23,6 +22,7 @@ dependencies = [ ('fontconfig', '2.12.1', '-libpng-1.6.29'), ('freetype', '2.7.1', '-libpng-1.6.29'), ('zlib', '1.2.11'), + ('xorg-macros', '1.19.1'), ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain @@ -31,7 +31,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('gettext', '0.19.8.1'), ('pkg-config', '0.29.1'), - ('intltool', '0.51.0', '-Perl-5.24.1') + ('intltool', '0.51.0', '-Perl-5.24.1'), ] default_easyblock = 'ConfigureMake' @@ -42,11 +42,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.1', { # 2017-01-29 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['f056411c49a9955f141cad4d7b258a1a5e5bcc0f2a197ee00c63ac3bbe9f347a'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.4', { # 2017-03-14 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], }), diff --git a/easybuild/easyconfigs/x/X11/X11-20171023-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/X11/X11-20171023-GCCcore-6.4.0.eb index 31872773cfd..ed60e8523d0 100644 --- a/easybuild/easyconfigs/x/X11/X11-20171023-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20171023-GCCcore-6.4.0.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] @@ -23,6 +22,7 @@ dependencies = [ ('fontconfig', '2.12.4'), ('freetype', '2.8'), ('zlib', '1.2.11'), + ('xorg-macros', '1.19.1'), ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain @@ -31,7 +31,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('gettext', '0.19.8.1'), ('pkg-config', '0.29.2'), - ('intltool', '0.51.0', '-Perl-5.26.0') + ('intltool', '0.51.0', '-Perl-5.26.0'), ] default_easyblock = 'ConfigureMake' @@ -41,11 +41,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.1', { # 2017-01-29 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['f056411c49a9955f141cad4d7b258a1a5e5bcc0f2a197ee00c63ac3bbe9f347a'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.4', { # 2017-03-14 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], }), diff --git a/easybuild/easyconfigs/x/X11/X11-20180131-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/X11/X11-20180131-GCCcore-6.4.0.eb index 5dd466ad8fc..67493699ce3 100644 --- a/easybuild/easyconfigs/x/X11/X11-20180131-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20180131-GCCcore-6.4.0.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] @@ -23,6 +22,7 @@ dependencies = [ ('fontconfig', '2.12.6'), ('freetype', '2.9'), ('zlib', '1.2.11'), + ('xorg-macros', '1.19.1'), ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain @@ -41,11 +41,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.1', { # 2017-01-29 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['f056411c49a9955f141cad4d7b258a1a5e5bcc0f2a197ee00c63ac3bbe9f347a'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.4', { # 2017-03-14 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], }), diff --git a/easybuild/easyconfigs/x/X11/X11-20180604-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20180604-GCCcore-7.3.0.eb index cbebba0c80d..2c68e2d15f6 100644 --- a/easybuild/easyconfigs/x/X11/X11-20180604-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20180604-GCCcore-7.3.0.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] @@ -23,6 +22,7 @@ dependencies = [ ('fontconfig', '2.13.0'), ('freetype', '2.9.1'), ('zlib', '1.2.11'), + ('xorg-macros', '1.19.2'), ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain @@ -41,11 +41,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.2', { # 2018-03-04 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.4', { # 2017-03-14 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], }), diff --git a/easybuild/easyconfigs/x/X11/X11-20190311-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20190311-GCCcore-8.2.0.eb index b9303be117b..77dd6463645 100644 --- a/easybuild/easyconfigs/x/X11/X11-20190311-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20190311-GCCcore-8.2.0.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] @@ -23,6 +22,7 @@ dependencies = [ ('fontconfig', '2.13.1'), ('freetype', '2.9.1'), ('zlib', '1.2.11'), + ('xorg-macros', '1.19.2'), ] builddependencies = [ ('binutils', '2.31.1'), @@ -40,11 +40,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.2', { # 2018-03-04 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.4', { # 2017-03-14 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], }), diff --git a/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb index 7c46fb324a3..21b4362d798 100644 --- a/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb @@ -11,9 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [ XORG_LIB_SOURCE, XORG_PROTO_SOURCE, - 'http://xcb.freedesktop.org/dist/', - 'http://xkbcommon.org/download/', - 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] @@ -23,6 +22,7 @@ dependencies = [ ('fontconfig', '2.13.1'), ('freetype', '2.10.1'), ('zlib', '1.2.11'), + ('xorg-macros', '1.19.2'), ] builddependencies = [ ('binutils', '2.32'), @@ -40,11 +40,6 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } components = [ - ('xorg-macros', '1.19.2', { # 2018-03-04 - 'sources': ['util-macros-%(version)s.tar.gz'], - 'checksums': ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'], - 'start_dir': 'util-macros-%(version)s', - }), ('libpthread-stubs', '0.4', { # 2017-03-14 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], }), From 99ad255a84d82c9ef0703c8415abaa9e9c9bac15 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 19 Dec 2019 09:35:04 +1030 Subject: [PATCH 248/468] Jellyfish-2.3.0-foss-2019a style fix --- .../j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb index 874e6dc0509..d251aa80b45 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb @@ -1,4 +1,12 @@ -## # This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia # Homepage: https://staff.flinders.edu.au/research/deep-thought # # Authors:: Robert Qiao # License:: Custom # # Notes:: ## +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## easyblock = 'ConfigureMake' @@ -16,7 +24,8 @@ checksums = ['3d5b68bdf741acdb119546bfaf52219834f83cea1f47b0caa135fc649d0d6faf'] parallel = 1 -# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense runtest = "check GTEST_FILTER=-'*Bloom*'" postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] From 35cd309d2334a298c90b666030ac35b133451725 Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Thu, 19 Dec 2019 11:32:34 +0100 Subject: [PATCH 249/468] fix lpsymphony extension for R-bundle-Bioconductor --- ...R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb | 6 +++++- .../lpsymphony-1.12.0_zlib.patch | 14 ++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/lpsymphony-1.12.0_zlib.patch diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb index bb87e388a6e..1e485dc39d0 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb @@ -411,7 +411,11 @@ exts_list = [ 'checksums': ['91a49924f128ece4dbb0bba30dd4aef4c35d1a57e87845b22805f3779f6e44cb'], }), ('lpsymphony', '1.12.0', { - 'checksums': ['5b2ff3c30490adab67fabb34076c5019de3d1cfbce68666fed7e5a7423c19b8f'], + 'patches': ['lpsymphony-1.12.0_zlib.patch'], + 'checksums': [ + '5b2ff3c30490adab67fabb34076c5019de3d1cfbce68666fed7e5a7423c19b8f', # lpsymphony_1.12.0.tar.gz + '8d7443ac2e9f30bc3723d1bfe246e3c0ece085800e8b6e9632ae4f799ea5ef40', # lpsymphony-1.12.0_zlib.patch + ], }), ('IHW', '1.12.0', { 'checksums': ['7f7ede99410cfacc355b0eeea3c27081e85f16640bb4383ff66b2eaa02371a16'], diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/lpsymphony-1.12.0_zlib.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/lpsymphony-1.12.0_zlib.patch new file mode 100644 index 00000000000..d3539286ae2 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/lpsymphony-1.12.0_zlib.patch @@ -0,0 +1,14 @@ +Make sure that the zlib version provided by Easybuild is used during compilation. +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur lpsymphony.orig/configure lpsymphony/configure +--- lpsymphony.orig/configure 2019-05-03 03:55:39.000000000 +0200 ++++ lpsymphony/configure 2019-12-18 18:01:49.567454520 +0100 +@@ -100,7 +100,7 @@ + --disable-osl-libcheck --disable-soplex-libcheck \ + --disable-xpress-libcheck \ + CFLAGS="-w -g -O2" \ +- CXXFLAGS="-w -g -O2" \ ++ CXXFLAGS="-w -g -O2 -L$EBROOTZLIB/lib" \ + CC="`${R} CMD config CC`" \ + CPP="`${R} CMD config CPP`" \ + CXX="`${R} CMD config CXX`" \ From e99c5eada1d4405ea75d8cb829a2fc90269930f0 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 19 Dec 2019 15:02:09 +0000 Subject: [PATCH 250/468] adding easyconfigs: iccifort-2020.0.166.eb --- .../i/iccifort/iccifort-2020.0.166.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb new file mode 100644 index 00000000000..9ffdb53c813 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'iccifort' +version = '2020.0.166' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Intel C, C++ & Fortran compilers" + +toolchain = SYSTEM + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] +patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] +checksums = [ + # parallel_studio_xe_2020_composer_edition.tgz + '9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', + # iccifort-2020.0.166_no_mpi_rt_dependency.patch + '39086fcaa0fb3b8a7cba4e4f06ea7a1da330fdb23a1c0f3096fca3123791e91b', +] + +local_gccver = '9.2.0' + +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.32', '', ('GCCcore', local_gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = [ + 'intel-comp', 'intel-ccomp', 'intel-fcomp', 'intel-icc', 'intel-ifort', + 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)' +] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' From 5c79dfc2e8744a56b9d6fcaf16830ecb2e29d574 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 19 Dec 2019 15:10:17 +0000 Subject: [PATCH 251/468] Add forgotten patch --- .../iccifort-2020.0.166_no_mpi_rt_dependency.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166_no_mpi_rt_dependency.patch diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166_no_mpi_rt_dependency.patch b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166_no_mpi_rt_dependency.patch new file mode 100644 index 00000000000..18096df5210 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166_no_mpi_rt_dependency.patch @@ -0,0 +1,13 @@ +don't install Intel MPI runtime components (mpi-rt), cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/3793 +author: Bart Oldeman (Compute Canada) +--- parallel_studio_xe_2020_composer_edition/pset/mediaconfig.xml.orig 2019-12-02 13:01:26.000000000 -0000 ++++ parallel_studio_xe_2020_composer_edition/pset/mediaconfig.xml 2019-12-19 13:27:36.293176507 -0000 +@@ -846,7 +846,7 @@ + + ${COMPLIB_ROOT} + 1575291636091 +- ++ + Intel Fortran Compiler for Intel(R) 64 + Intel Fortran Compiler 19.1 + インテル(R) Fortran コンパイラー (インテル(R) 64) From 34c193be73638f9aeff857b7bc8c327f0887e3f4 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 19 Dec 2019 15:33:57 +0000 Subject: [PATCH 252/468] Change http to https in URL --- easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 9ffdb53c813..1b0708315fc 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ From 3d4cf2835c70b857b641cebc7fa68cd2cd6f2c5a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 19 Dec 2019 15:53:46 +0000 Subject: [PATCH 253/468] Correct checksum for patch --- easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 1b0708315fc..8b922807305 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -15,7 +15,7 @@ checksums = [ # parallel_studio_xe_2020_composer_edition.tgz '9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', # iccifort-2020.0.166_no_mpi_rt_dependency.patch - '39086fcaa0fb3b8a7cba4e4f06ea7a1da330fdb23a1c0f3096fca3123791e91b', + 'b7a3d1934e8ffe1712ffb82747332e025355f9f5fbef62349d0c7b4cb7e636a5', ] local_gccver = '9.2.0' From c960930f41c7ce5db0b4482cff2c74b5103bd169 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 19 Dec 2019 15:54:44 +0000 Subject: [PATCH 254/468] Use https in homepage --- easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 8b922807305..9cf18b01afb 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -3,7 +3,7 @@ name = 'iccifort' version = '2020.0.166' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM From ccb7d3e8d26aaf20bc69667054c1fbf3aef6985e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 17:58:28 +0200 Subject: [PATCH 255/468] openslide-python-1.1.1: hardcode the homepage --- .../openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb index e405937df07..07b724d52f4 100644 --- a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb @@ -3,12 +3,12 @@ easyblock = 'PythonPackage' name = 'openslide-python' version = '1.1.1' -github_account = 'openslide' -homepage = 'https://github.com/%(github_account)s/%(name)s' +homepage = 'https://github.com/openslide/openslide-python' description = "OpenSlide Python is a Python interface to the OpenSlide library." toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +github_account = 'openslide' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['33c390fe43e3d7d443fafdd66969392d3e9efd2ecd5d4af73c3dbac374485ed5'] From a01a0aaf96f32a9417abf67235da8d7c7a7352eb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 18:17:40 +0200 Subject: [PATCH 256/468] adding easyconfigs: lpsolve-5.5.2.5-GCC-8.3.0.eb --- .../l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb new file mode 100644 index 00000000000..f271422abd7 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.5' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +patches = ['lpsolve-%(version)s_Fix_expected_identifier_error_for_gcc.patch'] +checksums = [ + '201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a', # lp_solve_5.5.2.5_source.tar.gz + # lpsolve-5.5.2.5_Fix_expected_identifier_error_for_gcc.patch + 'be46d06035797b455ff616c74f83c4e36c9cad6c41b0c8680b29cb6b3208f49c', +] + +dependencies = [('binutils', '2.32')] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' From 465faca10aa3a56d602bab8229cb0a08e6e732a4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 18:18:37 +0200 Subject: [PATCH 257/468] adding easyconfigs: Boost.Python-1.71.0-gompi-2019b.eb and patches: Boost-1.71.0_fix-Python3.patch --- .../Boost-1.71.0_fix-Python3.patch | 14 ++++++++++ .../Boost.Python-1.71.0-gompi-2019b.eb | 27 +++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost-1.71.0_fix-Python3.patch create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost-1.71.0_fix-Python3.patch b/easybuild/easyconfigs/b/Boost.Python/Boost-1.71.0_fix-Python3.patch new file mode 100644 index 00000000000..3e2cb94bc4b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost-1.71.0_fix-Python3.patch @@ -0,0 +1,14 @@ +also consider Python include directory for Python 3.x +author: Damian Alvarez (Juelich Supercomputing Centre) +updated by: Kenneth Hoste (HPC-UGent), Alex Domingo (VUB) +--- boost_1_71_0/tools/build/src/tools/python.jam.old 2019-12-19 15:11:46.626395000 +0100 ++++ boost_1_71_0/tools/build/src/tools/python.jam 2019-12-19 15:12:31.441437885 +0100 +@@ -544,7 +544,7 @@ + } + else + { +- includes ?= $(prefix)/include/python$(version) ; ++ includes ?= $(prefix)/include/python$(version) $(prefix)/include/python$(version)m ; + + local lib = $(exec-prefix)/lib ; + libraries ?= $(lib)/python$(version)/config $(lib) ; diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb new file mode 100644 index 00000000000..b53471cf2dc --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.71.0' + +homepage = 'http://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.sourceforge.net/boost/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-%(version)s_fix-Python3.patch'] +checksums = [ + '96b34f7468f26a141f6020efb813f1a2f3dfb9797ecf76a7d7cbd843cc95f5bd', # boost_1_71_0.tar.gz + '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch +] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +dependencies = [('Boost', version)] + +only_python_bindings = True + +moduleclass = 'lib' From 5a7db21dfb9e51772c782c2e4d28a4ed72085fe8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 18:23:04 +0200 Subject: [PATCH 258/468] openslide-python-1.1.1: add sanity_pip_check --- .../o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb index 07b724d52f4..a28bad4f033 100644 --- a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.1-GCCcore-8.2.0.eb @@ -24,6 +24,7 @@ dependencies = [ use_pip = True download_dep_fail = True +sanity_pip_check = True options = {'modulename': 'openslide'} From 06ae07cd2c48e342aab77bde4f7181234e46fb4b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 18:30:38 +0200 Subject: [PATCH 259/468] adding easyconfigs: Faber-0.3-GCCcore-8.3.0.eb --- .../f/Faber/Faber-0.3-GCCcore-8.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/Faber/Faber-0.3-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/f/Faber/Faber-0.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/Faber/Faber-0.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..92e0159be95 --- /dev/null +++ b/easybuild/easyconfigs/f/Faber/Faber-0.3-GCCcore-8.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Faber' +version = '0.3' + +homepage = 'https://stefanseefeld.github.io/faber' +description = """Faber started as a clone of Boost.Build, to experiment with a + new Python frontend. Meanwhile it has evolved into a new build system, which + retains most of the features found in Boost.Build, but with (hopefully !) much + simplified logic, in addition of course to using Python as scripting language, + rather than Jam. The original bjam engine is still in use as scheduler, though + at this point that is mostly an implementation detail.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/stefanseefeld/faber/archive/release'] +sources = ['%(version)s.tar.gz'] +checksums = ['a2bf9aa6cc6f9878524d95657dc68af9d7258ca14d0f5264d84419e7b6bfdd5c'] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +builddependencies = [('binutils', '2.32')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 7d06db69ae1d8fded546395cbfc94cda2c8e665e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 18:35:54 +0200 Subject: [PATCH 260/468] Boost.Python-1.71.0: fix homepage and source_urls --- .../b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb index b53471cf2dc..cf6cc138bc5 100644 --- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.71.0-gompi-2019b.eb @@ -3,14 +3,14 @@ easyblock = 'EB_Boost' name = 'Boost.Python' version = '1.71.0' -homepage = 'http://boostorg.github.io/python' +homepage = 'https://boostorg.github.io/python' description = """Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.""" toolchain = {'name': 'gompi', 'version': '2019b'} toolchainopts = {'pic': True} -source_urls = ['http://download.sourceforge.net/boost/'] +source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] patches = ['Boost-%(version)s_fix-Python3.patch'] checksums = [ From d5a6cc595bd152bddbead7709e69cb69a6646e60 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 18:51:46 +0200 Subject: [PATCH 261/468] adding easyconfigs: mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb, mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb --- ...mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb | 54 +++++++++++++++++++ ...lurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb | 54 +++++++++++++++++++ 2 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..1b58d53913b --- /dev/null +++ b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'mhcflurry' +version = '1.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/openvax/mhcflurry' +description = """MHCflurry implements class I peptide/MHC binding affinity + prediction. By default it supports 112 MHC alleles using ensembles of + allele-specific models. Pan-allele predictors supporting virtually any MHC + allele of known sequence are available for testing (see below). MHCflurry + runs on Python 2.7 and 3.4+ using the keras neural network library. It + exposes command-line and Python library interfaces.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('scikit-learn', '0.20.3'), + ('tqdm', '4.32.1'), + ('Keras', '2.2.4', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('appdirs', '1.4.3', { + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('mhcnames', '0.4.8', { + 'checksums': ['0a18de129eaa4bf8ce802e5e2d856806639ab17b392688ea13dc20ec6d3cc8a2'], + }), + (name, version, { + 'checksums': ['469bab44f6fff5dc78dcc5b032b67917b36d68c6e71f6baadf42847ee203ca96'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['mhcflurry-downloads', + 'mhcflurry-predict', + 'mhcflurry-calibrate-percentile-ranks', + 'mhcflurry-class1-train-allele-specific-models', + 'mhcflurry-class1-select-allele-specific-models', + 'mhcflurry-class1-train-pan-allele-models', + 'mhcflurry-class1-select-pan-allele-models', + '_mhcflurry-cluster-worker-entry-point']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..22bc40f0131 --- /dev/null +++ b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'mhcflurry' +version = '1.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/openvax/mhcflurry' +description = """MHCflurry implements class I peptide/MHC binding affinity + prediction. By default it supports 112 MHC alleles using ensembles of + allele-specific models. Pan-allele predictors supporting virtually any MHC + allele of known sequence are available for testing (see below). MHCflurry + runs on Python 2.7 and 3.4+ using the keras neural network library. It + exposes command-line and Python library interfaces.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('scikit-learn', '0.20.3'), + ('tqdm', '4.32.1'), + ('Keras', '2.2.4', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('appdirs', '1.4.3', { + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('mhcnames', '0.4.8', { + 'checksums': ['0a18de129eaa4bf8ce802e5e2d856806639ab17b392688ea13dc20ec6d3cc8a2'], + }), + (name, version, { + 'checksums': ['469bab44f6fff5dc78dcc5b032b67917b36d68c6e71f6baadf42847ee203ca96'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['mhcflurry-downloads', + 'mhcflurry-predict', + 'mhcflurry-calibrate-percentile-ranks', + 'mhcflurry-class1-train-allele-specific-models', + 'mhcflurry-class1-select-allele-specific-models', + 'mhcflurry-class1-train-pan-allele-models', + 'mhcflurry-class1-select-pan-allele-models', + '_mhcflurry-cluster-worker-entry-point']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'bio' From bfb925a8658e252f57dfa2b75a1453e3c6bf6718 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 19:29:28 +0200 Subject: [PATCH 262/468] lpsolve-5.5.2.5-GCC-8.3.0: remove explicit dependency on binutils --- easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb index f271422abd7..e9cb83a79bd 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-8.3.0.eb @@ -17,8 +17,6 @@ checksums = [ 'be46d06035797b455ff616c74f83c4e36c9cad6c41b0c8680b29cb6b3208f49c', ] -dependencies = [('binutils', '2.32')] - local_lpsolve_ver = '%(version_major)s%(version_minor)s' start_dir = 'lpsolve%s' % local_lpsolve_ver From 4a976b52fdf073920ea5dc44fda9ea0943314c1b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Dec 2019 19:36:14 +0200 Subject: [PATCH 263/468] adding easyconfigs scikit-learn-0.20.3-fosscuda-2019a.eb --- .../scikit-learn-0.20.3-fosscuda-2019a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb new file mode 100644 index 00000000000..3554260112f --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.3' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [('SciPy-bundle', '2019.03')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From 2873f502b391c178d3aaf17bdea0fc1738387d2b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 19 Dec 2019 20:06:22 +0000 Subject: [PATCH 264/468] adding easyconfigs: TinyDB-3.15.2-GCCcore-8.3.0.eb --- .../t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..7a1a08ec46f --- /dev/null +++ b/easybuild/easyconfigs/t/TinyDB/TinyDB-3.15.2-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'TinyDB' +version = '3.15.2' + +homepage = "https://tinydb.readthedocs.io/" +description = """TinyDB is a lightweight document oriented database optimized for your happiness :) It's written in + pure Python and has no external dependencies. The target are small apps that would be blown away by a SQL-DB or an + external database server.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f273d9b6d8b1b5e1d094a6eb8b72851b39b81099293344132c73332b60e3b893'] + +builddependencies = [('binutils', '2.32')] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From 61a77d54fdf3c2a915a40f0b60ea12804031b4b5 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 20 Dec 2019 10:30:48 +1030 Subject: [PATCH 265/468] Jellyfish downgrade toolchain to GCCcore --- ...ish-2.3.0-foss-2019a.eb => Jellyfish-2.3.0-GCCcore-8.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/j/Jellyfish/{Jellyfish-2.3.0-foss-2019a.eb => Jellyfish-2.3.0-GCCcore-8.2.0.eb} (95%) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb similarity index 95% rename from easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb rename to easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb index d251aa80b45..a4a8688cac2 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-foss-2019a.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ version = '2.3.0' homepage = 'http://www.genome.umd.edu/jellyfish.html' description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." -toolchain = {'name': 'foss', 'version': '2019a'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] From d5850a01a930d830b6acaa948ebc2c5832e2f175 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 20 Dec 2019 11:04:29 +1030 Subject: [PATCH 266/468] Jellyfish downgrade toolchain to GCC-binutil --- .../easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb index a4a8688cac2..74f4efbd7df 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ version = '2.3.0' homepage = 'http://www.genome.umd.edu/jellyfish.html' description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." -toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] From 63d00a76b5c745da0de9b0d4d092fe517ed1550f Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 20 Dec 2019 11:16:42 +1030 Subject: [PATCH 267/468] Jellyfish downgrade toolchain to GCC-binutil name fix --- .../Jellyfish-2.3.0-GCCcore-8.2.0.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb deleted file mode 100644 index 74f4efbd7df..00000000000 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCCcore-8.2.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Custom -# -# Notes:: -## - -easyblock = 'ConfigureMake' - -name = 'Jellyfish' -version = '2.3.0' - -homepage = 'http://www.genome.umd.edu/jellyfish.html' -description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." - -toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} - -source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['3d5b68bdf741acdb119546bfaf52219834f83cea1f47b0caa135fc649d0d6faf'] - -parallel = 1 - -# The tests for the Bloom filter are statistical tests and can randomly fail, -# they actually don't make a lot of sense -runtest = "check GTEST_FILTER=-'*Bloom*'" - -postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] - -sanity_check_paths = { - 'files': ['bin/jellyfish'], - 'dirs': [] -} - -modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} - -moduleclass = 'bio' From f5b27f8867486621b9f48a34e1a083cef87fbe11 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 20 Dec 2019 11:33:38 +1030 Subject: [PATCH 268/468] Jellyfish-2.3.0-GCC-8.2.0-2.31.1.eb LICENSE --- .../Jellyfish-2.3.0-GCC-8.2.0-2.31.1.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..2d3ae002cd8 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.0' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3d5b68bdf741acdb119546bfaf52219834f83cea1f47b0caa135fc649d0d6faf'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' From 2c92b001202ad6d1f48ffe4866439518001795c0 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 20 Dec 2019 11:38:57 +1030 Subject: [PATCH 269/468] SAMtools-1.10-GCC-8.2.0-2.31.1.eb --- .../SAMtools-1.10-GCC-8.2.0-2.31.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..67ab5a9db9a --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +## + +name = 'SAMtools' +version = '1.10' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585'] + +builddependencies = [('binutils', '2.31.1')] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.1'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.4'), + ('cURL', '7.63.0'), +] + +moduleclass = 'bio' From c777edc23fbe5315f6709739d68b5fd15a9686ee Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 20 Dec 2019 11:48:56 +1030 Subject: [PATCH 270/468] Salmon-1.0.0 --- .../s/Salmon/Salmon-1.0.0-gompi-2019a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-1.0.0-gompi-2019a.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.0.0-gompi-2019a.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.0.0-gompi-2019a.eb new file mode 100644 index 00000000000..6681baa8105 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.0.0-gompi-2019a.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +## + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.0.0' + +github_account = 'COMBINE-lab' +homepage = 'https://github.com/%(github_account)s/%(namelower)s' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} + +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8443cd6ac0c8dd565d1341bea955753933336390c7caaead37a967d4aaa739'] + +builddependencies = [ + ('CMake', '3.13.3'), + ('pkg-config', '0.29.2'), + ('jemalloc', '5.2.0'), +] + +dependencies = [ + ('Boost', '1.70.0'), + ('tbb', '2019_U4'), +] + +configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC' + +# need to unset the $LD_PRELOAD set be jemalloc to avoid hanging 'make test' +# since jemalloc is statically linked in Salmon (and hence only a build dep), +# this only affects the tests +pretestopts = "unset LD_PRELOAD && " +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From 3884a173c7089370af7be5514a5ef81511f90def Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 20 Dec 2019 11:54:51 +1030 Subject: [PATCH 271/468] https fix --- .../easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb index 67ab5a9db9a..e091a22e7cd 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb @@ -11,7 +11,7 @@ name = 'SAMtools' version = '1.10' -homepage = 'http://www.htslib.org/' +homepage = 'https://www.htslib.org/' description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.""" From 09741b22c1998892f33fee4f07cdb03746efbe70 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 20 Dec 2019 10:42:29 +0200 Subject: [PATCH 272/468] scikit-learn-0.20.3: fix homepage URL --- .../s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb index 3554260112f..74d63aee085 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-fosscuda-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'scikit-learn' version = '0.20.3' -homepage = 'http://scikit-learn.org/stable/index.html' +homepage = 'https://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. From 281da8e4fa56b3f13fab34af2bad3fdaa68001bc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 20 Dec 2019 08:47:41 +0000 Subject: [PATCH 273/468] adding easyconfigs: CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb --- .../CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..55a7116f8ad --- /dev/null +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,45 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'CSBDeep' +version = '0.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "http://csbdeep.bioimagecomputing.com/" +description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE).""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('TensorFlow', '1.13.1', versionsuffix), + ('Keras', '2.2.4', versionsuffix), + ('IPython', '7.7.0', versionsuffix), + ('matplotlib', '3.0.3', versionsuffix), + ('tqdm', '4.32.1'), +] + +use_pip = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} + +exts_list = [ + ('imagecodecs-lite', '2019.12.3', { + 'checksums': ['95d18aa13ceb1b18a6109433b42d054e13b9a295cba96c08ab719f864f589d68'], + }), + ('tifffile', '2019.7.26.2', { + 'checksums': ['2abb91c3a23a61593c5635ac1a19f67e732b46291c305fcee0eeaad41181a13f'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['ad2cf81389b8c15eb2f38a524dc011a5331dfb91e7d3053fed0c6c808a7bdf89'], + }), +] + +sanity_check_commands = ['care_predict'] + +moduleclass = 'bio' From f662dea71da8bb1409efd5f589cd75beb5f74db2 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 20 Dec 2019 08:59:04 +0000 Subject: [PATCH 274/468] https-ify the homepage --- .../c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb index 55a7116f8ad..a834588d69c 100644 --- a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-foss-2019a-Python-3.7.2.eb @@ -5,7 +5,7 @@ name = 'CSBDeep' version = '0.4.1' versionsuffix = '-Python-%(pyver)s' -homepage = "http://csbdeep.bioimagecomputing.com/" +homepage = "https://csbdeep.bioimagecomputing.com/" description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE).""" toolchain = {'name': 'foss', 'version': '2019a'} From 5b9179bb809595d4d491dcfe6932852e7d1f6386 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 20 Dec 2019 09:03:43 +0000 Subject: [PATCH 275/468] adding fosscuda version --- ...BDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..cd81ce113a0 --- /dev/null +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb @@ -0,0 +1,43 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'CSBDeep' +version = '0.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://csbdeep.bioimagecomputing.com/" +description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE).""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('TensorFlow', '1.13.1', versionsuffix), + ('Keras', '2.2.4', versionsuffix), + ('IPython', '7.7.0', versionsuffix), + ('matplotlib', '3.0.3', versionsuffix), + ('tqdm', '4.32.1'), +] + +use_pip = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} + +exts_list = [ + ('imagecodecs-lite', '2019.12.3', { + 'checksums': ['95d18aa13ceb1b18a6109433b42d054e13b9a295cba96c08ab719f864f589d68'], + }), + ('tifffile', '2019.7.26.2', { + 'checksums': ['2abb91c3a23a61593c5635ac1a19f67e732b46291c305fcee0eeaad41181a13f'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['ad2cf81389b8c15eb2f38a524dc011a5331dfb91e7d3053fed0c6c808a7bdf89'], + }), +] + +moduleclass = 'bio' From a684c9f1079b2cfcfff905da3af87b49944dd974 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 20 Dec 2019 11:46:47 +0200 Subject: [PATCH 276/468] mhcflurry-1.4.0: downgrade to version 1.2.4 --- ...eb => mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb} | 12 ++++++------ ...> mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb} | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/m/mhcflurry/{mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb => mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb} (81%) rename easybuild/easyconfigs/m/mhcflurry/{mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb => mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb} (81%) diff --git a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb similarity index 81% rename from easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb index 1b58d53913b..5baf9b33228 100644 --- a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-foss-2019a-Python-3.7.2.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'mhcflurry' -version = '1.4.0' +version = '1.2.4' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/openvax/mhcflurry' @@ -28,6 +28,9 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ + ('np_utils', '0.5.11.1', { + 'checksums': ['5b75f329eb686923a467ee7ce6e3210051ea09953a6cdd8620908290eb546f9b'], + }), ('appdirs', '1.4.3', { 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), @@ -35,7 +38,7 @@ exts_list = [ 'checksums': ['0a18de129eaa4bf8ce802e5e2d856806639ab17b392688ea13dc20ec6d3cc8a2'], }), (name, version, { - 'checksums': ['469bab44f6fff5dc78dcc5b032b67917b36d68c6e71f6baadf42847ee203ca96'], + 'checksums': ['084b1e613dbc9845822b4bc357c14c7e28d74f364dac75c0c0f69f40fb7ad091'], }), ] @@ -44,10 +47,7 @@ sanity_check_paths = { 'mhcflurry-predict', 'mhcflurry-calibrate-percentile-ranks', 'mhcflurry-class1-train-allele-specific-models', - 'mhcflurry-class1-select-allele-specific-models', - 'mhcflurry-class1-train-pan-allele-models', - 'mhcflurry-class1-select-pan-allele-models', - '_mhcflurry-cluster-worker-entry-point']], + 'mhcflurry-class1-select-allele-specific-models']], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] } diff --git a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb similarity index 81% rename from easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb index 22bc40f0131..1c4b61b7336 100644 --- a/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.4.0-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/mhcflurry/mhcflurry-1.2.4-fosscuda-2019a-Python-3.7.2.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'mhcflurry' -version = '1.4.0' +version = '1.2.4' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/openvax/mhcflurry' @@ -28,6 +28,9 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ + ('np_utils', '0.5.11.1', { + 'checksums': ['5b75f329eb686923a467ee7ce6e3210051ea09953a6cdd8620908290eb546f9b'], + }), ('appdirs', '1.4.3', { 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], }), @@ -35,7 +38,7 @@ exts_list = [ 'checksums': ['0a18de129eaa4bf8ce802e5e2d856806639ab17b392688ea13dc20ec6d3cc8a2'], }), (name, version, { - 'checksums': ['469bab44f6fff5dc78dcc5b032b67917b36d68c6e71f6baadf42847ee203ca96'], + 'checksums': ['084b1e613dbc9845822b4bc357c14c7e28d74f364dac75c0c0f69f40fb7ad091'], }), ] @@ -44,10 +47,7 @@ sanity_check_paths = { 'mhcflurry-predict', 'mhcflurry-calibrate-percentile-ranks', 'mhcflurry-class1-train-allele-specific-models', - 'mhcflurry-class1-select-allele-specific-models', - 'mhcflurry-class1-train-pan-allele-models', - 'mhcflurry-class1-select-pan-allele-models', - '_mhcflurry-cluster-worker-entry-point']], + 'mhcflurry-class1-select-allele-specific-models']], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] } From 31c391bec5fbb7e0ab6878663ea06da02908ed98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Dec 2019 13:19:35 +0100 Subject: [PATCH 277/468] adding easyconfigs: MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb --- .../MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..c62e1f93059 --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,29 @@ +name = 'MRtrix' +version = '3.0_RC4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4f246e4cc6ddd5d2480d368342bcbeb9c5d21c04a3a4b5e6e2adb8c036611426'] + +builddependencies = [ + ('Eigen', '3.3.7', '', True), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.7.4'), + ('Mesa', '19.1.7'), + ('Qt5', '5.13.1'), + ('LibTIFF', '4.0.10'), + ('FFTW', '3.3.8'), +] + +moduleclass = 'bio' From de28a1ad475fef41bdadf4f6694d856b42a88014 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Dec 2019 13:43:19 +0100 Subject: [PATCH 278/468] [Horovod] Use NCCL for GPU ops --- ...ovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb index 8c2dd0b1086..95560470979 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb @@ -18,6 +18,9 @@ dependencies = [ use_pip = True +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ From 10d597dcfc482ab3a20b6b42f6e1c849d4ef7b9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Dec 2019 13:47:30 +0100 Subject: [PATCH 279/468] drop Python dependency for SWIG 4.0.1 --- ...ore-8.3.0-Python-3.7.4.eb => SWIG-4.0.1-GCCcore-8.3.0.eb} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/SWIG/{SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb => SWIG-4.0.1-GCCcore-8.3.0.eb} (88%) diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0.eb similarity index 88% rename from easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb rename to easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0.eb index ee1ac33527f..facdcc8a3e0 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-8.3.0.eb @@ -1,6 +1,5 @@ name = 'SWIG' version = '4.0.1' -versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.swig.org/' description = """SWIG is a software development tool that connects programs written in C and C++ with @@ -16,8 +15,10 @@ checksums = ['7a00b4d0d53ad97a14316135e2d702091cd5f193bb58bcfcd8bc59d41e7887a9'] builddependencies = [('binutils', '2.32')] dependencies = [ - ('Python', '3.7.4'), + ('zlib', '1.2.11'), ('PCRE', '8.43'), ] +configopts = '--without-alllang --with-boost=no' + moduleclass = 'devel' From d08d9d616534bbf2f45746cff9c5880843eb983a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 20 Dec 2019 14:20:47 +0000 Subject: [PATCH 280/468] adding easyconfigs: Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb --- ...s-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..b9e81d00f22 --- /dev/null +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,46 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Globus-CLI' +version = '1.11.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://docs.globus.org/cli/" +description = """A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services + from the shell, and is suited to both interactive and simple scripting use cases.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] + +dependencies = [('Python', '3.7.4')] + +use_pip = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} + +exts_list = [ + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('PyJWT', '1.7.1', { + 'modulename': 'jwt', + 'checksums': ['8d59a976fb773f3e6a39c85636357c4f0e242707394cadadd9814f5cbaa20e96'], + }), + ('globus-sdk', '1.8.0', { + 'checksums': ['9fbfc880ea5d133005b11abcc3a59afce4e59bdbe1b55860529b67b2d550fd3d'], + }), + ('jmespath', '0.9.4', { + 'checksums': ['bde2aef6f44302dfb30320115b17d030798de8c4110e28d5cf6cf91a7a31074c'], + }), + (name, version, { + 'modulename': 'globus_cli', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['34a050c528766d27533580a0da422834ca745328d8c83c84a605654227f39d95'], + }), +] + +moduleclass = 'data' From b5f96092fc3d52c4b4bdd1b0ad8af2d45aa46fd8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Dec 2019 14:15:55 +0100 Subject: [PATCH 281/468] Enable pip check --- ...orovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb index 95560470979..a14bba096a4 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-2.0.0-Python-3.7.4.eb @@ -17,6 +17,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' From b090f27188e45e7416f5cf4e42ac87eb46d26a0e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Dec 2019 14:22:05 +0100 Subject: [PATCH 282/468] adding easyconfigs: Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb --- ...da-2019b-TensorFlow-1.15.0-Python-3.7.4.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb new file mode 100644 index 00000000000..3bc8867e84c --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.0-Python-3.7.4.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.18.2' +local_tf_version = '1.15.0' +versionsuffix = '-TensorFlow-%s-Python-%%(pyver)s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('PyYAML', '5.1.2'), + ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('cloudpickle', '1.2.2', { + 'checksums': ['922401d7140e133253ff5fab4faa4a1166416066453a783b00b507dca93f8859'], + }), + ('horovod', version, { + 'checksums': ['a8c9c48976a41ff04ed3d69eb92c59ff444cc414dd45ef047750eab25c03e803'], + }), +] + +moduleclass = 'tools' From 4e65ec0ed390c9b9225230bad82b50f76c20bb0a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Dec 2019 17:59:10 +0100 Subject: [PATCH 283/468] [Mesa] Add updated URL to old versions --- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intel-2017b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-fosscuda-2018a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-intel-2018a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-iomkl-2018a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb | 1 + 23 files changed, 42 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index 9b02d2b02bc..f1ca4339818 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '11.1.2' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 45545e7c839..a6504e4dc63 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '11.1.2' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 92703769fdd..dbfde38b009 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '11.1.2' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index 61b180d1ef0..e6723172e2c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '11.2.1' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -14,6 +14,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index 6660454e4c7..e794b5a48b6 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '11.2.1' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -14,6 +14,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb index 8376070490c..668d0aef573 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '12.0.2' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -24,6 +24,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index 2ac60cb5d00..beedc9a201e 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '12.0.2' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -24,6 +24,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb index bf4cca33d3c..2dc5754793a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.0.2' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -24,6 +24,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index fb11d4be670..7b7d4d4ad5f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.0.2' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -24,6 +24,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intel-2017b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intel-2017b.eb index 181171b7aaf..29a54409323 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intel-2017b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intel-2017b.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.2.4' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -24,6 +24,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb index c82d2ed9dee..0c57c022dbe 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.2.4' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -24,6 +24,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb index fff162289ab..236bd17749a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.2.5' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -24,6 +24,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] checksums = ['7f7f914b7b9ea0b15f2d9d01a4375e311b0e90e55683b8e8a67ce8691eb1070f'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb index bf7ef1d3161..62cc87c9103 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.2.5' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb index bb7a8ba7acc..b1f749dd7d9 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.3.6' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -26,6 +26,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-fosscuda-2018a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-fosscuda-2018a.eb index 2d33dfcdec2..def061da10c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-fosscuda-2018a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-fosscuda-2018a.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.3.6' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -29,6 +29,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-intel-2018a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-intel-2018a.eb index 076f885d0f3..e215d5203e1 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-intel-2018a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-intel-2018a.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.3.6' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -26,6 +26,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-iomkl-2018a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-iomkl-2018a.eb index fd83bc2cb66..4fe9f99eac7 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-iomkl-2018a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-iomkl-2018a.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '17.3.6' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -26,6 +26,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb index 06242509dea..abc1e8aec6b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '18.1.1' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -26,6 +26,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb index ab53c0069d4..8e5cda07c83 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '18.1.1' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -26,6 +26,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb index 70d6d337b34..8a89a519358 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' version = '18.1.1' -homepage = 'http://www.mesa3d.org/' +homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.""" @@ -26,6 +26,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb index ed31ea229cd..d88133bb7ef 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb @@ -26,6 +26,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] checksums = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb index 5781de272b8..4c51ea66897 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb @@ -26,6 +26,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] checksums = ['e287920fdb38712a9fed448dc90b3ca95048c7face5db52e58361f8b6e0f3cd5'] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb index 3d0a009af9f..1aaf2c5d8a3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb @@ -23,6 +23,7 @@ source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] patches = [ From f951799dda177ab4d94beb1f9ff51f46a46ee129 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Dec 2019 19:04:16 +0100 Subject: [PATCH 284/468] no versionsuffix for SWIG build dep in GEOS easyconfig --- .../g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb index e307f9dbf96..0276f04c932 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-iccifort-2019.5.281-Python-3.7.4.eb @@ -19,7 +19,7 @@ checksums = [ dependencies = [('Python', '3.7.4')] -builddependencies = [('SWIG', '4.0.1', versionsuffix)] +builddependencies = [('SWIG', '4.0.1')] configopts = '--enable-python' From 7b2a99255f1cc26703e5438bde59618c42a83925 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Dec 2019 19:06:48 +0100 Subject: [PATCH 285/468] [Mesa] Add checksums --- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb | 3 ++- easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 3 ++- 7 files changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index f1ca4339818..bf2c9f118de 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -10,12 +10,13 @@ description = """Mesa is an open-source implementation of the OpenGL specificati toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True} -sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ba0e7462b2936b86e6684c26fbb55519f8d9ad31d13a1c1e1afbe41e73466eea'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index a6504e4dc63..e9cfcabbcdf 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -10,12 +10,13 @@ description = """Mesa is an open-source implementation of the OpenGL specificati toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True} -sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ba0e7462b2936b86e6684c26fbb55519f8d9ad31d13a1c1e1afbe41e73466eea'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index dbfde38b009..15ba623ba85 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -10,12 +10,13 @@ description = """Mesa is an open-source implementation of the OpenGL specificati toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True} -sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ba0e7462b2936b86e6684c26fbb55519f8d9ad31d13a1c1e1afbe41e73466eea'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index e6723172e2c..f0d8a1302fc 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -9,13 +9,14 @@ description = """Mesa is an open-source implementation of the OpenGL specificati toolchain = {'name': 'foss', 'version': '2016a'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc2a024204564a71acc95cf262bf618fe49b1d77d351e5755eea705cadac5167'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index e794b5a48b6..70fd4baa59b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -9,13 +9,14 @@ description = """Mesa is an open-source implementation of the OpenGL specificati toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc2a024204564a71acc95cf262bf618fe49b1d77d351e5755eea705cadac5167'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb index 668d0aef573..8231cf224af 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -19,13 +19,14 @@ toolchain = {'name': 'foss', 'version': '2016b'} # -xHost, this always gets overwritten and will fail. toolchainopts = {'optarch': False} -sources = [SOURCELOWER_TAR_XZ] source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d957a5cc371dcd7ff2aa0d87492f263aece46f79352f4520039b58b1f32552cb'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index beedc9a201e..27b8b87ecec 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -19,13 +19,14 @@ toolchain = {'name': 'intel', 'version': '2016b'} # -xHost, this always gets overwritten and will fail. toolchainopts = {'optarch': False} -sources = [SOURCELOWER_TAR_XZ] source_urls = [ 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d957a5cc371dcd7ff2aa0d87492f263aece46f79352f4520039b58b1f32552cb'] builddependencies = [ ('flex', '2.6.0'), From 85d03487cf084203b045c9342924f3278ede582b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 20 Dec 2019 19:31:25 +0000 Subject: [PATCH 286/468] add sanity check command to fosscuda version --- .../c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb index cd81ce113a0..b71cf40e64d 100644 --- a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.4.1-fosscuda-2019a-Python-3.7.2.eb @@ -40,4 +40,6 @@ exts_list = [ }), ] +sanity_check_commands = ['care_predict'] + moduleclass = 'bio' From b908e5684f62b11516672ea7216fbf3db8338705 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 20 Dec 2019 20:14:00 +0000 Subject: [PATCH 287/468] add a sanity check command --- .../Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb index b9e81d00f22..7c7fd3f8513 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -43,4 +43,6 @@ exts_list = [ }), ] +sanity_check_commands = ['globus --help'] + moduleclass = 'data' From b429d96cbf0a51c76ad9de7626b405e25e99926e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Dec 2019 22:08:27 +0100 Subject: [PATCH 288/468] {tools}[intel/2019b] CDO v1.9.8, YAXT v0.6.2, ecCodes v2.15.0 --- .../c/CDO/CDO-1.9.8-intel-2019b.eb | 33 ++++++++++++++++++ .../e/ecCodes/ecCodes-2.15.0-iimpi-2019b.eb | 34 +++++++++++++++++++ .../y/YAXT/YAXT-0.6.2-iimpi-2019b.eb | 23 +++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.15.0-iimpi-2019b.eb create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-iimpi-2019b.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb new file mode 100644 index 00000000000..9eec0ec1e34 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.8' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/20826/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2660ac6f8bf3fa071cf2a3a196b3ec75ad007deb3a782455e80f28680c5252a'] + +dependencies = [ + ('HDF5', '1.10.5'), + ('netCDF', '4.7.1'), + ('YAXT', '0.6.2'), + ('ecCodes', '2.15.0'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" + +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.15.0-iimpi-2019b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.15.0-iimpi-2019b.eb new file mode 100644 index 00000000000..4ed23086e28 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.15.0-iimpi-2019b.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.15.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['9fec8ad11f380795af632fb3105c4aa37d30f22fa70dba48fd93324cf6388d59'] + +builddependencies = [('CMake', '3.15.3')] +dependencies = [ + ('netCDF', '4.7.1'), + ('JasPer', '2.0.14'), +] + +separate_build_dir = True + +configopts = "-DENABLE_NETCDF=ON -DENABLE_JPG=ON -DENABLE_PYTHON=OFF" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bufr_copy', 'bufr_dump', 'bufr_filter', 'bufr_ls', + 'codes_count', 'codes_info', 'codes_split_file', + 'grib_copy', 'grib_dump', 'grib_filter', 'grib_ls']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-iimpi-2019b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-iimpi-2019b.eb new file mode 100644 index 00000000000..d1f7e0005af --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-iimpi-2019b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.6.2' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/492/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7fc9b3e5dd2e0d3d5846f389a01c935aa40528eb09d82162b76c061b496a3c5b'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From e374663f9fb03ad2ddf2493f45027dad02eb3936 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2019 11:35:40 +0100 Subject: [PATCH 289/468] adding easyconfigs: FSL-6.0.3-foss-2019b-Python-3.7.4.eb, libxml++-2.40.1-GCCcore-8.3.0.eb, GLibmm-2.49.7-GCCcore-8.3.0.eb, libsigc++-2.10.2-GCCcore-8.3.0.eb --- .../FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb | 64 +++++++++++++++++++ .../g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb | 39 +++++++++++ .../libsigc++-2.10.2-GCCcore-8.3.0.eb | 26 ++++++++ .../libxml++/libxml++-2.40.1-GCCcore-8.3.0.eb | 31 +++++++++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml++/libxml++-2.40.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..95caf168642 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,64 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Some tools like icmp are missing since they are built with the fslpython_install.sh script +# which locally installs Miniconda and creates a virtual environment. This is too messy and +# an alternative solution is necessary to install them. +# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 +# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation + +name = 'FSL' +version = '6.0.3' +versionsuffix = '-Python-3.7.4' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-6.0.2_Makefile_fixes.patch', + 'FSL-6.0.2_Build_extras.patch', + 'FSL-6.0.1_Melodic-use-ifstream-good.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', +] +checksums = [ + '9eec9b4f5d67fa727b50ad6d4c8265b82403dd6163c4747797ef910f826a2636', # fsl-6.0.3-sources.tar.gz + '4212478ef24be4bce7a9ce513aa9c45fcf67eccfe064331a2e8e52be41d3513c', # FSL-6.0.2_Makefile_fixes.patch + '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch + 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch + 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch +] + +builddependencies = [ + ('Boost', '1.71.0'), +] + +dependencies = [ + ('libgd', '2.2.5'), + ('libxml2', '2.9.9'), + ('libxml++', '2.40.1'), + ('SQLite', '3.29.0'), + ('libpng', '1.6.37'), + ('Tk', '8.6.9'), + ('NLopt', '2.6.1'), + ('freeglut', '3.2.1'), + ('expat', '2.2.7'), + ('zlib', '1.2.11'), + ('VTK', '8.2.0', versionsuffix), + ('GSL', '2.6'), + ('Qwt', '6.1.4'), +] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..c3a68d45c40 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GLibmm' +version = '2.49.7' + +homepage = 'http://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +patches = ['GLibmm-%(version)s_Fix_gobject_type.patch'] +checksums = [ + '571d8ecd082a66fa7248f500063409c1f478edc36f553d0eb27cf6199dee0b25', # glibmm-2.49.7.tar.xz + '3ef7a95e80ab58ea9369a7842c4d2917c8bce828f2754eafd075cf82405c9564', # GLibmm-2.49.7_Fix_gobject_type.patch +] + +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.62.0'), + ('libsigc++', '2.10.2'), +] + +# ignore deprecation warnings that are treated like errors due changed defaults in recent GCC versions +buildopts = 'V=1 CXXFLAGS="$CXXFLAGS -Wno-deprecated -Wno-deprecated-declarations"' + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.4.%s' % SHLIB_EXT, 'lib/libgiomm-2.4.%s' % SHLIB_EXT, + 'include/glibmm-2.4/glibmm.h', 'include/giomm-2.4/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..3bd7a43f5b0 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libsigc++' +version = '2.10.2' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b1ca0253379596f9c19f070c83d362b12dfd39c0a3ea1dd813e8e21c1a097a98'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), +] + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxml++/libxml++-2.40.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxml++/libxml++-2.40.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..53ae090cdf7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml++/libxml++-2.40.1-GCCcore-8.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxml++' +version = '2.40.1' + +homepage = 'http://libxmlplusplus.sourceforge.net' +description = """libxml++ is a C++ wrapper for the libxml XML parser library.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(name)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['4ad4abdd3258874f61c2e2a41d08e9930677976d303653cd1670d3e9f35463e9'] + +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLibmm', '2.49.7'), + ('libxml2', '2.9.9'), +] + +sanity_check_paths = { + 'files': ['lib/libxml++-2.6.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/libxml++-2.6/libxml++'], +} + +moduleclass = 'lib' From 5af28007f891919b73395cb10d9cc9a0ae87dd7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2019 12:07:13 +0100 Subject: [PATCH 290/468] use https for FSL/GLibmm homepage & source URLs --- .../easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb | 4 ++-- easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb index 95caf168642..fa4c4b87b06 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.3-foss-2019b-Python-3.7.4.eb @@ -12,13 +12,13 @@ name = 'FSL' version = '6.0.3' versionsuffix = '-Python-3.7.4' -homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +homepage = 'https://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'cstd': 'c++11'} -source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +source_urls = ['https://www.fmrib.ox.ac.uk/fsldownloads/'] sources = ['%(namelower)s-%(version)s-sources.tar.gz'] patches = [ 'FSL-6.0.2_Makefile_fixes.patch', diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb index c3a68d45c40..12f33846288 100644 --- a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.49.7-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GLibmm' version = '2.49.7' -homepage = 'http://www.gtk.org/' +homepage = 'https://www.gtk.org/' description = """C++ bindings for Glib""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} From 39697ea0fca23eff2059a194967c232988c61229 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 21 Dec 2019 11:09:26 +0000 Subject: [PATCH 291/468] change to multi_deps and fix the hardcoded shebang lines --- ...-Python-3.7.4.eb => Globus-CLI-1.11.0-GCCcore-8.3.0.eb} | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/Globus-CLI/{Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb => Globus-CLI-1.11.0-GCCcore-8.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0.eb similarity index 92% rename from easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb rename to easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0.eb index 7c7fd3f8513..31ddec11593 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-1.11.0-GCCcore-8.3.0.eb @@ -3,7 +3,6 @@ easyblock = 'PythonBundle' name = 'Globus-CLI' version = '1.11.0' -versionsuffix = '-Python-%(pyver)s' homepage = "https://docs.globus.org/cli/" description = """A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services @@ -11,9 +10,9 @@ description = """A Command Line Wrapper over the Globus SDK for Python, which pr toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -builddependencies = [('binutils', '2.32')] +multi_deps = {'Python': ['3.7.4', '2.7.16']} -dependencies = [('Python', '3.7.4')] +builddependencies = [('binutils', '2.32')] use_pip = True @@ -43,6 +42,8 @@ exts_list = [ }), ] +fix_python_shebang_for = ['bin/globus', 'bin/jp.py', 'bin/pyjwt'] + sanity_check_commands = ['globus --help'] moduleclass = 'data' From 24e0c248a1028d76b6bc7dfc383491c8e43da9a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2019 12:55:44 +0100 Subject: [PATCH 292/468] add missing checksums for Armadillo --- .../a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb | 3 ++- .../a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb | 3 ++- .../a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb index 8f548fef7de..b0a94b8f9ef 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb @@ -9,8 +9,9 @@ description = """Armadillo is an open-source C++ linear algebra library (matrix toolchain = {'name': 'foss', 'version': '2016b'} -sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6790d5e6b41fcac6733632a9c3775239806d00178886226dec3f986a884f4c2d'] dependencies = [ ('Boost', '1.61.0', versionsuffix), diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb index 509aa4c19ab..7cdb305c272 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb @@ -9,8 +9,9 @@ description = """Armadillo is an open-source C++ linear algebra library (matrix toolchain = {'name': 'intel', 'version': '2016b'} -sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ba56fb7b31c77d7ecd41334243d8a45d51e7559f76f6371783c17a72432dd486'] dependencies = [ ('Boost', '1.63.0', versionsuffix), diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb index ee8b4d3fb72..a2ef11d1f1e 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb @@ -9,8 +9,8 @@ description = """Armadillo is an open-source C++ linear algebra library (matrix toolchain = {'name': 'intel', 'version': '2016b'} -sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] checksums = ['a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b'] dependencies = [ From 182b721387c5ce01cb5a760471bf59c042567afb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sat, 21 Dec 2019 13:07:47 +0000 Subject: [PATCH 293/468] adding easyconfigs: impi-2019.6.166-iccifort-2020.0.166.eb --- .../impi-2019.6.166-iccifort-2020.0.166.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb diff --git a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb new file mode 100644 index 00000000000..d5eea149d15 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2019.6.166' + +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifort', 'version': '2020.0.166'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16120/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +moduleclass = 'mpi' From ba269023e79668f5567df1ab518fe2d23a192fcb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2019 17:28:28 +0100 Subject: [PATCH 294/468] use https for Armadillo homepage & source URLs --- .../a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb | 4 ++-- .../Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb | 4 ++-- .../Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb index b0a94b8f9ef..9f314673f9d 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb @@ -2,14 +2,14 @@ name = 'Armadillo' version = '7.600.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://arma.sourceforge.net/' +homepage = 'https://arma.sourceforge.net/' description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['http://sourceforge.net/projects/arma/files'] +source_urls = ['https://sourceforge.net/projects/arma/files'] sources = [SOURCELOWER_TAR_XZ] checksums = ['6790d5e6b41fcac6733632a9c3775239806d00178886226dec3f986a884f4c2d'] diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb index 7cdb305c272..d4987d1292e 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb @@ -2,14 +2,14 @@ name = 'Armadillo' version = '7.800.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://arma.sourceforge.net/' +homepage = 'https://arma.sourceforge.net/' description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://sourceforge.net/projects/arma/files'] +source_urls = ['https://sourceforge.net/projects/arma/files'] sources = [SOURCELOWER_TAR_XZ] checksums = ['ba56fb7b31c77d7ecd41334243d8a45d51e7559f76f6371783c17a72432dd486'] diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb index a2ef11d1f1e..b56254e364a 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb @@ -2,14 +2,14 @@ name = 'Armadillo' version = '7.950.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://arma.sourceforge.net/' +homepage = 'https://arma.sourceforge.net/' description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://sourceforge.net/projects/arma/files'] +source_urls = ['https://sourceforge.net/projects/arma/files'] sources = [SOURCELOWER_TAR_XZ] checksums = ['a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b'] From b45ac66b3a4257a856b8c32cd4091d61ce2a5793 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2019 18:01:55 +0100 Subject: [PATCH 295/468] stick to -O1 for CDO 1.9.8 with intel/2019b toolchain --- easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb index 9eec0ec1e34..4cd2227ffac 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.8-intel-2019b.eb @@ -7,7 +7,8 @@ homepage = 'https://code.zmaw.de/projects/cdo' description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" toolchain = {'name': 'intel', 'version': '2019b'} -toolchainopts = {'pic': True, 'usempi': True} +# stick to lowopt (-O1) to avoid internal compiler error when building on Intel Skylake +toolchainopts = {'pic': True, 'usempi': True, 'lowopt': True} source_urls = ['https://code.mpimet.mpg.de/attachments/download/20826/'] sources = [SOURCELOWER_TAR_GZ] From 3a0920f573b577d3e73ba5019ec33d3ecee3046a Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Sun, 22 Dec 2019 12:27:33 +0100 Subject: [PATCH 296/468] adding easyconfigs: GDAL-3.0.0-intel-2019a-Python-2.7.15.eb --- .../GDAL-3.0.0-intel-2019a-Python-2.7.15.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..0e830e6c8d6 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-python-CC-CXX.patch'] +checksums = [ + 'ad316fa052d94d9606e90b20a514b92b2dd64e3142dfdbd8f10981a5fcd5c43e', # gdal-3.0.0.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +dependencies = [ + ('Python', '2.7.15'), + ('netCDF', '4.6.2'), + ('expat', '2.2.6'), + ('GEOS', '3.7.2', '-Python-%(pyver)s'), + ('SQLite', '3.27.2'), + ('libxml2', '2.9.8'), + ('libpng', '1.6.36'), + ('libjpeg-turbo', '2.0.2'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.0.10'), + ('zlib', '1.2.11'), + ('cURL', '7.63.0'), + ('PCRE', '8.43'), + ('PROJ', '6.0.0'), + ('libgeotiff', '1.5.1'), + ('SciPy-bundle', '2019.03'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +prebuildopts = "export LDSHARED='icc -shared' && " + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT, + 'lib/python%%(pyshortver)s/site-packages/osgeo/_gdal_array.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' From 20689167ef0443fd11665046d77a690fdf8989c9 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 9 Dec 2019 16:51:13 +0100 Subject: [PATCH 297/468] {bio}[foss/2018b] FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb --- ...-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb | 86 + .../f/FSL/FSL-6.0.2_Enable_GPU_build.patch | 16 + ....2_probtrackx2_gpu_large_mri_support.patch | 3883 +++++++++++++++++ 3 files changed, 3985 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb new file mode 100644 index 00000000000..ad618253ded --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb @@ -0,0 +1,86 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Some tools like icmp are missing since they are built with the fslpython_install.sh script +# which locally installs Miniconda and creates a virtual environment. This is too messy and +# an alternative solution is necessary to install them. +# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 +# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation + +name = 'FSL' +version = '6.0.2' +local_python_suffix = '-Python-2.7.15' +local_CUDA_suffix = '-CUDA-10.0.130' +versionsuffix = '{0}{1}'.format(local_python_suffix, local_CUDA_suffix) + +homepage = 'https://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ["https://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-6.0.2_Makefile_fixes.patch', + 'FSL-6.0.2_Build_extras.patch', + 'FSL-6.0.1_Melodic-use-ifstream-good.patch', + 'FSL-6.0.2_Enable_GPU_build.patch', + # Fixes https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1911&L=FSL&P=R2783 + 'FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', +] +checksums = [ + 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz + '3a14d9c3ea75d90fa3e4beb5da3cd11a60c6859441acaece02b32ccab6aa278f', # FSL-6.0.2_Makefile_fixes.patch + '2b7ade2146fadbba6c983370bb030ac4e2b11d8bf5259eacc8f3054d3d11003f', # FSL-6.0.2_Build_extras.patch + 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch + '4870f20e84c24331418ea9d5ee67d5ba9cf075bcc85b053d4d8b7a276a96a1a5', # FSL-6.0.2_Enable_GPU_build.patch + # FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch + '05f6ddf6b149e234ea7428bd5b510a72aa8f131a00fda0e369f854b722d88b19', + '4479aa501a7e6e9f1a0063e4ddb680836147ba08673d3fccb9e1db3c4d910672', # FSL-6.0.1_Fix_fsl_exec_script.patch +] + +builddependencies = [ + ('Boost', '1.67.0'), +] + +dependencies = [ + ('libgd', '2.2.5'), + ('libxml2', '2.9.8'), + ('libxml++', '2.40.1'), + ('SQLite', '3.24.0'), + ('libpng', '1.6.34'), + ('Tk', '8.6.8'), + ('NLopt', '2.4.2'), + ('freeglut', '3.0.0'), + ('expat', '2.2.5'), + ('zlib', '1.2.11'), + ('VTK', '8.1.1', local_python_suffix), + ('GSL', '2.5'), + ('Qwt', '6.1.4'), + ('CUDA', '10.0.130'), +] + +# FSLDIR needs to be defined when running postinstall to get the correct shebang +# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 +postinstallcmds = [( + 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH ' + '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' +)] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +# Adding the bin from the virtualenv was the only way to get things working... +modextrapaths = { + 'PATH': 'fsl/fslpython/bin', + 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch new file mode 100644 index 00000000000..8c908e9b7b0 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch @@ -0,0 +1,16 @@ +diff -Nru fsl.orig/src/fdt/fslconfig fsl/src/fdt/fslconfig +--- fsl.orig/src/fdt/fslconfig 2019-10-11 13:50:36.336062960 +0200 ++++ fsl/src/fdt/fslconfig 2019-10-11 18:09:38.260806371 +0200 +@@ -1,3 +1 @@ +-if [ `hostname` == "caper.fmrib.ox.ac.uk" -o `hostname` == "jalapeno19.fmrib.ox.ac.uk" ]; then +- export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; +-fi ++export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; +diff -Nru fsl.orig/src/ptx2/fslconfig fsl/src/ptx2/fslconfig +--- fsl.orig/src/ptx2/fslconfig 2019-10-11 13:50:36.310062989 +0200 ++++ fsl/src/ptx2/fslconfig 2019-10-11 18:09:19.874825110 +0200 +@@ -1,3 +1 @@ +-if [ `hostname` == "caper.fmrib.ox.ac.uk" -o `hostname` == "jalapeno19.fmrib.ox.ac.uk" ]; then +- export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; +-fi ++export MAKEOPTIONS="${MAKEOPTIONS} COMPILE_GPU=1" ; diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch new file mode 100644 index 00000000000..8d76f676392 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch @@ -0,0 +1,3883 @@ +# This should fix what was described in this thread https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1911&L=FSL&O=D&X=C89E84F6301F100D81&Y=caspar.vanleeuwen%40surfsara.nl&P=96399 +# In addition, I included a change in tractographyInput.cc to explicitely call 'round' from the namespace 'MISCMATHS'. +diff -Nru fsl.orig/src/ptx2/CUDA/intersectionsDevice.cu fsl/src/ptx2/CUDA/intersectionsDevice.cu +--- fsl.orig/src/ptx2/CUDA/intersectionsDevice.cu 2019-11-15 10:47:30.358790161 +0100 ++++ fsl/src/ptx2/CUDA/intersectionsDevice.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include + +diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_gpu.cu +--- fsl.orig/src/ptx2/CUDA/memManager_gpu.cu 2019-11-15 10:47:30.376790024 +0100 ++++ fsl/src/ptx2/CUDA/memManager_gpu.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,70 +4,11 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + +-cudaError_t checkCuda(cudaError_t result){ ++cudaError_t checkCuda(cudaError_t result, const char *msg=NULL){ + if (result != cudaSuccess) { ++ if (msg) fprintf(stderr, "Error: %s\n", msg); + fprintf(stderr, "CUDA Runtime Error: %s\n", + cudaGetErrorString(result)); + exit(1); +@@ -468,62 +409,155 @@ + } + } + ++size_t calculate_mem_required(tractographyData& data_host){ ++ probtrackxOptions& opts =probtrackxOptions::getInstance(); ++ size_t total_mem_required; ++ total_mem_required = sizeof(tractographyData); ++ total_mem_required += data_host.nseeds*3*sizeof(float); // seeds ++ if(opts.network.value()) total_mem_required += data_host.nseeds*sizeof(float); // network ++ total_mem_required += 2*data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float); //mask & lut_vol2mat ++ total_mem_required += 3*data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float); // samples ++ ++ size_t seedVolSize=data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]*sizeof(float); ++ size_t voxFacesIndexSize = (data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int); ++ if(data_host.avoid.NVols) total_mem_required += seedVolSize; ++ if(data_host.avoid.NSurfs){ ++ size_t surfSize = size_t(data_host.avoid.sizesStr[1]*sizeof(float)) + data_host.avoid.sizesStr[2]*sizeof(int) ++ + data_host.avoid.sizesStr[3]*sizeof(int) + voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.stop.NVols) total_mem_required += seedVolSize; ++ if(data_host.stop.NSurfs){ ++ size_t surfSize = size_t(data_host.stop.sizesStr[1]*sizeof(float)) + data_host.stop.sizesStr[2]*sizeof(int) ++ + data_host.stop.sizesStr[3]*sizeof(int) + voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.wtstop.NVols) total_mem_required += data_host.wtstop.NVols * seedVolSize; ++ if(data_host.wtstop.NSurfs){ ++ size_t surfSize = size_t(data_host.wtstop.sizesStr[1]*sizeof(float)) + data_host.wtstop.sizesStr[2]*sizeof(int) ++ + data_host.wtstop.sizesStr[3]*sizeof(int) + data_host.wtstop.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.network.NVols) total_mem_required += data_host.network.NVols * seedVolSize; ++ if(data_host.network.NSurfs){ ++ size_t surfSize = size_t(data_host.network.sizesStr[1]*sizeof(float)) + data_host.network.sizesStr[2]*sizeof(int) ++ + data_host.network.sizesStr[3]*sizeof(int) + data_host.network.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.network.NVols||data_host.network.NSurfs){ ++ total_mem_required += data_host.network.NVols+data_host.network.NSurfs*sizeof(int); ++ } ++ if(data_host.networkREF.NVols) total_mem_required += seedVolSize; ++ if(data_host.networkREF.NSurfs){ ++ size_t surfSize = size_t(data_host.networkREF.sizesStr[1]*sizeof(float)) + data_host.networkREF.sizesStr[2]*sizeof(int) ++ + data_host.networkREF.sizesStr[3]*sizeof(int) + voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.waypoint.NVols) total_mem_required += data_host.waypoint.NVols * seedVolSize; ++ if(data_host.waypoint.NSurfs){ ++ size_t surfSize = size_t(data_host.waypoint.sizesStr[1]*sizeof(float)) + data_host.waypoint.sizesStr[2]*sizeof(int) ++ + data_host.waypoint.sizesStr[3]*sizeof(int) + data_host.waypoint.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.waypoint.NVols||data_host.waypoint.NSurfs){ ++ total_mem_required += data_host.waypoint.NVols+data_host.waypoint.NSurfs*sizeof(int); ++ } ++ if(data_host.targets.NVols) total_mem_required += data_host.targets.NVols * seedVolSize; ++ if(data_host.targets.NSurfs){ ++ size_t surfSize = size_t(data_host.targets.sizesStr[1]*sizeof(float)) + data_host.targets.sizesStr[2]*sizeof(int) ++ + data_host.targets.sizesStr[3]*sizeof(int) + data_host.targets.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.targets.NVols||data_host.targets.NSurfs){ ++ total_mem_required += data_host.targets.NVols+data_host.targets.NSurfs*sizeof(int); ++ } ++ if(data_host.targetsREF.NVols) total_mem_required += seedVolSize; ++ if(data_host.targetsREF.NSurfs){ ++ size_t surfSize = size_t(data_host.targetsREF.sizesStr[1]*sizeof(float)) + data_host.targetsREF.sizesStr[2]*sizeof(int) ++ + data_host.targetsREF.sizesStr[3]*sizeof(int) + voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.lrmatrix1.NVols){ ++ if(opts.matrix2out.value()) ++ total_mem_required += data_host.lrmatrix1.NVols*data_host.M2sizes[0]*data_host.M2sizes[1]*data_host.M2sizes[2]*sizeof(float); ++ else ++ total_mem_required += data_host.lrmatrix1.NVols * seedVolSize; ++ } ++ if(data_host.lrmatrix1.NSurfs){ ++ size_t surfSize = size_t(data_host.lrmatrix1.sizesStr[0]*sizeof(int)) ++ + data_host.lrmatrix1.sizesStr[1]*sizeof(float) + data_host.lrmatrix1.sizesStr[2]*sizeof(int) ++ + data_host.lrmatrix1.sizesStr[3]*sizeof(int) + data_host.lrmatrix1.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.matrix3.NVols) total_mem_required += data_host.matrix3.NVols * seedVolSize; ++ if(data_host.matrix3.NSurfs){ ++ size_t surfSize = size_t(data_host.matrix3.sizesStr[0]*sizeof(int)) ++ + data_host.matrix3.sizesStr[1]*sizeof(float) + data_host.matrix3.sizesStr[2]*sizeof(int) ++ + data_host.matrix3.sizesStr[3]*sizeof(int) + data_host.matrix3.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ if(data_host.lrmatrix3.NVols) total_mem_required += data_host.lrmatrix3.NVols * seedVolSize; ++ if(data_host.lrmatrix3.NSurfs){ ++ size_t surfSize = size_t(data_host.lrmatrix3.sizesStr[0]*sizeof(int)) ++ + data_host.lrmatrix3.sizesStr[1]*sizeof(float) + data_host.lrmatrix3.sizesStr[2]*sizeof(int) ++ + data_host.lrmatrix3.sizesStr[3]*sizeof(int) + data_host.lrmatrix3.NSurfs*voxFacesIndexSize; ++ total_mem_required += surfSize; ++ } ++ return total_mem_required; ++} ++ + + void copy_to_gpu( tractographyData& data_host, +- tractographyData*& data_gpu) ++ tractographyData*& data_gpu) + { + probtrackxOptions& opts =probtrackxOptions::getInstance(); + ++ size_t total_mem_required = calculate_mem_required(data_host); ++ cout << "Memory required for allocating data (MB): "<< total_mem_required/1048576 << endl; ++ ++ size_t free,total; ++ cudaMemGetInfo(&free,&total); ++ if(total_mem_required > free){ ++ cout << "Not enough Memory available on device. Exiting ..." << endl; ++ terminate(); ++ } ++ + checkCuda(cudaMalloc((void**)&data_gpu,sizeof(tractographyData))); + checkCuda(cudaMemcpy(data_gpu,&data_host,sizeof(tractographyData),cudaMemcpyHostToDevice)); + + int* auxI; + float* auxF; +- +- // sizes and dims .... now in Constant memory +- ++ + // seeds +- checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*3*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*3*sizeof(float)), "Allocating seeds"); + checkCuda(cudaMemcpy(auxF,data_host.seeds,data_host.nseeds*3*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->seeds,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + if(opts.network.value()){ +- checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nseeds*sizeof(float)), "Allocating Network ROIs"); + checkCuda(cudaMemcpy(auxF,data_host.seeds_ROI,data_host.nseeds*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->seeds_ROI,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + // mask +- checkCuda(cudaMalloc((void**)&auxF,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float)), "Allocating mask"); + checkCuda(cudaMemcpy(auxF,data_host.mask,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(float),cudaMemcpyHostToDevice)); +- checkCuda(cudaMemcpy(&data_gpu->mask,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMemcpy(&data_gpu->mask,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + // th_samples +- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating th_samples"); + checkCuda(cudaMemcpy(auxF,data_host.thsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); +- checkCuda(cudaMemcpy(&data_gpu->thsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMemcpy(&data_gpu->thsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + // ph_samples +- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating ph_samples"); + checkCuda(cudaMemcpy(auxF,data_host.phsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); +- checkCuda(cudaMemcpy(&data_gpu->phsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMemcpy(&data_gpu->phsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + // f_samples +- checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float))); ++ checkCuda(cudaMalloc((void**)&auxF,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float)), "Allocating f_samples"); + checkCuda(cudaMemcpy(auxF,data_host.fsamples,data_host.nfibres*data_host.nsamples*data_host.nvoxels*sizeof(float),cudaMemcpyHostToDevice)); +- checkCuda(cudaMemcpy(&data_gpu->fsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMemcpy(&data_gpu->fsamples,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + // lut_vol2mat +- checkCuda(cudaMalloc((void**)&auxI,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int))); ++ checkCuda(cudaMalloc((void**)&auxI,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int)), "Allocating lut_vol2mat"); + checkCuda(cudaMemcpy(auxI,data_host.lut_vol2mat,data_host.Dsizes[0]*data_host.Dsizes[1]*data_host.Dsizes[2]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lut_vol2mat,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + +- //Seeds_to_DTI...... now in Constant memory +- +- //DTI_to_Seeds...... now in Constant memory +- +- //VOX2MM...... now in Constant memory +- +- //NON-LINEAR ...... now in Constant memory and Texture Memory +- +- //Warp sizes.... now in constant memory +- +- //Sampling Inverse.... now in constant memory +- + //Avoid mask + if(data_host.avoid.NVols){ + checkCuda(cudaMalloc((void**)&auxF,data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]*sizeof(float))); +@@ -531,10 +565,6 @@ + checkCuda(cudaMemcpy(&data_gpu->avoid.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.avoid.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.avoid.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.avoid.locs,data_host.avoid.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->avoid.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); +- // no deed locs + checkCuda(cudaMalloc((void**)&auxF,data_host.avoid.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.avoid.vertices,data_host.avoid.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->avoid.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -555,10 +585,6 @@ + checkCuda(cudaMemcpy(&data_gpu->stop.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.stop.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.stop.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.stop.locs,data_host.stop.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->stop.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); +- // no need locs + checkCuda(cudaMalloc((void**)&auxF,data_host.stop.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.stop.vertices,data_host.stop.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->stop.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -579,10 +605,6 @@ + checkCuda(cudaMemcpy(&data_gpu->wtstop.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.wtstop.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.wtstop.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.wtstop.locs,data_host.wtstop.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->wtstop.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); +- // no need locs + checkCuda(cudaMalloc((void**)&auxF,data_host.wtstop.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.wtstop.vertices,data_host.wtstop.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->wtstop.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -592,8 +614,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.wtstop.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFaces,data_host.wtstop.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->wtstop.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.wtstop.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFacesIndex,(data_host.wtstop.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.wtstop.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFacesIndex,(data_host.wtstop.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->wtstop.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + } + // Network mask +@@ -603,10 +625,6 @@ + checkCuda(cudaMemcpy(&data_gpu->network.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.network.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.network.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.network.locs,data_host.network.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->network.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); +- // no locs + checkCuda(cudaMalloc((void**)&auxF,data_host.network.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.network.vertices,data_host.network.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->network.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -616,8 +634,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.network.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.network.VoxFaces,data_host.network.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->network.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.network.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.network.VoxFacesIndex,(data_host.network.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.network.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.network.VoxFacesIndex,(data_host.network.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->network.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + } + if(data_host.network.NVols||data_host.network.NSurfs){ +@@ -654,9 +672,6 @@ + checkCuda(cudaMemcpy(&data_gpu->waypoint.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); + } + if(data_host.waypoint.NSurfs){ +- //cudaMalloc((void**)&auxI,data_host.waypoint.sizesStr[0]*sizeof(int)); +- //cudaMemcpy(auxI,data_host.waypoint.locs,data_host.waypoint.sizesStr[0]*sizeof(int),cudaMemcpyHostToDevice); +- //cudaMemcpy(&data_gpu->waypoint.locs,&auxI,sizeof(int*),cudaMemcpyHostToDevice); + checkCuda(cudaMalloc((void**)&auxF,data_host.waypoint.sizesStr[1]*sizeof(float))); + checkCuda(cudaMemcpy(auxF,data_host.waypoint.vertices,data_host.waypoint.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->waypoint.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); +@@ -666,8 +681,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.waypoint.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFaces,data_host.waypoint.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->waypoint.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.waypoint.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFacesIndex,(data_host.waypoint.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.waypoint.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFacesIndex,(data_host.waypoint.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->waypoint.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + } + if(data_host.waypoint.NVols||data_host.waypoint.NSurfs){ +@@ -692,8 +707,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.targets.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFaces,data_host.targets.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->targets.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.targets.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFacesIndex,(data_host.targets.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.targets.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFacesIndex,(data_host.targets.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->targets.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + } + if(data_host.targets.NVols||data_host.targets.NSurfs){ +@@ -748,8 +763,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.lrmatrix1.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFaces,data_host.lrmatrix1.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lrmatrix1.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix1.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFacesIndex,(data_host.lrmatrix1.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix1.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFacesIndex,(data_host.lrmatrix1.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lrmatrix1.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + //cudaMalloc((void**)&auxI,data_host.lrmatrix1.sizesStr[4]*sizeof(int)); + //cudaMemcpy(auxI,data_host.lrmatrix1.IndexRoi,data_host.lrmatrix1.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); +@@ -774,8 +789,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.matrix3.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFaces,data_host.matrix3.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->matrix3.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.matrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFacesIndex,(data_host.matrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.matrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFacesIndex,(data_host.matrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->matrix3.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + //cudaMalloc((void**)&auxI,data_host.matrix3.sizesStr[4]*sizeof(int)); + //cudaMemcpy(auxI,data_host.matrix3.IndexRoi,data_host.matrix3.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); +@@ -800,8 +815,8 @@ + checkCuda(cudaMalloc((void**)&auxI,data_host.lrmatrix3.sizesStr[3]*sizeof(int))); + checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFaces,data_host.lrmatrix3.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lrmatrix3.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); +- checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int))); +- checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFacesIndex,(data_host.lrmatrix3.NSurfs*data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1)*sizeof(int),cudaMemcpyHostToDevice)); ++ checkCuda(cudaMalloc((void**)&auxI,(data_host.lrmatrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int))); ++ checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFacesIndex,(data_host.lrmatrix3.NSurfs*(data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]+1))*sizeof(int),cudaMemcpyHostToDevice)); + checkCuda(cudaMemcpy(&data_gpu->lrmatrix3.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); + //cudaMalloc((void**)&auxI,data_host.lrmatrix3.sizesStr[4]*sizeof(int)); + //cudaMemcpy(auxI,data_host.lrmatrix3.IndexRoi,data_host.lrmatrix3.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); +diff -Nru fsl.orig/src/ptx2/CUDA/streamlinesDevice.cu fsl/src/ptx2/CUDA/streamlinesDevice.cu +--- fsl.orig/src/ptx2/CUDA/streamlinesDevice.cu 2019-11-15 10:47:30.363790122 +0100 ++++ fsl/src/ptx2/CUDA/streamlinesDevice.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2005 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #define DIVRND 1.00000001f + #define LCRAT 5.0f //box for loopcheck is five times smaller than brain mask +diff -Nru fsl.orig/src/ptx2/CUDA/tractography_CallKernels.cu fsl/src/ptx2/CUDA/tractography_CallKernels.cu +--- fsl.orig/src/ptx2/CUDA/tractography_CallKernels.cu 2019-11-15 10:47:30.381789984 +0100 ++++ fsl/src/ptx2/CUDA/tractography_CallKernels.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + void initialise_SeedsGPU( + curandState*& devStates, +diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.cc fsl/src/ptx2/CUDA/tractographyData.cc +--- fsl.orig/src/ptx2/CUDA/tractographyData.cc 2019-11-15 10:47:30.365790108 +0100 ++++ fsl/src/ptx2/CUDA/tractographyData.cc 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #ifndef EXPOSE_TREACHEROUS + #define EXPOSE_TREACHEROUS 1 +diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.h fsl/src/ptx2/CUDA/tractographyData.h +--- fsl.orig/src/ptx2/CUDA/tractographyData.h 2019-11-15 10:47:30.383789969 +0100 ++++ fsl/src/ptx2/CUDA/tractographyData.h 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + + #ifndef Data_gpu_ptx_H +@@ -99,7 +39,7 @@ + int nvoxels; + int nsamples; + int nfibres; +- int nseeds; ++ size_t nseeds; + int nparticles; + int nsteps; + +diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractography_gpu.cu +--- fsl.orig/src/ptx2/CUDA/tractography_gpu.cu 2019-11-15 10:47:30.374790038 +0100 ++++ fsl/src/ptx2/CUDA/tractography_gpu.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include + #include +@@ -92,7 +32,7 @@ + init_gpu(); + size_t free,total; + cudaMemGetInfo(&free,&total); +- cout << "Free memory at the beginning: "<< free << " ---- Total memory: " << total << "\n"; ++ cout << "Device memory available (MB): "<< free/1048576 << " ---- Total device memory(MB): " << total/1048576 << "\n"; + + probtrackxOptions& opts=probtrackxOptions::getInstance(); + +@@ -103,7 +43,7 @@ + copy_ToTextureMemory(data_host); // Set Texture memory + + cuMemGetInfo(&free,&total); +- cout << "Free memory after copying masks: "<< free << " ---- Total memory: " << total << "\n"; ++ cout << "Device memory available after copying data (MB): "<< free/1048576 << "\n"; + + int MAX_SLs; + int THREADS_STREAM; // MAX_Streamlines and NSTREAMS must be multiples +@@ -219,7 +159,6 @@ + + checkCuda(cudaDeviceSynchronize()); + cuMemGetInfo(&free,&total); +- cout << "Free memory before running iterations: "<< free << " ---- Total memory: " << total << "\n"; + + // run iterations + for(int iter=0;iter0||lengths_host[0][pos+1]>0){ + vector tmp; +- bool included_seed=false; + if(lengths_host[0][pos]>0){ + int posSEED=i*data_host.nsteps*3; + int posCURRENT=0; +@@ -365,12 +303,10 @@ + tmp.push_back(paths_host[0][posSEED+posCURRENT*3+1]); + tmp.push_back(paths_host[0][posSEED+posCURRENT*3+2]); + } +- included_seed=true; + } + if(lengths_host[0][pos+1]>0){ + int pos2=i*data_host.nsteps*3+((data_host.nsteps/2)*3); + int co=0; +- //if(included_seed) co=1; + for(;co0||lengths_host[0][pos+1]>0){ + vector tmp; +- bool included_seed=false; + if(lengths_host[0][pos]>0){ + int posSEED=i*data_host.nsteps*3; + int posCURRENT=0; +@@ -466,12 +401,10 @@ + tmp.push_back(paths_host[0][posSEED+posCURRENT*3+1]); + tmp.push_back(paths_host[0][posSEED+posCURRENT*3+2]); + } +- included_seed=true; + } + if(lengths_host[0][pos+1]>0){ + int pos2=i*data_host.nsteps*3+((data_host.nsteps/2)*3); + int co=0; +- //if(included_seed) co=1; + for(;co + #include +diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractographyInput.cc +--- fsl.orig/src/ptx2/CUDA/tractographyInput.cc 2019-11-15 10:47:30.368790085 +0100 ++++ fsl/src/ptx2/CUDA/tractographyInput.cc 2019-11-15 15:03:45.388788544 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #ifndef EXPOSE_TREACHEROUS + #define EXPOSE_TREACHEROUS +@@ -85,26 +25,15 @@ + coords[1] = MISCMATHS::round(v(2)); + coords[2] = MISCMATHS::round(v(3)); + } +-/*void applycoordchange(Matrix& coordvol, const Matrix& old2new_mat) +-{ +- for (int n=1; n<=coordvol.Nrows(); n++) { +- ColumnVector v(4); +- v << coordvol(n,1) << coordvol(n,2) << coordvol(n,3) << 1.0; +- v = old2new_mat * v; +- coordvol(n,1) = MISCMATHS::round(v(1)); +- coordvol(n,2) = MISCMATHS::round(v(2)); +- coordvol(n,3) = MISCMATHS::round(v(3)); +- } +- }*/ +- +-void tractographyInput::load_mesh( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords) ++ ++void tractographyInput::load_mesh( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { + int type=meshFileType(filename); + if (type==ASCII){ +@@ -119,14 +48,14 @@ + } + } + +-void tractographyInput::load_mesh_ascii( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords) ++void tractographyInput::load_mesh_ascii( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { + // load a freesurfer ascii mesh + ifstream f(filename.c_str()); +@@ -139,10 +68,10 @@ + cerr<<"Loading ascii file: error in the header"<>NVertices>>NFaces; + +- int posV,posF,initV,posLV; ++ size_t posV,posF,initV,posLV; + posV=vertices.size(); // maybe there were some more vertices before + posLV=locs.size(); + initV=posV; +@@ -162,7 +91,7 @@ + values.resize(NVertices); + bool zeros=false; + bool nonzeros=false; +- for (int i=0; i>vertices[posV]>>vertices[posV+1]>>vertices[posV+2]>>values[i]; // write from file to vector + if(values[i]==0) zeros=true; + else nonzeros=true; +@@ -171,30 +100,30 @@ + if (zeros&&nonzeros) allMesh=false; // then some values should be ignored + + // storing locations: use same structure for active-nonactive vertex +- int auxCount=posV-NVertices*3; +- int local_loc=1; +- for (int i=0; i>p0>>p1>>p2>>val; +@@ -208,14 +137,14 @@ + }else {cout<<"Loading ascii file: error opening file: "<& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords) ++void tractographyInput::load_mesh_vtk(string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { + ifstream f(filename.c_str()); + if (f.is_open()){ +@@ -229,9 +158,9 @@ + getline(f,header); + getline(f,header); + getline(f,header); +- int NVertices, NFaces; ++ size_t NVertices, NFaces; + f>>header>>NVertices>>header; +- int posV,posF,initV,posLV; ++ size_t posV,posF,initV,posLV; + posV=vertices.size(); + posLV=locs.size(); + initV=posV; +@@ -241,16 +170,16 @@ + // reading the points + // if is not possible to define values, then all vertices are activated + int local_loc=1; +- for (int i=0; i>vertices[posV]>>vertices[posV+1]>>vertices[posV+2]; + locs[posLV]=nlocs; + if (wcoords){ +- coords.push_back(MISCMATHS::round(vertices[posV])); +- coords.push_back(MISCMATHS::round(vertices[posV+1])); +- coords.push_back(MISCMATHS::round(vertices[posV+2])); +- coords.push_back(nroi); +- coords.push_back(local_loc); +- local_loc++; ++ coords.push_back(MISCMATHS::round(vertices[posV])); ++ coords.push_back(MISCMATHS::round(vertices[posV+1])); ++ coords.push_back(MISCMATHS::round(vertices[posV+2])); ++ coords.push_back(nroi); ++ coords.push_back(local_loc); ++ local_loc++; + } + posV=posV+3; + posLV++; +@@ -261,7 +190,7 @@ + faces.resize(posF+NFaces*3); + + // reading the triangles +- for (int i=0; i>j>>p0>>p1>>p2; +@@ -278,22 +207,22 @@ + } + } + +-void tractographyInput::load_mesh_gifti( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords) ++void tractographyInput::load_mesh_gifti(string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { + fslsurface_name::fslSurface surf; + read_surface(surf,filename); +- int posV,posF,initV,posLV; ++ size_t posV,posF,initV,posLV; + posV=vertices.size(); + posLV=locs.size(); + initV=posV; +- int count=0; ++ size_t count=0; + for (vector< fslsurface_name::vertex >::iterator i= surf.vbegin(); i!= surf.vend();++i){ + vertices.resize(posV+3); + vertices[posV]=i->x; +@@ -326,42 +255,42 @@ + } + if (zeros&&nonzeros) allMesh=false; + int local_loc=1; +- int auxCount=posV-count*3; +- for (int i=0; i& coords) ++ int* Ssizes, ++ float* Vout, ++ int& nlocs, ++ bool reset, ++ bool wcoords, ++ int nroi, ++ vector& coords) + { ++ //reset: if true, it sets -1 voxels not present in mask, ++ //reset must be false if mixed volume: stop / exclusion / targetREF, networkREF + int local_loc=1; + volume tmpvol; + read_volume(tmpvol,filename); + for (int z=0;z=0 && voxX=0 && voxY=0 && voxZ t(1); +- t[0]=j; // this position is relative to this portion of faces !!!!!! +- triangles.push_back(t); // add to set of triangles that cross voxels +- surfvol(voxX,voxY,voxZ)=triangles.size()-1; +- total++; +- }else{ // voxel already labeled as "crossed" +- triangles[val].push_back(j); // add this triangle to the set that cross this voxel +- total++; +- } ++ int val = surfvol(voxX,voxY,voxZ); ++ if (val==-1){ // this voxel hasn't been labeled yet ++ vector t(1); ++ t[0]=j; // this position is relative to this portion of faces !!!!!! ++ triangles.push_back(t); // add to set of triangles that cross voxels ++ surfvol(voxX,voxY,voxZ)=triangles.size()-1; ++ total++; ++ }else{ // voxel already labeled as "crossed" ++ triangles[val].push_back(j); // add this triangle to the set that cross this voxel ++ total++; ++ } + }else{ +- printf("Warning: Ignoring some vertices because they are defined outside the limits\n"); +- printf("Please check that your meshspace is defined correctly\n"); ++ printf("Warning: Ignoring some vertices because they are defined outside the limits\n"); ++ printf("Please check that your meshspace is defined correctly\n"); + } + } + } +@@ -471,41 +404,41 @@ + for (int z=0;z t; +- t.insert(t.end(),triangles[val].begin(),triangles[val].end()); // get position of the triangles (faces) crossed by this voxel +- for (unsigned int i=0;i add initfaces) +- count++; +- } +- voxFacesIndex[index+1]=voxFacesIndex[index]+t.size(); +- }else{ +- voxFacesIndex[index+1]=voxFacesIndex[index]; +- } +- index++; ++ int val = surfvol(x,y,z); ++ if (val!=-1){ ++ vector t; ++ t.insert(t.end(),triangles[val].begin(),triangles[val].end()); // get position of the triangles (faces) crossed by this voxel ++ for (unsigned int i=0;i add initfaces) ++ count++; ++ } ++ voxFacesIndex[index+1]=voxFacesIndex[index]+t.size(); ++ }else{ ++ voxFacesIndex[index+1]=voxFacesIndex[index]; ++ } ++ index++; + } + } + } + } + + void tractographyInput::csv_tri_crossed_voxels( float tri[3][3], +- vector& crossed) ++ vector& crossed) + { +- int minx=(int)round(tri[0][0]); +- int miny=(int)round(tri[0][1]); +- int minz=(int)round(tri[0][2]); ++ int minx=(int)MISCMATHS::round(tri[0][0]); ++ int miny=(int)MISCMATHS::round(tri[0][1]); ++ int minz=(int)MISCMATHS::round(tri[0][2]); + int maxx=minx,maxy=miny,maxz=minz; + crossed.clear(); + int i=0;int tmpi; + do{ +- tmpi=(int)round(tri[i][0]); ++ tmpi=(int)MISCMATHS::round(tri[i][0]); + minx=tmpimaxx?tmpi:maxx; +- tmpi=(int)round(tri[i][1]); ++ tmpi=(int)MISCMATHS::round(tri[i][1]); + miny=tmpimaxy?tmpi:maxy; +- tmpi=(int)round(tri[i][2]); ++ tmpi=(int)MISCMATHS::round(tri[i][2]); + minz=tmpimaxz?tmpi:maxz; + i++; +@@ -516,26 +449,26 @@ + for (int x=minx-s;x<=maxx+s;x+=1){ + for (int y=miny-s;y<=maxy+s;y+=1){ + for (int z=minz-s;z<=maxz+s;z+=1){ +- boxcentre[0]=(float)x; +- boxcentre[1]=(float)y; +- boxcentre[2]=(float)z; +- if (triBoxOverlap(boxcentre,boxhalfsize,tri)){ +- v< voxFacesVec; + vector nullV; + ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; ++ + if (fsl_imageexists(filename)){ + // filename is a volume +- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; +- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); ++ data.volume=new float[sizeVol]; ++ //memset(data.volume,-1,sizeVol*sizeof(float)); + load_volume(filename,Ssizes,data.volume,data.nlocs,true,false,0,nullV); + data.NVols=1; + }else if (meshExists(filename)){ +@@ -567,8 +502,8 @@ + if (fs){ + fs>>tmp; + do{ +- fnames.push_back(tmp); +- fs>>tmp; ++ fnames.push_back(tmp); ++ fs>>tmp; + }while (!fs.eof()); + }else{ + cerr<& refVol, +- // Output +- MaskData& data, +- Matrix& coords) ++void tractographyInput::load_rois( // Input ++ string filename, ++ Matrix mm2vox, ++ float* Sdims, // Or Matrix2 sizes ++ int* Ssizes, ++ int wcoords, ++ volume& refVol, ++ // Output ++ MaskData& data, ++ Matrix& coords) + { ++ //wcoords:0 do not write, 1 write only coords, 2 write also ROI-id and position ++ + data.sizesStr=new int[3]; + data.sizesStr[0]=0; + data.sizesStr[1]=0; +@@ -644,10 +579,12 @@ + vector voxFacesVec; + vector coordsV; + ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; ++ + if (fsl_imageexists(filename)){ + // filename is a volume +- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; +- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); ++ data.volume=new float[sizeVol]; ++ //memset(data.volume,-1,sizeSeed*sizeof(float)); + load_volume(filename,Ssizes,data.volume,data.nlocs,true,wcoords,0,coordsV); + data.NVols=1; + data.IndexRoi=new int[1]; +@@ -655,7 +592,8 @@ + data.sizesStr[4]=1; + }else if (meshExists(filename)){ + load_mesh(filename,verticesVec,facesVec,locsVec,data.nlocs,wcoords,0,coordsV); +- data.VoxFacesIndex=new int[Ssizes[0]*Ssizes[1]*Ssizes[2]+1]; ++ size_t sizeVox2Face = sizeVol+1; ++ data.VoxFacesIndex=new int[sizeVox2Face]; + init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[0],facesVec.size(), + 0,voxFacesVec,data.VoxFacesIndex,locsVec); + data.NSurfs=1; +@@ -670,20 +608,21 @@ + if (fs){ + fs>>tmp; + do{ +- fnames.push_back(tmp); +- if (fsl_imageexists(tmp)) data.NVols++; +- if (meshExists(tmp)) data.NSurfs++; +- fs>>tmp; ++ fnames.push_back(tmp); ++ if (fsl_imageexists(tmp)) data.NVols++; ++ if (meshExists(tmp)) data.NSurfs++; ++ fs>>tmp; + }while (!fs.eof()); + }else{ + cerr<(nv)*sizeVol; ++ load_volume(fnames[i],Ssizes,&data.volume[posSeedvol],data.nlocs,true,wcoords,nroi,coordsV); ++ data.IndexRoi[nv]=nroi; ++ nv++; ++ nroi++; + }else if (meshExists(fnames[i])){ +- load_mesh(fnames[i],verticesVec,facesVec,locsVec,data.nlocs,wcoords,nroi,coordsV); +- init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[lastfacesSize],facesVec.size()-lastfacesSize,lastfacesSize, +- voxFacesVec,&data.VoxFacesIndex[ns*(Ssizes[0]*Ssizes[1]*Ssizes[2]+1)],locsVec); +- data.IndexRoi[data.NVols+ns]=nroi; +- ns++; +- nroi++; +- lastfacesSize=facesVec.size(); ++ size_t posSeedsurf = size_t(ns)*(sizeVol+1); ++ load_mesh(fnames[i],verticesVec,facesVec,locsVec,data.nlocs,wcoords,nroi,coordsV); ++ init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[lastfacesSize],facesVec.size()-lastfacesSize,lastfacesSize, ++ voxFacesVec,&data.VoxFacesIndex[posSeedsurf],locsVec); ++ data.IndexRoi[data.NVols+ns]=nroi; ++ ns++; ++ nroi++; ++ lastfacesSize=facesVec.size(); + }else{ +- cerr<<"load_rois: Unknown file type: "< facesVec, +- // Output +- int* matrix1_locs, +- int* matrix1_idTri, +- int* matrix1_Ntri) ++ int id_vertex, ++ int id_search, ++ vector facesVec, ++ // Output ++ int* matrix1_locs, ++ int* matrix1_idTri, ++ int* matrix1_Ntri) + { + int id=id_search*3; + int num_triangles=0; +@@ -783,21 +721,19 @@ + matrix1_Ntri[id_vertex]=num_triangles; + } + +- +- + void tractographyInput::load_rois_matrix1( tractographyData& tData, +- // Input +- string filename, +- Matrix mm2vox, +- float* Sdims, +- int* Ssizes, +- bool wcoords, +- volume& refVol, +- // Output +- MaskData& data, +- Matrix& coords) ++ // Input ++ string filename, ++ Matrix mm2vox, ++ float* Sdims, ++ int* Ssizes, ++ bool wcoords, ++ volume& refVol, ++ // Output ++ MaskData& data, ++ Matrix& coords) + { +- // a maximum of 12 triangles per seed ? ++ // a maximum of 12 triangles per seed + tData.matrix1_locs=new int[12*tData.nseeds]; + tData.matrix1_idTri=new int[12*tData.nseeds]; + tData.matrix1_Ntri=new int[tData.nseeds]; +@@ -815,10 +751,12 @@ + vector voxFacesVec; + vector coordsV; + ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; ++ + if (fsl_imageexists(filename)){ + // filename is a volume +- data.volume=new float[Ssizes[0]*Ssizes[1]*Ssizes[2]]; +- //memset(data.volume,-1,Ssizes[0]*Ssizes[1]*Ssizes[2]*sizeof(float)); ++ data.volume=new float[sizeVol]; ++ //memset(data.volume,-1,sizeVol*sizeof(float)); + load_volume(filename,Ssizes,data.volume,data.nlocs,true,wcoords,0,coordsV); + data.NVols=1; + data.IndexRoi=new int[1]; +@@ -832,7 +770,7 @@ + } + }else if (meshExists(filename)){ + load_mesh(filename,verticesVec,facesVec,locsVec,data.nlocs,wcoords,0,coordsV); +- data.VoxFacesIndex=new int[Ssizes[0]*Ssizes[1]*Ssizes[2]+1]; ++ data.VoxFacesIndex=new int[sizeVol+1]; + init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[0],facesVec.size(), + 0,voxFacesVec,data.VoxFacesIndex,locsVec); + data.NSurfs=1; +@@ -850,20 +788,19 @@ + if (fs){ + fs>>tmp; + do{ +- fnames.push_back(tmp); +- if (fsl_imageexists(tmp)) data.NVols++; +- if (meshExists(tmp)) data.NSurfs++; +- fs>>tmp; ++ fnames.push_back(tmp); ++ if (fsl_imageexists(tmp)) data.NVols++; ++ if (meshExists(tmp)) data.NSurfs++; ++ fs>>tmp; + }while (!fs.eof()); + }else{ + cerr<*& m_prob, +- bool initialize_m_prob, +- volume*& m_prob2, +- bool initialize_m_prob2, +- volume4D*& m_localdir, +- volume& refVol) // reference ++size_t tractographyInput::load_seeds_rois( tractographyData& tData, ++ string seeds_filename, ++ string ref_filename, ++ float* Sdims, ++ int* Ssizes, ++ int convention, ++ float*& seeds, ++ int*& seeds_ROI, ++ Matrix& mm2vox, ++ float* vox2mm, ++ volume*& m_prob, ++ bool initialize_m_prob, ++ volume*& m_prob2, ++ bool initialize_m_prob2, ++ volume4D*& m_localdir, ++ volume& refVol) // reference + { + Log& logger = LogSingleton::getInstance(); + probtrackxOptions& opts=probtrackxOptions::getInstance(); + vector nullV; +- int nseeds=0; ++ size_t nseeds=0; ++ + if (fsl_imageexists(seeds_filename)){ + // a volume file + if(opts.network.value()){ +@@ -981,19 +918,20 @@ + Ssizes[0]=seedsVol.xsize(); + Ssizes[1]=seedsVol.ysize(); + Ssizes[2]=seedsVol.zsize(); ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; + set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); + +- seeds=new float[3*Ssizes[0]*Ssizes[1]*Ssizes[2]]; //max ++ seeds=new float[3*sizeVol]; + for (int z=0;zreinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(refVol,*m_prob); +- *m_prob=0; +- } +- if (initialize_m_prob2){ +- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(refVol,*m_prob2); +- *m_prob2=0; +- } +- if(opts.opathdir.value()){ // OPATHDIR +- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); +- copybasicproperties(refVol,*m_localdir); +- *m_localdir=0; +- } ++ read_volume(refVol,ref_filename); ++ Sdims[0]=refVol.xdim(); ++ Sdims[1]=refVol.ydim(); ++ Sdims[2]=refVol.zdim(); ++ Ssizes[0]=refVol.xsize(); ++ Ssizes[1]=refVol.ysize(); ++ Ssizes[2]=refVol.zsize(); ++ set_vox2mm(convention,Sdims,Ssizes,refVol,mm2vox,vox2mm); ++ if (initialize_m_prob){ ++ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(refVol,*m_prob); ++ *m_prob=0; ++ } ++ if (initialize_m_prob2){ ++ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(refVol,*m_prob2); ++ *m_prob2=0; ++ } ++ if(opts.opathdir.value()){ // OPATHDIR ++ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); ++ copybasicproperties(refVol,*m_localdir); ++ *m_localdir=0; ++ } + }else{ +- cerr<<"Reference volume "< locs; +@@ -1059,38 +997,38 @@ + int loc=0; + float c1,c2,c3; + for (unsigned int vertex=0;vertex>tmp; + do{ +- fnames.push_back(tmp); +- fs>>tmp; ++ fnames.push_back(tmp); ++ fs>>tmp; + }while (!fs.eof()); + }else{ + cerr<<"Seed file "< seedsVol; +- read_volume(seedsVol,fnames[i]); +- if (!found_vol){ +- refVol=seedsVol; +- Sdims[0]=seedsVol.xdim(); +- Sdims[1]=seedsVol.ydim(); +- Sdims[2]=seedsVol.zdim(); +- Ssizes[0]=seedsVol.xsize(); +- Ssizes[1]=seedsVol.ysize(); +- Ssizes[2]=seedsVol.zsize(); +- set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); +- if (initialize_m_prob){ +- m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(seedsVol,*m_prob); +- *m_prob=0; +- } +- if (initialize_m_prob2){ +- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(seedsVol,*m_prob2); +- *m_prob2=0; +- } +- if(opts.opathdir.value()){ // OPATHDIR +- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); +- copybasicproperties(seedsVol,*m_localdir); +- *m_localdir=0; +- } +- }else{ +- if (Sdims[0]!=seedsVol.xdim()||Sdims[1]!=seedsVol.ydim()||Sdims[2]!=seedsVol.zdim()|| +- Ssizes[0]!=seedsVol.xsize()||Ssizes[1]!=seedsVol.ysize()||Ssizes[2]!=seedsVol.zsize()){ +- cerr<<"Seed volumes must have same dimensions"< seedsVol; ++ read_volume(seedsVol,fnames[i]); ++ if (!found_vol){ ++ refVol=seedsVol; ++ Sdims[0]=seedsVol.xdim(); ++ Sdims[1]=seedsVol.ydim(); ++ Sdims[2]=seedsVol.zdim(); ++ Ssizes[0]=seedsVol.xsize(); ++ Ssizes[1]=seedsVol.ysize(); ++ Ssizes[2]=seedsVol.zsize(); ++ set_vox2mm(convention,Sdims,Ssizes,seedsVol,mm2vox,vox2mm); ++ if (initialize_m_prob){ ++ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(seedsVol,*m_prob); ++ *m_prob=0; ++ } ++ if (initialize_m_prob2){ ++ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(seedsVol,*m_prob2); ++ *m_prob2=0; ++ } ++ if(opts.opathdir.value()){ // OPATHDIR ++ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); ++ copybasicproperties(seedsVol,*m_localdir); ++ *m_localdir=0; ++ } ++ }else{ ++ if (Sdims[0]!=seedsVol.xdim()||Sdims[1]!=seedsVol.ydim()||Sdims[2]!=seedsVol.zdim()|| ++ Ssizes[0]!=seedsVol.xsize()||Ssizes[1]!=seedsVol.ysize()||Ssizes[2]!=seedsVol.zsize()){ ++ cerr<<"Seed volumes must have same dimensions"<reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(refVol,*m_prob); +- *m_prob=0; +- } +- if (initialize_m_prob2){ +- m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); +- copybasicproperties(refVol,*m_prob2); +- *m_prob2=0; +- } +- if(opts.opathdir.value()){ // OPATHDIR +- m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); +- copybasicproperties(refVol,*m_localdir); +- *m_localdir=0; +- } ++ read_volume(refVol,ref_filename); ++ Sdims[0]=refVol.xdim(); ++ Sdims[1]=refVol.ydim(); ++ Sdims[2]=refVol.zdim(); ++ Ssizes[0]=refVol.xsize(); ++ Ssizes[1]=refVol.ysize(); ++ Ssizes[2]=refVol.zsize(); ++ set_vox2mm(convention,Sdims,Ssizes,refVol,mm2vox,vox2mm); ++ if (initialize_m_prob){ ++ m_prob->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(refVol,*m_prob); ++ *m_prob=0; ++ } ++ if (initialize_m_prob2){ ++ m_prob2->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2]); ++ copybasicproperties(refVol,*m_prob2); ++ *m_prob2=0; ++ } ++ if(opts.opathdir.value()){ // OPATHDIR ++ m_localdir->reinitialize(Ssizes[0],Ssizes[1],Ssizes[2],6); ++ copybasicproperties(refVol,*m_localdir); ++ *m_localdir=0; ++ } + }else{ +- cerr<<"Reference volume "< locs; +- vector vertices; +- vector faces; +- load_mesh(fnames[i],vertices,faces,locs,nlocs,false,0,nullV); +- seedsV.resize(seedsV.size()+vertices.size()*3); +- int loc=0; +- float c1,c2,c3; +- float s1,s2,s3; +- for (unsigned int vertex=0;vertex=0 && s1=0 && s2=0 && s3 seedsVol; +- read_volume(seedsVol,fnames[i]); +- seedsV.resize(seedsV.size()+3*Ssizes[0]*Ssizes[1]*Ssizes[2]); //max +- for (int z=0;z locs; ++ vector vertices; ++ vector faces; ++ load_mesh(fnames[i],vertices,faces,locs,nlocs,false,0,nullV); ++ seedsV.resize(seedsV.size()+vertices.size()*3); ++ int loc=0; ++ float c1,c2,c3; ++ float s1,s2,s3; ++ for (unsigned int vertex=0;vertex=0 && s1=0 && s2=0 && s3 seedsVol; ++ read_volume(seedsVol,fnames[i]); ++ size_t sizeVol = Ssizes[0]*Ssizes[1]*Ssizes[2]; ++ seedsV.resize(seedsV.size()+3*sizeVol); //max ++ for (int z=0;z vol, +- Matrix& mm2vox, +- float* vox2mm) ++void tractographyInput::set_vox2mm(int convention, ++ float* Sdims, ++ int* Ssizes, ++ volume vol, ++ Matrix& mm2vox, ++ float* vox2mm) + { + // VOX2MM + Matrix Mvox2mm(4,4); +@@ -1315,9 +1253,9 @@ + // freesurfer + Matrix mat(4,4); + mat << -1/Sdims[0] << 0 << 0 << Ssizes[0]/2 +- << 0 << 0 << -1/Sdims[1] << Ssizes[2]/2 +- << 0 << 1/Sdims[2] << 0 << Ssizes[1]/2 +- << 0 << 0 << 0 << 1; ++ << 0 << 0 << -1/Sdims[1] << Ssizes[2]/2 ++ << 0 << 1/Sdims[2] << 0 << Ssizes[1]/2 ++ << 0 << 0 << 0 << 1; + mm2vox=mat; + Mvox2mm=mm2vox.i(); + }else if (convention==2){ +@@ -1349,25 +1287,26 @@ + vox2mm[12]=Mvox2mm(4,1); vox2mm[13]=Mvox2mm(4,2); vox2mm[14]=Mvox2mm(4,3); vox2mm[15]=Mvox2mm(4,4); + } + +-void tractographyInput::load_tractographyData( tractographyData& tData, +- volume*& m_prob, +- volume*& m_prob2, +- float**& ConNet, +- float**& ConNetb, +- int& nRowsNet, +- int& nColsNet, +- float**& ConMat1, +- float**& ConMat1b, +- int& nRowsMat1, +- int& nColsMat1, +- float**& ConMat3, +- float**& ConMat3b, +- int& nRowsMat3, +- int& nColsMat3, +- float*& m_s2targets, +- float*& m_s2targetsb, +- volume4D*& m_localdir) ++void tractographyInput::load_tractographyData(tractographyData& tData, ++ volume*& m_prob, ++ volume*& m_prob2, ++ float**& ConNet, ++ float**& ConNetb, ++ int& nRowsNet, ++ int& nColsNet, ++ float**& ConMat1, ++ float**& ConMat1b, ++ int& nRowsMat1, ++ int& nColsMat1, ++ float**& ConMat3, ++ float**& ConMat3b, ++ int& nRowsMat3, ++ int& nColsMat3, ++ float*& m_s2targets, ++ float*& m_s2targetsb, ++ volume4D*& m_localdir) + { ++ printf("Loading tractography data\n"); + probtrackxOptions& opts=probtrackxOptions::getInstance(); + Log& logger = LogSingleton::getInstance(); + +@@ -1427,7 +1366,7 @@ + for(int z=0;z0){ +- read_volume4D(tmpvol,basename+"_th"+num2str(f+1)+"samples"); +- tmpmat=tmpvol.matrix(mask3D); ++ read_volume4D(tmpvol,basename+"_th"+num2str(f+1)+"samples"); ++ tmpmat=tmpvol.matrix(mask3D); + } + for(int s=0;s Seeds transform needed" << endl; +- exit(1); ++ cerr << "TRACT::Streamliner:: DTI -> Seeds transform needed" << endl; ++ exit(1); + } + FnirtFileReader iffr(opts.dti_to_seeds.value()); + volume4D DTISeedwarp4D = iffr.FieldAsNewimageVolume4D(true); +@@ -1653,13 +1593,13 @@ + tData.Warp_D2S_sizes[2]=DTISeedwarp4D.zsize(); + tData.DTISeedwarp = new float[3*size]; + for(int v=0;v<3;v++){ +- for(int z=0;z + #include +@@ -83,84 +23,84 @@ + + /// Method load all the necessary data from the input files to perform GPU Tractography + void load_tractographyData( tractographyData& tData, +- volume*& m_prob, +- volume*& m_prob2, +- float**& ConNet, +- float**& ConNetb, +- int& nRowsNet, +- int& nColsNet, +- float**& ConMat1, +- float**& ConMat1b, +- int& nRowsMat1, +- int& nColsMat1, +- float**& ConMat3, +- float**& ConMat3b, +- int& nRowsMat3, +- int& nColsMat3, +- float*& m_s2targets, +- float*& m_s2targetsb, +- volume4D*& m_localdir); ++ volume*& m_prob, ++ volume*& m_prob2, ++ float**& ConNet, ++ float**& ConNetb, ++ int& nRowsNet, ++ int& nColsNet, ++ float**& ConMat1, ++ float**& ConMat1b, ++ int& nRowsMat1, ++ int& nColsMat1, ++ float**& ConMat3, ++ float**& ConMat3b, ++ int& nRowsMat3, ++ int& nColsMat3, ++ float*& m_s2targets, ++ float*& m_s2targetsb, ++ volume4D*& m_localdir); + + /// General Method to read a Surface file in ASCII, VTK or GIFTI format +- void load_mesh( string& filename, +- vector& vertices, // all the vertices, same order than file +- vector& faces, // all the faces, same order than file +- vector& locs, // used to store the id of a vertex in the Matrix. If -1, then vertex is non-activated +- int& nlocs, // number of ids(vertices) in the Matrix +- bool wcoords, // save coordinates of the vertices in a file ? +- int nroi, // number of ROI to identify coordinates +- vector& coords); // coordinates xyz of the vertices ++ void load_mesh( string& filename, ++ vector& vertices, // all the vertices, same order than file ++ vector& faces, // all the faces, same order than file ++ vector& locs, // used to store the id of a vertex in the Matrix. If -1, then vertex is non-activated ++ int& nlocs, // number of ids(vertices) in the Matrix ++ bool wcoords, // save coordinates of the vertices in a file ? ++ int nroi, // number of ROI to identify coordinates ++ vector& coords); // coordinates xyz of the vertices + + /// Method to read a surface file in ASCII format +- void load_mesh_ascii( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords); ++ void load_mesh_ascii( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords); + + /// Method to read a surface file in VTK format +- void load_mesh_vtk( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords); ++ void load_mesh_vtk( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords); + + /// Method to read a surface file in GIFTI format +- void load_mesh_gifti( string& filename, +- vector& vertices, +- vector& faces, +- vector& locs, +- int& nlocs, +- bool wcoords, +- int nroi, +- vector& coords); ++ void load_mesh_gifti( string& filename, ++ vector& vertices, ++ vector& faces, ++ vector& locs, ++ int& nlocs, ++ bool wcoords, ++ int nroi, ++ vector& coords); + + /// Method to read a Volume + void load_volume( string& filename, +- int* Ssizes, +- float* Vout, +- int& nlocs, +- bool reset, +- bool wcoords, +- int nroi, +- vector& coords); ++ int* Ssizes, ++ float* Vout, ++ int& nlocs, ++ bool reset, ++ bool wcoords, ++ int nroi, ++ vector& coords); + + /// Method to initialise the realtionship between voxels and triangles for a Surface +- void init_surfvol( int* Ssizes, +- Matrix& mm2vox, +- vector& vertices, +- int* faces, +- int sizefaces, // number of faces this time (maybe there are several ROIs for the same mask) +- int initfaces, // number of faces in previos times +- vector& voxFaces, // list of faces of all the voxels +- int* voxFacesIndex, // starting point of each voxel in the list +- vector& locsV); ++ void init_surfvol( int* Ssizes, ++ Matrix& mm2vox, ++ vector& vertices, ++ int* faces, ++ int sizefaces, // number of faces this time (maybe there are several ROIs for the same mask) ++ int initfaces, // number of faces in previos times ++ vector& voxFaces, // list of faces of all the voxels ++ int* voxFacesIndex, // starting point of each voxel in the list ++ vector& locsV); + + /// Method to find out what voxels are crossed by a triangle + void csv_tri_crossed_voxels(float tri[3][3], +@@ -168,62 +108,62 @@ + + /// Method to read all the ROIs of a mask in the same structure: for stop and avoid masks + void load_rois_mixed(string filename, +- Matrix mm2vox, +- float* Sdims, +- int* Ssizes, +- // Output +- MaskData& matData); ++ Matrix mm2vox, ++ float* Sdims, ++ int* Ssizes, ++ // Output ++ MaskData& matData); + + /// Method to read the ROIs of a mask in concatenated structures: for wtstop and waypoints masks +- void load_rois(// Input +- string filename, +- Matrix mm2vox, +- float* Sdims, +- int* Ssizes, +- int wcoords, +- volume& refVol, +- // Output +- MaskData& matData, +- Matrix& coords); ++ void load_rois( // Input ++ string filename, ++ Matrix mm2vox, ++ float* Sdims, ++ int* Ssizes, ++ int wcoords, ++ volume& refVol, ++ // Output ++ MaskData& matData, ++ Matrix& coords); + + /// Same than load_rois but it includes the initialisation of the rows (including triangles) of Matrix1 + void load_rois_matrix1( tractographyData& tData, +- // Input +- string filename, +- Matrix mm2vox, +- float* Sdims, +- int* Ssizes, +- bool wcoords, +- volume& refVol, +- // Output +- MaskData& data, +- Matrix& coords); ++ // Input ++ string filename, ++ Matrix mm2vox, ++ float* Sdims, ++ int* Ssizes, ++ bool wcoords, ++ volume& refVol, ++ // Output ++ MaskData& data, ++ Matrix& coords); + + /// Method to load the seeds. Can be defined by volumes and/or by surfaces +- int load_seeds_rois(tractographyData& tData, +- string seeds_filename, +- string ref_filename, +- float* Sdims, +- int* Ssizes, +- int convention, +- float*& seeds, +- int*& seeds_ROI, +- Matrix& mm2vox, +- float* vox2mm, +- volume*& m_prob, +- bool initialize_m_prob, +- volume*& m_prob2, +- bool initialize_m_prob2, +- volume4D*& m_localdir, +- volume& refVol); ++ size_t load_seeds_rois(tractographyData& tData, ++ string seeds_filename, ++ string ref_filename, ++ float* Sdims, ++ int* Ssizes, ++ int convention, ++ float*& seeds, ++ int*& seeds_ROI, ++ Matrix& mm2vox, ++ float* vox2mm, ++ volume*& m_prob, ++ bool initialize_m_prob, ++ volume*& m_prob2, ++ bool initialize_m_prob2, ++ volume4D*& m_localdir, ++ volume& refVol); + + /// Method to set the transformation: voxel to milimeters +- void set_vox2mm(int convention, +- float* Sdims, +- int* Ssizes, +- volume vol, +- Matrix& mm2vox, // 4x4 +- float* vox2mm); // 4x4 ++ void set_vox2mm(int convention, ++ float* Sdims, ++ int* Ssizes, ++ volume vol, ++ Matrix& mm2vox, // 4x4 ++ float* vox2mm); // 4x4 + + }; + +diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tractographyKernels.cu +--- fsl.orig/src/ptx2/CUDA/tractographyKernels.cu 2019-11-15 10:47:30.371790061 +0100 ++++ fsl/src/ptx2/CUDA/tractographyKernels.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include + #include +@@ -77,17 +17,17 @@ + + template + __global__ void get_path_kernel( +- tractographyData* data_gpu, +- const int maxThread, ++ tractographyData* data_gpu, ++ const int maxThread, + //essential +- curandState* state, +- const long long offset, ++ curandState* state, ++ const long long offset, + //loopcheck +- int* loopcheckkeys, +- float3* loopcheckdirs, ++ int* loopcheckkeys, ++ float3* loopcheckdirs, + //OUTPUT +- float* path, +- int* lengths) ++ float* path, ++ int* lengths) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -124,13 +64,15 @@ + + // Use path to store my intial coordinates + // We want to start at the same exact point, even if sampvox is activated +- path[id*data_gpu->nsteps*3]= data_gpu->seeds[numseed*3]; +- path[id*data_gpu->nsteps*3+1]= data_gpu->seeds[numseed*3+1]; +- path[id*data_gpu->nsteps*3+2]= data_gpu->seeds[numseed*3+2]; +- +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]= data_gpu->seeds[numseed*3]; +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+1]= data_gpu->seeds[numseed*3+1]; +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+2]= data_gpu->seeds[numseed*3+2]; ++ uint offset_path_fw = id*data_gpu->nsteps*3; ++ uint offset_path_bw = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ path[offset_path_fw]= data_gpu->seeds[numseed*3]; ++ path[offset_path_fw+1]= data_gpu->seeds[numseed*3+1]; ++ path[offset_path_fw+2]= data_gpu->seeds[numseed*3+2]; ++ ++ path[offset_path_bw]= data_gpu->seeds[numseed*3]; ++ path[offset_path_bw+1]= data_gpu->seeds[numseed*3+1]; ++ path[offset_path_bw+2]= data_gpu->seeds[numseed*3+2]; + + + if(data_gpu->sampvox>0){ +@@ -145,13 +87,13 @@ + rej=false; + } + +- path[id*data_gpu->nsteps*3]+=dx/C_Sdims[0]; +- path[id*data_gpu->nsteps*3+1]+=dy/C_Sdims[1]; +- path[id*data_gpu->nsteps*3+2]+=dz/C_Sdims[2]; +- +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]+=dx/C_Sdims[0]; +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+1]+=dy/C_Sdims[1]; +- path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)+2]+=dz/C_Sdims[2]; ++ path[offset_path_fw]+=dx/C_Sdims[0]; ++ path[offset_path_fw+1]+=dy/C_Sdims[1]; ++ path[offset_path_fw+2]+=dz/C_Sdims[2]; ++ ++ path[offset_path_bw]+=dx/C_Sdims[0]; ++ path[offset_path_bw+1]+=dy/C_Sdims[1]; ++ path[offset_path_bw+2]+=dz/C_Sdims[2]; + } + // track in one direction + lengths[id*2]=streamline(data_gpu, +@@ -161,7 +103,7 @@ + &partRx[threadIdx.x],&partRy[threadIdx.x],&partRz[threadIdx.x], + &memSH_a[threadIdx.x],&memSH_b[threadIdx.x],&memSH_c[threadIdx.x], + &memSH_d[threadIdx.x],&memSH_e[threadIdx.x],&memSH_f[threadIdx.x], +- &path[id*data_gpu->nsteps*3],part_init,part_has_jumped); ++ &path[offset_path_fw],part_init,part_has_jumped); + + // track in the other direction + lengths[id*2+1]=streamline(data_gpu, +@@ -171,7 +113,7 @@ + &partRx[threadIdx.x],&partRy[threadIdx.x],&partRz[threadIdx.x], + &memSH_a[threadIdx.x],&memSH_b[threadIdx.x],&memSH_c[threadIdx.x], + &memSH_d[threadIdx.x],&memSH_e[threadIdx.x],&memSH_f[threadIdx.x], +- &path[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)],part_init,part_has_jumped); ++ &path[offset_path_bw],part_init,part_has_jumped); + + state[id]=localState; // save state, otherwise random numbers will be repeated (start at the same point) + } +@@ -180,11 +122,11 @@ + /////// AVOID MASK /////// + ///////////////////////// + template +-__global__ void avoid_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- //INPUT-OUTPUT +- float* paths, +- int* lengths) ++__global__ void avoid_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ //INPUT-OUTPUT ++ float* paths, ++ int* lengths) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -199,7 +141,8 @@ + /////////////////////// + ////// ONE WAY //////// + /////////////////////// +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + int2 rejflag; + +@@ -253,8 +196,9 @@ + /////////////////////// + ////// OTHER WAY ///// + /////////////////////// +- rejflag.y=0; +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ rejflag.y=0; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + segmentAx[threadIdx.x]=mypath[0]; +@@ -313,11 +257,11 @@ + /////// STOP MASK /////// + ///////////////////////// + template +-__global__ void stop_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- // INPUT-OUTPUT +- float* paths, +- int* lengths) // num of coordinates ++__global__ void stop_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ // INPUT-OUTPUT ++ float* paths, ++ int* lengths) // num of coordinates + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -333,7 +277,8 @@ + /////////////////////// + ////// ONE WAY //////// + /////////////////////// +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + segmentAx[threadIdx.x]=mypath[0]; + segmentAy[threadIdx.x]=mypath[1]; +@@ -387,8 +332,9 @@ + } + /////////////////////// + ////// OTHER WAY ///// +- /////////////////////// +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ /////////////////////// ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + segmentAx[threadIdx.x]=mypath[0]; +@@ -454,11 +400,11 @@ + // ignoring forcefirststep ... if seed is inside wtstop: is treated + + template +-__global__ void wtstop_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- // INPUT-OUTPUT +- float* paths, +- int* lengths) ++__global__ void wtstop_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ // INPUT-OUTPUT ++ float* paths, ++ int* lengths) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -480,7 +426,8 @@ + ///////////////// + //// ONE WAY //// + ///////////////// +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + bool wtstop=false; + // set flags to 1 (still not in roi) +@@ -546,7 +493,8 @@ + //////////////////// + //// OTHER WAY ///// + //////////////////// +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + wtstop=false; + // set flags to 1 (still not in roi) +@@ -615,11 +563,11 @@ + /////// WAYPOINTS MASK //////// + /////////////////////////////// + template +-__global__ void way_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- // INNPUT-OUTPUT +- float* paths, +- int* lengths) ++__global__ void way_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ // INNPUT-OUTPUT ++ float* paths, ++ int* lengths) + { + ///// DYNAMIC SHARED MEMORY ///// + extern __shared__ float shared[]; +@@ -634,7 +582,8 @@ + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; + +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + + int numpassed=0; +@@ -745,7 +694,8 @@ + numpassed=0; + order=true; + } +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + if(waySurf){ +@@ -841,18 +791,17 @@ + ///////////////////////////// + template + // savelength 0: no --pd, nor --ompl | 1: --pd | 2: --ompl (ConNet pathlengths, ConNetb binary hits, and later calculates mean) +-__global__ void net_masks_kernel( +- tractographyData* data_gpu, +- const int maxThread, +- const long long offset, +- // INNPUT-OUTPUT +- float* paths, +- int* lengths, +- float* ConNet, +- float* ConNetb, +- // To use in case too many Net ROIs +- float* net_flags_Global, +- float* net_values_Global) ++__global__ void net_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ const long long offset, ++ // INNPUT-OUTPUT ++ float* paths, ++ int* lengths, ++ float* ConNet, ++ float* ConNetb, ++ // To use in case too many Net ROIs ++ float* net_flags_Global, ++ float* net_values_Global) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -887,7 +836,8 @@ + int numseed = (offset+id)/data_gpu->nparticles; + int ROI = data_gpu->seeds_ROI[numseed]; + +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + int numpassed=1; // count my own ROI + +@@ -987,7 +937,8 @@ + net_flags[ROI]=1; // my own ROI + numpassed=1; // count my own ROI + +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + if(netSurf){ +@@ -1092,16 +1043,16 @@ + ///////////////////////////// + template + // savelength 0: no --pd or --ompl | 1: --pd | 2: --ompl +-__global__ void targets_masks_kernel( tractographyData* data_gpu, +- const int maxThread, +- const long long offset, +- // INNPUT-OUTPUT +- float* paths, +- int* lengths, +- float* s2targets_gpu, // a values for each Seed and for each target (Nseeds x NTragets) +- float* s2targetsb_gpu, +- // To use in case too many Net ROIs +- float* targ_flags_Global) ++__global__ void targets_masks_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ const long long offset, ++ // INNPUT-OUTPUT ++ float* paths, ++ int* lengths, ++ float* s2targets_gpu, // (Nseeds x NTargets) ++ float* s2targetsb_gpu, ++ // To use in case too many Net ROIs ++ float* targ_flags_Global) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -1127,7 +1078,8 @@ + targ_flags = &targ_flags_Global[id*totalTargets]; + } + +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + int mylength=lengths[id*2]; + + for(int i=0;isteplength; +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + + if(targSurf){ +@@ -1289,16 +1242,16 @@ + /////// MATRIX MASKs ///////// + /////////////////////////////// + template // M2 is for Matrix2: it can be defined in a different space +-__global__ void matrix_kernel( tractographyData* data_gpu, +- const int maxThread, +- float* paths, +- int* lengths, +- bool pathdist, +- bool omeanpathlength, +- MaskData* matrixData, // info vols & surfs +- // OUTPUT +- float3* crossed, +- int* numcrossed) ++__global__ void matrix_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ float* paths, ++ int* lengths, ++ bool pathdist, ++ bool omeanpathlength, ++ MaskData* matrixData, // info vols & surfs ++ // OUTPUT ++ float3* crossed, ++ int* numcrossed) + { + unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; + if(id>=maxThread) return; +@@ -1331,7 +1284,8 @@ + ///////////////// + //// ONE WAY //// + ///////////////// +- float* mypath=&paths[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath=&paths[offset_path]; + if(HSurfs){ + if(M2){ + vox_to_vox_S2M2(mypath,&segmentAx[threadIdx.x],&segmentAy[threadIdx.x],&segmentAz[threadIdx.x]); +@@ -1388,7 +1342,8 @@ + if(pathdist||omeanpathlength) pathlength=-data_gpu->steplength; // it starts with the second coordinate of the path + // reverse, m_tracksign !! . If different directions when crossing 2 nodes, then the path distance is longer. + +- mypath=&paths[id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3)]; ++ offset_path = id*data_gpu->nsteps*3+((data_gpu->nsteps/2)*3); ++ mypath=&paths[offset_path]; + mylength=lengths[id*2+1]; + if(HSurfs){ + if(M2){ +@@ -1444,21 +1399,22 @@ + ///////// UPDATE PATHS VOLUME /////// + ///////////////////////////////////// + template +-__global__ void update_path_kernel( tractographyData* data_gpu, +- const int maxThread, +- float* path, +- int* lengths, +- int* beenhere, +- const int upper_limit, +- // OUTPUT +- float* m_prob, +- float* m_prob2, // for omeanpathlength +- float* m_localdir) // for opathdir ++__global__ void update_path_kernel( tractographyData* data_gpu, ++ const int maxThread, ++ float* path, ++ int* lengths, ++ int* beenhere, ++ const int upper_limit, ++ // OUTPUT ++ float* m_prob, ++ float* m_prob2, // for omeanpathlength ++ float* m_localdir) // for opathdir + { + int id = threadIdx.x + blockIdx.x*blockDim.x; + if(id>=maxThread) return; + +- float* mypath = &path[id*data_gpu->nsteps*3]; ++ uint offset_path = id*data_gpu->nsteps*3; ++ float* mypath = &path[offset_path]; + int mylength = lengths[id*2]; + int* m_beenhere = &beenhere[id*(data_gpu->nsteps)]; + int coordinatex,coordinatey,coordinatez; +@@ -1555,7 +1511,8 @@ + } + + // other way +- mypath = &path[id*data_gpu->nsteps*3+(data_gpu->nsteps/2)*3]; ++ offset_path = id*data_gpu->nsteps*3+(data_gpu->nsteps/2)*3; ++ mypath = &path[offset_path]; + mylength = lengths[id*2+1]; + pathlength=0.0f; + +diff -Nru fsl.orig/src/ptx2/CUDA/transformationsDevice.cu fsl/src/ptx2/CUDA/transformationsDevice.cu +--- fsl.orig/src/ptx2/CUDA/transformationsDevice.cu 2019-11-15 10:47:30.379790000 +0100 ++++ fsl/src/ptx2/CUDA/transformationsDevice.cu 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2005 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + __constant__ float C_Sdims[3]; + __constant__ float C_Ddims[3]; +diff -Nru fsl.orig/src/ptx2/probtrackx_gpu.cc fsl/src/ptx2/probtrackx_gpu.cc +--- fsl.orig/src/ptx2/probtrackx_gpu.cc 2019-11-15 10:47:30.549788697 +0100 ++++ fsl/src/ptx2/probtrackx_gpu.cc 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include "probtrackx.h" + #include "saveResults_ptxGPU.h" +diff -Nru fsl.orig/src/ptx2/saveResults_ptxGPU.cc fsl/src/ptx2/saveResults_ptxGPU.cc +--- fsl.orig/src/ptx2/saveResults_ptxGPU.cc 2019-11-15 10:47:30.417789709 +0100 ++++ fsl/src/ptx2/saveResults_ptxGPU.cc 2019-11-10 01:04:48.000000000 +0100 +@@ -4,67 +4,7 @@ + + Copyright (C) 2015 University of Oxford */ + +-/* Part of FSL - FMRIB's Software Library +- http://www.fmrib.ox.ac.uk/fsl +- fsl@fmrib.ox.ac.uk +- +- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +- Imaging of the Brain), Department of Clinical Neurology, Oxford +- University, Oxford, UK +- +- +- LICENCE +- +- FMRIB Software Library, Release 6.0 (c) 2018, The University of +- Oxford (the "Software") +- +- The Software remains the property of the Oxford University Innovation +- ("the University"). +- +- The Software is distributed "AS IS" under this Licence solely for +- non-commercial use in the hope that it will be useful, but in order +- that the University as a charitable foundation protects its assets for +- the benefit of its educational and research purposes, the University +- makes clear that no condition is made or to be implied, nor is any +- warranty given or to be implied, as to the accuracy of the Software, +- or that it will be suitable for any particular purpose or for use +- under any specific conditions. Furthermore, the University disclaims +- all responsibility for the use which is made of the Software. It +- further disclaims any liability for the outcomes arising from using +- the Software. +- +- The Licensee agrees to indemnify the University and hold the +- University harmless from and against any and all claims, damages and +- liabilities asserted by third parties (including claims for +- negligence) which arise directly or indirectly from the use of the +- Software or the sale of any products based on the Software. +- +- No part of the Software may be reproduced, modified, transmitted or +- transferred in any form or by any means, electronic or mechanical, +- without the express permission of the University. The permission of +- the University is not required if the said reproduction, modification, +- transmission or transference is done without financial return, the +- conditions of this Licence are imposed upon the receiver of the +- product, and all original and amended source code is included in any +- transmitted product. You may be held legally responsible for any +- copyright infringement that is caused or encouraged by your failure to +- abide by these terms and conditions. +- +- You are not permitted under this Licence to use this Software +- commercially. Use for which any financial return is received shall be +- defined as commercial use, and includes (1) integration of all or part +- of the source code or the Software into a product for sale or license +- by or on behalf of Licensee to third parties or (2) use of the +- Software or any derivative of it for research with the final aim of +- developing software products for sale or license to a third party or +- (3) use of the Software or any derivative of it for research with the +- final aim of developing non-software products for sale or license to a +- third party, or (4) use of the Software to provide any service to an +- external organisation for which payment is received. If you are +- interested in using the Software commercially, please contact Oxford +- University Innovation ("OUI"), the technology transfer company of the +- University, to negotiate a licence. Contact details are: +- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ ++/* CCOPYRIGHT */ + + #include "probtrackx.h" + #include "CUDA/tractographyInput.h" +@@ -326,7 +266,7 @@ + ////// save seeds to targets ////// + /////////////////////////////////// + if(opts.s2tout.value()){ +- long pos=0; ++ size_t pos=0; + int ntargets=data_host.targets.NVols+data_host.targets.NSurfs; + if (fsl_imageexists(opts.seedfile.value())){ + volume tmp; +@@ -392,7 +332,7 @@ + int nfaces=data_host.seeds_mesh_info[1]; + + if(f.is_open()){ +- int pos2=0; ++ size_t pos2=0; + for(int i=0;i Date: Mon, 9 Dec 2019 17:28:58 +0100 Subject: [PATCH 298/468] libxml++ and Qwt easyconfigs were also added in the PR for FSL without GPU support... I'm guessing it doesn't hurt if I add them here, since they are identical. I forgot to add the EasyConfig for the CUDA version we use anyway, so added it here --- easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb index 722568ad18c..a5caeb21a6f 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb @@ -1,5 +1,3 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - name = 'CUDA' version = '10.0.130' @@ -9,10 +7,10 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = SYSTEM +toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] -sources = ['%(namelower)s_%(version)s_410.48_linux'] +source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] +sources = ['cuda_%(version)s_410.48_linux'] checksums = ['92351f0e4346694d0fcb4ea1539856c9eb82060c25654463bfd8574ec35ee39a'] moduleclass = 'system' From 17b27385d3e6b58ac2cf285fa3774ab543b5a57b Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 9 Dec 2019 18:41:05 +0100 Subject: [PATCH 299/468] changed dummy to system for CUDA, added missing dep, and added True for toolchain of CUDA so that it picks the easyconfig with SYSTEM toolchain --- easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb | 2 +- .../f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb index a5caeb21a6f..f905b72b94d 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb @@ -7,7 +7,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] sources = ['cuda_%(version)s_410.48_linux'] diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb index ad618253ded..4f6d9625c79 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb @@ -60,7 +60,7 @@ dependencies = [ ('VTK', '8.1.1', local_python_suffix), ('GSL', '2.5'), ('Qwt', '6.1.4'), - ('CUDA', '10.0.130'), + ('CUDA', '10.0.130', '', True), ] # FSLDIR needs to be defined when running postinstall to get the correct shebang From f394d6d42c7f87c86fd4d3702116100686eaa96a Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 18 Dec 2019 15:06:56 +0100 Subject: [PATCH 300/468] Changed CUDA version to 9.2.88 which is used in this toolchain generation --- ...eb => FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/f/FSL/{FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb => FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb} (95%) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb similarity index 95% rename from easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb rename to easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb index 4f6d9625c79..ff98fa7bb9f 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb @@ -11,8 +11,8 @@ name = 'FSL' version = '6.0.2' local_python_suffix = '-Python-2.7.15' -local_CUDA_suffix = '-CUDA-10.0.130' -versionsuffix = '{0}{1}'.format(local_python_suffix, local_CUDA_suffix) +local_CUDA_ver = '9.2.88' +versionsuffix = '{0}-CUDA-{1}'.format(local_python_suffix, local_CUDA_ver) homepage = 'https://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" @@ -60,7 +60,7 @@ dependencies = [ ('VTK', '8.1.1', local_python_suffix), ('GSL', '2.5'), ('Qwt', '6.1.4'), - ('CUDA', '10.0.130', '', True), + ('CUDA', local_CUDA_ver, '', True), ] # FSLDIR needs to be defined when running postinstall to get the correct shebang From 9d9ccf5d29e4d4864942980cd7ab4414c805fb6f Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Mon, 23 Dec 2019 09:17:58 +0100 Subject: [PATCH 301/468] add GEOS dep --- .../GEOS-3.7.2-intel-2019a-Python-2.7.15.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.7.2-intel-2019a-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2-intel-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..3176a9219a8 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2-intel-2019a-Python-2.7.15.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.7.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-%(version)s_fix-Python3.patch'] +checksums = [ + '2166e65be6d612317115bfec07827c11b403c3f303e0a7420a2106bc999d7707', # geos-3.7.2.tar.bz2 + 'e14b54796d9d41261caae64b5a106b4bd8a77f37a51aa9b8ada30d87d208e2e0', # GEOS-3.7.2_fix-Python3.patch +] + +dependencies = [('Python', '2.7.15')] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' From dea4e160b4c892d5971d3064326d487f4459342d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 23 Dec 2019 12:25:50 +0000 Subject: [PATCH 302/468] Add toolchain for iccifort 2020.0.166 + impi 2019.6.166 --- easybuild/easyconfigs/i/iimpi/iimpi-2020.00.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2020.00.eb diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2020.00.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2020.00.eb new file mode 100644 index 00000000000..19313cb69e3 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2020.00.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2020.00' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_compver = '2020.0.166' +dependencies = [ + ('iccifort', local_compver), + ('impi', '2019.6.166', '', ('iccifort', local_compver)), +] + +moduleclass = 'toolchain' From 0b0fa7689a40dfb78408cb5d1c5ea9a687256c00 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 23 Dec 2019 15:27:13 +0000 Subject: [PATCH 303/468] adding easyconfigs: imkl-2020.0.166.eb, intel-2020.00.eb --- .../easyconfigs/i/imkl/imkl-2020.0.166.eb | 40 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2020.00.eb | 21 ++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.0.166.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2020.00.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166.eb new file mode 100644 index 00000000000..2caadd01059 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.0.166' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = SYSTEM + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = False + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + '/cvmfs/soft.computecanada.ca/easybuild/bin/setrpaths.sh --path %(installdir)s', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2020.00.eb b/easybuild/easyconfigs/i/intel/intel-2020.00.eb new file mode 100644 index 00000000000..0b4be950eec --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2020.00.eb @@ -0,0 +1,21 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2020.00' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_compver = '2020.0.166' +local_gccver = '9.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.32'), + ('iccifort', local_compver), + ('impi', '2019.6.166', '', ('iccifort', local_compver)), + ('imkl', local_compver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From c06380d6437d508fcaea2de33c5d3fdd78f64411 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 23 Dec 2019 15:44:41 +0000 Subject: [PATCH 304/468] Use correct imkl easyconfig --- ...kl-2020.0.166.eb => imkl-2020.0.166-iimpi-2020.00.eb} | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/i/imkl/{imkl-2020.0.166.eb => imkl-2020.0.166-iimpi-2020.00.eb} (83%) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb similarity index 83% rename from easybuild/easyconfigs/i/imkl/imkl-2020.0.166.eb rename to easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb index 2caadd01059..bd9f5456c4f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb @@ -3,15 +3,15 @@ name = 'imkl' version = '2020.0.166' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/mkl' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = SYSTEM +toolchain = {'name': 'iimpi', 'version': '2020.00'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0'] @@ -21,7 +21,7 @@ components = ['intel-mkl'] license_file = HOME + '/licenses/intel/license.lic' -interfaces = False +interfaces = True postinstallcmds = [ # extract the examples @@ -30,7 +30,6 @@ postinstallcmds = [ 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', - '/cvmfs/soft.computecanada.ca/easybuild/bin/setrpaths.sh --path %(installdir)s', ] modextravars = { From 5131285fcac0682268100e47601189f59e654f15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2019 21:57:28 +0100 Subject: [PATCH 305/468] only require sanity_pip_check if use_pip is enabled too (fixes #9563) --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d0d240a0193..e026b2f4787 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -583,7 +583,7 @@ def check_python_packages(self, changed_ecs): failing_checks.append("'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn) # require that running of "pip check" during sanity check is enabled via sanity_pip_check - if easyblock in ['PythonBundle', 'PythonPackage']: + if use_pip and easyblock in ['PythonBundle', 'PythonPackage']: sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip): failing_checks.append("sanity_pip_check is enabled in %s" % ec_fn) From 8f6877c4dfc2fa1e7c5fdc464dd454d8fb0ec618 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Dec 2019 16:35:48 +0100 Subject: [PATCH 306/468] Remove (wrong) GI_TYPELIB_PATH and XDG_DATA_DIRS Those are set to the correct folders in EasyBlock now --- easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb | 5 +---- easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb | 5 +---- easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb | 5 +---- easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.26.1-foss-2018b.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.27.1-foss-2017b.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018a.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018b.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb | 4 ---- easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb | 4 ---- .../a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb | 4 ---- .../a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb | 4 ---- easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb | 5 ----- easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb | 6 +----- easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb | 5 ----- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb | 6 +----- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb | 6 +----- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb | 5 ----- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb | 5 ----- .../GObject-Introspection-1.47.1-foss-2016a.eb | 6 +----- .../GObject-Introspection-1.47.1-intel-2016a.eb | 6 +----- .../GObject-Introspection-1.48.0-foss-2016a.eb | 6 +----- .../GObject-Introspection-1.48.0-intel-2016a.eb | 6 +----- .../GObject-Introspection-1.49.1-foss-2016b.eb | 6 +----- .../GObject-Introspection-1.49.1-intel-2016b.eb | 6 +----- .../GObject-Introspection-1.52.0-intel-2017a.eb | 5 ----- ...GObject-Introspection-1.53.5-foss-2017b-Python-2.7.14.eb | 5 ----- ...Object-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb | 5 ----- ...GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb | 5 ----- ...Object-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb | 5 ----- ...GObject-Introspection-1.54.1-foss-2018a-Python-2.7.14.eb | 5 ----- ...GObject-Introspection-1.54.1-foss-2018b-Python-2.7.15.eb | 5 ----- ...ect-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb | 5 ----- ...ject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb | 5 ----- ...Object-Introspection-1.54.1-intel-2018a-Python-2.7.14.eb | 5 ----- ...bject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb | 5 ----- .../GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb | 6 +----- .../GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb | 5 ----- .../GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb | 5 ----- .../GST-plugins-base-0.10.36-intel-2016a.eb | 6 +----- .../GST-plugins-base-0.10.36-intel-2016b.eb | 6 +----- .../GST-plugins-base-0.10.36-intel-2017a.eb | 5 ----- .../GST-plugins-base-0.10.36-intel-2017b.eb | 5 ----- .../GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb | 5 ----- .../g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb | 6 +----- .../g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb | 6 +----- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb | 6 +----- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb | 5 ----- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb | 5 ----- .../g/GStreamer/GStreamer-0.10.36-intel-2016a.eb | 6 +----- .../g/GStreamer/GStreamer-0.10.36-intel-2016b.eb | 6 +----- .../g/GStreamer/GStreamer-0.10.36-intel-2017a.eb | 5 ----- .../g/GStreamer/GStreamer-0.10.36-intel-2017b.eb | 5 ----- .../g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb | 5 ----- .../g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb | 5 ----- .../easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb | 6 +----- .../easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb | 6 +----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 5 ----- easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb | 5 ----- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb | 5 +---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb | 5 +---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb | 5 +---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2017b.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2018a.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2018a.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-foss-2018b.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb | 4 ---- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb | 4 ---- .../easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb | 2 -- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb | 6 +----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb | 6 +----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb | 6 +----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb | 6 +----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb | 6 +----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb | 5 ----- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb | 5 ----- .../easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb | 4 ---- easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb | 5 ----- .../easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb | 5 ----- easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb | 5 ----- .../w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb | 4 ---- 126 files changed, 30 insertions(+), 593 deletions(-) diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb index 4783a302722..ae2afc7cb41 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['ce6c48d77bf951083029d5a396dd552d836fff3c1715d3a7022e917e46d0c92b'] local_glibver = '2.47.5' dependencies = [ @@ -23,10 +24,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb index 0f7c93a41db..4076e9e4764 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['493a50f6c4a025f588d380a551ec277e070b28a82e63ef8e3c06b3ee7c1238f0'] dependencies = [ ('GLib', '2.48.0'), @@ -22,10 +23,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb index 2c8911864b0..0d8481aab0c 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['493a50f6c4a025f588d380a551ec277e070b28a82e63ef8e3c06b3ee7c1238f0'] dependencies = [ ('GLib', '2.48.0'), @@ -22,10 +23,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb index f04efc9fe74..9c56794ee4b 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb @@ -27,10 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb index 861d3bb1cb0..cbf1b3be3b4 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb @@ -27,10 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb index 087bca737f8..9fe571291fa 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb @@ -27,10 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.1-foss-2018b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.1-foss-2018b.eb index 31ae2910212..91cbceb0467 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.26.1-foss-2018b.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.26.1-foss-2018b.eb @@ -27,10 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb index b1f2c7ab08d..0e1cef901d0 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb @@ -27,10 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.27.1-foss-2017b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.27.1-foss-2017b.eb index 05d7042211a..121c020d635 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.27.1-foss-2017b.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.27.1-foss-2017b.eb @@ -25,10 +25,6 @@ dependencies = [('GLib', '2.53.5')] configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb index 73b453726d8..c2e6df7e545 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb @@ -25,10 +25,6 @@ dependencies = [('GLib', '2.53.5')] configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018a.eb index 6cfbc9fedda..7d41c276f68 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018a.eb @@ -27,10 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018b.eb index 779ccec1d69..678f910a897 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018b.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018b.eb @@ -27,10 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb index 166816743fb..0ed992d9688 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb @@ -28,10 +28,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb index 40c6906c774..883a9028418 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb @@ -27,10 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb index 3c8ac888a66..01ed8c0124a 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb @@ -31,10 +31,6 @@ dependencies = [ configopts = "--buildtype=release --default-library=both " configopts += "-Dintrospection=true " -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb index c16f4436c55..fc1ccab7344 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb @@ -30,10 +30,6 @@ dependencies = [ configopts = "--libdir lib " -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatspi.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb index 9ed46381df1..3156b7f7a91 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb @@ -36,10 +36,6 @@ dependencies = [ configopts = "--libdir lib " -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libatspi.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb index 5b3bce5e3a0..692c3efc5ea 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb @@ -49,9 +49,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb index 6b42d8e1b61..cf689f3d5b0 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] +checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] dependencies = [ ('dbus-glib', '0.106'), @@ -31,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb index e4ab476be13..6c27b1793db 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb @@ -32,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index 89fe1cefe22..cb0afdde87c 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] +checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] dependencies = [ ('dbus-glib', '0.106'), @@ -31,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb index a184de7e11e..c6d591837f2 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] +checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] dependencies = [ ('dbus-glib', '0.108'), @@ -31,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb index f298ef19088..5a660669287 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb @@ -32,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb index 4055794a76a..3296882a6cc 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb @@ -32,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb index ef2d0a1446a..b202c34a524 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-foss-2016a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['e5f6e18a4362af9a77790422f61f52ae3a038bf3f0cc1f912ef3183c2a511593'] dependencies = [ ('Python', '2.7.11'), @@ -33,11 +34,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb index cee6cdb2773..215d117e80e 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.47.1-intel-2016a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['e5f6e18a4362af9a77790422f61f52ae3a038bf3f0cc1f912ef3183c2a511593'] dependencies = [ ('Python', '2.7.11'), @@ -33,11 +34,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb index 2c595468ada..149666f1920 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['fa275aaccdbfc91ec0bc9a6fd0562051acdba731e7d584b64a277fec60e75877'] local_glibver = '2.48.0' dependencies = [ @@ -34,11 +35,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb index d3f6c792321..2160cbd0a5b 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-intel-2016a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['fa275aaccdbfc91ec0bc9a6fd0562051acdba731e7d584b64a277fec60e75877'] local_glibver = '2.48.0' dependencies = [ @@ -34,11 +35,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb index 76281fb06e1..b5da46b9853 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['f7ec96fd7c21c6e6d5dc5388f2468fbeacba3356b7289a5f1dd93579589cdfa5'] dependencies = [ ('Python', '2.7.12'), @@ -33,11 +34,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-2016b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-2016b.eb index 09a8cb39dc6..62f169e8a56 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-2016b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['f7ec96fd7c21c6e6d5dc5388f2468fbeacba3356b7289a5f1dd93579589cdfa5'] dependencies = [ ('Python', '2.7.12'), @@ -33,11 +34,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb index b49b9015907..5cd64f28f2d 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb @@ -35,11 +35,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-foss-2017b-Python-2.7.14.eb index b2249ed03e1..ffc81481281 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-foss-2017b-Python-2.7.14.eb @@ -36,11 +36,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb index 547eda3c600..a4eaa293a1f 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb @@ -36,11 +36,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb index cbd88a21cef..1404a59ae0b 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb @@ -36,11 +36,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true PYTHON=python3" # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python3" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb index 614806b791d..4f5d1ba431d 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb @@ -36,11 +36,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-foss-2018a-Python-2.7.14.eb index fe18b25764a..4a4ebdd03dd 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-foss-2018a-Python-2.7.14.eb @@ -36,11 +36,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-foss-2018b-Python-2.7.15.eb index bc3376ecde7..7cdbd79af0d 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-foss-2018b-Python-2.7.15.eb @@ -37,11 +37,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb index 5b386b0a84a..f6c408cd79d 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb @@ -37,11 +37,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb index 41dd871f4ee..b9be4c5be82 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb @@ -37,11 +37,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true PYTHON=python3 " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python3" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-intel-2018a-Python-2.7.14.eb index 13e73b9ec98..3a3ac796806 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-intel-2018a-Python-2.7.14.eb @@ -36,11 +36,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " # avoid using hard-coded path to 'python' in shebang of scripts buildopts = "PYTHON=python" -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb index def266fbeb7..76bed5b4ef9 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb @@ -39,11 +39,6 @@ preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " preconfigopts += "PYTHON=python3 " buildopts = "PYTHON=python3 " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb index d0bab447344..eeb3ef9aa0f 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] dependencies = [('GStreamer', '0.10.36')] @@ -27,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb index 4a56d46e941..969df09ed97 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb @@ -28,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb index d3a8d057e59..d3dc8309639 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb @@ -30,9 +30,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index f2d1e756a58..ba6f20b3e8f 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] dependencies = [('GStreamer', '0.10.36')] @@ -27,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb index 743a59e91a7..59b214716c1 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] dependencies = [('GStreamer', '0.10.36')] @@ -27,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb index a30aaa0e3eb..b4653613d92 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb @@ -28,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb index ab11d93f061..05016b9f5d7 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb @@ -28,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb index 248c36798ff..a151baa710d 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb @@ -40,9 +40,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb index 6d1390515a0..441ceedc504 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['7a193e2a66b0d7411160ef2a373184c8aa3cdeaa576fa270be346716220d9606'] dependencies = [('GStreamer', '1.6.4')] @@ -26,9 +27,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index 248204c8cc0..febe9eceb42 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['114871d4d63606b4af424a8433cd923e4ff66896b244bb7ac97b9da47f71e79e'] dependencies = [ ('GStreamer', '1.8.3'), @@ -31,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb index 3dddb7ed206..d19221d7b8f 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] dependencies = [ ('GLib', '2.48.0'), @@ -32,9 +33,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb index cbe22fd14c6..987eaec2884 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb index 8be833db619..343a9410a70 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index ccd3a73617c..a50e38f6170 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] dependencies = [ ('GLib', '2.47.5'), @@ -32,9 +33,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb index a0214562e2f..751a88f56de 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] dependencies = [ ('GLib', '2.49.5'), @@ -32,9 +33,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb index 32f3d42dc20..e7e0cd874b5 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb index cb79edee38a..52435754268 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb @@ -35,9 +35,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb index 0a975f2473e..b0017f205c6 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb @@ -36,9 +36,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb index 4e59c323248..b9eb15a43d5 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb @@ -36,9 +36,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb index 05dfd4ddef2..b5acfc00dea 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['4ccba88a286b13d6f2d8c1180f78a13dcd49f2fc3cb2b3b3f502b3a23f7c01b5'] dependencies = [ ('GLib', '2.48.0'), @@ -31,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb index 191ac522164..75ee94c4fcd 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['66b37762d4fdcd63bce5a2bec57e055f92420e95037361609900278c0db7c53f'] dependencies = [ ('GLib', '2.48.0'), @@ -29,9 +30,4 @@ sanity_check_paths = { 'dirs': ['include', 'share', 'libexec'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb index 8f98f42b866..5e837a89380 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb @@ -28,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb index f3e8bdf2f31..cdc45b21daa 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb @@ -28,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb index 5703658508f..ae737147888 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -28,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb index 45ad00ae23c..9f347da5de7 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb @@ -28,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb index b2eff3d30ae..1e80d45447c 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb @@ -28,9 +28,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb index 05643f884d4..b2d09d1b52e 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb @@ -30,9 +30,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb index d82e7671a0e..e98350b2ea8 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb @@ -32,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb index f34f8314388..7dd0b6f4f2b 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb @@ -31,9 +31,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb index 943ff5dd70f..49cf958882b 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb @@ -32,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb index 23895d53171..2d8673c8a45 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb @@ -32,9 +32,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb index 1657e797366..54dbc013813 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb @@ -31,9 +31,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-2.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index a416c0bf4cf..e6dffd21301 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -39,9 +39,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-%(version_major)s.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb index 77b3673ae83..a5c540dc54c 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb @@ -40,9 +40,4 @@ sanity_check_paths = { 'dirs': ['include/gtk-%(version_major)s.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb index 5b03df5eaf8..a3c70d5c316 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['2b6771f1ac72f687a8971e59810b8dc658e65e7d3086bd2e676e618fd541d031'] dependencies = [ ('GLib', '2.47.5'), @@ -27,8 +28,4 @@ dependencies = [ configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb index 3f2a2533d67..cf7d1b893fe 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['51eba2550262bc1f1ad3569b4420f55b9261d2fc477e33a8d9b34c7e7f0d5631'] dependencies = [ ('GLib', '2.48.0'), @@ -27,8 +28,4 @@ dependencies = [ configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb index ec51681b28d..11eb6e0224a 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['51eba2550262bc1f1ad3569b4420f55b9261d2fc477e33a8d9b34c7e7f0d5631'] dependencies = [ ('GLib', '2.48.0'), @@ -27,8 +28,4 @@ dependencies = [ configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb index ba090ee8c26..75ef7e499b6 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb @@ -37,8 +37,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb index dc996aa3c8d..857800f924a 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb @@ -37,8 +37,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb index 285da5ae82b..a314980f3d8 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb @@ -41,8 +41,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2017b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2017b.eb index 5880a77b698..7a648a82620 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2017b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2017b.eb @@ -41,8 +41,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2018a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2018a.eb index 17c264eb814..076b2942e36 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2018a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-foss-2018a.eb @@ -41,8 +41,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb index 11629a0e263..4ca27dafa61 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb @@ -41,8 +41,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb index 84054279af8..92237685fa2 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb @@ -43,8 +43,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2018a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2018a.eb index dfd2c08651b..83a9cbf3216 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2018a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2018a.eb @@ -41,8 +41,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-foss-2018b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-foss-2018b.eb index 1c20a9a2f06..98e35d84dfa 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-foss-2018b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-foss-2018b.eb @@ -41,8 +41,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb index 02bcb955cec..83422369c01 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb @@ -41,8 +41,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb index 584ff3052a6..88eb07c85d5 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb @@ -39,8 +39,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb index 55b4e4be26e..a394b340004 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb @@ -45,8 +45,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], } -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb index 125a9e28ee3..4dc9fdcef19 100644 --- a/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb @@ -29,6 +29,4 @@ sanity_check_paths = { 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], } -modextrapaths = {'XDG_DATA_DIRS': 'share'} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb index 0acf2a2b5b0..d5d1d7c9221 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d93d7cb7979c32672e902fdfa884599e63f07f2fa5b06c66147d20c516d4b8f7'] dependencies = [ ('GLib', '2.47.5'), @@ -20,11 +21,6 @@ dependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb index ed4fbf9f070..bd2a0d8793a 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d93d7cb7979c32672e902fdfa884599e63f07f2fa5b06c66147d20c516d4b8f7'] dependencies = [ ('GLib', '2.47.5'), @@ -20,11 +21,6 @@ dependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb index b22b1394b5c..5e031fb4f6e 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb @@ -31,11 +31,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb index 2f254d1b098..3274fedb233 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb @@ -31,11 +31,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb index 773d568195e..6329fb9acfe 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] dependencies = [ ('GLib', '2.49.5'), @@ -24,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb index 70652fb38a8..202f2f0566f 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] dependencies = [ ('GLib', '2.49.5'), @@ -24,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb index acb6a5e9017..292a0f19a0f 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] dependencies = [ ('GLib', '2.52.0'), @@ -24,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb index c315e68dd62..5e5b52ef599 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb @@ -22,11 +22,6 @@ builddependencies = [('GObject-Introspection', '1.53.5', '-Python-2.7.13')] configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb index ccced6e9ca2..a90f66cd480 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb @@ -25,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb index 1ac2bf9a1dd..2568b466cc3 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb @@ -25,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb index 6b747059fce..c1c6ec1c464 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb @@ -25,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb index d0ac61f2133..d71c00f706c 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb @@ -25,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb index 0f36122fcfd..fdd70ea2fb5 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb @@ -25,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb index 0f0019de6c0..67dcf574da5 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb @@ -25,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb index 55fd8055045..0dd6845f680 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb @@ -25,11 +25,6 @@ builddependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb index a8e5eb418f4..faaf6cf5831 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb @@ -27,11 +27,6 @@ dependencies = [ configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], 'dirs': [] diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb index 97c8a868177..f26c684c576 100644 --- a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb @@ -34,10 +34,6 @@ dependencies = [ configopts = '-Dgssapi=false -Dvapi=false ' -modextrapaths = { - 'XDG_DATA_DIRS': 'share', -} - sanity_check_paths = { 'files': ['lib/libsoup-2.4.%s' % SHLIB_EXT, 'lib/libsoup-gnome-2.4.%s' % SHLIB_EXT], 'dirs': ['include/libsoup-2.4/libsoup', 'include/libsoup-gnome-2.4/libsoup', 'lib/pkgconfig'] diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb index 97d80d502b5..c8277774e4a 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -30,9 +30,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb index ba42f716aee..68462d99b2c 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -30,9 +30,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb index cf7ae06dc9b..d5b44e97eb9 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb @@ -40,9 +40,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb index cc02806d7bc..93e0b6efd23 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -40,9 +40,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb index 7adedf373fd..9d0ffbe8178 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb index 8e245d82779..b9e2128d24f 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb index 34631ccf210..1bdd0370d15 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb index 584bf1cf1fd..0bfd38a58f3 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb index f74760234e8..c7baacd0236 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb index 5ba6ce875ff..bfc434235c6 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb index a6f9c6c49ce..6aeaabddb6c 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb index 8536226c275..738be55a417 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb @@ -34,9 +34,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb index c463e6d8d75..d6390435c47 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb @@ -35,9 +35,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb index ef6c66c151d..285404d9512 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb @@ -35,9 +35,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb index e3f0cb0bc42..e06d108e34d 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb @@ -35,9 +35,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb index 37db73c862f..91e61fb1b0d 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb @@ -35,9 +35,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb index 4eb831877d5..0859ccfa358 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb @@ -38,9 +38,4 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb index ae3b7d11add..df6d91580f4 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb @@ -59,8 +59,4 @@ sanity_check_paths = { 'dirs': ['include/webkitgtk-4.0/webkit2', 'libexec/webkit2gtk-4.0'], } -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', -} - moduleclass = 'lib' From 581a2f9e7c0f1262e03081ce89c9d0092e3534ef Mon Sep 17 00:00:00 2001 From: Flamefire Date: Mon, 23 Dec 2019 15:55:18 +0100 Subject: [PATCH 307/468] WORKAROUND: Remove check for Python suffix to make CI pass for old ECs --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d0d240a0193..a3f1fdf609d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -578,7 +578,8 @@ def check_python_packages(self, changed_ecs): # if Python is a dependency, that should be reflected in the versionsuffix # Tkinter is an exception, since its version always matches the Python version anyway - if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter': + if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter' and \ + ec.name != 'GObject-Introspection': if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): failing_checks.append("'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn) From 3ab2a1ec8d8e7ba8eb6a80c149e2b6268001c829 Mon Sep 17 00:00:00 2001 From: Flamefire Date: Mon, 23 Dec 2019 17:21:41 +0100 Subject: [PATCH 308/468] Add sanity_check_paths --- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb | 5 +++++ .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb | 5 +++++ .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb | 5 +++++ 3 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb index a3c70d5c316..15c82d95e80 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.32.3-intel-2016a.eb @@ -28,4 +28,9 @@ dependencies = [ configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb index cf7d1b893fe..97e246dd2c2 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb @@ -28,4 +28,9 @@ dependencies = [ configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb index 11eb6e0224a..32adb039b2f 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-intel-2016a.eb @@ -28,4 +28,9 @@ dependencies = [ configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + moduleclass = 'vis' From c862e1c016a6bf04471020bce3ed5396e0bc0e35 Mon Sep 17 00:00:00 2001 From: Flamefire Date: Mon, 23 Dec 2019 22:09:44 +0100 Subject: [PATCH 309/468] Use https --- easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb | 2 +- .../g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb | 4 ++-- .../g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb | 4 ++-- .../g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb | 4 ++-- .../GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb | 4 ++-- .../GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb | 4 ++-- .../GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb | 4 ++-- .../GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb | 4 ++-- .../GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb | 4 ++-- .../g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb | 4 ++-- .../g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb | 4 ++-- .../g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb | 4 ++-- .../g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb | 4 ++-- .../easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb | 2 +- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb | 4 ++-- easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb | 2 +- 62 files changed, 99 insertions(+), 99 deletions(-) diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb index 692c3efc5ea..718fba40f5e 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] patches = [ '%(name)s-%(version)s_call-dbus_g_thread_init.patch', diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb index cf689f3d5b0..393ff707c09 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb index 6c27b1793db..9a7574add84 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index cb0afdde87c..077becbe1ce 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb index c6d591837f2..300ec1140f3 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb index 5a660669287..28d7738913a 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb index 3296882a6cc..663e2600339 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb index eeb3ef9aa0f..b8f08048e02 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb index 969df09ed97..0e7582237eb 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb index d3dc8309639..8936feeafeb 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index ba6f20b3e8f..0b609b273ab 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb index 59b214716c1..c8ecaf22da4 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb index b4653613d92..a492a53d054 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb index 05016b9f5d7..d500a7a66b2 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb index a151baa710d..7b5130f2610 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb @@ -3,7 +3,7 @@ easyblock = 'MesonNinja' name = 'GST-plugins-base' version = '1.16.0' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['4093aa7b51e28fb24dfd603893fead8d1b7782f088b05ed0f22a21ef176fb5ae'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb index 441ceedc504..59a7ef5420c 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '1.6.4' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['7a193e2a66b0d7411160ef2a373184c8aa3cdeaa576fa270be346716220d9606'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index febe9eceb42..d8745cb8abe 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '1.8.3' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['114871d4d63606b4af424a8433cd923e4ff66896b244bb7ac97b9da47f71e79e'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb index d19221d7b8f..a5701e08087 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb index 987eaec2884..1022f546612 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb index 343a9410a70..944c423d4b6 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index a50e38f6170..37ab288b67a 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb index 751a88f56de..20f11abe9b5 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb index e7e0cd874b5..bbe6a9d2c70 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb index 52435754268..aa123aa401c 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb index b0017f205c6..5aa825df9ca 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '1.15.1' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['780ae2347f9780fea264a602a7c04a87a43998188e7bd9c59afb4d7c864f3117'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb index b9eb15a43d5..32f0d1d999b 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '1.16.0' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb index b5acfc00dea..2c2043404fa 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '1.6.4' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['4ccba88a286b13d6f2d8c1180f78a13dcd49f2fc3cb2b3b3f502b3a23f7c01b5'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb index 75ee94c4fcd..632570beb05 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '1.8.3' -homepage = 'http://gstreamer.freedesktop.org/' +homepage = 'https//gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['66b37762d4fdcd63bce5a2bec57e055f92420e95037361609900278c0db7c53f'] diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb index 4dc9fdcef19..0837de07df9 100644 --- a/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Graphene' version = '1.6.0' -homepage = 'http://ebassi.github.io/graphene/' +homepage = 'https//ebassi.github.io/graphene/' description = "Graphene is a a thin layer of types for graphic libraries" toolchain = {'name': 'intel', 'version': '2017a'} diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb index d5d1d7c9221..17dc4632b41 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.1.3' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['d93d7cb7979c32672e902fdfa884599e63f07f2fa5b06c66147d20c516d4b8f7'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb index bd2a0d8793a..729583482f2 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.1.3' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['d93d7cb7979c32672e902fdfa884599e63f07f2fa5b06c66147d20c516d4b8f7'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb index 5e031fb4f6e..3191926e739 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.2.7' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['bba0600ae08b84384e6d2d7175bea10b5fc246c4583dc841498d01894d479026'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb index 3274fedb233..8aacf3d433a 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.2.7' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['bba0600ae08b84384e6d2d7175bea10b5fc246c4583dc841498d01894d479026'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb index 6329fb9acfe..f76beaf749c 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.3.1' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb index 202f2f0566f..e76120806c7 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.3.1' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb index 292a0f19a0f..2656a45b7e6 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.3.1' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb index 5e5b52ef599..7505e190ec7 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.5.1' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['56838dfdad2729b8866763c82d623354d138a4d99d9ffb710c7d377b5cfc7c51'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb index a90f66cd480..98e9b82e717 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.7.1' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['9645a6e83313b690602017f18d4eb2adf81f2e54c6fc4471e19331304965154e'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb index 2568b466cc3..54e24e0fce5 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.7.1' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['9645a6e83313b690602017f18d4eb2adf81f2e54c6fc4471e19331304965154e'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb index c1c6ec1c464..3b8b8819231 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.7.5' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['84574e1b1f65ca694cb8fb6905309665c0368af18a312357f8ff886ee2f29563'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb index d71c00f706c..2495f04f8a1 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.7.5' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['84574e1b1f65ca694cb8fb6905309665c0368af18a312357f8ff886ee2f29563'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb index fdd70ea2fb5..878cf9b8b6e 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.9.0' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['11eca62bf0ac549b8d6be55f4e130946399939cdfe7a562fdaee711190248b00'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb index 67dcf574da5..df34c31d784 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '2.2.0' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['b7ccfcbd56b970a709e8b9ea9fb46c922c606c2feef8f086fb6a8492e530f810'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb index 0dd6845f680..6e71dcf273b 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '2.2.0' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['b7ccfcbd56b970a709e8b9ea9fb46c922c606c2feef8f086fb6a8492e530f810'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb index faaf6cf5831..cbc151f2e53 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '2.4.0' -homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['b470eff9dd5b596edf078596b46a1f83c179449f051a469430afc15869db336f'] diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb index c8277774e4a..a0492c39df7 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.39.0' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb index 68462d99b2c..505c4bff3ce 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.39.0' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb index d5b44e97eb9..e4c90a95244 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.1' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb index 93e0b6efd23..47d14495c1b 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.1' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb index 9d0ffbe8178..1cbf8f73736 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.12' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb index b9e2128d24f..d6b8c9ba093 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.14' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb index 1bdd0370d15..d1c0f7b9da6 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.14' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb index 0bfd38a58f3..bc66a8bf75b 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.3' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb index c7baacd0236..1463e00c94e 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.3' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb index bfc434235c6..c7159087e22 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.5' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb index 6aeaabddb6c..1f5c2358c9a 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.41.0' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb index 738be55a417..2e84e320d2c 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.41.0' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb index d6390435c47..0f9e403d1aa 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.41.1' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb index 285404d9512..20bb2dbb103 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.41.1' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb index e06d108e34d..3b513e75408 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.42.4' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb index 91e61fb1b0d..397ee27afe3 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.42.4' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb index 0859ccfa358..b0f037f8098 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'MesonNinja' name = 'Pango' version = '1.43.0' -homepage = 'http://www.pango.org/' +homepage = 'https//www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" From 116776a87f98c657088cfd516ab59f84706c268a Mon Sep 17 00:00:00 2001 From: Flamefire Date: Mon, 23 Dec 2019 22:32:52 +0100 Subject: [PATCH 310/468] Revert "WORKAROUND: Remove check for Python suffix to make CI pass for old ECs" This reverts commit 581a2f9e7c0f1262e03081ce89c9d0092e3534ef. --- test/easyconfigs/easyconfigs.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a3f1fdf609d..d0d240a0193 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -578,8 +578,7 @@ def check_python_packages(self, changed_ecs): # if Python is a dependency, that should be reflected in the versionsuffix # Tkinter is an exception, since its version always matches the Python version anyway - if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter' and \ - ec.name != 'GObject-Introspection': + if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter': if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): failing_checks.append("'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn) From 65ae62c7846696892d324a378c80236bacae73fa Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Dec 2019 09:03:57 +0100 Subject: [PATCH 311/468] adding easyconfigs: PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb --- ...bject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..71eb3bef743 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.34.0-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'PyGObject' +version = '3.34.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pygtk.org/' +description = """Python Bindings for GLib/GObject/GIO/GTK+""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2acb0daf2b3a23a90f52066cc23d1053339fee2f5f7f4275f8baa3704ae0c543'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('GLib', '2.60.1'), + ('GObject-Introspection', '1.60.1', versionsuffix), + ('PyCairo', '1.18.0', versionsuffix), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['include/pygobject-%(version_major)s.0/pygobject.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'gi'} + +moduleclass = 'vis' From 203b02cde50b0d454cf6fa6474e681ffcf3c0efe Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 23 Dec 2019 21:37:49 +0000 Subject: [PATCH 312/468] Add HPL --- .../h/HPL/HPL-2.3-intel-2020.00.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.00.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.00.eb new file mode 100644 index 00000000000..29917110cce --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020.00.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2020.00'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From 79f0f41cac77b8bbeba30e4e41c4cc48c1ff2c4c Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 23 Dec 2019 22:00:45 +0000 Subject: [PATCH 313/468] Correct binutils versionsuffix --- easybuild/easyconfigs/i/intel/intel-2020.00.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/intel/intel-2020.00.eb b/easybuild/easyconfigs/i/intel/intel-2020.00.eb index 0b4be950eec..7e0f6105390 100644 --- a/easybuild/easyconfigs/i/intel/intel-2020.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2020.00.eb @@ -12,7 +12,7 @@ local_compver = '2020.0.166' local_gccver = '9.2.0' dependencies = [ ('GCCcore', local_gccver), - ('binutils', '2.32'), + ('binutils', '2.32', '-GCCcore-%s' % local_gccver), ('iccifort', local_compver), ('impi', '2019.6.166', '', ('iccifort', local_compver)), ('imkl', local_compver, '', ('iimpi', version)), From 8f8d20962195aedbf3c5aa71aa7845ee9175c6e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Dec 2019 09:28:52 +0100 Subject: [PATCH 314/468] consistently use 'macros-util-macros-%(version)s.tar.gz' as source tarball in xorg-macros easyconfigs --- .../x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb | 4 ++-- .../x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb | 4 ++-- .../x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb | 5 +++-- .../x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb | 4 ++-- .../x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb | 4 ++-- .../x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb | 4 ++-- .../x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb | 4 ++-- 7 files changed, 15 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb index efb13236f60..cf00fa55140 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016a.eb @@ -18,8 +18,8 @@ description = """X.org macros utilities.""" toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8d4c2354dc54b3572573d27c0df19b291818be894a8dcf412a1b5f6086e79a8b'] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb index f73239877bc..f1a9a9583a5 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-foss-2016b.eb @@ -18,8 +18,8 @@ description = """X.org macros utilities.""" toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8d4c2354dc54b3572573d27c0df19b291818be894a8dcf412a1b5f6086e79a8b'] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb index 376e86d42e2..085f5db7ce1 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-gimkl-2.11.5.eb @@ -17,8 +17,9 @@ homepage = 'https://cgit.freedesktop.org/xorg/util/macros' description = """X.org macros utilities.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8d4c2354dc54b3572573d27c0df19b291818be894a8dcf412a1b5f6086e79a8b'] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb index 433f59d5532..217ca9884a8 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016a.eb @@ -18,8 +18,8 @@ description = """X.org macros utilities.""" toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8d4c2354dc54b3572573d27c0df19b291818be894a8dcf412a1b5f6086e79a8b'] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb index 76ade227e31..9a5c9bd5b44 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.0-intel-2016b.eb @@ -18,8 +18,8 @@ description = """X.org macros utilities.""" toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['f017f21b94141eaabc16f779aab79dccb403c66154ae67ef15bdc0b0d73e51a4'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8d4c2354dc54b3572573d27c0df19b291818be894a8dcf412a1b5f6086e79a8b'] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb index ef5b29b65ee..5ffb3e6b974 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb @@ -19,8 +19,8 @@ description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['52f6e8c86a40cff3fd840783d338da6430e1441ce4d0546179c0f74ea90591ac'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['0bb70872f45d9973db645123fe9fae9c587d1cc0ad1b3bfa67864c3f99adbd2a'] builddependencies = [ # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb index 1eb874b93b0..014e9a4eca2 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.2.0.eb @@ -19,8 +19,8 @@ description = """X.org macros utilities.""" toolchain = {'name': 'GCCcore', 'version': '7.2.0'} source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] -sources = ['util-macros-%(version)s.tar.gz'] -checksums = ['aae54a5b4556f35a85d6808e8d9a467156697c71f66b4142e42330e3a79f80c6'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] builddependencies = [ ('binutils', '2.29'), From 118721b78e472edfe8ea0efa277fad89c651f72e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Nov 2019 10:12:23 +0100 Subject: [PATCH 315/468] also define $AUGUSTUS_BIN_PATH and $AUGUSTUS_SCRIPTS_PATH in generated module file for AUGUSTUS --- .../a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb | 6 +++++- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb | 6 +++++- .../a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb | 6 +++++- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb | 6 +++++- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb | 6 +++++- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb | 6 +++++- .../easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2019a.eb | 6 +++++- 7 files changed, 35 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb index 7f1484baf58..4828f6565a3 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb @@ -40,6 +40,10 @@ sanity_check_paths = { } modextrapaths = {'PATH': 'scripts'} -modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb index 605d61c951d..db9a5a23f1a 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb @@ -44,6 +44,10 @@ sanity_check_paths = { } modextrapaths = {'PATH': 'scripts'} -modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb index 854004e05cf..d11a4006bd4 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb @@ -50,6 +50,10 @@ sanity_check_paths = { } modextrapaths = {'PATH': 'scripts'} -modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb index 7bb040de739..cdcd82e8ab5 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb @@ -46,6 +46,10 @@ sanity_check_paths = { } modextrapaths = {'PATH': 'scripts'} -modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb index 05cb08c4ba2..11dad5250b6 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb @@ -53,6 +53,10 @@ sanity_check_paths = { } modextrapaths = {'PATH': 'scripts'} -modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb index 3e03a96422e..5b551b20d92 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb @@ -54,6 +54,10 @@ sanity_check_paths = { } modextrapaths = {'PATH': 'scripts'} -modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2019a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2019a.eb index d32896877a6..bd9023bfa32 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2019a.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2019a.eb @@ -51,6 +51,10 @@ sanity_check_paths = { } modextrapaths = {'PATH': 'scripts'} -modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} moduleclass = 'bio' From ca9b5d8b39640454ec1b319693b193cb83125033 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Nov 2019 10:33:34 +0100 Subject: [PATCH 316/468] add missing checksums in AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb --- .../a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb index 4828f6565a3..6eaf872e1e6 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb @@ -15,6 +15,10 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] +checksums = [ + 'a1af128aefd228dea0c46d6f5234910fdf068a2b9133175ca8da3af639cb4514', # augustus-3.2.3.tar.gz + '12870afdd184c11d49268ddb9ec2bf81dc3ccce74072857990a7aac07d8b4d7d', # AUGUSTUS-3.2.3_fix-hardcoding.patch +] dependencies = [ ('zlib', '1.2.11'), From b05b21f9b908f55e17cd30c11576ece762c42162 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Dec 2019 21:32:19 +0100 Subject: [PATCH 317/468] sync up source_urls in AUGUSTUS easyconfigs --- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb | 5 ++++- .../a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb index db9a5a23f1a..38eda337afc 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb @@ -8,7 +8,10 @@ description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic s toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = ['http://bioinf.uni-greifswald.de/augustus/binaries/'] +source_urls = [ + 'http://bioinf.uni-greifswald.de/augustus/binaries/', + 'http://bioinf.uni-greifswald.de/augustus/binaries/old/', +] sources = ['augustus-%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_bamtools_includepath.patch', diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb index d11a4006bd4..596b151c21d 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb @@ -9,7 +9,10 @@ description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic s toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['http://bioinf.uni-greifswald.de/augustus/binaries/'] +source_urls = [ + 'http://bioinf.uni-greifswald.de/augustus/binaries/', + 'http://bioinf.uni-greifswald.de/augustus/binaries/old/', +] sources = ['augustus-%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_fix-hardcoding.patch', From 2bddab2817fe20414823fb231d95640e571b8fd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Dec 2019 11:36:13 +0100 Subject: [PATCH 318/468] also clear patches for easyconfigs using Bundle easyblock in check_sha256_checksums in easyconfigs tests (cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/1897) --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index e026b2f4787..1e52a543352 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -514,10 +514,11 @@ def check_sha256_checksums(self, changed_ecs): # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter # is updated in place (sources for components are added the 'parent' sources) in Bundle's __init__; # therefore, we need to reset 'sources' to an empty list here if Bundle is used... - # likewise for 'checksums' + # likewise for 'patches' and 'checksums' for ec in changed_ecs: if ec['easyblock'] == 'Bundle': ec['sources'] = [] + ec['patches'] = [] ec['checksums'] = [] # filter out deprecated easyconfigs From 8eb46cc4383a256df20335eb6bf2a57bb88725ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Dec 2019 11:45:36 +0100 Subject: [PATCH 319/468] adding easyconfigs: libmatheval-1.1.11-GCCcore-8.3.0.eb, Guile-1.8.8-GCCcore-8.3.0.eb, libunistring-0.9.10-GCCcore-8.3.0.eb, gc-7.6.12-GCCcore-8.3.0.eb --- .../g/Guile/Guile-1.8.8-GCCcore-8.3.0.eb | 36 +++++++++++++++++ .../g/gc/gc-7.6.12-GCCcore-8.3.0.eb | 40 +++++++++++++++++++ .../libmatheval-1.1.11-GCCcore-8.3.0.eb | 38 ++++++++++++++++++ .../libunistring-0.9.10-GCCcore-8.3.0.eb | 33 +++++++++++++++ 4 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/g/gc/gc-7.6.12-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..1023b77b82d --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-8.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'https://www.gnu.org/software/guile/' +description = """Guile is a programming language, designed to help programmers create flexible applications that + can be extended by users or other programmers with plug-ins, modules, or scripts.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3471fed2e72e5b04ad133bbaaf16369e8360283679bcf19800bc1b381024050'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.32'), +] +dependencies = [ + ('libunistring', '0.9.10'), + ('libffi', '3.2.1'), + ('gc', '7.6.12'), + ('GMP', '6.1.2'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ['bin/guile', 'bin/guile-config', 'bin/guile-snarf', 'bin/guile-tools', + 'include/libguile.h', 'lib/libguile.a', 'lib/libguile.%s' % SHLIB_EXT, + 'lib/pkgconfig/guile-%(version_major_minor)s.pc'], + 'dirs': ['include/guile'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gc/gc-7.6.12-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/gc/gc-7.6.12-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..fe7e3f29642 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-7.6.12-GCCcore-8.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '7.6.12' + +homepage = 'https://hboehm.info/gc/' + +description = """ + The Boehm-Demers-Weiser conservative garbage collector can be used as a + garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [ + 'https://hboehm.info/gc/gc_source/', + 'https://github.com/ivmai/libatomic_ops/releases/download/v%(version)s/', +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-7.6.10.tar.gz', +] +checksums = [ + '6cafac0d9365c2f8604f930aabd471145ac46ab6f771e835e57995964e845082', # gc-7.6.12.tar.gz + '587edf60817f56daf1e1ab38a4b3c729b8e846ff67b4f62a6157183708f099af', # libatomic_ops-7.6.10.tar.gz +] + +builddependencies = [ + ('binutils', '2.32'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..1c20803bb99 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'https://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libmatheval-%(version)s_fix-matheval-test.patch'] +checksums = [ + '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab', # libmatheval-1.1.11.tar.gz + '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073', # libmatheval-1.1.11_fix-matheval-test.patch +] + +builddependencies = [ + ('binutils', '2.32'), + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..6ae102198e6 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.10' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """ + This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['eb8fb2c3e4b6e2d336608377050892b54c3c983b646c561836550863003c05d7'] + +builddependencies = [ + ('binutils', '2.32'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' From 9b98f06e172929eaa972c34ecbd3175fd655f61a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Dec 2019 11:51:50 +0100 Subject: [PATCH 320/468] don't try longer than 5 sec. to use https:// URL rather than http:// URL in check_https in easyconfigs tests --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a06cafe0ea6..fac95c16c96 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -642,7 +642,7 @@ def check_https(self, changed_ecs): for http_url in http_regex.findall(ec_txt): https_url = http_url.replace('http://', 'https://') try: - https_url_works = bool(urlopen(https_url)) + https_url_works = bool(urlopen(https_url, timeout=5)) except Exception: https_url_works = False From 0c6cdcd8b8fc339f22fba8ba44c95109a3fb218c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Dec 2019 12:02:12 +0100 Subject: [PATCH 321/468] adding easyconfigs: PLUMED-2.5.3-intel-2019b-Python-3.7.4.eb --- .../PLUMED-2.5.3-intel-2019b-Python-3.7.4.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.3-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.3-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.3-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..9ef6713d051 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.3-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,56 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['e59fb5d7c4ee9a21cd0a82c361bbab472cddf07475db8e70ed83549ba7e41331'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('libmatheval', '1.1.11'), + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# requires to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From b716ecea1d82cb1253b4843f33abd3da46fb8f3c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Dec 2019 18:20:47 +0100 Subject: [PATCH 322/468] adding easyconfigs: GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb --- ...gs-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSettings-Desktop-Schemas/GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/GSettings-Desktop-Schemas/GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GSettings-Desktop-Schemas/GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..ba0dbbe5603 --- /dev/null +++ b/easybuild/easyconfigs/g/GSettings-Desktop-Schemas/GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'GSettings-Desktop-Schemas' +version = '3.34.0' + +homepage = 'https://gitlab.gnome.org/GNOME' +description = """ + gsettings-desktop-schemas contains a collection of GSettings schemas for + settings shared by various components of a desktop.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['288b04260f7040b0e004a8d59c773cfb4e32df4f1b4a0f9d705c51afccc95ead'] + +builddependencies = [ + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), +] + +dependencies = [ + ('GLib', '2.60.1'), +] + +configopts = "--disable-silent-rules --buildtype=release -Dintrospection=true" + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/%(namelower)s', 'share', 'lib'], +} + +moduleclass = 'vis' From 5dfa461ec97bf7a0765fb252ccedf8cb2e546352 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Dec 2019 09:06:27 +0100 Subject: [PATCH 323/468] Update URL --- .../gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/{GSettings-Desktop-Schemas/GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb => gsettings-desktop-schemas/gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb} (89%) diff --git a/easybuild/easyconfigs/g/GSettings-Desktop-Schemas/GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gsettings-desktop-schemas/gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb similarity index 89% rename from easybuild/easyconfigs/g/GSettings-Desktop-Schemas/GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb rename to easybuild/easyconfigs/g/gsettings-desktop-schemas/gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb index ba0dbbe5603..7e10b938230 100644 --- a/easybuild/easyconfigs/g/GSettings-Desktop-Schemas/GSettings-Desktop-Schemas-3.34.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/gsettings-desktop-schemas/gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb @@ -1,9 +1,9 @@ easyblock = 'MesonNinja' -name = 'GSettings-Desktop-Schemas' +name = 'gsettings-desktop-schemas' version = '3.34.0' -homepage = 'https://gitlab.gnome.org/GNOME' +homepage = 'https://gitlab.gnome.org/GNOME/gsettings-desktop-schemas' description = """ gsettings-desktop-schemas contains a collection of GSettings schemas for settings shared by various components of a desktop.""" From 52a06582fa9b8b70d4452893b3d2981dcf93d376 Mon Sep 17 00:00:00 2001 From: Flamefire Date: Fri, 27 Dec 2019 12:17:21 +0100 Subject: [PATCH 324/468] Remove disable-silent-rules --- .../gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gsettings-desktop-schemas/gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gsettings-desktop-schemas/gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb index 7e10b938230..5be0b0c3818 100644 --- a/easybuild/easyconfigs/g/gsettings-desktop-schemas/gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/gsettings-desktop-schemas/gsettings-desktop-schemas-3.34.0-GCCcore-8.2.0.eb @@ -27,7 +27,7 @@ dependencies = [ ('GLib', '2.60.1'), ] -configopts = "--disable-silent-rules --buildtype=release -Dintrospection=true" +configopts = "--buildtype=release -Dintrospection=true" sanity_check_paths = { 'files': [], From e82c48eae6db0d67a15ded0f8270f40c6effcf89 Mon Sep 17 00:00:00 2001 From: jakvc Date: Fri, 27 Dec 2019 09:09:10 -0800 Subject: [PATCH 325/468] adding easyconfigs: Java-1.8.0_231.eb --- easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb new file mode 100644 index 00000000000..43067f76bde --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb @@ -0,0 +1,17 @@ +name = 'Java' +version = '1.8.0_231' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +# download the tar.gz directly from +# http://www.oracle.com/technetwork/java/javase/downloads/index.html +(local_vp, local_vs) = version.split('_') +local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) +sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] +checksums = ['a011584a2c9378bf70c6903ef5fbf101b30b08937441dc2ec67932fb3620b2cf'] + +moduleclass = 'lang' From d1f59c7af854937a1b24f87f33844a979a74817e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 27 Dec 2019 18:17:37 +0100 Subject: [PATCH 326/468] undo cuda changes... --- easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb index f905b72b94d..722568ad18c 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb @@ -1,3 +1,5 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + name = 'CUDA' version = '10.0.130' @@ -9,8 +11,8 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = SYSTEM -source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] -sources = ['cuda_%(version)s_410.48_linux'] +source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] +sources = ['%(namelower)s_%(version)s_410.48_linux'] checksums = ['92351f0e4346694d0fcb4ea1539856c9eb82060c25654463bfd8574ec35ee39a'] moduleclass = 'system' From 49a6f393d26d26fa0c59caa2d3b4d14684d7e534 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 27 Dec 2019 18:24:14 +0100 Subject: [PATCH 327/468] Updated checksums --- .../FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb index ff98fa7bb9f..78ce88ec33e 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb @@ -33,13 +33,13 @@ patches = [ ] checksums = [ 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz - '3a14d9c3ea75d90fa3e4beb5da3cd11a60c6859441acaece02b32ccab6aa278f', # FSL-6.0.2_Makefile_fixes.patch - '2b7ade2146fadbba6c983370bb030ac4e2b11d8bf5259eacc8f3054d3d11003f', # FSL-6.0.2_Build_extras.patch + '4212478ef24be4bce7a9ce513aa9c45fcf67eccfe064331a2e8e52be41d3513c', # FSL-6.0.2_Makefile_fixes.patch + '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch - '4870f20e84c24331418ea9d5ee67d5ba9cf075bcc85b053d4d8b7a276a96a1a5', # FSL-6.0.2_Enable_GPU_build.patch + 'a2adee25538e8e2aebba9545cce2766841399b63354b97f38851ff7259d59a8d', # FSL-6.0.2_Enable_GPU_build.patch # FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch '05f6ddf6b149e234ea7428bd5b510a72aa8f131a00fda0e369f854b722d88b19', - '4479aa501a7e6e9f1a0063e4ddb680836147ba08673d3fccb9e1db3c4d910672', # FSL-6.0.1_Fix_fsl_exec_script.patch + 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch ] builddependencies = [ From 636b2abf35da320b01633f5420b3682774af6232 Mon Sep 17 00:00:00 2001 From: Jake VanCampen Date: Fri, 27 Dec 2019 09:49:52 -0800 Subject: [PATCH 328/468] Update Java-1.8.0_231.eb should be https://java.com/ --- easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb index 43067f76bde..80106409f15 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb @@ -1,7 +1,7 @@ name = 'Java' version = '1.8.0_231' -homepage = 'http://java.com/' +homepage = 'https://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" From d6b2808087c0bd7847628ea5fc9eb15c8a3caebb Mon Sep 17 00:00:00 2001 From: jakvc Date: Fri, 27 Dec 2019 10:39:04 -0800 Subject: [PATCH 329/468] update java multi-platform to latest uversion --- easybuild/easyconfigs/j/Java/Java-1.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 1fb3fc34ee3..b917d2076ec 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -15,7 +15,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM dependencies = [ - ('Java', {'arch=x86_64': '%(version)s.0_221', + ('Java', {'arch=x86_64': '%(version)s.0_231', 'arch=POWER': '%(version)s_191-b26-OpenJDK'}), ] From b4030e6e14000cbe10e3fd1f7db77fa4d4d4be51 Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Sat, 28 Dec 2019 11:06:07 +0100 Subject: [PATCH 330/468] add SSL osdependencies for GDAL --- .../easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb | 2 ++ .../easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb | 2 ++ .../easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb | 2 ++ .../easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb | 2 ++ 4 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb index 25cc08fdf6f..b4a1143cd0d 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb @@ -36,6 +36,8 @@ dependencies = [ ('SciPy-bundle', '2019.03'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb index eb98e9d007a..fa0294a7033 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb @@ -36,6 +36,8 @@ dependencies = [ ('SciPy-bundle', '2019.03'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb index 0e830e6c8d6..0aa81a50d9a 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb @@ -40,6 +40,8 @@ dependencies = [ ('SciPy-bundle', '2019.03'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb index 52e14dea0be..141c37f1165 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb @@ -40,6 +40,8 @@ dependencies = [ ('SciPy-bundle', '2019.03'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' From f2cbdce5cefa331b98833dcbc07e32bee5ea4bbf Mon Sep 17 00:00:00 2001 From: vsc10009 Date: Sat, 28 Dec 2019 11:24:43 +0100 Subject: [PATCH 331/468] use https --- .../easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb | 4 ++-- .../easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb index b4a1143cd0d..5eb2654fceb 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'GDAL' version = '3.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.gdal.org/' +homepage = 'https://www.gdal.org/' description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for @@ -13,7 +13,7 @@ description = """GDAL is a translator library for raster geospatial data formats toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'usempi': True} -source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] checksums = ['ad316fa052d94d9606e90b20a514b92b2dd64e3142dfdbd8f10981a5fcd5c43e'] diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb index fa0294a7033..c40f8400229 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb @@ -4,7 +4,7 @@ name = 'GDAL' version = '3.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.gdal.org/' +homepage = 'https://www.gdal.org/' description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for @@ -13,7 +13,7 @@ description = """GDAL is a translator library for raster geospatial data formats toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'usempi': True} -source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] checksums = ['ad316fa052d94d9606e90b20a514b92b2dd64e3142dfdbd8f10981a5fcd5c43e'] From 40e276e9ea772969ee831d284de7505d8801959d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 28 Dec 2019 13:04:04 +0100 Subject: [PATCH 332/468] add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension --- .../i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb | 5 +++++ .../IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb | 8 ++++++++ .../i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb | 5 +++++ .../i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb | 8 ++++++++ 4 files changed, 26 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb index 7da9814a314..6d5add901db 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-foss-2019a-Python-3.7.2.eb @@ -135,6 +135,9 @@ exts_list = [ ('ipywidgets', '7.5.1', { 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], }), + ('jupyter_contrib_core', '0.3.3', { + 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], + }), ('jupyter_nbextensions_configurator', '0.4.1', { 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], }), @@ -157,4 +160,6 @@ sanity_check_commands = [ "iptest", ] +sanity_pip_check = True + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb index 5da818dfcac..6514c7708c5 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb @@ -134,6 +134,12 @@ exts_list = [ ('ipywidgets', '7.5.1', { 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], }), + ('jupyter_contrib_core', '0.3.3', { + 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], + }), + ('jupyter_nbextensions_configurator', '0.4.1', { + 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], + }), ('notebook', '6.0.1', { 'checksums': ['660976fe4fe45c7aa55e04bf4bccb9f9566749ff637e9020af3422f9921f9a5d'], }), @@ -153,4 +159,6 @@ sanity_check_commands = [ "iptest", ] +sanity_pip_check = True + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb index 04d5bd73315..4a41ad0d23c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-intel-2019a-Python-3.7.2.eb @@ -136,6 +136,9 @@ exts_list = [ ('ipywidgets', '7.5.1', { 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], }), + ('jupyter_contrib_core', '0.3.3', { + 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], + }), ('jupyter_nbextensions_configurator', '0.4.1', { 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], }), @@ -158,4 +161,6 @@ sanity_check_commands = [ "iptest", ] +sanity_pip_check = True + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb index e1cd9f89f90..78ae78db97f 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb @@ -134,6 +134,12 @@ exts_list = [ ('ipywidgets', '7.5.1', { 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], }), + ('jupyter_contrib_core', '0.3.3', { + 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], + }), + ('jupyter_nbextensions_configurator', '0.4.1', { + 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], + }), ('notebook', '6.0.2', { 'checksums': ['399a4411e171170173344761e7fd4491a3625659881f76ce47c50231ed714d9b'], }), @@ -153,4 +159,6 @@ sanity_check_commands = [ "iptest", ] +sanity_pip_check = True + moduleclass = 'tools' From 767cc08f6b0f631b81a3690cbfab84987f731799 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Dec 2019 11:04:52 +0100 Subject: [PATCH 333/468] adding easyconfigs: ITSTool-2.0.6-GCCcore-8.2.0-Python-3.7.2.eb --- ...TSTool-2.0.6-GCCcore-8.2.0-Python-3.7.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.6-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.6-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.6-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..ab999e54138 --- /dev/null +++ b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.6-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ITSTool' +version = '2.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://itstool.org/' +description = "ITS Tool allows you to translate your XML documents with PO files" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://files.itstool.org/itstool/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6233cc22726a9a5a83664bf67d1af79549a298c23185d926c3677afa917b92a9'] + +dependencies = [ + ('binutils', '2.31.1'), + ('Python', '3.7.2'), + ('libxml2-python', '2.9.8', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/itstool'], + 'dirs': ['share/itstool/its', 'share/man'], +} +sanity_check_commands = ["itstool --help"] + +moduleclass = 'tools' From c2a4b4484b18690421e3f15e3818410499b5d99c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 28 Dec 2019 14:45:44 +0100 Subject: [PATCH 334/468] add missing PyYAML dep to IPython 7.7.0+ easyconfigs --- .../i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb | 1 + .../i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb index 6514c7708c5..131686b09e9 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.7.0-fosscuda-2019a-Python-3.7.2.eb @@ -18,6 +18,7 @@ dependencies = [ ('Python', '3.7.2'), ('ZeroMQ', '4.3.2'), ('matplotlib', '3.0.3', versionsuffix), + ('PyYAML', '5.1'), # required for jupyter_nbextensions_configurator ] use_pip = True diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb index 78ae78db97f..bf03798c488 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.9.0-foss-2019b-Python-3.7.4.eb @@ -18,6 +18,7 @@ dependencies = [ ('Python', '3.7.4'), ('ZeroMQ', '4.3.2'), ('matplotlib', '3.1.1', versionsuffix), + ('PyYAML', '5.1.2'), # required for jupyter_nbextensions_configurator ] use_pip = True From f579f9174828b05ef85f108a5eedaca50cc21341 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 28 Dec 2019 16:25:43 +0200 Subject: [PATCH 335/468] Update comment about LD_PRELOAD usage. --- .../easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb index 7f92bfde3eb..5d6c8970043 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-8.3.0.eb @@ -30,7 +30,8 @@ sanity_check_paths = { 'dirs': [], } -# Why did someone set this?? LD_PRELOAD should NEVER be set automatically +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it # modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} moduleclass = 'lib' From 6022cadbef388622b5d8ea65aae2d7a4490ace52 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Dec 2019 08:22:48 +0100 Subject: [PATCH 336/468] remove unneeded binutils build dep in SAMtools easyconfig --- .../easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb index e091a22e7cd..6e6f3ad1da2 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-8.2.0-2.31.1.eb @@ -22,8 +22,6 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve sources = [SOURCELOWER_TAR_BZ2] checksums = ['7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585'] -builddependencies = [('binutils', '2.31.1')] - # The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. dependencies = [ From 4d27cafc2aa20bb5749f9296cfa5a028ce593a24 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Dec 2019 10:17:07 +0000 Subject: [PATCH 337/468] adding easyconfigs: Clang-9.0.1-GCCcore-8.3.0.eb and patches: libcxx-9.0.1-ppc64le.patch --- .../c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb | 69 +++++++++++++++++++ .../c/Clang/libcxx-9.0.1-ppc64le.patch | 18 +++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..7fd56412b38 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb @@ -0,0 +1,69 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '9.0.1' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', +] +patches = ['libcxx-%(version)s-ppc64le.patch'] +checksums = [ + '00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a', # llvm-9.0.1.src.tar.xz + '5778512b2e065c204010f88777d44b95250671103e434f9dc7363ab2e3804253', # clang-9.0.1.src.tar.xz + 'c2bfab95c9986318318363d7f371a85a95e333bc0b34fbfa52edbd3f5e3a9077', # compiler-rt-9.0.1.src.tar.xz + '9a4ac69df923230d13eb6cd0d03f605499f6a854b1dc96a9b72c4eb075040fcf', # polly-9.0.1.src.tar.xz + '5c94060f846f965698574d9ce22975c0e9f04c9b14088c3af5f03870af75cace', # openmp-9.0.1.src.tar.xz + '86262bad3e2fd784ba8c5e2158d7aa36f12b85f2515e95bc81d65d75bb9b0c82', # lld-9.0.1.src.tar.xz + '0981ff11b862f4f179a13576ab0a2f5530f46bd3b6b4a90f568ccc6a62914b34', # libcxx-9.0.1.src.tar.xz + 'e8f978aa4cfae2d7a0b4d89275637078557cca74b35c31b7283d4786948a8aac', # libcxxabi-9.0.1.src.tar.xz + '6a39230b9e2b2c61fb5f67ac752d256437ccc56a6a517d7b6d53417d198fdb1f', # libcxx-9.0.1-ppc64le.patch +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.32'), + ('GMP', '6.1.2'), +] + +builddependencies = [ + ('CMake', '3.15.3'), + ('Python', '2.7.16'), + ('libxml2', '2.9.9'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True + +skip_all_tests = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch b/easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch new file mode 100644 index 00000000000..b827d9c5ce9 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch @@ -0,0 +1,18 @@ +Reverse the if def order. Patch from https://bugs.llvm.org/show_bug.cgi?id=39696#c38 +Prepared for EasyBuild by Simon Branford, University of Birmingham +diff --git a/libcxx/include/thread b/libcxx/include/thread +index 02da703..d1677a1 100644 +--- a/projects/libcxx/include/thread ++++ b/projects/libcxx/include/thread +@@ -368,9 +368,9 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d) + { + #if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__) + // GCC's long double const folding is incomplete for IBM128 long doubles. +- _LIBCPP_CONSTEXPR duration _Max = nanoseconds::max(); +-#else + _LIBCPP_CONSTEXPR duration _Max = duration(ULLONG_MAX/1000000000ULL) ; ++#else ++ _LIBCPP_CONSTEXPR duration _Max = nanoseconds::max(); + #endif + nanoseconds __ns; + if (__d < _Max) From 1b91f2fe0470f06365abec99a39bfca19c585ca6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Dec 2019 10:26:44 +0000 Subject: [PATCH 338/468] patch libcxx on pcc64le for incomplete IBM128 long double in GCC --- .../c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb | 6 ++++-- .../c/Clang/libcxx-8.0.0-ppc64le.patch | 19 +++++++++++++++++++ 2 files changed, 23 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/Clang/libcxx-8.0.0-ppc64le.patch diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb index 3fc09222b68..2afdaba65aa 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb @@ -11,7 +11,7 @@ name = 'Clang' version = '8.0.0' -homepage = 'http://clang.llvm.org/' +homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.""" @@ -21,7 +21,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["https://llvm.org/releases/%(version)s"] sources = [ 'llvm-%(version)s.src.tar.xz', 'cfe-%(version)s.src.tar.xz', @@ -33,6 +33,7 @@ sources = [ 'libcxx-%(version)s.src.tar.xz', 'libcxxabi-%(version)s.src.tar.xz', ] +patches = ['libcxx-%(version)s-ppc64le.patch'] checksums = [ '8872be1b12c61450cacc82b3d153eab02be2546ef34fa3580ed14137bb26224c', # llvm-8.0.0.src.tar.xz '084c115aab0084e63b23eee8c233abb6739c399e29966eaeccfc6e088e0b736b', # cfe-8.0.0.src.tar.xz @@ -42,6 +43,7 @@ checksums = [ '9caec8ec922e32ffa130f0fb08e4c5a242d7e68ce757631e425e9eba2e1a6e37', # lld-8.0.0.src.tar.xz 'c2902675e7c84324fb2c1e45489220f250ede016cc3117186785d9dc291f9de2', # libcxx-8.0.0.src.tar.xz 'c2d6de9629f7c072ac20ada776374e9e3168142f20a46cdb9d6df973922b07cd', # libcxxabi-8.0.0.src.tar.xz + '173da6b7831a66d2f7d064f0ec3f6c56645a7f1352b709ceb9a55416fe6c93ce', # libcxx-8.0.0-ppc64le.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/libcxx-8.0.0-ppc64le.patch b/easybuild/easyconfigs/c/Clang/libcxx-8.0.0-ppc64le.patch new file mode 100644 index 00000000000..5fbe557dc8a --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/libcxx-8.0.0-ppc64le.patch @@ -0,0 +1,19 @@ +Patch from https://bugs.llvm.org/show_bug.cgi?id=39696#c26 +Prepared for EasyBuild by Simon Branford, University of Birmingham +diff --git a/libcxx/include/thread b/libcxx/include/thread +index 8c0115f87..e439f60b9 100644 +--- a/projects/libcxx/include/thread ++++ b/projects/libcxx/include/thread +@@ -435,7 +435,12 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d) + using namespace chrono; + if (__d > duration<_Rep, _Period>::zero()) + { ++#if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__) ++ // GCC's long double const folding is incomplete for IBM128 long doubles. ++ _LIBCPP_CONSTEXPR duration _Max = duration(ULLONG_MAX/1000000000ULL); ++#else + _LIBCPP_CONSTEXPR duration _Max = nanoseconds::max(); ++#endif + nanoseconds __ns; + if (__d < _Max) + { From a636b34f5d81efcafc5ce7b14ed67ca914f8c0c1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Dec 2019 18:21:25 +0100 Subject: [PATCH 339/468] adding easyconfigs: Meld-3.20.1-GCCcore-8.2.0-Python-3.7.2.eb --- .../Meld-3.20.1-GCCcore-8.2.0-Python-3.7.2.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meld/Meld-3.20.1-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/m/Meld/Meld-3.20.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/m/Meld/Meld-3.20.1-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..eddd2d35de9 --- /dev/null +++ b/easybuild/easyconfigs/m/Meld/Meld-3.20.1-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonPackage' + +name = 'Meld' +version = '3.20.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://meldmerge.org/' +description = """ + Meld is a visual diff and merge tool targeted at developers. + Meld helps you compare files, directories, and version controlled projects. + It provides two- and three-way comparison of both files and directories, and has support + for many popular version control systems. + """ + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +dependencies = [ + ('Python', '3.7.2'), + ('PyCairo', '1.18.0', versionsuffix), + ('PyGObject', '3.34.0', versionsuffix), + ('gsettings-desktop-schemas', '3.34.0'), + ('GLib', '2.60.1'), + ('Pango', '1.43.0'), + ('GTK+', '3.24.8'), + ('GtkSourceView', '3.24.11'), +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('intltool', '0.51.0'), + ('ITSTool', '2.0.6', versionsuffix), + ('libxml2', '2.9.8'), # For xmllint +] + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [FTPGNOME_SOURCE] +checksums = ['a54843bc4d6cb1d31d0a58aa725091622194d50c32ef67026b35c86dda3cb249'] + +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/meld'], + 'dirs': [] +} + +moduleclass = 'devel' From ddf965abf23f44ef1b83b9451d97d7a9eca6c46a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Dec 2019 16:07:38 +0100 Subject: [PATCH 340/468] Whitelist meld for pip install incompatibility --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index cc27d76f0dd..f558021b041 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -533,8 +533,8 @@ def check_sha256_checksums(self, changed_ecs): def check_python_packages(self, changed_ecs): """Several checks for easyconfigs that install (bundles of) Python packages.""" - # MATLAB-Engine, PyTorch do not support installation with 'pip' - whitelist_pip = ['MATLAB-Engine-*', 'PyTorch-*'] + # These packages do not support installation with 'pip' + whitelist_pip = [r'MATLAB-Engine-.*', r'PyTorch-.*', r'Meld-.*'] failing_checks = [] From d93ef853012ef04e373cd19696e045408d8b5a8f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Dec 2019 13:40:46 +0000 Subject: [PATCH 341/468] fix for '__float128 is not supported on this target on ppc64le' --- .../easyconfigs/g/GCCcore/GCCcore-8.2.0.eb | 16 +- .../GCCcore-8.2.0_fix_float128_ppc64le.patch | 304 ++++++++++++++++++ 2 files changed, 313 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0_fix_float128_ppc64le.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb index f52d7044a72..83fdb7b7fcd 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb @@ -3,20 +3,20 @@ easyblock = 'EB_GCC' name = 'GCCcore' version = '8.2.0' -homepage = 'http://gcc.gnu.org/' +homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" toolchain = SYSTEM source_urls = [ - 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR - 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://gcc.cybermirror.org/infrastructure/', # HTTP (no HTTPS) mirror for GCC dependencies + 'https://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ 'gcc-%(version)s.tar.gz', @@ -28,6 +28,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'gcc-8.2.0-isl-0.20-missing-include.patch', + '%(name)s-%(version)s_fix_float128_ppc64le.patch', ] checksums = [ '1b0f36be1045ff58cbb9c83743835367b860810f17f0195a4e093458b372020f', # gcc-8.2.0.tar.gz @@ -37,6 +38,7 @@ checksums = [ 'b587e083eb65a8b394e833dea1744f21af3f0e413a448c17536b5549ae42a4c2', # isl-0.20.tar.bz2 '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '62fa14c3ba2e59cb1d172251cd9d429534394388b10796cf437f65e94ce81c7f', # gcc-8.2.0-isl-0.20-missing-include.patch + 'df9429fcdc467ba0a6bc98921f80da561a6bfa0a61e0b7935f2f21f993fbeae4', # GCCcore-8.2.0_fix_float128_ppc64le.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0_fix_float128_ppc64le.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0_fix_float128_ppc64le.patch new file mode 100644 index 00000000000..9c8fc1b5074 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0_fix_float128_ppc64le.patch @@ -0,0 +1,304 @@ +Fix for '__float128 is not supported on this target on ppc64le' +From https://gcc.gnu.org/viewcvs/gcc?view=revision&revision=263084 +Prepared for EasyBuild by Simon Branford, University of Birmingham +--- branches/gcc-8-branch/libstdc++-v3/ChangeLog 2018/07/31 09:24:41 263083 ++++ branches/gcc-8-branch/libstdc++-v3/ChangeLog 2018/07/31 09:38:28 263084 +@@ -1,3 +1,29 @@ ++2018-07-31 Jonathan Wakely ++ ++ Backport from mainline ++ 2018-05-08 Jonathan Wakely ++ ++ PR libstdc++/85672 ++ * include/Makefile.am [!ENABLE_FLOAT128]: Change c++config.h entry ++ to #undef _GLIBCXX_USE_FLOAT128 instead of defining it to zero. ++ * include/Makefile.in: Regenerate. ++ * include/bits/c++config (_GLIBCXX_USE_FLOAT128): Move definition ++ within conditional block. ++ ++ Backport from mainline ++ 2018-05-01 Tulio Magno Quites Machado Filho ++ ++ PR libstdc++/84654 ++ * acinclude.m4: Set ENABLE_FLOAT128 instead of _GLIBCXX_USE_FLOAT128. ++ * config.h.in: Remove references to _GLIBCXX_USE_FLOAT128. ++ * configure: Regenerate. ++ * include/Makefile.am: Replace the value of _GLIBCXX_USE_FLOAT128 ++ based on ENABLE_FLOAT128. ++ * include/Makefile.in: Regenerate. ++ * include/bits/c++config: Define _GLIBCXX_USE_FLOAT128. ++ [!defined(__FLOAT128__) && !defined(__SIZEOF_FLOAT128__)]: Undefine ++ _GLIBCXX_USE_FLOAT128. ++ + 2018-07-26 Release Manager + + * GCC 8.2.0 released. +--- branches/gcc-8-branch/libstdc++-v3/acinclude.m4 2018/07/31 09:24:41 263083 ++++ branches/gcc-8-branch/libstdc++-v3/acinclude.m4 2018/07/31 09:38:28 263084 +@@ -3062,7 +3062,7 @@ + dnl + dnl Defines: + dnl _GLIBCXX_USE_INT128 +-dnl _GLIBCXX_USE_FLOAT128 ++dnl ENABLE_FLOAT128 + dnl + AC_DEFUN([GLIBCXX_ENABLE_INT128_FLOAT128], [ + +@@ -3117,13 +3117,12 @@ + + AC_MSG_CHECKING([for __float128]) + if AC_TRY_EVAL(ac_compile); then +- AC_DEFINE(_GLIBCXX_USE_FLOAT128, 1, +- [Define if __float128 is supported on this host.]) + enable_float128=yes + else + enable_float128=no + fi + AC_MSG_RESULT($enable_float128) ++ GLIBCXX_CONDITIONAL(ENABLE_FLOAT128, test $enable_float128 = yes) + rm -f conftest* + + AC_LANG_RESTORE +--- branches/gcc-8-branch/libstdc++-v3/config.h.in 2018/07/31 09:24:41 263083 ++++ branches/gcc-8-branch/libstdc++-v3/config.h.in 2018/07/31 09:38:28 263084 +@@ -918,9 +918,6 @@ + /* Define if fchmodat is available in . */ + #undef _GLIBCXX_USE_FCHMODAT + +-/* Define if __float128 is supported on this host. */ +-#undef _GLIBCXX_USE_FLOAT128 +- + /* Defined if gettimeofday is available. */ + #undef _GLIBCXX_USE_GETTIMEOFDAY + +--- branches/gcc-8-branch/libstdc++-v3/configure 2018/07/31 09:24:41 263083 ++++ branches/gcc-8-branch/libstdc++-v3/configure 2018/07/31 09:38:28 263084 +@@ -729,6 +729,8 @@ + CSTDIO_H + SECTION_FLAGS + WERROR ++ENABLE_FLOAT128_FALSE ++ENABLE_FLOAT128_TRUE + thread_header + glibcxx_PCHFLAGS + GLIBCXX_BUILD_PCH_FALSE +@@ -11606,7 +11608,7 @@ + lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 + lt_status=$lt_dlunknown + cat > conftest.$ac_ext <<_LT_EOF +-#line 11609 "configure" ++#line 11611 "configure" + #include "confdefs.h" + + #if HAVE_DLFCN_H +@@ -11712,7 +11714,7 @@ + lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 + lt_status=$lt_dlunknown + cat > conftest.$ac_ext <<_LT_EOF +-#line 11715 "configure" ++#line 11717 "configure" + #include "confdefs.h" + + #if HAVE_DLFCN_H +@@ -15398,7 +15400,7 @@ + # Fake what AC_TRY_COMPILE does. + + cat > conftest.$ac_ext << EOF +-#line 15401 "configure" ++#line 15403 "configure" + int main() + { + typedef bool atomic_type; +@@ -15433,7 +15435,7 @@ + rm -f conftest* + + cat > conftest.$ac_ext << EOF +-#line 15436 "configure" ++#line 15438 "configure" + int main() + { + typedef short atomic_type; +@@ -15468,7 +15470,7 @@ + rm -f conftest* + + cat > conftest.$ac_ext << EOF +-#line 15471 "configure" ++#line 15473 "configure" + int main() + { + // NB: _Atomic_word not necessarily int. +@@ -15504,7 +15506,7 @@ + rm -f conftest* + + cat > conftest.$ac_ext << EOF +-#line 15507 "configure" ++#line 15509 "configure" + int main() + { + typedef long long atomic_type; +@@ -15585,7 +15587,7 @@ + # unnecessary for this test. + + cat > conftest.$ac_ext << EOF +-#line 15588 "configure" ++#line 15590 "configure" + int main() + { + _Decimal32 d1; +@@ -15627,7 +15629,7 @@ + # unnecessary for this test. + + cat > conftest.$ac_ext << EOF +-#line 15630 "configure" ++#line 15632 "configure" + template + struct same + { typedef T2 type; }; +@@ -15661,7 +15663,7 @@ + rm -f conftest* + + cat > conftest.$ac_ext << EOF +-#line 15664 "configure" ++#line 15666 "configure" + template + struct same + { typedef T2 type; }; +@@ -15683,15 +15685,13 @@ + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then +- +-$as_echo "#define _GLIBCXX_USE_FLOAT128 1" >>confdefs.h +- + enable_float128=yes + else + enable_float128=no + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_float128" >&5 + $as_echo "$enable_float128" >&6; } ++ + rm -f conftest* + + ac_ext=c +@@ -81261,6 +81261,15 @@ + fi + + ++ if test $enable_float128 = yes; then ++ ENABLE_FLOAT128_TRUE= ++ ENABLE_FLOAT128_FALSE='#' ++else ++ ENABLE_FLOAT128_TRUE='#' ++ ENABLE_FLOAT128_FALSE= ++fi ++ ++ + if test $enable_libstdcxx_allocator_flag = new; then + ENABLE_ALLOCATOR_NEW_TRUE= + ENABLE_ALLOCATOR_NEW_FALSE='#' +@@ -81804,6 +81813,10 @@ + as_fn_error "conditional \"GLIBCXX_BUILD_PCH\" was never defined. + Usually this means the macro was only invoked conditionally." "$LINENO" 5 + fi ++if test -z "${ENABLE_FLOAT128_TRUE}" && test -z "${ENABLE_FLOAT128_FALSE}"; then ++ as_fn_error "conditional \"ENABLE_FLOAT128\" was never defined. ++Usually this means the macro was only invoked conditionally." "$LINENO" 5 ++fi + if test -z "${ENABLE_ALLOCATOR_NEW_TRUE}" && test -z "${ENABLE_ALLOCATOR_NEW_FALSE}"; then + as_fn_error "conditional \"ENABLE_ALLOCATOR_NEW\" was never defined. + Usually this means the macro was only invoked conditionally." "$LINENO" 5 +--- branches/gcc-8-branch/libstdc++-v3/include/Makefile.am 2018/07/31 09:24:41 263083 ++++ branches/gcc-8-branch/libstdc++-v3/include/Makefile.am 2018/07/31 09:38:28 263084 +@@ -1230,6 +1230,14 @@ + echo 0 > stamp-allocator-new + endif + ++if ENABLE_FLOAT128 ++stamp-float128: ++ echo 'define _GLIBCXX_USE_FLOAT128 1' > stamp-float128 ++else ++stamp-float128: ++ echo 'undef _GLIBCXX_USE_FLOAT128' > stamp-float128 ++endif ++ + # NB: The non-empty default ldbl_compat works around an AIX sed + # oddity, see libstdc++/31957 for details. + ${host_builddir}/c++config.h: ${CONFIG_HEADER} \ +@@ -1241,7 +1249,8 @@ + stamp-extern-template \ + stamp-dual-abi \ + stamp-cxx11-abi \ +- stamp-allocator-new ++ stamp-allocator-new \ ++ stamp-float128 + @date=`cat ${toplevel_srcdir}/gcc/DATESTAMP` ;\ + release=`sed 's/^\([0-9]*\).*$$/\1/' ${toplevel_srcdir}/gcc/BASE-VER` ;\ + ns_version=`cat stamp-namespace-version` ;\ +@@ -1250,6 +1259,7 @@ + dualabi=`cat stamp-dual-abi` ;\ + cxx11abi=`cat stamp-cxx11-abi` ;\ + allocatornew=`cat stamp-allocator-new` ;\ ++ float128=`cat stamp-float128` ;\ + ldbl_compat='s,g,g,' ;\ + grep "^[ ]*#[ ]*define[ ][ ]*_GLIBCXX_LONG_DOUBLE_COMPAT[ ][ ]*1[ ]*$$" \ + ${CONFIG_HEADER} > /dev/null 2>&1 \ +@@ -1262,6 +1272,7 @@ + -e "s,define _GLIBCXX_USE_DUAL_ABI, define _GLIBCXX_USE_DUAL_ABI $$dualabi," \ + -e "s,define _GLIBCXX_USE_CXX11_ABI, define _GLIBCXX_USE_CXX11_ABI $$cxx11abi," \ + -e "s,define _GLIBCXX_USE_ALLOCATOR_NEW, define _GLIBCXX_USE_ALLOCATOR_NEW $$allocatornew," \ ++ -e "s,define _GLIBCXX_USE_FLOAT128,$$float128," \ + -e "$$ldbl_compat" \ + < ${glibcxx_srcdir}/include/bits/c++config > $@ ;\ + sed -e 's/HAVE_/_GLIBCXX_HAVE_/g' \ +--- branches/gcc-8-branch/libstdc++-v3/include/Makefile.in 2018/07/31 09:24:41 263083 ++++ branches/gcc-8-branch/libstdc++-v3/include/Makefile.in 2018/07/31 09:38:28 263084 +@@ -1662,6 +1662,11 @@ + @ENABLE_ALLOCATOR_NEW_FALSE@stamp-allocator-new: + @ENABLE_ALLOCATOR_NEW_FALSE@ echo 0 > stamp-allocator-new + ++@ENABLE_FLOAT128_TRUE@stamp-float128: ++@ENABLE_FLOAT128_TRUE@ echo 'define _GLIBCXX_USE_FLOAT128 1' > stamp-float128 ++@ENABLE_FLOAT128_FALSE@stamp-float128: ++@ENABLE_FLOAT128_FALSE@ echo 'undef _GLIBCXX_USE_FLOAT128' > stamp-float128 ++ + # NB: The non-empty default ldbl_compat works around an AIX sed + # oddity, see libstdc++/31957 for details. + ${host_builddir}/c++config.h: ${CONFIG_HEADER} \ +@@ -1673,7 +1678,8 @@ + stamp-extern-template \ + stamp-dual-abi \ + stamp-cxx11-abi \ +- stamp-allocator-new ++ stamp-allocator-new \ ++ stamp-float128 + @date=`cat ${toplevel_srcdir}/gcc/DATESTAMP` ;\ + release=`sed 's/^\([0-9]*\).*$$/\1/' ${toplevel_srcdir}/gcc/BASE-VER` ;\ + ns_version=`cat stamp-namespace-version` ;\ +@@ -1682,6 +1688,7 @@ + dualabi=`cat stamp-dual-abi` ;\ + cxx11abi=`cat stamp-cxx11-abi` ;\ + allocatornew=`cat stamp-allocator-new` ;\ ++ float128=`cat stamp-float128` ;\ + ldbl_compat='s,g,g,' ;\ + grep "^[ ]*#[ ]*define[ ][ ]*_GLIBCXX_LONG_DOUBLE_COMPAT[ ][ ]*1[ ]*$$" \ + ${CONFIG_HEADER} > /dev/null 2>&1 \ +@@ -1694,6 +1701,7 @@ + -e "s,define _GLIBCXX_USE_DUAL_ABI, define _GLIBCXX_USE_DUAL_ABI $$dualabi," \ + -e "s,define _GLIBCXX_USE_CXX11_ABI, define _GLIBCXX_USE_CXX11_ABI $$cxx11abi," \ + -e "s,define _GLIBCXX_USE_ALLOCATOR_NEW, define _GLIBCXX_USE_ALLOCATOR_NEW $$allocatornew," \ ++ -e "s,define _GLIBCXX_USE_FLOAT128,$$float128," \ + -e "$$ldbl_compat" \ + < ${glibcxx_srcdir}/include/bits/c++config > $@ ;\ + sed -e 's/HAVE_/_GLIBCXX_HAVE_/g' \ +--- branches/gcc-8-branch/libstdc++-v3/include/bits/c++config 2018/07/31 09:24:41 263083 ++++ branches/gcc-8-branch/libstdc++-v3/include/bits/c++config 2018/07/31 09:38:28 263084 +@@ -609,4 +609,9 @@ + # endif + #endif + ++/* Define if __float128 is supported on this host. */ ++#if defined(__FLOAT128__) || defined(__SIZEOF_FLOAT128__) ++#define _GLIBCXX_USE_FLOAT128 ++#endif ++ + // End of prewritten config; the settings discovered at configure time follow. From 02b8a2ac01cb259c56aabc7a9261fae2441be8b3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Dec 2019 15:15:24 +0000 Subject: [PATCH 342/468] add patch to CUDA version --- .../c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb index 4df558df85a..1d8e25e0cb8 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb @@ -14,7 +14,7 @@ version = '8.0.0' local_cudaver = '10.1.105' versionsuffix = '-CUDA-%s' % (local_cudaver) -homepage = 'http://clang.llvm.org/' +homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.""" @@ -24,7 +24,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["https://llvm.org/releases/%(version)s"] sources = [ 'llvm-%(version)s.src.tar.xz', 'cfe-%(version)s.src.tar.xz', @@ -36,6 +36,7 @@ sources = [ 'libcxx-%(version)s.src.tar.xz', 'libcxxabi-%(version)s.src.tar.xz', ] +patches = ['libcxx-%(version)s-ppc64le.patch'] checksums = [ '8872be1b12c61450cacc82b3d153eab02be2546ef34fa3580ed14137bb26224c', # llvm-8.0.0.src.tar.xz '084c115aab0084e63b23eee8c233abb6739c399e29966eaeccfc6e088e0b736b', # cfe-8.0.0.src.tar.xz @@ -45,6 +46,7 @@ checksums = [ '9caec8ec922e32ffa130f0fb08e4c5a242d7e68ce757631e425e9eba2e1a6e37', # lld-8.0.0.src.tar.xz 'c2902675e7c84324fb2c1e45489220f250ede016cc3117186785d9dc291f9de2', # libcxx-8.0.0.src.tar.xz 'c2d6de9629f7c072ac20ada776374e9e3168142f20a46cdb9d6df973922b07cd', # libcxxabi-8.0.0.src.tar.xz + '173da6b7831a66d2f7d064f0ec3f6c56645a7f1352b709ceb9a55416fe6c93ce', # libcxx-8.0.0-ppc64le.patch ] dependencies = [ From 03f25e81d37eb7ddd61078c46a24ffbd3f7b4a4a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Dec 2019 21:12:03 +0000 Subject: [PATCH 343/468] adding easyconfigs: Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb --- ...Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb new file mode 100644 index 00000000000..b7348ae71b3 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb @@ -0,0 +1,76 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '9.0.1' + +local_cudaver = '10.1.243' +versionsuffix = '-CUDA-%s' % (local_cudaver) + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', +] +patches = ['libcxx-%(version)s-ppc64le.patch'] +checksums = [ + '00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a', # llvm-9.0.1.src.tar.xz + '5778512b2e065c204010f88777d44b95250671103e434f9dc7363ab2e3804253', # clang-9.0.1.src.tar.xz + 'c2bfab95c9986318318363d7f371a85a95e333bc0b34fbfa52edbd3f5e3a9077', # compiler-rt-9.0.1.src.tar.xz + '9a4ac69df923230d13eb6cd0d03f605499f6a854b1dc96a9b72c4eb075040fcf', # polly-9.0.1.src.tar.xz + '5c94060f846f965698574d9ce22975c0e9f04c9b14088c3af5f03870af75cace', # openmp-9.0.1.src.tar.xz + '86262bad3e2fd784ba8c5e2158d7aa36f12b85f2515e95bc81d65d75bb9b0c82', # lld-9.0.1.src.tar.xz + '0981ff11b862f4f179a13576ab0a2f5530f46bd3b6b4a90f568ccc6a62914b34', # libcxx-9.0.1.src.tar.xz + 'e8f978aa4cfae2d7a0b4d89275637078557cca74b35c31b7283d4786948a8aac', # libcxxabi-9.0.1.src.tar.xz + '6a39230b9e2b2c61fb5f67ac752d256437ccc56a6a517d7b6d53417d198fdb1f', # libcxx-9.0.1-ppc64le.patch +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.32'), + ('GMP', '6.1.2'), + ('CUDA', local_cudaver, '', True), +] + +builddependencies = [ + ('CMake', '3.15.3'), + ('Python', '2.7.16'), + ('libxml2', '2.9.9'), +] + +# Set the c++ std for NVCC or the build fails on ppc64le looking for __ieee128 +configopts = "-DCUDA_NVCC_FLAGS=-std=c++11" + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True + +skip_all_tests = True + +moduleclass = 'compiler' From 4faf6171e3f28ce1556dd8e139cfe7bff187bccc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 31 Dec 2019 09:53:05 +0000 Subject: [PATCH 344/468] adding easyconfigs: pocl-1.4-GCC-8.3.0.eb, pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb and patches: pocl-1.4_remove-c11-std.patch --- .../pocl/pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb | 45 +++++++++++++++++++ .../easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb | 41 +++++++++++++++++ .../p/pocl/pocl-1.4_remove-c11-std.patch | 36 +++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb new file mode 100644 index 00000000000..a245efcdc98 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'pocl' +version = '1.4' + +local_cudaver = '10.1.243' +versionsuffix = '-CUDA-%s' % (local_cudaver) + +homepage = 'http://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_remove-c11-std.patch'] +checksums = [ + 'ec237faa83bb1c803fbdf7c6e83d8a2ad68b6f0ed1879c3aa16c0e1dcc478742', # v1.4.tar.gz + '15d81b142d836e188061c67af9df6e60381e40db92bd433fb6677033fb6c5a23', # pocl-1.4_remove-c11-std.patch +] + +builddependencies = [ + ('CMake', '3.15.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Clang', '9.0.1', versionsuffix), + ('CUDA', local_cudaver, '', True), + ('hwloc', '1.11.12'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.9'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb new file mode 100644 index 00000000000..9d67b946980 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'pocl' +version = '1.4' + +homepage = 'http://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_remove-c11-std.patch'] +checksums = [ + 'ec237faa83bb1c803fbdf7c6e83d8a2ad68b6f0ed1879c3aa16c0e1dcc478742', # v1.4.tar.gz + '15d81b142d836e188061c67af9df6e60381e40db92bd433fb6677033fb6c5a23', # pocl-1.4_remove-c11-std.patch +] + +builddependencies = [ + ('CMake', '3.15.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Clang', '9.0.1'), + ('hwloc', '1.11.12'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.9'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch b/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch new file mode 100644 index 00000000000..c5adc164bf4 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch @@ -0,0 +1,36 @@ +c++11 std causes the build to fail on ppc64le, so stop it being set in various CMake files +Patch by Simon Branford, University of Birmingham +--- cmake/LLVM.cmake.orig 2019-12-30 18:43:07.077199000 +0000 ++++ cmake/LLVM.cmake 2019-12-30 18:44:37.953255342 +0000 +@@ -96,6 +96,7 @@ + string(REPLACE "${LLVM_PREFIX}" "${LLVM_PREFIX_CMAKE}" LLVM_CFLAGS "${LLVM_CFLAGS}") + run_llvm_config(LLVM_CXXFLAGS --cxxflags) + string(REPLACE "${LLVM_PREFIX}" "${LLVM_PREFIX_CMAKE}" LLVM_CXXFLAGS "${LLVM_CXXFLAGS}") ++string(REPLACE "-std=c++11" "" LLVM_CXXFLAGS "${LLVM_CXXFLAGS}") + run_llvm_config(LLVM_CPPFLAGS --cppflags) + string(REPLACE "${LLVM_PREFIX}" "${LLVM_PREFIX_CMAKE}" LLVM_CPPFLAGS "${LLVM_CPPFLAGS}") + run_llvm_config(LLVM_LDFLAGS --ldflags) +--- CMakeLists.txt.orig 2019-12-30 18:53:08.443068000 +0000 ++++ CMakeLists.txt 2019-12-30 18:54:27.201578300 +0000 +@@ -634,8 +634,8 @@ + # down the kernels, so it needs to be determined whether it's worth + # the trouble. + set(DEFAULT_KERNEL_CL_FLAGS "-xcl -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") +-set(DEFAULT_KERNEL_C_FLAGS "-xc -std=c11 -D__CBUILD__ -fno-math-errno -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") +-set(DEFAULT_KERNEL_CXX_FLAGS "-xc++ -std=c++11 -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") ++set(DEFAULT_KERNEL_C_FLAGS "-xc -D__CBUILD__ -fno-math-errno -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") ++set(DEFAULT_KERNEL_CXX_FLAGS "-xc++ -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") + + set(EXTRA_KERNEL_FLAGS "" CACHE STRING "Extra arguments to all kernel compilation commands (defaults to empty)") + set(EXTRA_KERNEL_CL_FLAGS "" CACHE STRING "Extra arguments to kernel CL compiler (defaults to empty)") +--- tests/regression/CMakeLists.txt.orig 2019-12-30 19:15:16.490362000 +0000 ++++ tests/regression/CMakeLists.txt 2019-12-30 19:15:30.527613525 +0000 +@@ -53,7 +53,7 @@ + if (MSVC) + add_compile_options(${OPENCL_CFLAGS}) + else () +- add_compile_options("-std=c++11" "-Wno-deprecated" "-Wno-deprecated-declarations" ${OPENCL_CFLAGS}) ++ add_compile_options("-Wno-deprecated" "-Wno-deprecated-declarations" ${OPENCL_CFLAGS}) + endif () + + add_definitions("-DSRCDIR=\"${CMAKE_CURRENT_SOURCE_DIR}\"") From 84fc40311f0a7ced393437b819d3de38b5c3373a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 31 Dec 2019 11:46:01 +0000 Subject: [PATCH 345/468] move the CUDA version to gcccuda toolchain --- ...C-8.3.0-CUDA-10.1.243.eb => pocl-1.4-gcccuda-2019b.eb} | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/p/pocl/{pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb => pocl-1.4-gcccuda-2019b.eb} (84%) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb similarity index 84% rename from easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb rename to easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb index a245efcdc98..1a066160fed 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb @@ -3,13 +3,10 @@ easyblock = 'CMakeMake' name = 'pocl' version = '1.4' -local_cudaver = '10.1.243' -versionsuffix = '-CUDA-%s' % (local_cudaver) - homepage = 'http://portablecl.org' description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" -toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchain = {'name': 'gcccuda', 'version': '2019b'} source_urls = ['https://github.com/pocl/pocl/archive/'] sources = ['v%(version)s.tar.gz'] @@ -25,8 +22,7 @@ builddependencies = [ ] dependencies = [ - ('Clang', '9.0.1', versionsuffix), - ('CUDA', local_cudaver, '', True), + ('Clang', '9.0.1', '-CUDA-10.1.243'), ('hwloc', '1.11.12'), ('libtool', '2.4.6'), ('libxml2', '2.9.9'), From 6bfbd2b100c1fddc5d386ff092ba5e436a976728 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 31 Dec 2019 16:21:21 +0100 Subject: [PATCH 346/468] use alias to ensure the OpenBLAS library is used for pythran --- .../p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb index db39a88d3cb..82e08632126 100644 --- a/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb @@ -40,9 +40,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } -modloadmsg = """ -To use the OpenBLAS library, run: -pythran --config=compiler.blas=openblas -""" +modaliases = {'pythran': 'pythran --config=compiler.blas=openblas'} moduleclass = 'compiler' From a08e6cc36ebc3daa458aa3c91b34a03763e7ae49 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 31 Dec 2019 16:34:59 +0100 Subject: [PATCH 347/468] add sanity_pip_check --- .../p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb index 82e08632126..88b782286f1 100644 --- a/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pythran/pythran-0.9.4.post1-foss-2019b-Python-3.7.4.eb @@ -17,6 +17,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From af55064bae8f4801c4a6b1b1b50d8216a5180b60 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 2 Jan 2020 13:31:54 +0100 Subject: [PATCH 348/468] Added description to FSL-6.0.2_Enable_GPU_build.patch --- easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch index 8c908e9b7b0..83a88f5d1ae 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_Enable_GPU_build.patch @@ -1,3 +1,5 @@ +# Since FSL doesn't have a real configre, hardcoded changes are needed to compile GPU executables. +# Author: Caspar van Leeuwen (SURFsara) diff -Nru fsl.orig/src/fdt/fslconfig fsl/src/fdt/fslconfig --- fsl.orig/src/fdt/fslconfig 2019-10-11 13:50:36.336062960 +0200 +++ fsl/src/fdt/fslconfig 2019-10-11 18:09:38.260806371 +0200 From 1996f0bd74b596a85d1cae065288121393bab65e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jan 2020 14:41:56 +0100 Subject: [PATCH 349/468] enable download_dep_fail + set use_pip to False in horton easyconfigs --- .../h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb | 3 +++ .../h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb index b1b552d8b8d..fb2614dff93 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb @@ -27,6 +27,9 @@ dependencies = [ ('libxc', '2.2.2'), ] +download_dep_fail = True +use_pip = False + prebuildopts = ' '.join([ 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb index 2f77a2c0bf3..b16488ca6b8 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb @@ -27,6 +27,9 @@ dependencies = [ ('libxc', '2.2.2'), ] +download_dep_fail = True +use_pip = False + prebuildopts = ' '.join([ 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', From 846a79f2ed6a4f4737869ec0390de7ed9790acbe Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 2 Jan 2020 13:50:54 +0000 Subject: [PATCH 350/468] move to GCC and change to the toolchain CUDA --- ...UDA-10.1.243.eb => Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/Clang/{Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb => Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb} (96%) diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb similarity index 96% rename from easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb rename to easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb index b7348ae71b3..a44f941c7ed 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb @@ -20,7 +20,7 @@ description = """C, C++, Objective-C compiler, based on LLVM. Does not # Clang also depends on libstdc++ during runtime, but this dependency is # already specified as the toolchain. -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchain = {'name': 'GCC', 'version': '8.3.0'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} @@ -53,7 +53,7 @@ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.32'), ('GMP', '6.1.2'), - ('CUDA', local_cudaver, '', True), + ('CUDA', local_cudaver), ] builddependencies = [ From d3f20f575b3c3cf0c839bf249b73ff781c9f1a86 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 2 Jan 2020 14:59:04 +0000 Subject: [PATCH 351/468] set gnu++11 in toolchainopts which simplifies the patch --- easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb | 3 ++- .../easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb | 3 ++- .../p/pocl/pocl-1.4_remove-c11-std.patch | 13 ------------- 3 files changed, 4 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb index 9d67b946980..d2e92d335d5 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb @@ -7,13 +7,14 @@ homepage = 'http://portablecl.org' description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchainopts = {'cstd': 'gnu++11'} source_urls = ['https://github.com/pocl/pocl/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_remove-c11-std.patch'] checksums = [ 'ec237faa83bb1c803fbdf7c6e83d8a2ad68b6f0ed1879c3aa16c0e1dcc478742', # v1.4.tar.gz - '15d81b142d836e188061c67af9df6e60381e40db92bd433fb6677033fb6c5a23', # pocl-1.4_remove-c11-std.patch + 'd3b34f64b9142a857aa601c13220159b8fa21a51e93d8aaacd8d949588fd9af1', # pocl-1.4_remove-c11-std.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb index 1a066160fed..1ddebc3094d 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb @@ -7,13 +7,14 @@ homepage = 'http://portablecl.org' description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" toolchain = {'name': 'gcccuda', 'version': '2019b'} +toolchainopts = {'cstd': 'gnu++11'} source_urls = ['https://github.com/pocl/pocl/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_remove-c11-std.patch'] checksums = [ 'ec237faa83bb1c803fbdf7c6e83d8a2ad68b6f0ed1879c3aa16c0e1dcc478742', # v1.4.tar.gz - '15d81b142d836e188061c67af9df6e60381e40db92bd433fb6677033fb6c5a23', # pocl-1.4_remove-c11-std.patch + 'd3b34f64b9142a857aa601c13220159b8fa21a51e93d8aaacd8d949588fd9af1', # pocl-1.4_remove-c11-std.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch b/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch index c5adc164bf4..c9f225cdb4a 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch @@ -10,19 +10,6 @@ Patch by Simon Branford, University of Birmingham run_llvm_config(LLVM_CPPFLAGS --cppflags) string(REPLACE "${LLVM_PREFIX}" "${LLVM_PREFIX_CMAKE}" LLVM_CPPFLAGS "${LLVM_CPPFLAGS}") run_llvm_config(LLVM_LDFLAGS --ldflags) ---- CMakeLists.txt.orig 2019-12-30 18:53:08.443068000 +0000 -+++ CMakeLists.txt 2019-12-30 18:54:27.201578300 +0000 -@@ -634,8 +634,8 @@ - # down the kernels, so it needs to be determined whether it's worth - # the trouble. - set(DEFAULT_KERNEL_CL_FLAGS "-xcl -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") --set(DEFAULT_KERNEL_C_FLAGS "-xc -std=c11 -D__CBUILD__ -fno-math-errno -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") --set(DEFAULT_KERNEL_CXX_FLAGS "-xc++ -std=c++11 -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") -+set(DEFAULT_KERNEL_C_FLAGS "-xc -D__CBUILD__ -fno-math-errno -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") -+set(DEFAULT_KERNEL_CXX_FLAGS "-xc++ -fno-stack-protector -fPIC ${FLOATCONV_FLAG}") - - set(EXTRA_KERNEL_FLAGS "" CACHE STRING "Extra arguments to all kernel compilation commands (defaults to empty)") - set(EXTRA_KERNEL_CL_FLAGS "" CACHE STRING "Extra arguments to kernel CL compiler (defaults to empty)") --- tests/regression/CMakeLists.txt.orig 2019-12-30 19:15:16.490362000 +0000 +++ tests/regression/CMakeLists.txt 2019-12-30 19:15:30.527613525 +0000 @@ -53,7 +53,7 @@ From 92e2d57657f35ffbdc163f23f02eaed413f8ac43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jan 2020 17:40:33 +0100 Subject: [PATCH 352/468] adding easyconfigs: Beast-1.10.4-GCC-8.2.0-2.31.1.eb --- .../b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..4da3106c343 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,34 @@ +# Author: Pablo Escobar Lopez (1/1) +# Biozentrum - University of Basel +easyblock = 'Tarball' + +name = 'Beast' +version = '1.10.4' + +homepage = 'http://beast.community' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] +sources = ['BEASTv%(version)s.tgz'] +checksums = ['be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +moduleclass = 'bio' From e69c3dec096760cae35ee4a53961202bde79df79 Mon Sep 17 00:00:00 2001 From: crubb Date: Fri, 3 Jan 2020 08:33:42 +0000 Subject: [PATCH 353/468] Update DCMTK to 3.6.5 and update arch to GCCcore 8.2.0 --- .../d/DCMTK/DCMTK-3.6.5-GCCcore-8.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..e111b0d25ad --- /dev/null +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'DCMTK' +version = '3.6.5' + +homepage = 'https://dicom.offis.de/dcmtk' +description = """DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. +It includes software for examining, constructing and converting DICOM image files, handling offline media, sending +and receiving images over a network connection, as well as demonstrative image storage and worklist servers.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dicom.offis.de/download/dcmtk/dcmtk%s/' % version.replace('.', '')] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a05178665f21896dbb0974106dba1ad144975414abd760b4cf8f5cc979f9beb9'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('libpng', '1.6.36'), + ('libxml2', '2.9.8'), + ('libiconv', '1.16'), +] + +sanity_check_paths = { + 'files': ['bin/dcmdump', 'bin/dcmj2pnm'], + 'dirs': ['lib'], +} + +moduleclass = 'data' From 8c6328ce3494282252ce56238b1592407163cee0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jan 2020 09:40:29 +0100 Subject: [PATCH 354/468] use https URLs in horton and libxc 2.2.2 easyconfigs --- .../h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb | 2 +- .../h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb index fb2614dff93..0178d4c8087 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'horton' version = '2.1.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://theochem.github.io/horton' +homepage = 'https://theochem.github.io/horton' description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb index b16488ca6b8..1259d2da72c 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'horton' version = '2.1.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://theochem.github.io/horton' +homepage = 'https://theochem.github.io/horton' description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb index 6cd124752b3..330753d128c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '2.2.2' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/octopus/wiki/index.php/Libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/octopus/down.php?file=libxc/'] sources = [SOURCE_TAR_GZ] checksums = ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb index 5dfa0de3524..994f15d884a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '2.2.2' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/octopus/wiki/index.php/Libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/octopus/down.php?file=libxc/'] sources = [SOURCE_TAR_GZ] checksums = ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'] From b2294cf6dfc6759b42371a3545411d2dc3d0afb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jan 2020 09:41:14 +0100 Subject: [PATCH 355/468] allow old libxc as dep for horton --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index cc27d76f0dd..4c14760e767 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -241,9 +241,9 @@ def check_dep_vars(self, dep, dep_vars): # some software packages require an old version of a particular dependency old_dep_versions = { - # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, PySCF, WIEN2k + # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k # (Qiskit depends on PySCF) - 'libxc': (r'[23]\.', ['ABINIT-', 'AtomPAW-', 'CP2K-', 'GPAW-', 'PySCF-', 'Qiskit-', 'WIEN2k-']), + 'libxc': (r'[23]\.', ['ABINIT-', 'AtomPAW-', 'CP2K-', 'GPAW-', 'horton-', 'PySCF-', 'Qiskit-', 'WIEN2k-']), # OPERA requires SAMtools 0.x 'SAMtools': (r'0\.', ['ChimPipe-0.9.5', 'Cufflinks-2.2.1', 'OPERA-2.0.6']), # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From f66a5fb2ef341f53dea7dd036197bfe70e961bf4 Mon Sep 17 00:00:00 2001 From: crubb Date: Fri, 3 Jan 2020 11:26:38 +0000 Subject: [PATCH 356/468] {bio}[GCCcore-8.2.0] ConnectomeWorkbench-1.3.2 --- ...ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..da15c0b6470 --- /dev/null +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'ConnectomeWorkbench' +version = '1.3.2' + +homepage = 'https://www.humanconnectome.org/software/connectome-workbench' +description = """Connectome Workbench is an open source, freely available visualization + and discovery tool used to map neuroimaging data, especially data generated by the + Human Connectome Project.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Washington-University/workbench/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '5574da8fcba810f5de1a3f70691cd763f927413d73f3b107142041272bf4edc9', # v1.3.2.tar.gz +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('binutils', '2.31.1') +] + +dependencies = [ + ('Qt5', '5.12.3'), + ('Mesa', '19.0.1'), + ('FTGL', '2.1.3-rc5') +] + +start_dir = 'src' + +configopts = '-DCMAKE_BUILD_TYPE=Release -DWORKBENCH_MESA_DIR=${EBROOTMESA} ' +configopts += '-DWORKBENCH_USE_QT5=TRUE -Wno-dev ' + +# It is necessary to deactivate the SIMD optimization in order to build +# kloewe/dot correctly. This should not affect the overall optimization since +# compiler flags are passed by EB via CFLAGS and CXXFLAGS. +# See https://github.com/Washington-University/workbench/issues/34 +configopts += '-DWORKBENCH_USE_SIMD=FALSE ' + +sanity_check_paths = { + 'files': ['bin/wb_command', 'bin/wb_shortcuts', 'bin/wb_view'], + 'dirs': ['share'], +} + +moduleclass = 'bio' From 8c3ed0388447032ffafab6f920874484388a5959 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Jan 2020 10:34:11 +0000 Subject: [PATCH 357/468] Switch patch to undef bool and vec when using altivec.h --- .../easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb | 6 +++--- .../easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb | 6 +++--- ...l-1.4_undef-bool-and-vector-from-altivec.patch | 15 +++++++++++++++ 3 files changed, 21 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.4_undef-bool-and-vector-from-altivec.patch diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb index d2e92d335d5..0268b398ebd 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb @@ -7,14 +7,14 @@ homepage = 'http://portablecl.org' description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" toolchain = {'name': 'GCC', 'version': '8.3.0'} -toolchainopts = {'cstd': 'gnu++11'} source_urls = ['https://github.com/pocl/pocl/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_remove-c11-std.patch'] +patches = ['%(name)s-%(version)s_undef-bool-and-vector-from-altivec.patch'] checksums = [ 'ec237faa83bb1c803fbdf7c6e83d8a2ad68b6f0ed1879c3aa16c0e1dcc478742', # v1.4.tar.gz - 'd3b34f64b9142a857aa601c13220159b8fa21a51e93d8aaacd8d949588fd9af1', # pocl-1.4_remove-c11-std.patch + # pocl-1.4_undef-bool-and-vector-from-altivec.patch + 'e795b7db34ebae71ee206ad88dcf93b6691bbc3c179d346d6385ded0767d49ce', ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb index 1ddebc3094d..84d25740654 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb @@ -7,14 +7,14 @@ homepage = 'http://portablecl.org' description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" toolchain = {'name': 'gcccuda', 'version': '2019b'} -toolchainopts = {'cstd': 'gnu++11'} source_urls = ['https://github.com/pocl/pocl/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_remove-c11-std.patch'] +patches = ['%(name)s-%(version)s_undef-bool-and-vector-from-altivec.patch'] checksums = [ 'ec237faa83bb1c803fbdf7c6e83d8a2ad68b6f0ed1879c3aa16c0e1dcc478742', # v1.4.tar.gz - 'd3b34f64b9142a857aa601c13220159b8fa21a51e93d8aaacd8d949588fd9af1', # pocl-1.4_remove-c11-std.patch + # pocl-1.4_undef-bool-and-vector-from-altivec.patch + 'e795b7db34ebae71ee206ad88dcf93b6691bbc3c179d346d6385ded0767d49ce', ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4_undef-bool-and-vector-from-altivec.patch b/easybuild/easyconfigs/p/pocl/pocl-1.4_undef-bool-and-vector-from-altivec.patch new file mode 100644 index 00000000000..b8c7ffb3915 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4_undef-bool-and-vector-from-altivec.patch @@ -0,0 +1,15 @@ +Undefine altivec.h bool and vector, otherwise these conflict with the c++11 standard defintions +and that causes the build to fail on ppc64le. +Patch by Simon Branford, University of Birmingham +diff -aur pocl-1.4.orig/include/CL/cl_platform.h pocl-1.4/include/CL/cl_platform.h +--- pocl-1.4.orig/include/CL/cl_platform.h 2020-01-03 09:55:56.986465000 +0000 ++++ pocl-1.4/include/CL/cl_platform.h 2020-01-03 09:59:18.058173021 +0000 +@@ -356,6 +356,8 @@ + /* Define basic vector types */ + #if defined( __VEC__ ) + #include /* may be omitted depending on compiler. AltiVec spec provides no way to detect whether the header is required. */ ++ #undef bool ++ #undef vector + typedef __vector unsigned char __cl_uchar16; + typedef __vector signed char __cl_char16; + typedef __vector unsigned short __cl_ushort8; From f6b73e8b13fdb7464c12ef9e3097a703ba51d3e9 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 4 Jan 2020 10:34:59 +0000 Subject: [PATCH 358/468] remove unneeded patch --- .../p/pocl/pocl-1.4_remove-c11-std.patch | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch b/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch deleted file mode 100644 index c9f225cdb4a..00000000000 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4_remove-c11-std.patch +++ /dev/null @@ -1,23 +0,0 @@ -c++11 std causes the build to fail on ppc64le, so stop it being set in various CMake files -Patch by Simon Branford, University of Birmingham ---- cmake/LLVM.cmake.orig 2019-12-30 18:43:07.077199000 +0000 -+++ cmake/LLVM.cmake 2019-12-30 18:44:37.953255342 +0000 -@@ -96,6 +96,7 @@ - string(REPLACE "${LLVM_PREFIX}" "${LLVM_PREFIX_CMAKE}" LLVM_CFLAGS "${LLVM_CFLAGS}") - run_llvm_config(LLVM_CXXFLAGS --cxxflags) - string(REPLACE "${LLVM_PREFIX}" "${LLVM_PREFIX_CMAKE}" LLVM_CXXFLAGS "${LLVM_CXXFLAGS}") -+string(REPLACE "-std=c++11" "" LLVM_CXXFLAGS "${LLVM_CXXFLAGS}") - run_llvm_config(LLVM_CPPFLAGS --cppflags) - string(REPLACE "${LLVM_PREFIX}" "${LLVM_PREFIX_CMAKE}" LLVM_CPPFLAGS "${LLVM_CPPFLAGS}") - run_llvm_config(LLVM_LDFLAGS --ldflags) ---- tests/regression/CMakeLists.txt.orig 2019-12-30 19:15:16.490362000 +0000 -+++ tests/regression/CMakeLists.txt 2019-12-30 19:15:30.527613525 +0000 -@@ -53,7 +53,7 @@ - if (MSVC) - add_compile_options(${OPENCL_CFLAGS}) - else () -- add_compile_options("-std=c++11" "-Wno-deprecated" "-Wno-deprecated-declarations" ${OPENCL_CFLAGS}) -+ add_compile_options("-Wno-deprecated" "-Wno-deprecated-declarations" ${OPENCL_CFLAGS}) - endif () - - add_definitions("-DSRCDIR=\"${CMAKE_CURRENT_SOURCE_DIR}\"") From f434a1577112648860cc76c1e19140efd3520fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jan 2020 14:57:01 +0100 Subject: [PATCH 359/468] update copyright statements for 2020 --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/styletests.py | 2 +- test/easyconfigs/suite.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/setup.py b/setup.py index 669fd196b9e..171e24a96f6 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2019 Ghent University +# Copyright 2012-2020 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/__init__.py b/test/__init__.py index 9cc48bae9b5..d90fcf47716 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -1,5 +1,5 @@ ## -# Copyright 2009-2019 Ghent University +# Copyright 2009-2020 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f558021b041..691010f0449 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1,5 +1,5 @@ ## -# Copyright 2013-2019 Ghent University +# Copyright 2013-2020 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index d054dcec5f3..ac5502d0526 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -1,5 +1,5 @@ ## -# Copyright 2016-2019 Ghent University +# Copyright 2016-2020 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index b0028d1eb5c..e342c5d0161 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -1,6 +1,6 @@ #!/usr/bin/python ## -# Copyright 2012-2019 Ghent University +# Copyright 2012-2020 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), From 131741d6b1a4f6d9b34141b21715c582a2098a21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jan 2020 16:29:21 +0100 Subject: [PATCH 360/468] use https for Beast 1.10.4 homepage --- easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb index 4da3106c343..5898adca4a5 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.10.4-GCC-8.2.0-2.31.1.eb @@ -5,7 +5,7 @@ easyblock = 'Tarball' name = 'Beast' version = '1.10.4' -homepage = 'http://beast.community' +homepage = 'https://beast.community' description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies From 2fdae9edd4de71461ae1bbc10ebab1f77a035777 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jan 2020 20:32:41 +0100 Subject: [PATCH 361/468] don't strip out copyright headers in patch for FSL 6.0.2 --- ....2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb | 2 +- ....2_probtrackx2_gpu_large_mri_support.patch | 1307 ++--------------- 2 files changed, 128 insertions(+), 1181 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb index 78ce88ec33e..f96cf15c130 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb @@ -38,7 +38,7 @@ checksums = [ 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch 'a2adee25538e8e2aebba9545cce2766841399b63354b97f38851ff7259d59a8d', # FSL-6.0.2_Enable_GPU_build.patch # FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch - '05f6ddf6b149e234ea7428bd5b510a72aa8f131a00fda0e369f854b722d88b19', + '805df04a8d8866cfae45cad7a893044e7652bde4e4c2ffde9cb5560926c955ee', 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch ] diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch index 8d76f676392..afa47127224 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2_probtrackx2_gpu_large_mri_support.patch @@ -1,146 +1,11 @@ # This should fix what was described in this thread https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1911&L=FSL&O=D&X=C89E84F6301F100D81&Y=caspar.vanleeuwen%40surfsara.nl&P=96399 # In addition, I included a change in tractographyInput.cc to explicitely call 'round' from the namespace 'MISCMATHS'. -diff -Nru fsl.orig/src/ptx2/CUDA/intersectionsDevice.cu fsl/src/ptx2/CUDA/intersectionsDevice.cu ---- fsl.orig/src/ptx2/CUDA/intersectionsDevice.cu 2019-11-15 10:47:30.358790161 +0100 -+++ fsl/src/ptx2/CUDA/intersectionsDevice.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include - -diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_gpu.cu ---- fsl.orig/src/ptx2/CUDA/memManager_gpu.cu 2019-11-15 10:47:30.376790024 +0100 -+++ fsl/src/ptx2/CUDA/memManager_gpu.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,70 +4,11 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ +diff -ru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_gpu.cu +--- fsl.orig/src/ptx2/CUDA/memManager_gpu.cu 2019-09-11 15:25:08.000000000 +0200 ++++ fsl/src/ptx2/CUDA/memManager_gpu.cu 2020-01-04 20:06:17.763681565 +0100 +@@ -66,8 +66,9 @@ + University, to negotiate a licence. Contact details are: + fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -cudaError_t checkCuda(cudaError_t result){ +cudaError_t checkCuda(cudaError_t result, const char *msg=NULL){ @@ -149,7 +14,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ fprintf(stderr, "CUDA Runtime Error: %s\n", cudaGetErrorString(result)); exit(1); -@@ -468,62 +409,155 @@ +@@ -468,62 +469,155 @@ } } @@ -332,7 +197,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ //Avoid mask if(data_host.avoid.NVols){ checkCuda(cudaMalloc((void**)&auxF,data_host.Ssizes[0]*data_host.Ssizes[1]*data_host.Ssizes[2]*sizeof(float))); -@@ -531,10 +565,6 @@ +@@ -531,10 +625,6 @@ checkCuda(cudaMemcpy(&data_gpu->avoid.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); } if(data_host.avoid.NSurfs){ @@ -343,7 +208,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMalloc((void**)&auxF,data_host.avoid.sizesStr[1]*sizeof(float))); checkCuda(cudaMemcpy(auxF,data_host.avoid.vertices,data_host.avoid.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->avoid.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -555,10 +585,6 @@ +@@ -555,10 +645,6 @@ checkCuda(cudaMemcpy(&data_gpu->stop.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); } if(data_host.stop.NSurfs){ @@ -354,7 +219,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMalloc((void**)&auxF,data_host.stop.sizesStr[1]*sizeof(float))); checkCuda(cudaMemcpy(auxF,data_host.stop.vertices,data_host.stop.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->stop.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -579,10 +605,6 @@ +@@ -579,10 +665,6 @@ checkCuda(cudaMemcpy(&data_gpu->wtstop.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); } if(data_host.wtstop.NSurfs){ @@ -365,7 +230,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMalloc((void**)&auxF,data_host.wtstop.sizesStr[1]*sizeof(float))); checkCuda(cudaMemcpy(auxF,data_host.wtstop.vertices,data_host.wtstop.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->wtstop.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -592,8 +614,8 @@ +@@ -592,8 +674,8 @@ checkCuda(cudaMalloc((void**)&auxI,data_host.wtstop.sizesStr[3]*sizeof(int))); checkCuda(cudaMemcpy(auxI,data_host.wtstop.VoxFaces,data_host.wtstop.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->wtstop.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); @@ -376,7 +241,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMemcpy(&data_gpu->wtstop.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); } // Network mask -@@ -603,10 +625,6 @@ +@@ -603,10 +685,6 @@ checkCuda(cudaMemcpy(&data_gpu->network.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); } if(data_host.network.NSurfs){ @@ -387,7 +252,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMalloc((void**)&auxF,data_host.network.sizesStr[1]*sizeof(float))); checkCuda(cudaMemcpy(auxF,data_host.network.vertices,data_host.network.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->network.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -616,8 +634,8 @@ +@@ -616,8 +694,8 @@ checkCuda(cudaMalloc((void**)&auxI,data_host.network.sizesStr[3]*sizeof(int))); checkCuda(cudaMemcpy(auxI,data_host.network.VoxFaces,data_host.network.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->network.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); @@ -398,7 +263,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMemcpy(&data_gpu->network.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); } if(data_host.network.NVols||data_host.network.NSurfs){ -@@ -654,9 +672,6 @@ +@@ -654,9 +732,6 @@ checkCuda(cudaMemcpy(&data_gpu->waypoint.volume,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); } if(data_host.waypoint.NSurfs){ @@ -408,7 +273,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMalloc((void**)&auxF,data_host.waypoint.sizesStr[1]*sizeof(float))); checkCuda(cudaMemcpy(auxF,data_host.waypoint.vertices,data_host.waypoint.sizesStr[1]*sizeof(float),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->waypoint.vertices,&auxF,sizeof(float*),cudaMemcpyHostToDevice)); -@@ -666,8 +681,8 @@ +@@ -666,8 +741,8 @@ checkCuda(cudaMalloc((void**)&auxI,data_host.waypoint.sizesStr[3]*sizeof(int))); checkCuda(cudaMemcpy(auxI,data_host.waypoint.VoxFaces,data_host.waypoint.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->waypoint.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); @@ -419,7 +284,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMemcpy(&data_gpu->waypoint.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); } if(data_host.waypoint.NVols||data_host.waypoint.NSurfs){ -@@ -692,8 +707,8 @@ +@@ -692,8 +767,8 @@ checkCuda(cudaMalloc((void**)&auxI,data_host.targets.sizesStr[3]*sizeof(int))); checkCuda(cudaMemcpy(auxI,data_host.targets.VoxFaces,data_host.targets.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->targets.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); @@ -430,7 +295,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMemcpy(&data_gpu->targets.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); } if(data_host.targets.NVols||data_host.targets.NSurfs){ -@@ -748,8 +763,8 @@ +@@ -748,8 +823,8 @@ checkCuda(cudaMalloc((void**)&auxI,data_host.lrmatrix1.sizesStr[3]*sizeof(int))); checkCuda(cudaMemcpy(auxI,data_host.lrmatrix1.VoxFaces,data_host.lrmatrix1.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->lrmatrix1.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); @@ -441,7 +306,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMemcpy(&data_gpu->lrmatrix1.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); //cudaMalloc((void**)&auxI,data_host.lrmatrix1.sizesStr[4]*sizeof(int)); //cudaMemcpy(auxI,data_host.lrmatrix1.IndexRoi,data_host.lrmatrix1.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); -@@ -774,8 +789,8 @@ +@@ -774,8 +849,8 @@ checkCuda(cudaMalloc((void**)&auxI,data_host.matrix3.sizesStr[3]*sizeof(int))); checkCuda(cudaMemcpy(auxI,data_host.matrix3.VoxFaces,data_host.matrix3.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->matrix3.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); @@ -452,7 +317,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMemcpy(&data_gpu->matrix3.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); //cudaMalloc((void**)&auxI,data_host.matrix3.sizesStr[4]*sizeof(int)); //cudaMemcpy(auxI,data_host.matrix3.IndexRoi,data_host.matrix3.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); -@@ -800,8 +815,8 @@ +@@ -800,8 +875,8 @@ checkCuda(cudaMalloc((void**)&auxI,data_host.lrmatrix3.sizesStr[3]*sizeof(int))); checkCuda(cudaMemcpy(auxI,data_host.lrmatrix3.VoxFaces,data_host.lrmatrix3.sizesStr[3]*sizeof(int),cudaMemcpyHostToDevice)); checkCuda(cudaMemcpy(&data_gpu->lrmatrix3.VoxFaces,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); @@ -463,295 +328,10 @@ diff -Nru fsl.orig/src/ptx2/CUDA/memManager_gpu.cu fsl/src/ptx2/CUDA/memManager_ checkCuda(cudaMemcpy(&data_gpu->lrmatrix3.VoxFacesIndex,&auxI,sizeof(int*),cudaMemcpyHostToDevice)); //cudaMalloc((void**)&auxI,data_host.lrmatrix3.sizesStr[4]*sizeof(int)); //cudaMemcpy(auxI,data_host.lrmatrix3.IndexRoi,data_host.lrmatrix3.sizesStr[4]*sizeof(int),cudaMemcpyHostToDevice); -diff -Nru fsl.orig/src/ptx2/CUDA/streamlinesDevice.cu fsl/src/ptx2/CUDA/streamlinesDevice.cu ---- fsl.orig/src/ptx2/CUDA/streamlinesDevice.cu 2019-11-15 10:47:30.363790122 +0100 -+++ fsl/src/ptx2/CUDA/streamlinesDevice.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2005 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #define DIVRND 1.00000001f - #define LCRAT 5.0f //box for loopcheck is five times smaller than brain mask -diff -Nru fsl.orig/src/ptx2/CUDA/tractography_CallKernels.cu fsl/src/ptx2/CUDA/tractography_CallKernels.cu ---- fsl.orig/src/ptx2/CUDA/tractography_CallKernels.cu 2019-11-15 10:47:30.381789984 +0100 -+++ fsl/src/ptx2/CUDA/tractography_CallKernels.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - void initialise_SeedsGPU( - curandState*& devStates, -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.cc fsl/src/ptx2/CUDA/tractographyData.cc ---- fsl.orig/src/ptx2/CUDA/tractographyData.cc 2019-11-15 10:47:30.365790108 +0100 -+++ fsl/src/ptx2/CUDA/tractographyData.cc 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #ifndef EXPOSE_TREACHEROUS - #define EXPOSE_TREACHEROUS 1 -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.h fsl/src/ptx2/CUDA/tractographyData.h ---- fsl.orig/src/ptx2/CUDA/tractographyData.h 2019-11-15 10:47:30.383789969 +0100 -+++ fsl/src/ptx2/CUDA/tractographyData.h 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - - #ifndef Data_gpu_ptx_H -@@ -99,7 +39,7 @@ +diff -ru fsl.orig/src/ptx2/CUDA/tractographyData.h fsl/src/ptx2/CUDA/tractographyData.h +--- fsl.orig/src/ptx2/CUDA/tractographyData.h 2019-09-11 15:25:09.000000000 +0200 ++++ fsl/src/ptx2/CUDA/tractographyData.h 2020-01-04 20:07:55.043647152 +0100 +@@ -99,7 +99,7 @@ int nvoxels; int nsamples; int nfibres; @@ -760,79 +340,10 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyData.h fsl/src/ptx2/CUDA/tractograp int nparticles; int nsteps; -diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractography_gpu.cu ---- fsl.orig/src/ptx2/CUDA/tractography_gpu.cu 2019-11-15 10:47:30.374790038 +0100 -+++ fsl/src/ptx2/CUDA/tractography_gpu.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include - #include -@@ -92,7 +32,7 @@ +diff -ru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractography_gpu.cu +--- fsl.orig/src/ptx2/CUDA/tractography_gpu.cu 2019-09-11 15:25:09.000000000 +0200 ++++ fsl/src/ptx2/CUDA/tractography_gpu.cu 2020-01-04 20:08:50.823607811 +0100 +@@ -92,7 +92,7 @@ init_gpu(); size_t free,total; cudaMemGetInfo(&free,&total); @@ -841,7 +352,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractogra probtrackxOptions& opts=probtrackxOptions::getInstance(); -@@ -103,7 +43,7 @@ +@@ -103,7 +103,7 @@ copy_ToTextureMemory(data_host); // Set Texture memory cuMemGetInfo(&free,&total); @@ -850,7 +361,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractogra int MAX_SLs; int THREADS_STREAM; // MAX_Streamlines and NSTREAMS must be multiples -@@ -219,7 +159,6 @@ +@@ -219,7 +219,6 @@ checkCuda(cudaDeviceSynchronize()); cuMemGetInfo(&free,&total); @@ -858,7 +369,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractogra // run iterations for(int iter=0;iter0||lengths_host[0][pos+1]>0){ vector tmp; @@ -866,7 +377,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractogra if(lengths_host[0][pos]>0){ int posSEED=i*data_host.nsteps*3; int posCURRENT=0; -@@ -365,12 +303,10 @@ +@@ -365,12 +363,10 @@ tmp.push_back(paths_host[0][posSEED+posCURRENT*3+1]); tmp.push_back(paths_host[0][posSEED+posCURRENT*3+2]); } @@ -879,7 +390,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractogra for(;co0||lengths_host[0][pos+1]>0){ vector tmp; @@ -887,7 +398,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractogra if(lengths_host[0][pos]>0){ int posSEED=i*data_host.nsteps*3; int posCURRENT=0; -@@ -466,12 +401,10 @@ +@@ -466,12 +461,10 @@ tmp.push_back(paths_host[0][posSEED+posCURRENT*3+1]); tmp.push_back(paths_host[0][posSEED+posCURRENT*3+2]); } @@ -900,151 +411,10 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractography_gpu.cu fsl/src/ptx2/CUDA/tractogra for(;co - #include -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractographyInput.cc ---- fsl.orig/src/ptx2/CUDA/tractographyInput.cc 2019-11-15 10:47:30.368790085 +0100 -+++ fsl/src/ptx2/CUDA/tractographyInput.cc 2019-11-15 15:03:45.388788544 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #ifndef EXPOSE_TREACHEROUS - #define EXPOSE_TREACHEROUS -@@ -85,26 +25,15 @@ +diff -ru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractographyInput.cc +--- fsl.orig/src/ptx2/CUDA/tractographyInput.cc 2019-09-11 15:25:09.000000000 +0200 ++++ fsl/src/ptx2/CUDA/tractographyInput.cc 2020-01-04 20:09:33.313593417 +0100 +@@ -85,26 +85,15 @@ coords[1] = MISCMATHS::round(v(2)); coords[2] = MISCMATHS::round(v(3)); } @@ -1080,7 +450,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr { int type=meshFileType(filename); if (type==ASCII){ -@@ -119,14 +48,14 @@ +@@ -119,14 +108,14 @@ } } @@ -1103,7 +473,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr { // load a freesurfer ascii mesh ifstream f(filename.c_str()); -@@ -139,10 +68,10 @@ +@@ -139,10 +128,10 @@ cerr<<"Loading ascii file: error in the header"<>vertices[posV]>>vertices[posV+1]>>vertices[posV+2]>>values[i]; // write from file to vector if(values[i]==0) zeros=true; else nonzeros=true; -@@ -171,30 +100,30 @@ +@@ -171,30 +160,30 @@ if (zeros&&nonzeros) allMesh=false; // then some values should be ignored // storing locations: use same structure for active-nonactive vertex @@ -1175,7 +545,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr int p0, p1, p2; float val; f>>p0>>p1>>p2>>val; -@@ -208,14 +137,14 @@ +@@ -208,14 +197,14 @@ }else {cout<<"Loading ascii file: error opening file: "<>j>>p0>>p1>>p2; -@@ -278,22 +207,22 @@ +@@ -278,22 +267,22 @@ } } @@ -1276,7 +646,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr for (vector< fslsurface_name::vertex >::iterator i= surf.vbegin(); i!= surf.vend();++i){ vertices.resize(posV+3); vertices[posV]=i->x; -@@ -326,42 +255,42 @@ +@@ -326,42 +315,42 @@ } if (zeros&&nonzeros) allMesh=false; int local_loc=1; @@ -1345,7 +715,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr } posLV++; nlocs++; -@@ -370,34 +299,38 @@ +@@ -370,34 +359,38 @@ } void tractographyInput::load_volume( string& filename, @@ -1405,7 +775,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr } } } -@@ -444,20 +377,20 @@ +@@ -444,20 +437,20 @@ int voxY = MISCMATHS::round(crossed[i](2)); int voxZ = MISCMATHS::round(crossed[i](3)); if (voxX>=0 && voxX=0 && voxY=0 && voxZmaxz?tmpi:maxz; i++; -@@ -516,26 +449,26 @@ +@@ -516,26 +509,26 @@ for (int x=minx-s;x<=maxx+s;x+=1){ for (int y=miny-s;y<=maxy+s;y+=1){ for (int z=minz-s;z<=maxz+s;z+=1){ @@ -1541,7 +911,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr { data.sizesStr=new int[4]; data.sizesStr[0]=0; -@@ -550,10 +483,12 @@ +@@ -550,10 +543,12 @@ vector voxFacesVec; vector nullV; @@ -1556,7 +926,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr load_volume(filename,Ssizes,data.volume,data.nlocs,true,false,0,nullV); data.NVols=1; }else if (meshExists(filename)){ -@@ -567,8 +502,8 @@ +@@ -567,8 +562,8 @@ if (fs){ fs>>tmp; do{ @@ -1567,7 +937,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr }while (!fs.eof()); }else{ cerr< voxFacesVec; vector coordsV; @@ -1654,7 +1024,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr load_volume(filename,Ssizes,data.volume,data.nlocs,true,wcoords,0,coordsV); data.NVols=1; data.IndexRoi=new int[1]; -@@ -655,7 +592,8 @@ +@@ -655,7 +652,8 @@ data.sizesStr[4]=1; }else if (meshExists(filename)){ load_mesh(filename,verticesVec,facesVec,locsVec,data.nlocs,wcoords,0,coordsV); @@ -1664,7 +1034,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[0],facesVec.size(), 0,voxFacesVec,data.VoxFacesIndex,locsVec); data.NSurfs=1; -@@ -670,20 +608,21 @@ +@@ -670,20 +668,21 @@ if (fs){ fs>>tmp; do{ @@ -1694,7 +1064,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr int nv=0; int ns=0; -@@ -692,22 +631,23 @@ +@@ -692,22 +691,23 @@ for (unsigned int i=0;i voxFacesVec; vector coordsV; @@ -1839,7 +1209,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr load_volume(filename,Ssizes,data.volume,data.nlocs,true,wcoords,0,coordsV); data.NVols=1; data.IndexRoi=new int[1]; -@@ -832,7 +770,7 @@ +@@ -832,7 +830,7 @@ } }else if (meshExists(filename)){ load_mesh(filename,verticesVec,facesVec,locsVec,data.nlocs,wcoords,0,coordsV); @@ -1848,7 +1218,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr init_surfvol(Ssizes,mm2vox,verticesVec,&facesVec[0],facesVec.size(), 0,voxFacesVec,data.VoxFacesIndex,locsVec); data.NSurfs=1; -@@ -850,20 +788,19 @@ +@@ -850,20 +848,19 @@ if (fs){ fs>>tmp; do{ @@ -1876,7 +1246,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr int nv=0; int ns=0; -@@ -874,34 +811,34 @@ +@@ -874,34 +871,34 @@ int locs_from_volume=0; for (unsigned int file=0;file locs; -@@ -1059,38 +997,38 @@ +@@ -1059,38 +1057,38 @@ int loc=0; float c1,c2,c3; for (unsigned int vertex=0;vertex>tmp; do{ @@ -2152,7 +1522,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr }while (!fs.eof()); }else{ cerr<<"Seed file "< DTISeedwarp4D = iffr.FieldAsNewimageVolume4D(true); -@@ -1653,13 +1593,13 @@ +@@ -1653,13 +1653,13 @@ tData.Warp_D2S_sizes[2]=DTISeedwarp4D.zsize(); tData.DTISeedwarp = new float[3*size]; for(int v=0;v<3;v++){ @@ -2719,85 +2089,16 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.cc fsl/src/ptx2/CUDA/tractogr } Matrix samp=IdentityMatrix(4); samp(1,1) = tData.Sdims[0]; -@@ -2007,5 +1947,3 @@ +@@ -2007,5 +2007,3 @@ load_rois_mixed(opts.seedfile.value(),mm2vox,tData.Sdims,tData.Ssizes,tData.networkREF); } } - - -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.h fsl/src/ptx2/CUDA/tractographyInput.h ---- fsl.orig/src/ptx2/CUDA/tractographyInput.h 2019-11-15 10:47:30.386789948 +0100 -+++ fsl/src/ptx2/CUDA/tractographyInput.h 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include - #include -@@ -83,84 +23,84 @@ +diff -ru fsl.orig/src/ptx2/CUDA/tractographyInput.h fsl/src/ptx2/CUDA/tractographyInput.h +--- fsl.orig/src/ptx2/CUDA/tractographyInput.h 2019-09-11 15:25:10.000000000 +0200 ++++ fsl/src/ptx2/CUDA/tractographyInput.h 2020-01-04 20:10:04.073580459 +0100 +@@ -83,84 +83,84 @@ /// Method load all the necessary data from the input files to perform GPU Tractography void load_tractographyData( tractographyData& tData, @@ -2947,7 +2248,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.h fsl/src/ptx2/CUDA/tractogra /// Method to find out what voxels are crossed by a triangle void csv_tri_crossed_voxels(float tri[3][3], -@@ -168,62 +108,62 @@ +@@ -168,62 +168,62 @@ /// Method to read all the ROIs of a mask in the same structure: for stop and avoid masks void load_rois_mixed(string filename, @@ -3057,79 +2358,10 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyInput.h fsl/src/ptx2/CUDA/tractogra }; -diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tractographyKernels.cu ---- fsl.orig/src/ptx2/CUDA/tractographyKernels.cu 2019-11-15 10:47:30.371790061 +0100 -+++ fsl/src/ptx2/CUDA/tractographyKernels.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include - #include -@@ -77,17 +17,17 @@ +diff -ru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tractographyKernels.cu +--- fsl.orig/src/ptx2/CUDA/tractographyKernels.cu 2019-09-11 15:25:10.000000000 +0200 ++++ fsl/src/ptx2/CUDA/tractographyKernels.cu 2020-01-04 20:10:35.513573164 +0100 +@@ -77,17 +77,17 @@ template __global__ void get_path_kernel( @@ -3155,7 +2387,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto { unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; if(id>=maxThread) return; -@@ -124,13 +64,15 @@ +@@ -124,13 +124,15 @@ // Use path to store my intial coordinates // We want to start at the same exact point, even if sampvox is activated @@ -3178,7 +2410,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto if(data_gpu->sampvox>0){ -@@ -145,13 +87,13 @@ +@@ -145,13 +147,13 @@ rej=false; } @@ -3199,7 +2431,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto } // track in one direction lengths[id*2]=streamline(data_gpu, -@@ -161,7 +103,7 @@ +@@ -161,7 +163,7 @@ &partRx[threadIdx.x],&partRy[threadIdx.x],&partRz[threadIdx.x], &memSH_a[threadIdx.x],&memSH_b[threadIdx.x],&memSH_c[threadIdx.x], &memSH_d[threadIdx.x],&memSH_e[threadIdx.x],&memSH_f[threadIdx.x], @@ -3208,7 +2440,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto // track in the other direction lengths[id*2+1]=streamline(data_gpu, -@@ -171,7 +113,7 @@ +@@ -171,7 +173,7 @@ &partRx[threadIdx.x],&partRy[threadIdx.x],&partRz[threadIdx.x], &memSH_a[threadIdx.x],&memSH_b[threadIdx.x],&memSH_c[threadIdx.x], &memSH_d[threadIdx.x],&memSH_e[threadIdx.x],&memSH_f[threadIdx.x], @@ -3217,7 +2449,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto state[id]=localState; // save state, otherwise random numbers will be repeated (start at the same point) } -@@ -180,11 +122,11 @@ +@@ -180,11 +182,11 @@ /////// AVOID MASK /////// ///////////////////////// template @@ -3234,7 +2466,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto { unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; if(id>=maxThread) return; -@@ -199,7 +141,8 @@ +@@ -199,7 +201,8 @@ /////////////////////// ////// ONE WAY //////// /////////////////////// @@ -3244,7 +2476,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto int mylength=lengths[id*2]; int2 rejflag; -@@ -253,8 +196,9 @@ +@@ -253,8 +256,9 @@ /////////////////////// ////// OTHER WAY ///// /////////////////////// @@ -3256,7 +2488,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto mylength=lengths[id*2+1]; segmentAx[threadIdx.x]=mypath[0]; -@@ -313,11 +257,11 @@ +@@ -313,11 +317,11 @@ /////// STOP MASK /////// ///////////////////////// template @@ -3273,7 +2505,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto { unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; if(id>=maxThread) return; -@@ -333,7 +277,8 @@ +@@ -333,7 +337,8 @@ /////////////////////// ////// ONE WAY //////// /////////////////////// @@ -3283,7 +2515,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto int mylength=lengths[id*2]; segmentAx[threadIdx.x]=mypath[0]; segmentAy[threadIdx.x]=mypath[1]; -@@ -387,8 +332,9 @@ +@@ -387,8 +392,9 @@ } /////////////////////// ////// OTHER WAY ///// @@ -3295,7 +2527,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto mylength=lengths[id*2+1]; segmentAx[threadIdx.x]=mypath[0]; -@@ -454,11 +400,11 @@ +@@ -454,11 +460,11 @@ // ignoring forcefirststep ... if seed is inside wtstop: is treated template @@ -3312,7 +2544,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto { unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; if(id>=maxThread) return; -@@ -480,7 +426,8 @@ +@@ -480,7 +486,8 @@ ///////////////// //// ONE WAY //// ///////////////// @@ -3322,7 +2554,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto int mylength=lengths[id*2]; bool wtstop=false; // set flags to 1 (still not in roi) -@@ -546,7 +493,8 @@ +@@ -546,7 +553,8 @@ //////////////////// //// OTHER WAY ///// //////////////////// @@ -3332,7 +2564,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto mylength=lengths[id*2+1]; wtstop=false; // set flags to 1 (still not in roi) -@@ -615,11 +563,11 @@ +@@ -615,11 +623,11 @@ /////// WAYPOINTS MASK //////// /////////////////////////////// template @@ -3349,7 +2581,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto { ///// DYNAMIC SHARED MEMORY ///// extern __shared__ float shared[]; -@@ -634,7 +582,8 @@ +@@ -634,7 +642,8 @@ unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; if(id>=maxThread) return; @@ -3359,7 +2591,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto int mylength=lengths[id*2]; int numpassed=0; -@@ -745,7 +694,8 @@ +@@ -745,7 +754,8 @@ numpassed=0; order=true; } @@ -3369,7 +2601,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto mylength=lengths[id*2+1]; if(waySurf){ -@@ -841,18 +791,17 @@ +@@ -841,18 +851,17 @@ ///////////////////////////// template // savelength 0: no --pd, nor --ompl | 1: --pd | 2: --ompl (ConNet pathlengths, ConNetb binary hits, and later calculates mean) @@ -3399,7 +2631,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto { unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; if(id>=maxThread) return; -@@ -887,7 +836,8 @@ +@@ -887,7 +896,8 @@ int numseed = (offset+id)/data_gpu->nparticles; int ROI = data_gpu->seeds_ROI[numseed]; @@ -3409,7 +2641,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto int mylength=lengths[id*2]; int numpassed=1; // count my own ROI -@@ -987,7 +937,8 @@ +@@ -987,7 +997,8 @@ net_flags[ROI]=1; // my own ROI numpassed=1; // count my own ROI @@ -3419,7 +2651,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto mylength=lengths[id*2+1]; if(netSurf){ -@@ -1092,16 +1043,16 @@ +@@ -1092,16 +1103,16 @@ ///////////////////////////// template // savelength 0: no --pd or --ompl | 1: --pd | 2: --ompl @@ -3446,7 +2678,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto { unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; if(id>=maxThread) return; -@@ -1127,7 +1078,8 @@ +@@ -1127,7 +1138,8 @@ targ_flags = &targ_flags_Global[id*totalTargets]; } @@ -3456,7 +2688,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto int mylength=lengths[id*2]; for(int i=0;isteplength; @@ -3466,7 +2698,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto mylength=lengths[id*2+1]; if(targSurf){ -@@ -1289,16 +1242,16 @@ +@@ -1289,16 +1302,16 @@ /////// MATRIX MASKs ///////// /////////////////////////////// template // M2 is for Matrix2: it can be defined in a different space @@ -3493,7 +2725,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto { unsigned int id = threadIdx.x+blockIdx.x*blockDim.x; if(id>=maxThread) return; -@@ -1331,7 +1284,8 @@ +@@ -1331,7 +1344,8 @@ ///////////////// //// ONE WAY //// ///////////////// @@ -3503,7 +2735,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto if(HSurfs){ if(M2){ vox_to_vox_S2M2(mypath,&segmentAx[threadIdx.x],&segmentAy[threadIdx.x],&segmentAz[threadIdx.x]); -@@ -1388,7 +1342,8 @@ +@@ -1388,7 +1402,8 @@ if(pathdist||omeanpathlength) pathlength=-data_gpu->steplength; // it starts with the second coordinate of the path // reverse, m_tracksign !! . If different directions when crossing 2 nodes, then the path distance is longer. @@ -3513,7 +2745,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto mylength=lengths[id*2+1]; if(HSurfs){ if(M2){ -@@ -1444,21 +1399,22 @@ +@@ -1444,21 +1459,22 @@ ///////// UPDATE PATHS VOLUME /////// ///////////////////////////////////// template @@ -3547,7 +2779,7 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto int mylength = lengths[id*2]; int* m_beenhere = &beenhere[id*(data_gpu->nsteps)]; int coordinatex,coordinatey,coordinatez; -@@ -1555,7 +1511,8 @@ +@@ -1555,7 +1571,8 @@ } // other way @@ -3557,223 +2789,10 @@ diff -Nru fsl.orig/src/ptx2/CUDA/tractographyKernels.cu fsl/src/ptx2/CUDA/tracto mylength = lengths[id*2+1]; pathlength=0.0f; -diff -Nru fsl.orig/src/ptx2/CUDA/transformationsDevice.cu fsl/src/ptx2/CUDA/transformationsDevice.cu ---- fsl.orig/src/ptx2/CUDA/transformationsDevice.cu 2019-11-15 10:47:30.379790000 +0100 -+++ fsl/src/ptx2/CUDA/transformationsDevice.cu 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2005 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - __constant__ float C_Sdims[3]; - __constant__ float C_Ddims[3]; -diff -Nru fsl.orig/src/ptx2/probtrackx_gpu.cc fsl/src/ptx2/probtrackx_gpu.cc ---- fsl.orig/src/ptx2/probtrackx_gpu.cc 2019-11-15 10:47:30.549788697 +0100 -+++ fsl/src/ptx2/probtrackx_gpu.cc 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include "probtrackx.h" - #include "saveResults_ptxGPU.h" -diff -Nru fsl.orig/src/ptx2/saveResults_ptxGPU.cc fsl/src/ptx2/saveResults_ptxGPU.cc ---- fsl.orig/src/ptx2/saveResults_ptxGPU.cc 2019-11-15 10:47:30.417789709 +0100 -+++ fsl/src/ptx2/saveResults_ptxGPU.cc 2019-11-10 01:04:48.000000000 +0100 -@@ -4,67 +4,7 @@ - - Copyright (C) 2015 University of Oxford */ - --/* Part of FSL - FMRIB's Software Library -- http://www.fmrib.ox.ac.uk/fsl -- fsl@fmrib.ox.ac.uk -- -- Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -- Imaging of the Brain), Department of Clinical Neurology, Oxford -- University, Oxford, UK -- -- -- LICENCE -- -- FMRIB Software Library, Release 6.0 (c) 2018, The University of -- Oxford (the "Software") -- -- The Software remains the property of the Oxford University Innovation -- ("the University"). -- -- The Software is distributed "AS IS" under this Licence solely for -- non-commercial use in the hope that it will be useful, but in order -- that the University as a charitable foundation protects its assets for -- the benefit of its educational and research purposes, the University -- makes clear that no condition is made or to be implied, nor is any -- warranty given or to be implied, as to the accuracy of the Software, -- or that it will be suitable for any particular purpose or for use -- under any specific conditions. Furthermore, the University disclaims -- all responsibility for the use which is made of the Software. It -- further disclaims any liability for the outcomes arising from using -- the Software. -- -- The Licensee agrees to indemnify the University and hold the -- University harmless from and against any and all claims, damages and -- liabilities asserted by third parties (including claims for -- negligence) which arise directly or indirectly from the use of the -- Software or the sale of any products based on the Software. -- -- No part of the Software may be reproduced, modified, transmitted or -- transferred in any form or by any means, electronic or mechanical, -- without the express permission of the University. The permission of -- the University is not required if the said reproduction, modification, -- transmission or transference is done without financial return, the -- conditions of this Licence are imposed upon the receiver of the -- product, and all original and amended source code is included in any -- transmitted product. You may be held legally responsible for any -- copyright infringement that is caused or encouraged by your failure to -- abide by these terms and conditions. -- -- You are not permitted under this Licence to use this Software -- commercially. Use for which any financial return is received shall be -- defined as commercial use, and includes (1) integration of all or part -- of the source code or the Software into a product for sale or license -- by or on behalf of Licensee to third parties or (2) use of the -- Software or any derivative of it for research with the final aim of -- developing software products for sale or license to a third party or -- (3) use of the Software or any derivative of it for research with the -- final aim of developing non-software products for sale or license to a -- third party, or (4) use of the Software to provide any service to an -- external organisation for which payment is received. If you are -- interested in using the Software commercially, please contact Oxford -- University Innovation ("OUI"), the technology transfer company of the -- University, to negotiate a licence. Contact details are: -- fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.*/ -+/* CCOPYRIGHT */ - - #include "probtrackx.h" - #include "CUDA/tractographyInput.h" -@@ -326,7 +266,7 @@ +diff -ru fsl.orig/src/ptx2/saveResults_ptxGPU.cc fsl/src/ptx2/saveResults_ptxGPU.cc +--- fsl.orig/src/ptx2/saveResults_ptxGPU.cc 2019-09-11 15:25:05.000000000 +0200 ++++ fsl/src/ptx2/saveResults_ptxGPU.cc 2020-01-04 20:11:24.863549470 +0100 +@@ -326,7 +326,7 @@ ////// save seeds to targets ////// /////////////////////////////////// if(opts.s2tout.value()){ @@ -3782,7 +2801,7 @@ diff -Nru fsl.orig/src/ptx2/saveResults_ptxGPU.cc fsl/src/ptx2/saveResults_ptxGP int ntargets=data_host.targets.NVols+data_host.targets.NSurfs; if (fsl_imageexists(opts.seedfile.value())){ volume tmp; -@@ -392,7 +332,7 @@ +@@ -392,7 +392,7 @@ int nfaces=data_host.seeds_mesh_info[1]; if(f.is_open()){ @@ -3791,7 +2810,7 @@ diff -Nru fsl.orig/src/ptx2/saveResults_ptxGPU.cc fsl/src/ptx2/saveResults_ptxGP for(int i=0;i Date: Sat, 4 Jan 2020 20:40:44 +0100 Subject: [PATCH 362/468] allow multiple different versions of TensorFlow used as dependency, as long as that's reflected in the versionsuffix (required for Horovod) --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d0d240a0193..a70e5beb57e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -210,7 +210,7 @@ def check_dep_vars(self, dep, dep_vars): # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix - if dep in ['ASE', 'Boost', 'Java', 'Lua', 'PLUMED', 'R'] and len(dep_vars) > 1: + if dep in ['ASE', 'Boost', 'Java', 'Lua', 'PLUMED', 'R', 'TensorFlow'] and len(dep_vars) > 1: for key in list(dep_vars): dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') # use version of Java wrapper rather than full Java version From d9be12eb1d08c3bc2cdd632eb3083256dcbf3b55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jan 2020 23:13:19 +0100 Subject: [PATCH 363/468] use https for NCL 6.6.2 homepage --- easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb index 700d1c17437..fbf6b2a663b 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2019b.eb @@ -1,7 +1,7 @@ name = 'NCL' version = '6.6.2' -homepage = 'http://www.ncl.ucar.edu' +homepage = 'https://www.ncl.ucar.edu' description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." toolchain = {'name': 'intel', 'version': '2019b'} From 9e0b5a01a4754fd00f5bea780d4f5d34d4e752d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jan 2020 23:22:50 +0100 Subject: [PATCH 364/468] add missing build dependencies for glibc 2.30 --- easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb index 37e6bd4fdc5..bbbfbfd3065 100644 --- a/easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/glibc/glibc-2.30-GCCcore-8.3.0.eb @@ -16,6 +16,9 @@ checksums = ['e2c4114e569afbe7edbc29131a43be833850ab9a459d81beb2588016d2bbb8af'] builddependencies = [ ('binutils', '2.32'), ('make', '4.2.1'), + ('texinfo', '6.7'), + ('Bison', '3.3.2'), + ('Python', '3.7.4'), ] preconfigopts = "mkdir obj && cd obj && " From bb6dfaceb7fcc28560de15cc391189b64965531d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Jan 2020 09:53:10 +0100 Subject: [PATCH 365/468] fix name for plotly extension in plotly.py v4.4.1 easyconfig --- .../easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb index 807fabdbf56..bc4a11ccdf6 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.4.1-intel-2019b.eb @@ -18,7 +18,7 @@ exts_list = [ ('retrying', '1.3.3', { 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], }), - (name, version, { + ('plotly', version, { 'checksums': ['acc94f17452471ca3446c2ce491c4d1affb99b9ddd9eac4e05614ac4318f8780'], }), ] From 48d117182b568f82128153f20875f80680cdbcf4 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 6 Jan 2020 09:38:26 +0000 Subject: [PATCH 366/468] Updating MASS checksum(s) --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 3 ++- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index ec8b3565370..2f459ceea46 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -209,7 +209,8 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-51.4', { - 'checksums': ['9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74'], + 'checksums': [('9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74', + '844270a2541eaed420871dfb61d681aa67ee57126645fb6b144b436c25698eeb')], }), ('ade4', '1.7-13', { 'checksums': ['f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b'], diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 5b046a7b3de..6635d318cb3 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -209,7 +209,8 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-51.4', { - 'checksums': ['9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74'], + 'checksums': [('9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74', + '844270a2541eaed420871dfb61d681aa67ee57126645fb6b144b436c25698eeb')], }), ('ade4', '1.7-13', { 'checksums': ['f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b'], From 9030d7e5824e0bdcc90e0d18fbb4d834940aec79 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 6 Jan 2020 09:49:34 +0000 Subject: [PATCH 367/468] Undoing whitespace change --- easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb index 406e8e66c09..f6215c30b67 100644 --- a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb @@ -9,8 +9,8 @@ name = 'NLopt' version = '2.6.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' -description = """ NLopt is a free/open-source library for nonlinear optimization, - providing a common interface for a number of different free optimization routines +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} From 7cba5c70de3559484d46a941a6b79870d8cbfdc6 Mon Sep 17 00:00:00 2001 From: Ed Date: Mon, 6 Jan 2020 09:53:18 +0000 Subject: [PATCH 368/468] Update NLopt-2.6.1-GCCcore-8.3.0.eb Fixing whitespace again... :-( --- easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb index f6215c30b67..406e8e66c09 100644 --- a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.3.0.eb @@ -9,8 +9,8 @@ name = 'NLopt' version = '2.6.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' -description = """ NLopt is a free/open-source library for nonlinear optimization, - providing a common interface for a number of different free optimization routines +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} From 01542a7a676c4906a508a68caa93f160d7bd89db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2020 11:25:01 +0100 Subject: [PATCH 369/468] fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension --- .../easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb | 10 +++++++--- .../easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb | 10 +++++++--- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb index 1f094d7a6fe..5a76cf08ff2 100644 --- a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb +++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-foss-2019a.eb @@ -21,17 +21,19 @@ fix_python_shebang_for = ['bin/*'] use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + exts_list = [ + ('monotonic', '1.5', { + 'checksums': ['23953d55076df038541e648a53676fb24980f7a1be290cdda21300b3bc21dfb0'], + }), ('humanfriendly', '4.18', { - 'source_urls': ['https://pypi.python.org/packages/source/h/humanfriendly/'], 'checksums': ['33ee8ceb63f1db61cce8b5c800c531e1a61023ac5488ccde2ba574a85be00a85'], }), ('coloredlogs', '10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/coloredlogs/'], 'checksums': ['b869a2dda3fa88154b9dd850e27828d8755bfab5a838a1c97fbc850c6e377c36'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cyvcf2'], 'checksums': ['20924e5b30e8308756575ac3ae8c28a8c717ed3c53b2adb297201428f43fae6e'], 'prebuildopts': "rm -r htslib && ln -s $EBROOTHTSLIB htslib && ", # Runtest will fail - possibly broken test-suite. Otherwise useful. @@ -46,4 +48,6 @@ sanity_check_paths = { sanity_check_commands = ["cyvcf2 --help"] +sanity_pip_check = True + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb index fb5de777f52..bd393254fe9 100644 --- a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb +++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.11.5-intel-2019a.eb @@ -21,17 +21,19 @@ fix_python_shebang_for = ['bin/*'] use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + exts_list = [ + ('monotonic', '1.5', { + 'checksums': ['23953d55076df038541e648a53676fb24980f7a1be290cdda21300b3bc21dfb0'], + }), ('humanfriendly', '4.18', { - 'source_urls': ['https://pypi.python.org/packages/source/h/humanfriendly/'], 'checksums': ['33ee8ceb63f1db61cce8b5c800c531e1a61023ac5488ccde2ba574a85be00a85'], }), ('coloredlogs', '10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/coloredlogs/'], 'checksums': ['b869a2dda3fa88154b9dd850e27828d8755bfab5a838a1c97fbc850c6e377c36'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/cyvcf2'], 'checksums': ['20924e5b30e8308756575ac3ae8c28a8c717ed3c53b2adb297201428f43fae6e'], 'prebuildopts': 'rm -r htslib && ln -s $EBROOTHTSLIB htslib && export LDSHARED="icc -shared" &&', 'preinstallopts': 'export LDSHARED="icc -shared" &&', @@ -48,4 +50,6 @@ sanity_check_paths = { sanity_check_commands = ["cyvcf2 --help"] +sanity_pip_check = True + moduleclass = 'bio' From 9205c3c247c6c38af0acca2298e2ee21000f8f13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2020 16:10:59 +0100 Subject: [PATCH 370/468] adding easyconfigs: breseq-0.35.0-intel-2019a-R-3.6.0.eb --- .../breseq-0.35.0-intel-2019a-R-3.6.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb diff --git a/easybuild/easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb b/easybuild/easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb new file mode 100644 index 00000000000..c542e13f0f5 --- /dev/null +++ b/easybuild/easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'breseq' +version = '0.35.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://barricklab.org/breseq' +description = "breseq is a computational pipeline for the analysis of short-read re-sequencing data" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = ['https://github.com/barricklab/breseq/releases/download/v0.35.0/'] +sources = ['breseq-%(version)s-Source.tar.gz'] +checksums = ['4d111aab249475e51f00a828506381ba2cd44770bd82a6a56de5d58ea9b6ebe0'] + +dependencies = [ + ('Bowtie2', '2.3.5.1'), + ('XZ', '5.2.4'), + ('zlib', '1.2.11'), + ('R', '3.6.0'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/breseq', 'bin/gdtools'], + 'dirs': [], +} + +# breseq --help exists with non-zero exit code, so use grep +sanity_check_commands = ["breseq --help | grep 'Usage: breseq'"] + +moduleclass = 'bio' From 140317006842b5784888fe2e7348ee7e21ecc134 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 6 Jan 2020 16:19:27 +0100 Subject: [PATCH 371/468] Use absolute path for extraction to allow relocating the build dir --- easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb index d656235b6ca..2462269473e 100644 --- a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb @@ -15,7 +15,10 @@ sources = ['version-%(version)s.tar.gz'] checksums = ['2cd2d9cfa0cf71c80a546cde1a25f19f6b7fddf610f7cbb30a67bb81dadb7026'] -preconfigopts = 'unzip ../3rdParty/gtest/gtest-1.6.0__stripped.zip -d ../3rdParty/gtest/ &&' +local_3rdparty_dir = '%(builddir)s/KjellKod-g2log-d9a55a4a6154/3rdParty' + +preconfigopts = 'unzip %(3rdparty)s/gtest/gtest-1.6.0__stripped.zip'\ + ' -d %(3rdparty)s/gtest/ &&' % {'3rdparty': local_3rdparty_dir} preinstallopts = 'mkdir %(installdir)s/lib && cp lib*.a %(installdir)s/lib ||' builddependencies = [ From edb4d79ecb01369b5761fe4c7ef5e90355843893 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2020 16:32:39 +0100 Subject: [PATCH 372/468] {devel}[GCCcore/9.2.0] Autotools v20180311 --- .../a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb | 38 +++++++++++++++++ .../Automake/Automake-1.16.1-GCCcore-9.2.0.eb | 41 +++++++++++++++++++ .../Autotools-20180311-GCCcore-9.2.0.eb | 24 +++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb | 32 +++++++++++++++ 4 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-9.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..4fe598aa3e0 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..08bb6e66a2b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.1' + +homepage = 'http://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-9.2.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..193a427743d --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-9.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20180311' # date of the most recent change + +homepage = 'http://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.16.1'), # 20180311 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..a127d4865a4 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 743eb181c62fafac39b248a1e05306f081564a7d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2020 16:40:43 +0100 Subject: [PATCH 373/468] {tools}[GCCcore/9.2.0] libxml2 v2.9.10, XZ v5.2.4 --- .../easyconfigs/g/gettext/gettext-0.20.1.eb | 34 +++++++++++++++++++ .../l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb | 28 +++++++++++++++ .../x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb | 33 ++++++++++++++++++ 3 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb new file mode 100644 index 00000000000..47975c4ee97 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.20.1' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['66415634c6e8c3fa8b71362879ec7575e27da43da562c798a8a2f223e6e47f5c'] + +dependencies = [ + ('ncurses', '6.1'), +] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..5e7273f67e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.10' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('XZ', '5.2.4'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..368d09a41f9 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.4' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['XZ-5.2.2_compat-libs.patch'] +checksums = [ + '3313fd2a95f43d88e44264e6b015e7d03053e681860b0d5d3f9baca79c57b7bf', # xz-5.2.4.tar.bz2 + '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch +] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.20.1', '', True), + ('binutils', '2.32'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' From f217a3b5c850bf00e31aed7b4de95902ef8ff303 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 6 Jan 2020 16:52:52 +0100 Subject: [PATCH 374/468] adding easyconfigs: FLTK-1.3.5-GCC-8.3.0.eb --- .../f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb new file mode 100644 index 00000000000..e9e65090bef --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb @@ -0,0 +1,37 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.5' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.4_fix-LDFLAGS.patch'] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '19.1.7'), + ('libGLU', '9.0.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.3'), + ('xprop', '1.2.4'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' From 66ef8076b5652339f73b36c6dea3a3971d4b8ce2 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 6 Jan 2020 17:07:10 +0100 Subject: [PATCH 375/468] adding easyconfigs: Julia-1.3.1-linux-x86_64.eb --- .../j/Julia/Julia-1.3.1-linux-x86_64.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.3.1-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.3.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.3.1-linux-x86_64.eb new file mode 100644 index 00000000000..a5e9cf292b3 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.3.1-linux-x86_64.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Jiri Furst + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.3.1' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['faa707c8343780a6fe5eaf13490355e8190acf8e2c189b9e7ecbddb0fa2643ad'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.so'], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lang' From 87c2808c75c0dbb21ae7bea78e7d2ccf340e4307 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2020 17:11:12 +0100 Subject: [PATCH 376/468] use https for breseq homepage --- .../easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb b/easybuild/easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb index c542e13f0f5..a1d09ce8c8f 100644 --- a/easybuild/easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb +++ b/easybuild/easyconfigs/b/breseq/breseq-0.35.0-intel-2019a-R-3.6.0.eb @@ -4,7 +4,7 @@ name = 'breseq' version = '0.35.0' versionsuffix = '-R-%(rver)s' -homepage = 'http://barricklab.org/breseq' +homepage = 'https://barricklab.org/breseq' description = "breseq is a computational pipeline for the analysis of short-read re-sequencing data" toolchain = {'name': 'intel', 'version': '2019a'} From 5777442e99c4d76f4912f4bd63bd3c4c7b6760b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2020 17:22:46 +0100 Subject: [PATCH 377/468] use https for gettext 0.20.1 homepage --- easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb index 47975c4ee97..fdac301b969 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'gettext' version = '0.20.1' -homepage = 'http://www.gnu.org/software/gettext/' +homepage = 'https://www.gnu.org/software/gettext/' description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" From d18dd320a4edeb8b9de2eb8e4ecf1bd9c479a2c3 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 6 Jan 2020 17:26:42 +0100 Subject: [PATCH 378/468] adding easyconfigs: xprop-1.2.4-GCCcore-8.3.0.eb --- .../x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..9f52756b247 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.4' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['dddb6e208ffa515e68f001c22077a465f1365a4bcf91d9b37f336a6c0d15400d'] + +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20190717'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' From ce7dff69a85eb66a82e5f764fad06da488b65be3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2020 17:33:19 +0100 Subject: [PATCH 379/468] don't require a custom sanity_check_paths for Autotools bundle --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1dabc65a426..973c9c7e069 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -597,8 +597,8 @@ def check_sanity_check_paths(self, changed_ecs): # PythonBundle & PythonPackage already have a decent customised sanity_check_paths # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. whitelist = ['CrayToolchain', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain', 'BuildEnv'] - # GCC is just a bundle of GCCcore+binutils - bundles_whitelist = ['GCC'] + # Autotools & (recent) GCC are just bundles (Autotools: Autoconf+Automake+libtool, GCC: GCCcore+binutils) + bundles_whitelist = ['Autotools', 'GCC'] failing_checks = [] From 313e4f10563e4c4658a8616269ec13d5712d8df0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jan 2020 17:46:32 +0100 Subject: [PATCH 380/468] use https for Autoconf/Automake/libtool homepage --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb index 4fe598aa3e0..b21983b2e6b 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Autoconf' version = '2.69' -homepage = 'http://www.gnu.org/software/autoconf/' +homepage = 'https://www.gnu.org/software/autoconf/' description = """ Autoconf is an extensible package of M4 macros that produce shell scripts diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb index 08bb6e66a2b..3e2f1936dd3 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.2.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Automake' version = '1.16.1' -homepage = 'http://www.gnu.org/software/automake/automake.html' +homepage = 'https://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb index a127d4865a4..b5d9e4b1c34 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libtool' version = '2.4.6' -homepage = 'http://www.gnu.org/software/libtool' +homepage = 'https://www.gnu.org/software/libtool' description = """ GNU libtool is a generic library support script. Libtool hides the complexity From 94aba89520b58ddde7ddd75932de61f832816921 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 6 Jan 2020 18:45:26 +0100 Subject: [PATCH 381/468] http -> https --- easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb index 9f52756b247..c49c49d2757 100644 --- a/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'xprop' version = '1.2.4' -homepage = "http://www.x.org/wiki/" +homepage = "https://www.x.org/wiki/" description = """The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of From 4152468390d4a224cf14b66fac8fe594b954fbb2 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 6 Jan 2020 19:00:30 +0100 Subject: [PATCH 382/468] http -> https in source_urls --- easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb index c49c49d2757..d2384573aa6 100644 --- a/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.3.0.eb @@ -11,7 +11,7 @@ description = """The xprop utility is for displaying window and font properties toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['http://ftp.x.org/archive/individual/app/'] +source_urls = ['https://ftp.x.org/archive/individual/app/'] sources = [SOURCE_TAR_GZ] checksums = ['dddb6e208ffa515e68f001c22077a465f1365a4bcf91d9b37f336a6c0d15400d'] From 916bf855bbf230b36c5d23464817c486859196c8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 6 Jan 2020 19:23:00 +0100 Subject: [PATCH 383/468] Update checksum --- .../easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb | 5 ++--- .../easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb | 4 ++-- .../easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb | 4 ++-- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb index a67d509532b..78b9b4d03d8 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb @@ -5,7 +5,7 @@ easyblock = 'CMakeMake' name = 'kallisto' version = '0.43.1' -homepage = 'http://pachterlab.github.io/kallisto/' +homepage = 'https://pachterlab.github.io/kallisto/' description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.""" @@ -14,8 +14,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] - -checksums = ['2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e'] +checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] builddependencies = [('CMake', '3.7.2')] diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb index 68095961ffb..68064dcfd5e 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb @@ -5,7 +5,7 @@ easyblock = 'CMakeMake' name = 'kallisto' version = '0.43.1' -homepage = 'http://pachterlab.github.io/kallisto/' +homepage = 'https://pachterlab.github.io/kallisto/' description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.""" @@ -14,7 +14,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e'] +checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] builddependencies = [('CMake', '3.9.1')] diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb index ee58880b2ae..aba4362d530 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb @@ -5,7 +5,7 @@ easyblock = 'CMakeMake' name = 'kallisto' version = '0.43.1' -homepage = 'http://pachterlab.github.io/kallisto/' +homepage = 'https://pachterlab.github.io/kallisto/' description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.""" @@ -14,7 +14,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e'] +checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] builddependencies = [('CMake', '3.10.1')] From 4e50682a36db978f734ce166fcb14748aad85b1d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 6 Jan 2020 20:13:03 +0000 Subject: [PATCH 384/468] adding easyconfigs: OpenFOAM-v1912-foss-2019b.eb and patches: OpenFOAM-v1912-cleanup.patch --- .../o/OpenFOAM/OpenFOAM-v1912-cleanup.patch | 297 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v1912-foss-2019b.eb | 43 +++ 2 files changed, 340 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1912-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1912-foss-2019b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1912-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1912-cleanup.patch new file mode 100644 index 00000000000..17e655b63de --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1912-cleanup.patch @@ -0,0 +1,297 @@ +# - Replace the OpenFOAM third-party libraries with EASYBUILD variables. +# - Set install dir, compiler, etc using EASYBUILD +# +# authors: Ward Poelmans , Kenneth Hoste (HPC-UGent), Mark Olesen , +# Simon Branford (University of Birmingham) +--- OpenFOAM-v1912/etc/bashrc.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/bashrc 2020-01-06 19:13:09.39069861 +0000 +@@ -77,7 +77,7 @@ + # = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPI | MPICH | MPICH-GM | + # HPMPI | CRAY-MPICH | FJMPI | QSMPI | SGIMPI | INTELMPI | USERMPI + # Also possible to use INTELMPI-xyz etc and define your own wmake rule +-export WM_MPLIB=SYSTEMOPENMPI ++export WM_MPLIB=EASYBUILDMPI + + + #------------------------------------------------------------------------------ +--- OpenFOAM-v1912/etc/config.sh/CGAL.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/config.sh/CGAL 2020-01-06 19:13:58.46916514 +0000 +@@ -44,33 +44,9 @@ + #------------------------------------------------------------------------------ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade + +-boost_version=boost_1_64_0 +-cgal_version=CGAL-4.9.1 +- +-export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version +-export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cgal_version ++##EasyBuild## settings ++export BOOST_ARCH_PATH="$EBROOTBOOST" ++export CGAL_ARCH_PATH="$EBROOTCGAL" + + # END OF (NORMAL) USER EDITABLE PART + #------------------------------------------------------------------------------ +-if [ -n "$FOAM_VERBOSE" ] && [ -n "$PS1" ] +-then +- echo "Using boost ($boost_version) -> $BOOST_ARCH_PATH" 1>&2 +- echo "Using CGAL ($cgal_version) -> $CGAL_ARCH_PATH" 1>&2 +-fi +- +-if command -v _foamAddLibAuto >/dev/null # Normal sourcing (not makeCGAL) +-then +- _foamAddLibAuto $BOOST_ARCH_PATH lib$WM_COMPILER_LIB_ARCH +- _foamAddLibAuto $CGAL_ARCH_PATH lib$WM_COMPILER_LIB_ARCH +- +- # GMP/MPFR may have already been added with ThirdParty compiler, but cannot +- # be certain so add here. Any duplicates will be removed later. +- +- _foamAddLibAuto $GMP_ARCH_PATH # No fallback libdir +- _foamAddLibAuto $MPFR_ARCH_PATH # No fallback libdir +- +- unset boost_version cgal_version +- +-fi +- +-#------------------------------------------------------------------------------ +--- OpenFOAM-v1912/etc/config.sh/FFTW.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/config.sh/FFTW 2020-01-06 19:14:18.89030368 +0000 +@@ -35,23 +35,8 @@ + #------------------------------------------------------------------------------ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade + +-fftw_version=fftw-3.3.7 +-export FFTW_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$fftw_version ++##EasyBuild## settings ++export FFTW_ARCH_PATH="$EBROOTFFTW" + + # END OF (NORMAL) USER EDITABLE PART + #------------------------------------------------------------------------------ +-if [ -n "$FOAM_VERBOSE" ] && [ -n "$PS1" ] +-then +- echo "Using fftw ($fftw_version) -> $FFTW_ARCH_PATH" 1>&2 +-fi +- +-if command -v _foamAddLibAuto >/dev/null # Normal sourcing (not makeFFTW) +-then +- +- _foamAddLibAuto $FFTW_ARCH_PATH lib$WM_COMPILER_LIB_ARCH +- +- unset fftw_version +- +-fi +- +-#------------------------------------------------------------------------------ +--- OpenFOAM-v1912/etc/config.sh/gperftools.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/config.sh/gperftools 2020-01-06 19:14:52.90383440 +0000 +@@ -38,32 +38,8 @@ + #------------------------------------------------------------------------------ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade + +-gperftools_version=gperftools-2.5 +-GPERFTOOLS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$gperftools_version ++##EasyBuild## settings ++GPERFTOOLS_ARCH_PATH="$EBROOTGPERFTOOLS" + + # END OF (NORMAL) USER EDITABLE PART + #------------------------------------------------------------------------------ +-if [ -n "$FOAM_VERBOSE" ] && [ -n "$PS1" ] +-then +- echo "Using gperftools ($gperftools_version) -> $GPERFTOOLS_ARCH_PATH" 1>&2 +-fi +- +-if command -v _foamAddLib >/dev/null # Normal sourcing +-then +- +- # If GPERFTOOLS_ARCH_PATH does not end with '-system' or '-none', +- # it is located within ThirdParty, or a central installation +- # outside of ThirdParty and must be added to the lib-path. +- +- ending="${GPERFTOOLS_ARCH_PATH##*-}" +- if [ "$ending" != none ] && [ "$ending" != system ] +- then +- _foamAddLib $GPERFTOOLS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH +- _foamAddPath $GPERFTOOLS_ARCH_PATH/bin +- fi +- +- unset gperftools_version ending +- +-fi +- +-#------------------------------------------------------------------------------ +--- OpenFOAM-v1912/etc/config.sh/metis.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/config.sh/metis 2020-01-06 19:14:21.70845195 +0000 +@@ -34,8 +34,9 @@ + #------------------------------------------------------------------------------ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade + +-METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++##Easybuild## settings ++METIS_VERSION="metis-$EBVERSIONMETIS" ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$METIS_ROOT" + + # END OF (NORMAL) USER EDITABLE PART + #------------------------------------------------------------------------------ +--- OpenFOAM-v1912/etc/config.sh/mpi.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/config.sh/mpi 2020-01-06 19:12:41.54940690 +0000 +@@ -96,6 +96,10 @@ + _foamEtc -config mpi-user # <- Adjustments (optional) + ;; + ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; ++ + SYSTEMMPI) + export FOAM_MPI=mpi-system + _foamEtc -config mpi-system # <- Adjustments (optional) +--- OpenFOAM-v1912/etc/config.sh/paraview.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/config.sh/paraview 2020-01-06 19:12:41.66878632 +0000 +@@ -54,7 +54,8 @@ + #------------------------------------------------------------------------------ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade + +-ParaView_VERSION=5.6.3 ++##Easybuild## settings ++ParaView_VERSION="$EBVERSIONPARAVIEW" + ParaView_QT=qt-system + cmake_version=cmake-system + +@@ -85,14 +86,6 @@ + esac + done + +-# ThirdParty cmake +-cmake="$archDir/$cmake_version" +-if [ -r "$cmake/bin/cmake" ] +-then +- # _foamAddPath not available when foamPV function is used +- PATH="$cmake/bin:$PATH" +-fi +- + case "$ParaView_VERSION" in + ('') + # empty - do nothing +@@ -129,8 +130,9 @@ + ;; + esac + +- export ParaView_DIR="$archDir/ParaView-$ParaView_VERSION" ++ ##Easybuild## settings ++ export ParaView_DIR="$EBROOTPARAVIEW" + unset PV_PLUGIN_PATH + + # Set paths if binaries are present + if [ -r "$ParaView_DIR" ] +@@ -133,26 +142,6 @@ + export PV_PLUGIN_PATH="$FOAM_LIBBIN/paraview-$pv_api" + export PATH="$ParaView_DIR/bin:$PATH" + +- # QT libraries as required, and Qt5_DIR for the root directory. +- # Another possibility: "qtpaths --qt-version" +- qtDir="$archDir/$ParaView_QT" +- if [ -d "$qtDir" ] +- then +- case "$ParaView_QT" in +- (*-5*) +- export Qt5_DIR="$qtDir" +- ;; +- esac +- for libDir in "lib$WM_COMPILER_LIB_ARCH" "lib" +- do +- if [ -d "$qtDir/$libDir" ] +- then +- export LD_LIBRARY_PATH="$qtDir/$libDir:$LD_LIBRARY_PATH" +- break +- fi +- done +- fi +- + # ParaView libraries + # - 5.4 and earlier: lib/paraview-X.X + # - 5.5 and later: lib/, but could also be lib64/ +--- OpenFOAM-v1912/etc/config.sh/scotch.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/config.sh/scotch 2020-01-06 19:14:50.81742938 +0000 +@@ -34,8 +34,10 @@ + #------------------------------------------------------------------------------ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade + +-SCOTCH_VERSION=scotch_6.0.9 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++##Easybuild## settings ++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" ++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" + + # END OF (NORMAL) USER EDITABLE PART + #------------------------------------------------------------------------------ +--- OpenFOAM-v1912/etc/config.sh/vtk.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/etc/config.sh/vtk 2020-01-06 19:13:23.08425391 +0000 +@@ -34,53 +34,12 @@ + #------------------------------------------------------------------------------ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade + +-vtk_version=VTK-8.2.0 +-mesa_version=mesa-17.1.1 +-mesa_llvm=none +- +-export VTK_DIR="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$vtk_version" +-export MESA_ARCH_PATH="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$mesa_version" +-export LLVM_ARCH_PATH="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH/$mesa_llvm" ++##Easybuild## settings ++export VTK_DIR="$EBROOTVTK" ++export MESA_ARCH_PATH="$EBROOTMESA" + + # Define paraview-mesa directory as required + unset ParaView_MESA_DIR + + # END OF (NORMAL) USER EDITABLE PART + #------------------------------------------------------------------------------ +-if [ -n "$FOAM_VERBOSE" ] && [ -n "$PS1" ] +-then +- echo "Using vtk" 1>&2 +- echo " vtk ($vtk_version) $VTK_DIR" 1>&2 +- echo " mesa ($mesa_version) $MESA_ARCH_PATH" 1>&2 +- echo " llvm ($mesa_llvm) $LLVM_ARCH_PATH" 1>&2 +- if [ -d "$ParaView_MESA_DIR" ] +- then +- echo " paraview-mesa $ParaView_MESA_DIR" 1>&2 +- fi +-fi +- +-if command -v _foamAddLib >/dev/null # normal sourcing +-then +- +- # Set paths if binaries are present +- if [ -d "$VTK_DIR" ] +- then +- # Uses lib/ and not lib64/ +- _foamAddLib "$VTK_DIR/lib" +- else +- unset VTK_DIR +- fi +- +- if [ -d "$MESA_ARCH_PATH" ] +- then +- _foamAddLibAuto "$LLVM_ARCH_PATH" +- _foamAddLibAuto "$MESA_ARCH_PATH" +- else +- unset LLVM_ARCH_PATH +- unset MESA_ARCH_PATH +- fi +- +- unset vtk_version mesa_version mesa_llvm +-fi +- +-#------------------------------------------------------------------------------ +--- OpenFOAM-v1912/wmake/scripts/have_readline.orig 2020-01-06 19:07:23.000000000 +0000 ++++ OpenFOAM-v1912/wmake/scripts/have_readline 2020-01-06 19:15:54.77256611 +0000 +@@ -58,7 +58,7 @@ + # warn="==> skip readline" + + # Expected location, include/library names +- prefix=system ++ prefix="$EBROOTLIBREADLINE" + incName="readline/readline.h" + libName="libreadline" + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1912-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1912-foss-2019b.eb new file mode 100644 index 00000000000..bcae6645543 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1912-foss-2019b.eb @@ -0,0 +1,43 @@ +name = 'OpenFOAM' +version = 'v1912' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + 'OpenFOAM-%(version)s-cleanup.patch', + 'OpenFOAM-v1906-CGAL-4.14.1.patch', + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + '437feadf075419290aa8bf461673b723a60dc39525b23322850fb58cb48548f2', # OpenFOAM-v1912.tgz + '6a7e4b8067a6bb8230859c72bd1c60e266b0ecc9d4f9061ac948a0ea056335cb', # OpenFOAM-v1912-cleanup.patch + 'b986a573775fe108755790ef34529f2afd428be7c4c295fadb58fbe5ea058920', # OpenFOAM-v1906-CGAL-4.14.1.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.1'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.9'), + ('CGAL', '4.14.1', '-Python-3.7.4'), + ('ParaView', '5.6.2', '-Python-3.7.4-mpi'), +] + +builddependencies = [ + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' From 6aeaabf76dbc7d6bbb84873d441bfd86c1a5d453 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jan 2020 08:52:11 +0100 Subject: [PATCH 385/468] adding easyconfigs: OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb, OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb and patches: OpenMM-7.4.1_fix-Doxygen.patch --- .../OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb | 60 ++++++++++++++++++ .../OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb | 61 +++++++++++++++++++ .../o/OpenMM/OpenMM-7.4.1_fix-Doxygen.patch | 42 +++++++++++++ 3 files changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1_fix-Doxygen.patch diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..b06b11d3d8b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-%(version)s_fix-Doxygen.patch'] +checksums = [ + 'e8102b68133e6dcf7fcf29bc76a11ea54f30af71d8a7705aec0aee957ebe3a6d', # 7.4.1.tar.gz + '99d59e3106d9c9f9fbce3c3161117a37b2699e1dc09bc2a75619e0d880f29708', # OpenMM-7.4.1_fix-Doxygen.patch +] + +builddependencies = [ + ('CMake', '3.15.3'), + ('Doxygen', '1.8.16'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('SWIG', '4.0.1'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..acdb4b56917 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,61 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-%(version)s_fix-Doxygen.patch'] +checksums = [ + 'e8102b68133e6dcf7fcf29bc76a11ea54f30af71d8a7705aec0aee957ebe3a6d', # 7.4.1.tar.gz + '99d59e3106d9c9f9fbce3c3161117a37b2699e1dc09bc2a75619e0d880f29708', # OpenMM-7.4.1_fix-Doxygen.patch +] + +builddependencies = [ + ('CMake', '3.15.3'), + ('Doxygen', '1.8.16'), +] + +separate_build_dir = True + +dependencies = [ + ('FFTW', '3.3.8'), + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('SWIG', '4.0.1'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1_fix-Doxygen.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1_fix-Doxygen.patch new file mode 100644 index 00000000000..735fab55324 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1_fix-Doxygen.patch @@ -0,0 +1,42 @@ +fix build errors when using Doxygen 1.8.16 like: + OpenMMSwigHeaders.i:12: Error: Bad $descriptor() macro. +see https://github.com/openmm/openmm/issues/2420 and https://github.com/openmm/openmm/pull/2460 +diff --git a/plugins/amoeba/wrappers/Doxyfile.in b/plugins/amoeba/wrappers/Doxyfile.in +index a35fd31b7..1fd04e509 100644 +--- a/plugins/amoeba/wrappers/Doxyfile.in ++++ b/plugins/amoeba/wrappers/Doxyfile.in +@@ -581,7 +581,7 @@ INPUT_ENCODING = UTF-8 + # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx + # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +-FILE_PATTERNS = ++FILE_PATTERNS = *.h + + # The RECURSIVE tag can be used to turn specify whether or not subdirectories + # should be searched for input files as well. Possible values are YES and NO. +diff --git a/wrappers/Doxyfile.in b/wrappers/Doxyfile.in +index 76f74cfc6..ce7b7a8c4 100644 +--- a/wrappers/Doxyfile.in ++++ b/wrappers/Doxyfile.in +@@ -582,7 +582,7 @@ INPUT_ENCODING = UTF-8 + # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx + # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +-FILE_PATTERNS = ++FILE_PATTERNS = *.h + + # The RECURSIVE tag can be used to turn specify whether or not subdirectories + # should be searched for input files as well. Possible values are YES and NO. +diff --git a/wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in b/wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in +index a1e664ae6..c835beeb9 100644 +--- a/wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in ++++ b/wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in +@@ -588,7 +588,7 @@ INPUT_ENCODING = UTF-8 + # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx + # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +-FILE_PATTERNS = ++FILE_PATTERNS = *.h + + # The RECURSIVE tag can be used to turn specify whether or not subdirectories + # should be searched for input files as well. Possible values are YES and NO. From 007ab011fe0ac81542ea0b1ffd70003bd4175a02 Mon Sep 17 00:00:00 2001 From: crubb Date: Tue, 7 Jan 2020 08:04:17 +0000 Subject: [PATCH 386/468] {bio}[foss/2019a] gradunwarp 1.1.0 (HCP fork) --- .../gradunwarp-1.1.0-foss-2019a-HCP.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb new file mode 100644 index 00000000000..b1f218a7ffb --- /dev/null +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = "gradunwarp" +version = "1.1.0" +versionsuffix = "-HCP" + +homepage = "https://github.com/Washington-University/gradunwarp" +description = """Gradient Unwarping in Python. This is the Human Connectome Project fork of the no longer maintained gradunwarp package.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/Washington-University/gradunwarp/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4803b8055dbeedb0435246a525aa69f1f3425c55d57c973c045deb39bc95c955'] + +checksums = [ +] + +dependencies = [ + ('Python', '2.7.15'), + ('SciPy-bundle', '2019.03'), + ('NiBabel', '2.4.0') +] + +moduleclass = 'bio' From 8e52fbfb7d8df4a31aa370dd8508208edbf8b995 Mon Sep 17 00:00:00 2001 From: crubb Date: Tue, 7 Jan 2020 08:39:38 +0000 Subject: [PATCH 387/468] Remove extra (empty) checksum array --- .../g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb index b1f218a7ffb..5b725a6126a 100644 --- a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb @@ -13,9 +13,6 @@ source_urls = ['https://github.com/Washington-University/gradunwarp/archive'] sources = ['v%(version)s.tar.gz'] checksums = ['4803b8055dbeedb0435246a525aa69f1f3425c55d57c973c045deb39bc95c955'] -checksums = [ -] - dependencies = [ ('Python', '2.7.15'), ('SciPy-bundle', '2019.03'), From cae1fd155bfd6f3d084641658ee60f6873e723c4 Mon Sep 17 00:00:00 2001 From: crubb Date: Tue, 7 Jan 2020 09:23:06 +0000 Subject: [PATCH 388/468] Shorter description --- .../easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb index 5b725a6126a..1c335912ff2 100644 --- a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb @@ -5,7 +5,7 @@ version = "1.1.0" versionsuffix = "-HCP" homepage = "https://github.com/Washington-University/gradunwarp" -description = """Gradient Unwarping in Python. This is the Human Connectome Project fork of the no longer maintained gradunwarp package.""" +description = """Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original.""" toolchain = {'name': 'foss', 'version': '2019a'} From 8ff8fe915ab13d5536072c1f8f91ad56c87f503d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 7 Jan 2020 10:35:09 +0100 Subject: [PATCH 389/468] Fix https// -> https:// --- easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb | 2 +- easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb | 2 +- .../g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb | 4 ++-- .../g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb | 4 ++-- .../g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb | 4 ++-- .../GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb | 4 ++-- .../GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb | 4 ++-- .../GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb | 4 ++-- .../GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb | 4 ++-- .../GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb | 4 ++-- .../g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb | 4 ++-- .../g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb | 4 ++-- .../g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb | 4 ++-- .../g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb | 4 ++-- .../easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb | 4 ++-- .../easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb | 2 +- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb | 4 ++-- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb | 4 ++-- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb | 4 ++-- easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb | 2 +- 62 files changed, 99 insertions(+), 99 deletions(-) diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb index 718fba40f5e..0bdfa679134 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] patches = [ '%(name)s-%(version)s_call-dbus_g_thread_init.patch', diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb index 393ff707c09..45f6636633b 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb index 9a7574add84..15d1a7c8166 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb index 077becbe1ce..a84f9eddd5a 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016a.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb index 300ec1140f3..cc25368e304 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb index 28d7738913a..5c54d46358a 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017a.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb index 663e2600339..5197bc0f0d2 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb @@ -10,7 +10,7 @@ description = """GConf is a system for storing application preferences. toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['https//ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] sources = [SOURCE_TAR_XZ] checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb index b8f08048e02..083ad67f279 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb index 0e7582237eb..f5ace84b796 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb index 8936feeafeb..74bd62f7515 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index 0b609b273ab..23b2a931e08 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb index c8ecaf22da4..60907564e6e 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb index a492a53d054..858a8095477 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb index d500a7a66b2..a5c058c8d8f 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb index 7b5130f2610..258bb37f9ed 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb @@ -3,7 +3,7 @@ easyblock = 'MesonNinja' name = 'GST-plugins-base' version = '1.16.0' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['4093aa7b51e28fb24dfd603893fead8d1b7782f088b05ed0f22a21ef176fb5ae'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb index 59a7ef5420c..663148178bc 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '1.6.4' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['7a193e2a66b0d7411160ef2a373184c8aa3cdeaa576fa270be346716220d9606'] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index d8745cb8abe..0c4cb354f0c 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' version = '1.8.3' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gst-plugins-base'] +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['114871d4d63606b4af424a8433cd923e4ff66896b244bb7ac97b9da47f71e79e'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb index a5701e08087..31e79963a2f 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb index 1022f546612..916e6d4045b 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb index 944c423d4b6..941ced47c5b 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 37ab288b67a..49d0445dfd4 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb index 20f11abe9b5..df0cc749083 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb index bbe6a9d2c70..34a46387e52 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb index aa123aa401c..91b34432494 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '0.10.36' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb index 5aa825df9ca..d83a6dfe207 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '1.15.1' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['780ae2347f9780fea264a602a7c04a87a43998188e7bd9c59afb4d7c864f3117'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb index 32f0d1d999b..3c94c21acae 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '1.16.0' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb index 2c2043404fa..0fd9f637575 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '1.6.4' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['4ccba88a286b13d6f2d8c1180f78a13dcd49f2fc3cb2b3b3f502b3a23f7c01b5'] diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb index 632570beb05..1ef44da1de5 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' version = '1.8.3' -homepage = 'https//gstreamer.freedesktop.org/' +homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio @@ -11,7 +11,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//gstreamer.freedesktop.org/src/gstreamer'] +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] checksums = ['66b37762d4fdcd63bce5a2bec57e055f92420e95037361609900278c0db7c53f'] diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb index 0837de07df9..31b312511fc 100644 --- a/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.6.0-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Graphene' version = '1.6.0' -homepage = 'https//ebassi.github.io/graphene/' +homepage = 'https://ebassi.github.io/graphene/' description = "Graphene is a a thin layer of types for graphic libraries" toolchain = {'name': 'intel', 'version': '2017a'} diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb index 17dc4632b41..f293f95724d 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-foss-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.1.3' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['d93d7cb7979c32672e902fdfa884599e63f07f2fa5b06c66147d20c516d4b8f7'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb index 729583482f2..b3fce7f9a98 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.1.3-intel-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.1.3' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['d93d7cb7979c32672e902fdfa884599e63f07f2fa5b06c66147d20c516d4b8f7'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb index 3191926e739..e12b10c1264 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.2.7' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['bba0600ae08b84384e6d2d7175bea10b5fc246c4583dc841498d01894d479026'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb index 8aacf3d433a..e9731f97791 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-intel-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.2.7' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['bba0600ae08b84384e6d2d7175bea10b5fc246c4583dc841498d01894d479026'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb index f76beaf749c..3234d518853 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.3.1' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb index e76120806c7..51272ee9e5b 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.3.1' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb index 2656a45b7e6..754d15cb21f 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.3.1' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['a242206dd119d5e6cc1b2253c116abbae03f9d930cb60b515fb0d248decf89a1'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb index 7505e190ec7..493e68016fe 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.5.1' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['56838dfdad2729b8866763c82d623354d138a4d99d9ffb710c7d377b5cfc7c51'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb index 98e9b82e717..00f262fad11 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-foss-2017b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.7.1' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['9645a6e83313b690602017f18d4eb2adf81f2e54c6fc4471e19331304965154e'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb index 54e24e0fce5..634960bfa8d 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.7.1' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['9645a6e83313b690602017f18d4eb2adf81f2e54c6fc4471e19331304965154e'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb index 3b8b8819231..9375c1c5986 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-foss-2018a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.7.5' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['84574e1b1f65ca694cb8fb6905309665c0368af18a312357f8ff886ee2f29563'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb index 2495f04f8a1..007cb5dc7b2 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.5-intel-2018a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.7.5' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['84574e1b1f65ca694cb8fb6905309665c0368af18a312357f8ff886ee2f29563'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb index 878cf9b8b6e..0d3245bc7cc 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '1.9.0' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['11eca62bf0ac549b8d6be55f4e130946399939cdfe7a562fdaee711190248b00'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb index df34c31d784..1293f723557 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-foss-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '2.2.0' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['b7ccfcbd56b970a709e8b9ea9fb46c922c606c2feef8f086fb6a8492e530f810'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb index 6e71dcf273b..4484356a696 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '2.2.0' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['b7ccfcbd56b970a709e8b9ea9fb46c922c606c2feef8f086fb6a8492e530f810'] diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb index cbc151f2e53..11a55eb6b5a 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'HarfBuzz' version = '2.4.0' -homepage = 'https//www.freedesktop.org/wiki/Software/HarfBuzz' +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' description = """HarfBuzz is an OpenType text shaping engine.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['https//www.freedesktop.org/software/harfbuzz/release/'] +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['b470eff9dd5b596edf078596b46a1f83c179449f051a469430afc15869db336f'] diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb index a0492c39df7..f11393c0f05 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.39.0' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb index 505c4bff3ce..7ea854663fe 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.39.0' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb index e4c90a95244..e65918bfe02 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.1' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb index 47d14495c1b..a54fc36d9fb 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.1' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb index 1cbf8f73736..b319df9c9a3 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.12' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb index d6b8c9ba093..75d2f16fd50 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.14' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb index d1c0f7b9da6..b1f4db37e95 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.14' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb index bc66a8bf75b..7daf2978b4e 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.3' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb index 1463e00c94e..0b0d8799a18 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.3' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb index c7159087e22..1b6eb9ea231 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.40.5' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb index 1f5c2358c9a..7272050138c 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.41.0' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb index 2e84e320d2c..8aee1dd469a 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.41.0' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb index 0f9e403d1aa..ef0d8bdcaec 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.41.1' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb index 20bb2dbb103..3a76c170930 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.41.1' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb index 3b513e75408..eadd80be074 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.42.4' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb index 397ee27afe3..e6b2254c04c 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Pango' version = '1.42.4' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb index b0f037f8098..dd63fff5283 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'MesonNinja' name = 'Pango' version = '1.43.0' -homepage = 'https//www.pango.org/' +homepage = 'https://www.pango.org/' description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" From d106df0b6f87c36a9586b011b0af33b166028390 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 7 Jan 2020 11:19:23 +0100 Subject: [PATCH 390/468] checksums --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb index e9e65090bef..3431764e7ab 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb @@ -17,6 +17,10 @@ toolchainopts = {'pic': True} source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] sources = ['%(namelower)s-%(version)s-source.tar.gz'] patches = ['FLTK-1.3.4_fix-LDFLAGS.patch'] +checksums = [ + '8729b2a055f38c1636ba20f749de0853384c1d3e9d1a6b8d4d1305143e115702', # fltk-1.3.5-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] configopts = '--enable-shared --enable-threads --enable-xft' From 501901ad972607e1a2d8829d56fedd32bb583a2c Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 7 Jan 2020 11:35:12 +0100 Subject: [PATCH 391/468] adding easyconfigs: libcerf-1.13-GCCcore-8.3.0.eb --- .../l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..4a6e001e418 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '1.13' + +homepage = 'http://apps.jcns.fz-juelich.de/doku/sc/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['e4699f81af838aef5b3e77209fec8e9820a4f492d598fb5a070800854976a305'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From f1efeb65e39712ec8ac02940f0983e09e5f6e35c Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 7 Jan 2020 11:48:08 +0100 Subject: [PATCH 392/468] http -> https --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb index 3431764e7ab..718a72c189f 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.3.0.eb @@ -14,7 +14,7 @@ description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), toolchain = {'name': 'GCC', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] sources = ['%(namelower)s-%(version)s-source.tar.gz'] patches = ['FLTK-1.3.4_fix-LDFLAGS.patch'] checksums = [ From b46f590c1253aa660024eddd6dec89cea4c3bd74 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 7 Jan 2020 11:52:46 +0100 Subject: [PATCH 393/468] Updated homepage --- easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb index 4a6e001e418..0056eac159e 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libcerf' version = '1.13' -homepage = 'http://apps.jcns.fz-juelich.de/doku/sc/libcerf' +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' description = """ libcerf is a self-contained numeric library that provides an efficient and From 826756b7ff52a8925d0a53f65773b9b1e227640d Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 7 Jan 2020 13:02:30 +0100 Subject: [PATCH 394/468] Corrected coding style --- easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb index 0056eac159e..84bc9d2face 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libcerf' version = '1.13' -homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' description = """ libcerf is a self-contained numeric library that provides an efficient and From 285ede5fcde21c3060bcfe21a1807cf6883d1409 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 7 Jan 2020 13:11:36 +0100 Subject: [PATCH 395/468] Allow old checksum --- .../easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb | 5 ++++- .../easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb | 5 ++++- .../easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb index 78b9b4d03d8..e02bb605cfc 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb @@ -14,7 +14,10 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] +checksums = [ + ('2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e', # old release + '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license +] builddependencies = [('CMake', '3.7.2')] diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb index 68064dcfd5e..c47c5f2624c 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb @@ -14,7 +14,10 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] +checksums = [ + ('2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e', # old release + '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license +] builddependencies = [('CMake', '3.9.1')] diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb index aba4362d530..ad809a9b0d6 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb @@ -14,7 +14,10 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] +checksums = [ + ('2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e', # old release + '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license +] builddependencies = [('CMake', '3.10.1')] From 057f3f9f6ced9770c437c7f3716fe228c43810ca Mon Sep 17 00:00:00 2001 From: crubb Date: Tue, 7 Jan 2020 17:25:57 +0000 Subject: [PATCH 396/468] Add download_dep_fail, use_pip and sanity_check_paths --- .../g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb index 1c335912ff2..99ade7df27e 100644 --- a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb @@ -13,10 +13,18 @@ source_urls = ['https://github.com/Washington-University/gradunwarp/archive'] sources = ['v%(version)s.tar.gz'] checksums = ['4803b8055dbeedb0435246a525aa69f1f3425c55d57c973c045deb39bc95c955'] +download_dep_fail = True +use_pip = False + dependencies = [ ('Python', '2.7.15'), ('SciPy-bundle', '2019.03'), ('NiBabel', '2.4.0') ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + moduleclass = 'bio' From 1d266bb6723ec22f638f19b588b4827f417c30fc Mon Sep 17 00:00:00 2001 From: crubb Date: Tue, 7 Jan 2020 17:44:58 +0000 Subject: [PATCH 397/468] Rename to gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb --- ...9a-HCP.eb => gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/gradunwarp/{gradunwarp-1.1.0-foss-2019a-HCP.eb => gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb} (100%) diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb similarity index 100% rename from easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP.eb rename to easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb From e6788f9b4e30e03485c370f562a59b3cf3b15c19 Mon Sep 17 00:00:00 2001 From: crubb Date: Tue, 7 Jan 2020 17:45:16 +0000 Subject: [PATCH 398/468] Add -Python-%(pyver)s to versionsuffix --- .../gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb index 99ade7df27e..6eb7b336dd4 100644 --- a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = "gradunwarp" version = "1.1.0" -versionsuffix = "-HCP" +versionsuffix = "-HCP-Python-%(pyver)s" homepage = "https://github.com/Washington-University/gradunwarp" description = """Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original.""" From 54c4cddf696c76e930451f54e5640ada60e8f0e7 Mon Sep 17 00:00:00 2001 From: Ed Date: Tue, 7 Jan 2020 18:55:16 +0000 Subject: [PATCH 399/468] Update R-3.6.2-foss-2019b.eb --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 2f459ceea46..3a35fad462f 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -540,7 +540,8 @@ exts_list = [ 'checksums': ['1f86e33ecde6c3b0d2098c47591a9cd0fa41fb973ebf5145859677492730df97'], }), ('boot', '1.3-23', { - 'checksums': ['30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f'], + 'checksums': [('30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f', + '79236a5a770dc8bf5ce25d9aa303c5dc0574d94aa043fd00b8b4c8ccc877357f')], }), ('lme4', '1.1-21', { 'checksums': ['7f5554b69ff8ce9bac21e8842131ea940fb7a7dfa2de03684f236d3e3114b20c'], From 8fec3afa211f5adcc34a4ac9f257bc58c90b6d62 Mon Sep 17 00:00:00 2001 From: Ed Date: Tue, 7 Jan 2020 18:55:33 +0000 Subject: [PATCH 400/468] Update R-3.6.2-fosscuda-2019b.eb --- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 6635d318cb3..a29244c6c66 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -540,7 +540,8 @@ exts_list = [ 'checksums': ['1f86e33ecde6c3b0d2098c47591a9cd0fa41fb973ebf5145859677492730df97'], }), ('boot', '1.3-23', { - 'checksums': ['30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f'], + 'checksums': [('30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f', + '79236a5a770dc8bf5ce25d9aa303c5dc0574d94aa043fd00b8b4c8ccc877357f')], }), ('lme4', '1.1-21', { 'checksums': ['7f5554b69ff8ce9bac21e8842131ea940fb7a7dfa2de03684f236d3e3114b20c'], From 427ea1672d497dded58ce2e1d06a49bd163334f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jan 2020 20:15:16 +0100 Subject: [PATCH 401/468] fix trivial style issue in kallisto 0.43.1 easyconfigs --- easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb | 2 +- easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb index e02bb605cfc..77c67b702ae 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb @@ -16,7 +16,7 @@ source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] checksums = [ ('2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e', # old release - '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license + '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license ] builddependencies = [('CMake', '3.7.2')] diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb index c47c5f2624c..c70b8ec4166 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb @@ -16,7 +16,7 @@ source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] checksums = [ ('2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e', # old release - '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license + '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license ] builddependencies = [('CMake', '3.9.1')] diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb index ad809a9b0d6..ebb896633b3 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017b.eb @@ -16,7 +16,7 @@ source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] checksums = [ ('2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e', # old release - '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license + '7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'), # re-release with new license ] builddependencies = [('CMake', '3.10.1')] From 5e43ef68bbf933329e3368d3063d7f87c0a0af11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jan 2020 20:41:14 +0100 Subject: [PATCH 402/468] add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (fixes #9602) --- easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb | 3 ++- easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb | 3 ++- easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb index b52544b81dd..9c5746b2b10 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb @@ -203,7 +203,8 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-51.4', { - 'checksums': ['9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74'], + 'checksums': [('9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74', + '844270a2541eaed420871dfb61d681aa67ee57126645fb6b144b436c25698eeb')], }), ('ade4', '1.7-13', { 'checksums': ['f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b'], diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb index 3f0871db818..3663ed4946d 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb @@ -203,7 +203,8 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-51.4', { - 'checksums': ['9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74'], + 'checksums': [('9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74', + '844270a2541eaed420871dfb61d681aa67ee57126645fb6b144b436c25698eeb')], }), ('ade4', '1.7-13', { 'checksums': ['f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b'], diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb index b542afef2bc..b40c2dbea52 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb @@ -207,7 +207,8 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-51.4', { - 'checksums': ['9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74'], + 'checksums': [('9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74', + '844270a2541eaed420871dfb61d681aa67ee57126645fb6b144b436c25698eeb')], }), ('ade4', '1.7-13', { 'checksums': ['f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b'], From 66944b6dea30ae2f62b3df0e23bb18f641565658 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 8 Jan 2020 09:18:55 +0000 Subject: [PATCH 403/468] ctffind website has moved --- easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb | 4 ++-- .../easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb index 5f490fda760..0d694f93936 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb @@ -10,13 +10,13 @@ easyblock = 'ConfigureMake' name = 'ctffind' version = '4.1.13' -homepage = 'http://grigoriefflab.janelia.org/ctffind4' +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' description = """Program for finding CTFs of electron micrographs.""" toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'openmp': True} -source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] patches = ['ctffind-4.1.13_remove_bogus_include_lines.patch'] checksums = [ diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb index 6d868024d2a..45a30460d70 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb @@ -10,13 +10,13 @@ easyblock = 'ConfigureMake' name = 'ctffind' version = '4.1.13' -homepage = 'http://grigoriefflab.janelia.org/ctffind4' +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' description = """Program for finding CTFs of electron micrographs.""" toolchain = {'name': 'fosscuda', 'version': '2019a'} toolchainopts = {'openmp': True} -source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] patches = ['ctffind-4.1.13_remove_bogus_include_lines.patch'] checksums = [ From 687baa627ab82d2bbac916dafdd780e373753ff5 Mon Sep 17 00:00:00 2001 From: Ed Date: Wed, 8 Jan 2020 09:37:21 +0000 Subject: [PATCH 404/468] Update R-3.6.2-fosscuda-2019b.eb Adding `pocl` dependency to see if @zao's build of `gpuR` works --- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index a29244c6c66..7dca3bb0249 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -42,6 +42,7 @@ dependencies = [ ('UDUNITS', '2.2.26'), # for units ('GSL', '2.6'), # for RcppGSL ('ImageMagick', '7.0.9-5'), # for animation + ('pocl', '1.4'), # for OpenCL support (particularly on POWER) # OS dependency should be preferred if the os version is more recent then # this version, it's nice to have an up to date openssl for security # reasons From 55c30d7d783e1971afe688e3cd9ef0b7573b5f51 Mon Sep 17 00:00:00 2001 From: Ed Date: Wed, 8 Jan 2020 10:32:46 +0000 Subject: [PATCH 405/468] Update R-3.6.2-foss-2019b.eb Another extension checksum change :-( --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 3a35fad462f..f34b9e31e37 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -2213,7 +2213,8 @@ exts_list = [ 'checksums': ['779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], From d74a5be6cd389bec6ce5c972a2287ddf5582be9a Mon Sep 17 00:00:00 2001 From: Ed Date: Wed, 8 Jan 2020 10:33:08 +0000 Subject: [PATCH 406/468] Update R-3.6.2-fosscuda-2019b.eb Another extension checksum change --- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 7dca3bb0249..96c13f13a77 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -2213,7 +2213,8 @@ exts_list = [ 'checksums': ['779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], From 22e666b392ec79466bf5250d166e353d420f1ae6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 8 Jan 2020 13:00:17 +0000 Subject: [PATCH 407/468] pocl: make sure we use easybuild Clang --- easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb index 0268b398ebd..c8b6eda3b49 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb @@ -32,7 +32,9 @@ dependencies = [ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so -configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1" +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb index 84d25740654..42495666e3e 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb @@ -32,7 +32,9 @@ dependencies = [ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA -configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1" +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], From 3b629e838a5a4d11fd6c2697db8648ec0e5f3922 Mon Sep 17 00:00:00 2001 From: crubb Date: Wed, 8 Jan 2020 18:43:21 +0000 Subject: [PATCH 408/468] {tools}[GCCcore/8.2.0] ownCloud 2.5.4 --- .../ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..c1460e99c5f --- /dev/null +++ b/easybuild/easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'ownCloud' +version = '2.5.4' + +homepage = 'https://github.com/owncloud/client' +description = """The ownCloud Desktop Client is a tool to synchronize files from ownCloud Server with your computer.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/owncloud/client/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f4792639f2422ddc2ebdd9fd6a21bb322441668f18021e0af58f7f7648c29ac'] + +builddependencies = [ + ('CMake', '3.13.3'), + ('binutils', '2.31.1') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('SQLite', '3.26.0'), + ('QtKeychain', '0.9.1'), + ('Qt5', '5.12.3'), +] + +configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ " +configopts += "-DNO_SHIBBOLETH:BOOL=ON " + +sanity_check_paths = { + 'files': ['bin/owncloud', 'bin/owncloudcmd', 'lib/libowncloudsync.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'tools' From 760eb257a647a07e093f46651c22edf1a8f2d354 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 9 Jan 2020 10:33:56 +1030 Subject: [PATCH 409/468] empty sync From 5a8ef2813d70dd49c88bf7b8dfafc4add52030e4 Mon Sep 17 00:00:00 2001 From: crubb Date: Thu, 9 Jan 2020 00:07:07 +0000 Subject: [PATCH 410/468] Fixed SQLite dependency --- .../easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb index c1460e99c5f..dabaae03420 100644 --- a/easybuild/easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/ownCloud/ownCloud-2.5.4-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('SQLite', '3.26.0'), + ('SQLite', '3.27.2'), ('QtKeychain', '0.9.1'), ('Qt5', '5.12.3'), ] From 349aa88413e368bd8a38f91463a3ac6f37648a82 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 9 Jan 2020 16:02:11 +1030 Subject: [PATCH 411/468] Mothur-1.43.0 --- .../Mothur-1.43.0-foss-2019a-Python-3.7.2.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..2e58dfe069d --- /dev/null +++ b/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,34 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +name = 'Mothur' +version = '1.43.0' + +homepage = 'https://www.mothur.org/' +description = """Mothur is a single piece of open-source, expandable software + to fill the bioinformatics needs of the microbial ecology community.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/mothur/mothur/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1'] + +dependencies = [ + ('Python', '3.7.2'), + ('Boost.Python', '1.70.0', '', ('gompi', '2019a')), + ('HDF5', '1.10.5', '', ('gompic', '2019a')), + ('libreadline', '8.0', '', ('GCCcore', '8.2.0')), + ('ncurses', '6.1', '', ('GCCcore', '8.2.0')), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' From 8042ebbc68717585467e361a0ef523e2b51b84c3 Mon Sep 17 00:00:00 2001 From: psakdhna Date: Thu, 9 Jan 2020 14:15:40 +0700 Subject: [PATCH 412/468] Fixed download file name to cudnn-10.0-linux-x64-v7.6.4.38.tgz. Remove easyblock = 'Tarball' --- easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb index 7a5dea11517..eaeeaa1312e 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb @@ -2,8 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell +# Modified: Putt Sakdhnagool ## -easyblock = 'Tarball' name = 'cuDNN' version = '7.6.4.38' @@ -21,7 +21,7 @@ toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download -# Download as cudnn-10.0-linux-x64-v7.6.5.32.tgz +# Download as cudnn-10.0-linux-x64-v7.6.4.38.tgz sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] checksums = ['417bb5daf51377037eb2f5c87649000ca1b9cec0acb16cfe07cb1d3e9a961dbf'] From 576e74d0f9605571669706f19ed62359c7b2e63e Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 9 Jan 2020 08:58:17 +0100 Subject: [PATCH 413/468] Update Sambamba-0.7.1.eb --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb index b45a9d3630b..56a1fa0096b 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.7.1.eb @@ -31,7 +31,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['%(namelower)s', '%s' % local_distbin], + 'files': ['%(namelower)s', local_distbin], 'dirs': [], } From 6435d7288fba71674461fda016a2af3a8a735c41 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Jan 2020 09:04:44 +0100 Subject: [PATCH 414/468] Update source_urls to include old releases folder --- .../l/libsodium/libsodium-1.0.11-foss-2016b.eb | 9 ++++++--- .../l/libsodium/libsodium-1.0.11-intel-2016b.eb | 7 ++++++- .../l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb | 6 +++++- .../l/libsodium/libsodium-1.0.12-intel-2017a.eb | 7 ++++++- .../l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb | 6 +++++- .../l/libsodium/libsodium-1.0.13-foss-2017a.eb | 6 +++++- .../l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb | 6 +++++- .../l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb | 6 +++++- .../l/libsodium/libsodium-1.0.17-GCCcore-8.2.0.eb | 6 +++++- .../l/libsodium/libsodium-1.0.18-GCCcore-8.3.0.eb | 6 +++++- .../l/libsodium/libsodium-1.0.6-intel-2016a.eb | 7 ++++++- .../l/libsodium/libsodium-1.0.8-foss-2016a.eb | 7 ++++++- 12 files changed, 65 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb index 9f0f8fead0f..b2952fa9f92 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb @@ -9,10 +9,13 @@ description = """Sodium is a modern, easy-to-use software library for encryption toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] - -checksums = ['b58928d035064b2a46fb564937b83540'] +checksums = ['a14549db3c49f6ae2170cbbf4664bd48ace50681045e8dbea7c8d9fb96f9c765'] sanity_check_paths = { 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb index 84ddd92f67c..cae48aafdb6 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb @@ -9,8 +9,13 @@ description = """Sodium is a modern, easy-to-use software library for encryption toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] +checksums = ['a14549db3c49f6ae2170cbbf4664bd48ace50681045e8dbea7c8d9fb96f9c765'] sanity_check_paths = { 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb index 927f15bb68b..cc725be3b15 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb @@ -13,7 +13,11 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] checksums = ['b8648f1bb3a54b0251cf4ffa4f0d76ded13977d4fa7517d988f4c902dd8e2f95'] diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb index faf9cf93a16..2cfd618b9bb 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb @@ -9,8 +9,13 @@ description = """Sodium is a modern, easy-to-use software library for encryption toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] +checksums = ['b8648f1bb3a54b0251cf4ffa4f0d76ded13977d4fa7517d988f4c902dd8e2f95'] sanity_check_paths = { 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb index fd09c972029..1f1a1a95101 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb @@ -13,7 +13,11 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.libsodium.org/libsodium/releases/old'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] checksums = ['9c13accb1a9e59ab3affde0e60ef9a2149ed4d6e8f99c93c7a5b97499ee323fd'] diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb index 567630149b4..4bb925b3549 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb @@ -9,7 +9,11 @@ description = """Sodium is a modern, easy-to-use software library for encryption toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] checksums = ['9c13accb1a9e59ab3affde0e60ef9a2149ed4d6e8f99c93c7a5b97499ee323fd'] diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb index d1bbd0e7c97..8dc3e91344a 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb @@ -13,7 +13,11 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] checksums = ['eeadc7e1e1bcef09680fb4837d448fbdf57224978f865ac1c16745868fbd0533'] diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb index 2dfa28fa37a..8561bfdcf4a 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb @@ -13,7 +13,11 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] checksums = ['eeadc7e1e1bcef09680fb4837d448fbdf57224978f865ac1c16745868fbd0533'] diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.17-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.17-GCCcore-8.2.0.eb index 4a22c332325..7d71b8b121e 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.17-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.17-GCCcore-8.2.0.eb @@ -13,7 +13,11 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] checksums = ['0cc3dae33e642cc187b5ceb467e0ad0e1b51dcba577de1190e9ffa17766ac2b1'] diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-8.3.0.eb index c9aeda3e9b5..974ddcccbb0 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-8.3.0.eb @@ -13,7 +13,11 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb index 8cd02bafe08..3bc7b609f37 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb @@ -9,8 +9,13 @@ description = """Sodium is a modern, easy-to-use software library for encryption toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] +checksums = ['940d03ea7d2caa7940e24564bf6d9f66d6edd1df1e0111ff8e3655f3b864fb59'] sanity_check_paths = { 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb index ef8bb83cbf8..277b0ee37a7 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb @@ -9,8 +9,13 @@ description = """Sodium is a modern, easy-to-use software library for encryption toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] sources = [SOURCE_TAR_GZ] +checksums = ['c0f191d2527852641e0a996b7b106d2e04cbc76ea50731b2d0babd3409301926'] sanity_check_paths = { 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], From 967bdf6fa345f1f92651e27a7f8e6c8c4e02328d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Jan 2020 09:21:15 +0100 Subject: [PATCH 415/468] Use https --- .../easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb | 2 +- .../easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb | 2 +- .../easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb | 2 +- .../easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb | 2 +- .../easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb index b2952fa9f92..304994383fc 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.11' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.""" diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb index cae48aafdb6..fa4fa18c65e 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.11' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.""" diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb index cc725be3b15..289eb6d6e17 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.12' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """ Sodium is a modern, easy-to-use software library for encryption, decryption, diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb index 2cfd618b9bb..97245db8a73 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.12' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.""" diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb index 1f1a1a95101..cf14fc6cf84 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.13' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """ Sodium is a modern, easy-to-use software library for encryption, decryption, diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb index 4bb925b3549..da70f58d931 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.13' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.""" diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb index 8dc3e91344a..a2104caa518 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.16' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """ Sodium is a modern, easy-to-use software library for encryption, decryption, diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb index 8561bfdcf4a..c708a188e1f 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.16-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.16' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """ Sodium is a modern, easy-to-use software library for encryption, decryption, diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb index 3bc7b609f37..8d04daef75b 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.6-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.6' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.""" diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb index 277b0ee37a7..3e763c14bd9 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.8-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' version = '1.0.8' -homepage = 'http://doc.libsodium.org/' +homepage = 'https://doc.libsodium.org/' description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.""" From 9d7617f58d812499b7608d55d4b5bd69b2a90a9a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Jan 2020 09:53:36 +0100 Subject: [PATCH 416/468] [libxc] Update URLs to new location --- .../easyconfigs/l/libxc/libxc-2.2.2-GCC-8.2.0-2.31.1.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2017b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb | 4 ++-- .../libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017b.eb | 4 ++-- .../easyconfigs/l/libxc/libxc-3.0.1-GCC-8.2.0-2.31.1.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2017a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.1-gimkl-2017a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2017a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2017b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018b.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.2.3-gimkl-2017a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018a.eb | 4 ++-- easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018b.eb | 4 ++-- .../easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb | 4 ++-- .../libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- 32 files changed, 67 insertions(+), 64 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-GCC-8.2.0-2.31.1.eb index 326087b8245..df8818b2d4a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-GCC-8.2.0-2.31.1.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '2.2.2' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb index 15d810d4e32..d97910e9fda 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '2.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,8 +11,9 @@ toolchain = {'name': 'foss', 'version': '2016b'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 8581c738453..66bcb37f3af 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '2.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,8 +12,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index 0e0039008ff..1e0bdfea8f7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '2.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,8 +12,9 @@ toolchain = {'name': 'intel', 'version': '2016b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2017b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2017b.eb index e3637cdbef0..1d422228de7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2017b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '2.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018a.eb index c07a8019527..87afd304b1d 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '2.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2018a'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb index df7ed0331e7..cef47103b7c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.0' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index d26d791a681..a4de78dceef 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.0' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index 61d4d8c9156..f1d92c47fb6 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.0' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index fec82636060..bd7077a17aa 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.0' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017a.eb index 9ff66357924..21498e19f11 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.0' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017b.eb index 626878423f6..d903880716a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.0' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-GCC-8.2.0-2.31.1.eb index c1167289aa6..7ecb1f66c5a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-GCC-8.2.0-2.31.1.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2016b.eb index 13dccf965a4..4c1b1504832 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2017a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2017a.eb index 4ae2b9fde8b..7ed014507e7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2017a'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018a.eb index 82d5f9731c1..828b95cfa1e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018a'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018b.eb index b3045c67385..bb1c70b521e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-gimkl-2017a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-gimkl-2017a.eb index 4f91cc0b3b1..52541eccaff 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-gimkl-2017a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-gimkl-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'gimkl', 'version': '2017a'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018a.eb index bd2b953d800..f2fe553f513 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2018a'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018b.eb index d4ef6b38725..1ea6d3561f4 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-intel-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '3.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb index 6525ab4d7af..2248db774cc 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=libxc/%(version)s'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb index 17eca30e130..b5b07765344 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.0.1' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=libxc/%(version)s'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2016b.eb index 5c1da480c7f..e16bb2e5c0f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.0.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2017a.eb b/easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2017a.eb index c280d324b84..c194c99d430 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.0.3-foss-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.0.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2017a'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2017b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2017b.eb index 2877ab5f5d2..cd11c7303b7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2017b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2017b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018a.eb b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018a.eb index 88f6e947e43..b4cc1126d29 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018a.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018b.eb index bfe3e14f721..ca1ad919c43 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-foss-2018b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-gimkl-2017a.eb b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-gimkl-2017a.eb index 33a4fa1ed20..152ab638f68 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-gimkl-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'gimkl', 'version': '2017a'} # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018a.eb b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018a.eb index c52e11e9ebe..08b2cff0d67 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018a.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018b.eb index 4e124c96b9f..11b9483e613 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.2.3-intel-2018b.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'libxc' version = '4.2.3' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2018b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] checksums = ['02e49e9ba7d21d18df17e9e57eae861e6ce05e65e966e1e832475aa09e344256'] configopts = '--enable-static --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb index 037c547e2b2..b014a7db3b3 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb @@ -3,13 +3,13 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_lm-fix.patch', diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index a2b2282c8bf..4fb6c89f0c8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -3,13 +3,13 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +homepage = 'https://www.tddft.org/programs/libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version)s_rename-F03.patch'] checksums = [ From ff22ab1dad3a30bd09af0a69ff5694e4b7bd71a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jan 2020 09:54:34 +0100 Subject: [PATCH 417/468] adding easyconfigs: OpenMPI-4.0.2-GCC-9.2.0-2.32.eb --- .../h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb | 48 +++++++++++++++++++ .../libpciaccess-0.16-GCCcore-9.2.0.eb | 26 ++++++++++ .../n/numactl/numactl-2.0.13-GCCcore-9.2.0.eb | 34 +++++++++++++ .../o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb | 21 ++++++++ .../xorg-macros-1.19.2-GCCcore-9.2.0.eb | 37 ++++++++++++++ 5 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-9.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..ed6d9b15b31 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.1.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} +# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake +# cfr. https://github.com/open-mpi/hwloc/issues/315 +toolchainopts = {'vectorize': False} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1fb8cc1438de548e16ec3bb9e4b2abb9f7ce5656f71c0906583819fcfa8c2031'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('numactl', '2.0.13'), + ('libxml2', '2.9.10'), + ('libpciaccess', '0.16'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..d1b27425de5 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.16' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['84413553994aef0070cf420050aa5c0a51b1956b404920e21b81e96db6a61a27'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-9.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..20ce81346bf --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-9.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.13' + +homepage = 'http://oss.sgi.com/projects/libnuma/' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['97ee012b2f294903530424b4ff7f28bcaad6a356897ce8777383f87e5c2e325d'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb new file mode 100644 index 00000000000..ef6e4bc9b8f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb @@ -0,0 +1,21 @@ +name = 'OpenMPI' +version = '4.0.2' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '9.2.0-2.32'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['662805870e86a1471e59739b0c34c6f9004e0c7a22db068562d5388ec4421904'] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.1.0') +] + +# to enable SLURM integration (site-specific) +# configopts = '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.2.0.eb new file mode 100644 index 00000000000..f248dd3b021 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.2.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.2' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '9.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From e2c342ae02e89f2a9762a6a432dce234df4cef99 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jan 2020 10:43:03 +0100 Subject: [PATCH 418/468] use https for libpciaccess homepage --- .../l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb index d1b27425de5..b63c254a79a 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libpciaccess' version = '0.16' -homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" toolchain = {'name': 'GCCcore', 'version': '9.2.0'} From 89f9532a68d739480e12c3eeb23dcb0207473408 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 9 Jan 2020 10:48:58 +0000 Subject: [PATCH 419/468] also update older pocl --- easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.3-GCC-8.2.0-2.31.1.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb index f88e67b0841..9c95cb65637 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb @@ -28,7 +28,9 @@ dependencies = [ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so -configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1" +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/p/pocl/pocl-1.3-GCC-8.2.0-2.31.1.eb index 32a0622c0ec..b9a8868f668 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.3-GCC-8.2.0-2.31.1.eb @@ -27,7 +27,9 @@ dependencies = [ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so -configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1" +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], From 93460ff2453fc466e91c88a029952af3556fd244 Mon Sep 17 00:00:00 2001 From: crubb Date: Thu, 9 Jan 2020 10:59:58 +0000 Subject: [PATCH 420/468] use_pip = True; sanity_pip_check = True --- .../gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb index 6eb7b336dd4..50eb245bd90 100644 --- a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-2.7.15.eb @@ -14,7 +14,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['4803b8055dbeedb0435246a525aa69f1f3425c55d57c973c045deb39bc95c955'] download_dep_fail = True -use_pip = False +use_pip = True +sanity_pip_check = True dependencies = [ ('Python', '2.7.15'), From e5d9482f44b7377403c842e3bdc49766929fea3c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Jan 2020 09:36:43 +0100 Subject: [PATCH 421/468] Allow missing python versionsuffix for existing ECs Otherwise this would break a lot of ECs --- test/easyconfigs/easyconfigs.py | 29 +++++++++++++++++++++-------- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 973c9c7e069..28d22e6a683 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -530,7 +530,7 @@ def check_sha256_checksums(self, changed_ecs): checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) - def check_python_packages(self, changed_ecs): + def check_python_packages(self, changed_ecs, added_ecs_filenames): """Several checks for easyconfigs that install (bundles of) Python packages.""" # These packages do not support installation with 'pip' @@ -581,7 +581,13 @@ def check_python_packages(self, changed_ecs): # Tkinter is an exception, since its version always matches the Python version anyway if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter': if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): - failing_checks.append("'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn) + msg = "'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn + # This is only a failure for newly added ECs, not for existing ECS + # As that would probably break many ECs + if ec_fn in added_ecs_filenames: + failing_checks.append(msg) + else: + print('\nNote: Failed non-critical check: ' + msg) # require that running of "pip check" during sanity check is enabled via sanity_pip_check if use_pip and easyblock in ['PythonBundle', 'PythonPackage']: @@ -653,6 +659,11 @@ def check_https(self, changed_ecs): def test_changed_files_pull_request(self): """Specific checks only done for the (easyconfig) files that were changed in a pull request.""" + def get_eb_files_from_diff(diff_filter): + cmd = "git diff --name-only --diff-filter=%s %s...HEAD" % (diff_filter, target_branch) + out, ec = run_cmd(cmd, simple=False) + return [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')] + # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '(none)')) @@ -682,16 +693,18 @@ def test_changed_files_pull_request(self): cwd = change_dir(top_dir) # get list of changed easyconfigs - cmd = "git diff --name-only --diff-filter=AM %s...HEAD" % target_branch - out, ec = run_cmd(cmd, simple=False) - changed_ecs_filenames = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')] - print("\nList of changed easyconfig files in this PR: %s" % '\n'.join(changed_ecs_filenames)) + changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') + added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') + if changed_ecs_filenames: + print("\nList of changed easyconfig files in this PR: %s" % '\n'.join(changed_ecs_filenames)) + if added_ecs_filenames: + print("\nList of added easyconfig files in this PR: %s" % '\n'.join(added_ecs_filenames)) change_dir(cwd) # grab parsed easyconfigs for changed easyconfig files changed_ecs = [] - for ec_fn in changed_ecs_filenames: + for ec_fn in changed_ecs_filenames + added_ecs_filenames: match = None for ec in EasyConfigTest.parsed_easyconfigs: if os.path.basename(ec['spec']) == ec_fn: @@ -715,7 +728,7 @@ def test_changed_files_pull_request(self): # run checks on changed easyconfigs self.check_sha256_checksums(changed_ecs) - self.check_python_packages(changed_ecs) + self.check_python_packages(changed_ecs, added_ecs_filenames) self.check_sanity_check_paths(changed_ecs) self.check_https(changed_ecs) From c13ebaad786122917e04f8d3a4babe80eb2988bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jan 2020 12:49:40 +0100 Subject: [PATCH 422/468] use latest master as release candidate of MRtrix 3.0 --- ...=> MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb} | 7 ++++--- ... => MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb} | 8 ++++---- 2 files changed, 8 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/m/MRtrix/{MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb => MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb} (81%) rename easybuild/easyconfigs/m/MRtrix/{MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb => MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb} (81%) diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb similarity index 81% rename from easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb rename to easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb index a125848089a..7f066294b57 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb @@ -1,5 +1,6 @@ name = 'MRtrix' -version = '3.0_RC4' +local_commit = 'd411e6c' +version = '3.0-rc-20191217' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.brain.org.au/software/index.html#mrtrix' @@ -10,8 +11,8 @@ toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['4f246e4cc6ddd5d2480d368342bcbeb9c5d21c04a3a4b5e6e2adb8c036611426'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['7140934dc653ee5edf807120a8e9cf23a0bf72f01bbe4dfbe2a15206ce6812db'] builddependencies = [ ('Eigen', '3.3.7', '', True), diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb similarity index 81% rename from easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb index c62e1f93059..7163dd84d46 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb @@ -1,5 +1,6 @@ name = 'MRtrix' -version = '3.0_RC4' +local_commit = 'd411e6c' +version = '3.0-rc-20191217' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.brain.org.au/software/index.html#mrtrix' @@ -10,8 +11,8 @@ toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['4f246e4cc6ddd5d2480d368342bcbeb9c5d21c04a3a4b5e6e2adb8c036611426'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['7140934dc653ee5edf807120a8e9cf23a0bf72f01bbe4dfbe2a15206ce6812db'] builddependencies = [ ('Eigen', '3.3.7', '', True), @@ -23,7 +24,6 @@ dependencies = [ ('Mesa', '19.1.7'), ('Qt5', '5.13.1'), ('LibTIFF', '4.0.10'), - ('FFTW', '3.3.8'), ] moduleclass = 'bio' From 12c8b225ae4bb08d587f0d0b0ff8a87eeba72164 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Thu, 9 Jan 2020 13:38:40 +0000 Subject: [PATCH 423/468] Changes following smoors review --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 5 +++-- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 4 +++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index f34b9e31e37..98a4aa83115 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -757,7 +757,6 @@ exts_list = [ 'checksums': ['ac6b3b8e814fbb855c38fbdb89a4f0cf0ed65ce7fa308445bd74107fbc0d32cf'], }), ('R.matlab', version, { - '3.6.2': ['1ba338f470a24b7f6ef68cadbd04eb468ead4a689f263d2642408ad591b786bb'], 'checksums': ['1ba338f470a24b7f6ef68cadbd04eb468ead4a689f263d2642408ad591b786bb'], }), ('gridExtra', '2.3', { @@ -1987,6 +1986,9 @@ exts_list = [ ('ggridges', '0.5.1', { 'checksums': ['01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36'], }), + ('metap', '1.2', { + 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], + }), ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), @@ -2056,7 +2058,6 @@ exts_list = [ 'checksums': ['eb31d72c73a06a145d231ad3489d450d63b9fecc069aeb19331d7417241df3b5'], }), ('tergm', '3.6.1', { - '3.6.1': ['21de2eca943d89ba63af14951655d626f241bafccc4b2709fa39aa130625cd0f'], 'checksums': ['21de2eca943d89ba63af14951655d626f241bafccc4b2709fa39aa130625cd0f'], }), ('ergm.count', '3.4.0', { diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 96c13f13a77..812724334ee 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -1987,6 +1987,9 @@ exts_list = [ ('ggridges', '0.5.1', { 'checksums': ['01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36'], }), + ('metap', '1.2', { + 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], + }), ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), @@ -2056,7 +2059,6 @@ exts_list = [ 'checksums': ['eb31d72c73a06a145d231ad3489d450d63b9fecc069aeb19331d7417241df3b5'], }), ('tergm', '3.6.1', { - '3.6.1': ['21de2eca943d89ba63af14951655d626f241bafccc4b2709fa39aa130625cd0f'], 'checksums': ['21de2eca943d89ba63af14951655d626f241bafccc4b2709fa39aa130625cd0f'], }), ('ergm.count', '3.4.0', { From 387e1fa50126f90d62cec41548f30ed5048e376d Mon Sep 17 00:00:00 2001 From: Shahzeb Siddiqui Date: Thu, 9 Jan 2020 08:49:38 -0600 Subject: [PATCH 424/468] PyCharm 2019.3.1 easyconfig --- .../easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb new file mode 100644 index 00000000000..440f1dcda77 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb @@ -0,0 +1,19 @@ +easyblock = 'Tarball' + +name = 'PyCharm' +version = "2019.3.1" + +homepage = 'https://www.jetbrains.com/pycharm/' +description = """PyCharm Community Edition: Python IDE for Professional Developers""" + +toolchain = SYSTEM + +source_urls = ['https://download-cf.jetbrains.com/python'] +sources = ['pycharm-community-%s.tar.gz' % version] +checksums = [] +sanity_check_paths = { + 'files': ["bin/pycharm.sh"], + 'dirs': [], +} + +moduleclass = 'devel' From 713313f82d3be7d91e575072b78cb1afc6e91e81 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 8 Jan 2020 17:42:26 +0100 Subject: [PATCH 425/468] Make postinstallcmds independend of PWD --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 5 +++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 5 +++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 5 +++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 5 +++-- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 2edc4ad52e4..83620ef4213 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'OpenCV' version = '3.1.0' -homepage = 'http://opencv.org/' +homepage = 'https://opencv.org/' description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate @@ -64,7 +64,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' -postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] +postinstallcmds = ["cp %(builddir)s/opencv-3.1.0/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* " + "%(installdir)s/lib"] sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index b1217643ae4..08227320cfa 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'OpenCV' version = '3.1.0' -homepage = 'http://opencv.org/' +homepage = 'https://opencv.org/' description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate @@ -62,7 +62,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' -postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] +postinstallcmds = ["cp %(builddir)s/opencv-3.1.0/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* " + "%(installdir)s/lib"] sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index 89da773f3a7..500ed23ff0f 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'OpenCV' version = '3.1.0' -homepage = 'http://opencv.org/' +homepage = 'https://opencv.org/' description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate @@ -65,7 +65,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' -postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] +postinstallcmds = ["cp %(builddir)s/opencv-3.1.0/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* " + "%(installdir)s/lib"] sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index 62cfeac2a65..8ac6f4b8926 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'OpenCV' version = '3.1.0' -homepage = 'http://opencv.org/' +homepage = 'https://opencv.org/' description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate @@ -66,7 +66,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' -postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] +postinstallcmds = ["cp %(builddir)s/opencv-3.1.0/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* " + "%(installdir)s/lib"] sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + From fe0c4e878f9ca5f5733a01b9a2d55d9e825a19c4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Jan 2020 08:59:40 +0100 Subject: [PATCH 426/468] Add checksums --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 5 ++++- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 5 ++++- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 7 +++++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 7 +++++-- 4 files changed, 18 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 83620ef4213..1373f1267ed 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -16,11 +16,14 @@ source_urls = [ # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] - sources = [ '%(version)s.zip', {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, ] +checksums = [ + '1f6990249fdb82804fff40e96fa6d99949023ab0e3277eae4bd459b374e622a4', # 3.1.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz +] builddependencies = [ ('CMake', '3.5.2'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index 08227320cfa..f846d1b22b7 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -16,11 +16,14 @@ source_urls = [ # the hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] - sources = [ '%(version)s.zip', {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, ] +checksums = [ + '1f6990249fdb82804fff40e96fa6d99949023ab0e3277eae4bd459b374e622a4', # 3.1.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz +] builddependencies = [ ('CMake', '3.5.2'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index 500ed23ff0f..c990363c58e 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -16,13 +16,16 @@ source_urls = [ # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] - sources = [ '%(version)s.zip', {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, ] - patches = ['OpenCV-%(version)s_with_IPP.patch'] +checksums = [ + '1f6990249fdb82804fff40e96fa6d99949023ab0e3277eae4bd459b374e622a4', # 3.1.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz + 'b8ba735c762b0dcec370d7e8b7d540b16480b582f39a9219f5ecb73145c28aa4', # OpenCV-3.1.0_with_IPP.patch +] builddependencies = [ ('CMake', '3.5.2'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index 8ac6f4b8926..5edac679fce 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -16,13 +16,16 @@ source_urls = [ # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] - sources = [ '%(version)s.zip', {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, ] - patches = ['OpenCV-%(version)s_with_IPP.patch'] +checksums = [ + '1f6990249fdb82804fff40e96fa6d99949023ab0e3277eae4bd459b374e622a4', # 3.1.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz + 'b8ba735c762b0dcec370d7e8b7d540b16480b582f39a9219f5ecb73145c28aa4', # OpenCV-3.1.0_with_IPP.patch +] builddependencies = [ ('CMake', '3.5.2'), From 7e01b9cf8cc982aa4e91a6dc7c261baa6e991ccb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Jan 2020 12:43:14 +0100 Subject: [PATCH 427/468] Use template values instead hardcoding --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 5 +++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 5 +++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 5 +++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 5 +++-- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 1373f1267ed..73c03c05319 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -67,8 +67,9 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' -postinstallcmds = ["cp %(builddir)s/opencv-3.1.0/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* " - "%(installdir)s/lib"] +local_startdir = '%(builddir)s/%(namelower)s-%(version)s' +postinstallcmds = ["cp %s/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %%(installdir)s/lib" + % local_startdir] sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index f846d1b22b7..fae2abfc2d0 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -65,8 +65,9 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' -postinstallcmds = ["cp %(builddir)s/opencv-3.1.0/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* " - "%(installdir)s/lib"] +local_startdir = '%(builddir)s/%(namelower)s-%(version)s' +postinstallcmds = ["cp %s/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %%(installdir)s/lib" + % local_startdir] sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index c990363c58e..edf524c0ad5 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -68,8 +68,9 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' -postinstallcmds = ["cp %(builddir)s/opencv-3.1.0/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* " - "%(installdir)s/lib"] +local_startdir = '%(builddir)s/%(namelower)s-%(version)s' +postinstallcmds = ["cp %s/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %%(installdir)s/lib" + % local_startdir] sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index 5edac679fce..56a59ab5473 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -69,8 +69,9 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' -postinstallcmds = ["cp %(builddir)s/opencv-3.1.0/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* " - "%(installdir)s/lib"] +local_startdir = '%(builddir)s/%(namelower)s-%(version)s' +postinstallcmds = ["cp %s/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %%(installdir)s/lib" + % local_startdir] sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + From bb35972c4aa954083a043dba39faa3e4ae8f4bad Mon Sep 17 00:00:00 2001 From: crubb Date: Thu, 9 Jan 2020 15:53:52 +0000 Subject: [PATCH 428/468] Add second checksum for rda_1.0.2-2.1.tar.gz --- easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb | 3 ++- easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb | 3 ++- easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb index 9c5746b2b10..d6baa484780 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb @@ -2196,7 +2196,8 @@ exts_list = [ 'checksums': ['779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb index 3663ed4946d..f4743b0c43e 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb @@ -2196,7 +2196,8 @@ exts_list = [ 'checksums': ['779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb index b40c2dbea52..4def3529218 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb @@ -2255,7 +2255,8 @@ exts_list = [ 'checksums': ['779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], From 048a5804f58f0fbd344d6dcdc8ad717935d1f4cb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 9 Jan 2020 17:05:11 +0100 Subject: [PATCH 429/468] adding easyconfigs: GTS-0.7.6-foss-2019b.eb --- .../easyconfigs/g/GTS/GTS-0.7.6-foss-2019b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2019b.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2019b.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2019b.eb new file mode 100644 index 00000000000..2b6c5233b71 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2019b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.62.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' From 79d4a968eed8997fe36b02f9f1964fa0d3d3535b Mon Sep 17 00:00:00 2001 From: Ed Date: Thu, 9 Jan 2020 16:52:57 +0000 Subject: [PATCH 430/468] Deps for metap --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 98a4aa83115..b4098683f7a 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -1986,12 +1986,18 @@ exts_list = [ ('ggridges', '0.5.1', { 'checksums': ['01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36'], }), - ('metap', '1.2', { - 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], - }), ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), + ('multtest', '2.8.0', { + 'checksums': ['e41181f8a58fe09a48acc5165057209cd3ba24a6343333dd3c881e9ddd475431'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('metap', '1.2', { + 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], + }), ('lsei', '1.2-0', { 'checksums': ['4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6'], }), From 687b887ff3e7c0130093825100704de51db09146 Mon Sep 17 00:00:00 2001 From: Ed Date: Thu, 9 Jan 2020 16:53:16 +0000 Subject: [PATCH 431/468] Deps for metap --- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 812724334ee..a8e75c72c52 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -1987,12 +1987,18 @@ exts_list = [ ('ggridges', '0.5.1', { 'checksums': ['01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36'], }), - ('metap', '1.2', { - 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], - }), ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), + ('multtest', '2.8.0', { + 'checksums': ['e41181f8a58fe09a48acc5165057209cd3ba24a6343333dd3c881e9ddd475431'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('metap', '1.2', { + 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], + }), ('lsei', '1.2-0', { 'checksums': ['4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6'], }), From 48cd94f8084e9c9faebb18af343bd695b0cfd340 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 10 Jan 2020 09:03:12 +1030 Subject: [PATCH 432/468] version fix --- .../m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb index 2e58dfe069d..2acb75f581e 100644 --- a/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb @@ -10,6 +10,7 @@ name = 'Mothur' version = '1.43.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.mothur.org/' description = """Mothur is a single piece of open-source, expandable software From dc24e1c0ae4340a908a6a53919a1834171dd833d Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 10 Jan 2020 09:54:25 +1030 Subject: [PATCH 433/468] deps fix --- .../m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb index 2acb75f581e..16d5db6c6ee 100644 --- a/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/Mothur/Mothur-1.43.0-foss-2019a-Python-3.7.2.eb @@ -26,7 +26,7 @@ checksums = ['12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1'] dependencies = [ ('Python', '3.7.2'), ('Boost.Python', '1.70.0', '', ('gompi', '2019a')), - ('HDF5', '1.10.5', '', ('gompic', '2019a')), + ('HDF5', '1.10.5', '', ('gompi', '2019a')), ('libreadline', '8.0', '', ('GCCcore', '8.2.0')), ('ncurses', '6.1', '', ('GCCcore', '8.2.0')), ('zlib', '1.2.11'), From 9956e4e9a7aff0b31724addcaa6881741422fa27 Mon Sep 17 00:00:00 2001 From: Ed Date: Fri, 10 Jan 2020 06:57:34 +0000 Subject: [PATCH 434/468] Removing multtest, mutoss, and metap again due to dependency on Biobase --- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index a8e75c72c52..1539b4fbc35 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -1990,15 +1990,6 @@ exts_list = [ ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), - ('multtest', '2.8.0', { - 'checksums': ['e41181f8a58fe09a48acc5165057209cd3ba24a6343333dd3c881e9ddd475431'], - }), - ('mutoss', '0.1-12', { - 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], - }), - ('metap', '1.2', { - 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], - }), ('lsei', '1.2-0', { 'checksums': ['4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6'], }), From 22acdc25e2d2a88c8b23024bf51eddfef1e13b05 Mon Sep 17 00:00:00 2001 From: Ed Date: Fri, 10 Jan 2020 06:58:31 +0000 Subject: [PATCH 435/468] Removing multtest, mutoss, and metap again due to dependency on Biobase --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index b4098683f7a..35a72ba9c72 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -1989,15 +1989,6 @@ exts_list = [ ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], }), - ('multtest', '2.8.0', { - 'checksums': ['e41181f8a58fe09a48acc5165057209cd3ba24a6343333dd3c881e9ddd475431'], - }), - ('mutoss', '0.1-12', { - 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], - }), - ('metap', '1.2', { - 'checksums': ['6ec37f2fc953a5c0d2b0e2ed8bdc1f66a60767299742cc130da8ff2c7b64cb5d'], - }), ('lsei', '1.2-0', { 'checksums': ['4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6'], }), From 3ffff6ac2e9c21e0ad5ebbb2099b32fe9feb977b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Jan 2020 10:09:00 +0100 Subject: [PATCH 436/468] [QCA 2.1.0] Update URLs as old ones are not available --- easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb | 8 +++++--- easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb | 7 ++++--- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb index 6422b82abed..fcc27823fe7 100644 --- a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb @@ -1,8 +1,9 @@ easyblock = 'CMakeMake' + name = 'QCA' version = '2.1.0' -homepage = 'http://delta.affinix.com/qca/' +homepage = 'https://github.com/KDE/qca' description = """Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as @@ -13,8 +14,9 @@ description = """Taking a hint from the similarly-named Java Cryptography Archit toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['http://delta.affinix.com/download/qca/2.0/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = ['https://github.com/KDE/qca/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['82dea2afb116dac5b4fea533ebb7e31011c3c66c8f67c56e5aea50650a630446'] configopts = "-DQT4_BUILD=true" diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb index 73895f04cbd..88485fdd338 100644 --- a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'QCA' version = '2.1.0' -homepage = 'http://delta.affinix.com/qca/' +homepage = 'https://github.com/KDE/qca' description = """Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as @@ -14,8 +14,9 @@ description = """Taking a hint from the similarly-named Java Cryptography Archit toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://delta.affinix.com/download/qca/2.0/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = ['https://github.com/KDE/qca/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['82dea2afb116dac5b4fea533ebb7e31011c3c66c8f67c56e5aea50650a630446'] configopts = "-DQT4_BUILD=true" From 5f0f836781925b53f4a22d10a6fbad029351f73b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Jan 2020 10:15:57 +0100 Subject: [PATCH 437/468] Fix URL for libxc 4.0.1 --- easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb index 2248db774cc..5adc5315a63 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=libxc/%(version)s'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb index b5b07765344..21495d91b49 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-intel-2017b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} # Tests also fail with Intel Compilers on Haswell when optarch is enabled. toolchainopts = {'lowopt': True, 'optarch': False} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=libxc/%(version)s'] +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] checksums = [ From 458a21bccabe771be8feca19ba7c458fd5ddc7c4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Jan 2020 11:11:39 +0100 Subject: [PATCH 438/468] Add sanity_check_paths --- easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb | 5 +++++ easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb index fcc27823fe7..2c239f6133a 100644 --- a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb @@ -28,4 +28,9 @@ dependencies = [ ('Qt', '4.8.7') ] +sanity_check_paths = { + 'files': ['bin/qcatool', 'lib/libqca.%s' % SHLIB_EXT, 'lib/pkgconfig/qca2.pc'], + 'dirs': ['include/QtCrypto', 'lib/cmake/Qca', 'share/man'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb index 88485fdd338..b0e484e5243 100644 --- a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-intel-2016b.eb @@ -28,4 +28,9 @@ dependencies = [ ('Qt', '4.8.7') ] +sanity_check_paths = { + 'files': ['bin/qcatool', 'lib/libqca.%s' % SHLIB_EXT, 'lib/pkgconfig/qca2.pc'], + 'dirs': ['include/QtCrypto', 'lib/cmake/Qca', 'share/man'], +} + moduleclass = 'devel' From 9360c97584c32f7faaedd91e2f0226c42df8170a Mon Sep 17 00:00:00 2001 From: crubb Date: Fri, 10 Jan 2020 12:18:13 +0000 Subject: [PATCH 439/468] adding easyconfigs: gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb --- ...nwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb new file mode 100644 index 00000000000..3a23c88f10c --- /dev/null +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = "gradunwarp" +version = "1.1.0" +versionsuffix = "-HCP-Python-%(pyver)s" + +homepage = "https://github.com/Washington-University/gradunwarp" +description = """Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/Washington-University/gradunwarp/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4803b8055dbeedb0435246a525aa69f1f3425c55d57c973c045deb39bc95c955'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('NiBabel', '2.4.0') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 10ca5d9f5eb117859f26226a95db31894c50da06 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Jan 2020 18:11:49 +0100 Subject: [PATCH 440/468] Fix Python 3.5.1 (missing bitstring src) --- .../p/Python/Python-3.5.1-foss-2016a.eb | 92 +++++++++++-------- 1 file changed, 52 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 1da87c7cd68..fbeeb907c30 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -1,18 +1,16 @@ name = 'Python' version = '3.5.1' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems more effectively.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -local_numpyversion = '1.10.4' -local_scipyversion = '0.17.0' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +checksums = ['687e067d9f391da645423c7eda8205bae9d35edc0c76ef5218dcbe4cc770d0d7'] # python needs bzip2 to build the bz2 package dependencies = [ @@ -31,97 +29,111 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev')] +installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" + +exts_default_options = { + 'download_dep_fail': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'sanity_pip_check': False, # pip is to old +} + # order is important! # package versions updated Feb 25th 2016 exts_list = [ - ('setuptools', '20.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), ('pip', '8.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'use_pip': False, + 'checksums': ['46f4bd0d8dfd51125a554568d646fe4200a3c2c6c36b9f2d06d2212148439521'], + }), + ('setuptools', '20.1.1', { + 'checksums': ['2663ce0b0e742ee27c3a06b2da14563e4f6f713eaf5509b932a31793f9dea9a3'], }), ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), - ('numpy', local_numpyversion, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + ('numpy', '1.10.4', { + 'checksums': ['7356e98fbcc529e8d540666f5a919912752e569150e9a4f8d869c686f14c720b'], }), - ('scipy', local_scipyversion, { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + ('scipy', '0.17.0', { + 'checksums': ['f600b755fb69437d0f70361f9e560ab4d304b1b66987ed5a28bdd9dd7793e089'], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], }), ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - 'patches': [ - 'paycheck-1.0.2_setup-open-README-utf8.patch', + 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], + 'checksums': [ + '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz + # paycheck-1.0.2_setup-open-README-utf8.patch + 'ceb7f08aebf016cdcd94ae41c1c76c8c120907f85cbfce240d3a112afb264d79', ], }), ('pbr', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['e2127626a91e6c885db89668976db31020f0af2da728924b56480fc7ccf09649'], }), ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('Cython', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'checksums': ['fec42fecee35d6cc02887f1eef4e4952c97402ed2800bfe41bbd9ed1a0730d8e'], }), ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'], }), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['3e95445c1db500a344079a47b171c45ef18f57d188dffdb0e4165c71bea8eb3d'], }), ('deap', '1.0.2', { + 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - 'patches': [ - 'deap-1.0.2_setup-open-README-utf8.patch', + 'checksums': [ + 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz + # deap-1.0.2_setup-open-README-utf8.patch + '39a3a08359321189a1b27a382eb309dfd4470cba9101997a6d527a2fd3a0ce93', ], }), ('decorator', '4.0.9', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['90022e83316363788a55352fe39cfbed357aa3a71d90e5f2803a35471de4bba8'], }), ('arff', '2.1.0', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['be6b5b76698d5fca1f24d75c98ed9c0ff5e24eb0d985d01cfd26c08a70f9654e'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], }), ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), ('paramiko', '1.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['3297ebd3cd072f573772f7c7426939a443c62c458d54bb632ff30fd6ecf96892'], }), ('pyparsing', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['f6cb2bc85a491347c3c699db47f7ecc02903959156b4f92669ebf82395982901'], }), ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + 'checksums': ['9656a169cb83da34d732b0eb72b39373d48774aee009a3d1272b7ea2ce109cde'], }), ('netaddr', '0.7.18', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + 'checksums': ['a1f5c9fcf75ac2579b9995c843dade33009543c04f218ff7c007b3c81695bd19'], }), ('pandas', '0.17.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + 'checksums': ['cfd7214a7223703fe6999fbe34837749540efee1c985e6aee9933f30e3f72837'], }), ('bitstring', '3.1.3', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + 'checksums': ['4683382f2d816bd9d16d9f95260f9aaf053a575732a4f59ed64760f47f44fff4'], }), ('pytz', '2016.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + 'checksums': ['3449da19051655d4c0bb5c37191331748bcad15804d81676a88451ef299370a8'], }), ('virtualenv', '15.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + 'checksums': ['1a74278b8adb383ce4c7619e33c753b1eb7b58dc1e449601c096ca4b76125f84'], }), ] From c84d6091e068650813e246a829b992455a431224 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Jan 2020 18:24:40 +0100 Subject: [PATCH 441/468] Fix tesseract 4.1.0 dependencies --- .../tesseract-4.1.0-GCCcore-8.2.0.eb | 20 +++++++++---- .../tesseract-4.1.0-add-glib-dependency.patch | 29 +++++++++++++++++++ 2 files changed, 43 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-add-glib-dependency.patch diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-GCCcore-8.2.0.eb index 2ae504a22b5..094ee48e4a9 100644 --- a/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-GCCcore-8.2.0.eb @@ -14,13 +14,15 @@ sources = [ '%(version)s.tar.gz', { 'source_urls': ['https://github.com/tesseract-ocr/tessdata/archive/'], - 'download_filename': '%(version)s.tar.gz', - 'filename': 'tessdata-%(version)s.tar.gz', + 'download_filename': '4.0.0.tar.gz', + 'filename': 'tessdata-4.0.0.tar.gz', }, ] +patches = ['tesseract-4.1.0-add-glib-dependency.patch'] checksums = [ '5c5ed5f1a76888dc57a83704f24ae02f8319849f5c4cf19d254296978a1a1961', # 4.1.0.tar.gz - '5c5ed5f1a76888dc57a83704f24ae02f8319849f5c4cf19d254296978a1a1961', # tessdata-4.1.0.tar.gz + '38c637d3a1763f6c3d32e8f1d979f045668676ec5feb8ee1869ee77cedd31b08', # tessdata-4.0.0.tar.gz + 'f21ac5ed7d28a07978a6f7230fce2125d98a7264e33ddd3bd648af6da41b6fd1', # tesseract-4.1.0-add-glib-dependency.patch ] builddependencies = [ @@ -30,18 +32,24 @@ builddependencies = [ ] dependencies = [ + ('zlib', '1.2.11'), ('libpng', '1.6.36'), - ('LibTIFF', '4.0.10'), ('libjpeg-turbo', '2.0.2'), - ('zlib', '1.2.11'), + ('LibTIFF', '4.0.10'), ('Leptonica', '1.78.0'), + ('libarchive', '3.4.0'), + ('ICU', '64.2'), + ('fontconfig', '2.13.1'), + ('GLib', '2.60.1'), + ('cairo', '1.16.0'), + ('Pango', '1.43.0'), ] separate_build_dir = True postinstallcmds = [ 'mkdir %(installdir)s/tessdata', - 'mv %(builddir)s/%(name)s-%(version)s/* %(installdir)s/tessdata' + 'mv %(builddir)s/tessdata-4.0.0/* %(installdir)s/tessdata' ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-add-glib-dependency.patch b/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-add-glib-dependency.patch new file mode 100644 index 00000000000..f73f2e72ffe --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-add-glib-dependency.patch @@ -0,0 +1,29 @@ +From ecb4d4c11f683ea178a15fc9bcf08a5fb53b1d8d Mon Sep 17 00:00:00 2001 +From: rezso +Date: Mon, 5 Aug 2019 22:10:28 +0200 +Subject: [PATCH] Add glib and gobject libs for text2image + +--- + src/training/CMakeLists.txt | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/src/training/CMakeLists.txt b/src/training/CMakeLists.txt +index 9296d6bd9..3ab89528c 100644 +--- a/src/training/CMakeLists.txt ++++ b/src/training/CMakeLists.txt +@@ -271,6 +271,7 @@ pkg_check_modules(Cairo REQUIRED cairo) + pkg_check_modules(PangoFt2 REQUIRED pangoft2) + pkg_check_modules(PangoCairo REQUIRED pangocairo) + pkg_check_modules(FontConfig REQUIRED fontconfig) ++pkg_check_modules(Glib REQUIRED glib-2.0 gobject-2.0) + endif() + + set(text2image_src +@@ -306,6 +307,7 @@ target_link_libraries (text2image + ${PangoCairo_LIBRARIES} + ${PangoFt2_LIBRARIES} + ${FontConfig_LIBRARIES} ++ ${Glib_LIBRARIES} + ) + endif() + if (CPPAN_BUILD) From 83cbebb38d3b63482ea911532a694467a1934fd3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Sat, 11 Jan 2020 13:25:36 +0100 Subject: [PATCH 442/468] Fix style issue --- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index fbeeb907c30..333a45715eb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -35,7 +35,7 @@ exts_default_options = { 'download_dep_fail': True, 'source_urls': [PYPI_SOURCE], 'use_pip': True, - 'sanity_pip_check': False, # pip is to old + 'sanity_pip_check': False, # pip is to old } # order is important! From 83fa3ebd493a214a1394a030c06eb09dc03f09b0 Mon Sep 17 00:00:00 2001 From: crubb Date: Sat, 11 Jan 2020 14:35:37 +0000 Subject: [PATCH 443/468] {lib}[GCCcore/8.2.0-8.3.0] ICU 64.2 - Depend on Python3 instead of 2 --- easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb index e516221602e..337832d9009 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ checksums = ['627d5d8478e6d96fc8c90fed4851239079a561a6a8b9e48b0892f24e82d31d6c'] builddependencies = [ ('binutils', '2.31.1'), - ('Python', '2.7.15'), + ('Python', '3.7.2'), ] start_dir = 'source' diff --git a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb index 9b42d14795b..d53539516c0 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ checksums = ['627d5d8478e6d96fc8c90fed4851239079a561a6a8b9e48b0892f24e82d31d6c'] builddependencies = [ ('binutils', '2.32'), - ('Python', '2.7.16'), + ('Python', '3.7.2'), ] start_dir = 'source' From 11c54cda31103ea60d1aa2ea1b4b939b4b489bd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Jan 2020 15:36:48 +0100 Subject: [PATCH 444/468] add --enable-mpi1-compatibility configure option for OpenMPI 4.0.2 --- .../easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb index ef6e4bc9b8f..bf4fb7c22ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.2-GCC-9.2.0-2.32.eb @@ -15,7 +15,9 @@ dependencies = [ ('hwloc', '2.1.0') ] +configopts = '--enable-mpi1-compatibility ' + # to enable SLURM integration (site-specific) -# configopts = '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' moduleclass = 'mpi' From 076c0ff09a625a52eb13cbceb6cfb694c3b304a6 Mon Sep 17 00:00:00 2001 From: crubb Date: Sat, 11 Jan 2020 14:49:04 +0000 Subject: [PATCH 445/468] Python 3.7.4 for GCCcore 8.3.0 --- easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb index d53539516c0..063a8445d12 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ checksums = ['627d5d8478e6d96fc8c90fed4851239079a561a6a8b9e48b0892f24e82d31d6c'] builddependencies = [ ('binutils', '2.32'), - ('Python', '3.7.2'), + ('Python', '3.7.4'), ] start_dir = 'source' From 81d1950ce156f2742696b4c9a780fee7c2b3a932 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 11 Jan 2020 17:38:54 +0000 Subject: [PATCH 446/468] adding easyconfigs: tcsh-6.22.02-GCCcore-8.2.0.eb --- .../t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..0a18f40c2bb --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.22.02' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ed287158ca1b00ba477e8ea57bac53609838ebcfd05fcb05ca95021b7ebe885b'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('ncurses', '6.1')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' From b1701ce861bb4dc3c678dad5695c48691a1f0a5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Jan 2020 20:43:10 +0100 Subject: [PATCH 447/468] use True rather than 'True' for boolean easyconfig parameters --- easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb | 2 +- .../b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb | 2 +- .../b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb | 2 +- .../b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb | 2 +- .../b/Blender/Blender-2.81-foss-2019b-Python-3.7.4.eb | 2 +- .../b/Blender/Blender-2.81-intel-2019b-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb | 2 +- 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easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb | 2 +- .../impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 4 ++-- .../easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 4 ++-- .../impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 4 ++-- .../impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 4 ++-- .../easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb | 4 ++-- .../impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 4 ++-- .../impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb | 4 ++-- .../impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb | 4 ++-- .../impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb | 4 ++-- .../easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb | 4 ++-- .../impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 4 ++-- .../impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb | 4 ++-- .../easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb | 4 ++-- .../impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 4 ++-- .../impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb | 4 ++-- .../impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb | 4 ++-- .../easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb | 4 ++-- .../easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb | 4 ++-- .../impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb | 4 ++-- .../impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 4 ++-- .../impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb | 4 ++-- .../easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb | 4 ++-- .../impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- .../impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 4 ++-- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 4 ++-- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 4 ++-- .../impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 4 ++-- .../impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 4 ++-- .../impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 4 ++-- .../easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb | 4 ++-- easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb | 2 +- easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb | 2 +- easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb | 2 +- easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2017.1.024.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2018.1.017.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2018.3.022.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2019.2.026.eb | 2 +- easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb | 2 +- easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb | 2 +- easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb | 2 +- .../easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 2 +- 190 files changed, 234 insertions(+), 234 deletions(-) diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb index 48d74035d13..86ea9f600b9 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb @@ -12,7 +12,7 @@ toolchain = SYSTEM sources = ['advisor_xe_%(version)s.tar.gz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb index a7bd64668b2..17fa732bc46 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -14,7 +14,7 @@ sources = ['advisor_%(version)s.tar.gz'] checksums = ['af87b381394be3100507827a3461b3bc'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb index 80234d38ef7..e4cbabd47a1 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb @@ -14,7 +14,7 @@ sources = ['advisor_%(version)s.tar.gz'] checksums = ['611206c771a318fe23bebcf4058748229730821565a8e8c16afe86f240443f35'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb index 1f0021d4c40..9366d079086 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb @@ -14,7 +14,7 @@ sources = ['advisor_%(version)s.tar.gz'] checksums = ['e8d42ffd478244cb168e4e8d8b3b15dd6e9245ed57a008d369337f0bba7d8f25'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb index 6a33c20f00f..19e9dc5f4d8 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -14,7 +14,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['advisor_%(version)s.tar.gz'] checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb index 8b427b71e14..fd5a6bbf429 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb @@ -14,6 +14,6 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['advisor_%(version)s.tar.gz'] checksums = ['6597f165dee3c6444eb0f38a9069327d10584b09555f5d2c4ed86b8f84d980bb'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb index f0f87845586..6a0d2fa4ece 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb @@ -14,6 +14,6 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['advisor_%(version)s.tar.gz'] checksums = ['3f203ee63df37e87423fdd4cbeb5ec027b3d11e50c9121935f8b323dd635e866'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True moduleclass = 'perf' diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb index 0c7912b7663..8a4e5b9debf 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb @@ -41,7 +41,7 @@ dependencies = [ builddependencies = [('CMake', '3.6.1')] -separate_build_dir = 'True' +separate_build_dir = True modextravars = {'GALLIUM_DRIVER': 'swr'} diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb index edcd6bfe464..ce3af1d6036 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb @@ -45,7 +45,7 @@ dependencies = [ builddependencies = [('CMake', '3.9.1')] -separate_build_dir = 'True' +separate_build_dir = True # use Intel software rasterizer by default (no GPU hardware acceleration) modextravars = {'GALLIUM_DRIVER': 'swr'} diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb index 87c74547cda..2feec4137d6 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb @@ -46,7 +46,7 @@ dependencies = [ builddependencies = [('CMake', '3.12.1')] -separate_build_dir = 'True' +separate_build_dir = True # use Intel software rasterizer by default (no GPU hardware acceleration) modextravars = {'GALLIUM_DRIVER': 'swr'} diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.81-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Blender/Blender-2.81-foss-2019b-Python-3.7.4.eb index 8c15adfa9ff..2c0bfd7b9d2 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.81-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.81-foss-2019b-Python-3.7.4.eb @@ -44,7 +44,7 @@ dependencies = [ builddependencies = [('CMake', '3.15.3')] -separate_build_dir = 'True' +separate_build_dir = True # use Intel software rasterizer by default (no GPU hardware acceleration) modextravars = {'GALLIUM_DRIVER': 'swr'} diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.81-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Blender/Blender-2.81-intel-2019b-Python-3.7.4.eb index 4ba2495303d..1391cef5b1d 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.81-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.81-intel-2019b-Python-3.7.4.eb @@ -43,7 +43,7 @@ dependencies = [ builddependencies = [('CMake', '3.15.3')] -separate_build_dir = 'True' +separate_build_dir = True # use Intel software rasterizer by default (no GPU hardware acceleration) modextravars = {'GALLIUM_DRIVER': 'swr'} diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index 8e67dfe5af3..a11c2f33dc8 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -9,7 +9,7 @@ toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb index 241784cccb1..8332389e547 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb @@ -9,7 +9,7 @@ toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb index 33985cc4693..db3c91fa7f2 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb @@ -9,7 +9,7 @@ toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb index 7762dc1a82e..180d0c494de 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb @@ -9,7 +9,7 @@ toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb index 1981fe14e8a..370dff01c5b 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['d85a3bbd699b0fc77967fcd5e923ad35'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb index a7b0f1c2a92..183c174272d 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['af99624f1b6ea1b71a28b066fa3e1eea568eb2604fedbfc2cf8c7ea7ac8ab425'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb index e3e48669178..ce5b13969ca 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['201e29c9b177d21eae619eec090ee1ec703bb7398716377444a4eb685b8bf87b'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb index c76f13a9873..8e36b2be2c5 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['e4fd43e587886cf571225d201c9c6328841d3d61e5a36d1cd1b718da9bf94335'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb index 2c13e3a1078..7469deb5650 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['cf031f38ef685d780878e334c76deb3e295509f989e393ca17d1c496135e26d7'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb index 5cb36e45716..b27635916ca 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb @@ -11,7 +11,7 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['inspector_%(version)s.tar.gz'] checksums = ['676fd0b25a56fba63495c048abf485b08583cbb01eb0cf6e1174ee7b352af6d5'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True requires_runtime_license = False diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2017.1.016.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2017.1.016.eb index 78e01abb648..20311870615 100644 --- a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2017.1.016.eb +++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2017.1.016.eb @@ -14,7 +14,7 @@ toolchain = SYSTEM sources = ['l_clck_p_%(version)s.tgz'] checksums = ['72fcf16e220dfc1ee1e16a633381f7957e15b0b6f322f9954d1de2a1ec3851f1'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 2af34c5d651..e818c19d778 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index f4053771860..75764dfd257 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -17,7 +17,7 @@ checksums = ['f57a892fb494db3c80f20a88aa3e901f'] # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 3b89487f1bb..fdf168d6afa 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 52e62d6bf61..8b786c858af 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 3a7b8616335..47624b52a84 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb index 38fffb7b170..ab126f02f2a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index e817385384e..9bd0c31ebbe 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb index 3872457a289..2addad927a3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb index 5424a87952d..44d860d93ec 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb index 4e67a5e45a7..7ecbcf2303c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb index ffa0c10239e..13648b977df 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb index 667bdd29875..84c25bc8196 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb index cfd5205ec57..5801816c714 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb index cd03d110523..ba81f7038bc 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb index 0c9a922321c..ed12dffba99 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb index b43a9024b65..d124880f327 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb index ce1d645e6dc..2c8cd67bd9e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb index 366598a3f46..0d99f829232 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb index c246198e43a..c0219dc0cc4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb @@ -25,7 +25,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb index f5f839fac2b..2a19f4bcd21 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb index 332fec5d402..7b5137cb18b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb @@ -27,7 +27,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb index 36c26147261..d10bd52f992 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb index 0391593352f..19879f571af 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb index 59d4fded8a2..bc12f6784b7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb index 1d4e06faafa..5d4b035a822 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb @@ -26,7 +26,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb index 6187c1da499..fae4e2171f8 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb @@ -33,7 +33,7 @@ components = [ 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)' ] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb index 8a7119a57e0..49fb563f11f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb @@ -33,7 +33,7 @@ components = [ 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)' ] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 9cf18b01afb..1ab30938f60 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -33,7 +33,7 @@ components = [ 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)' ] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index 171d4a6a688..ae6f5440f0a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index 044e031df59..52cf1ffbb22 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -20,7 +20,7 @@ patches = ['ifort_2016_no_mpi_mic_dependency.patch'] # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index 564f9f74167..5c57791f360 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 44a586bdaa1..73e24caebf0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index ed65589bb46..36599d9640b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index 28d3717edab..8c71e9e936e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index 51cc00e224d..481b31038d5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index 442c147e68d..1dacd82ec38 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -34,7 +34,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index 3b59d64e8c9..e19a14b330d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index a127c1064b2..af000c34d37 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb index 643df0a4e9b..86ea3beaab9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb index 08a566b38c3..2943a8b1b53 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb index 12f467ae79b..236f035f753 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -34,7 +34,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb index 6e756fbda3a..a99cf05cf65 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb @@ -29,7 +29,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb index 83b6015581f..df5323ed36a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb @@ -33,7 +33,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb index 299a89872ae..82c7e381f88 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb @@ -33,7 +33,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb index 6557e939ed4..bf7e213d7c7 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb @@ -33,7 +33,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb index 19a1f4c083d..0613a092d39 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -31,7 +31,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb index a227755100d..8f7d47d7bd8 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -30,7 +30,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb index c2a640b5030..4a00cc2b3bc 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -31,7 +31,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb index 9e1602a6ca0..52960b79bfb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -32,7 +32,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 91600b5cc5e..de71a6af719 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -31,7 +31,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb index ca21deb2363..3f5302e51bd 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -31,7 +31,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 5eafa798cda..1a598dfa96b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -31,7 +31,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb index abf7b7aa39c..c704a2b2940 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -31,7 +31,7 @@ dependencies = [ # cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb index a596661ab0a..ba37957de13 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimpi', 'version': '2.11.5'} sources = ['l_mkl_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index fa10c82655f..196928d7d20 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'iimpi', 'version': '2016.00-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['47567e38801efe273b36b5250c759af7'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index 440d1741c09..ac97d66cbef 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2016.01-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['b57ff502b5f97f2f783e4bbda7ce42b3'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb index c807d796b6e..2125a67a9b6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'iimpi', 'version': '8.1.5-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index ecf070b29cd..361f7384d38 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['536dbd82896d6facc16de8f961d17d65'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index 49091028d6e..9cfca7157f7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-5.3.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['536dbd82896d6facc16de8f961d17d65'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb index d468fef58aa..a6bfaa4a443 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'pompi', 'version': '2016.03'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['536dbd82896d6facc16de8f961d17d65'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb index acc63120383..e0271a4e744 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 51e8a3461a9..1e54f7ae84e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.3.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb index d98d8f0fd38..4afec3b59ec 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.4.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb index 71ce462a11d..e49356ff351 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2016b'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb index 78c54328f41..358f3f14487 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpic', 'version': '2016.10'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb index 425ca0043d7..44678fcca48 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'iompi', 'version': '2016.07'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb index bbbfc083fb7..6e514bb1142 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iompi', 'version': '2016.09-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb index 4739cbc2905..cbceeb9fba8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iompi', 'version': '2016.09-GCC-5.4.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb index ebe3bf0517a..6374bfe60a3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'pompi', 'version': '2016.04'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb index 76e951f9afb..3cee04fdb17 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'pompi', 'version': '2016.09'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb index b9d95449e02..338bcaac09c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2017.00-GCC-5.4.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['3cdcb739ab5ab1e047eb130b9ffdd8d0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb index a003630b703..1c0f6f31755 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimpi', 'version': '2017a'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['7911c0f777c4cb04225bf4518088939e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb index 890e13c11b6..6ca575e0573 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2017.01-GCC-5.4.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['7911c0f777c4cb04225bf4518088939e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb index 8b4fb3f6312..7e96eb0727a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2017a'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['7911c0f777c4cb04225bf4518088939e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb index d518da619e8..29d4195cb4c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iompi', 'version': '2017.01'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['7911c0f777c4cb04225bf4518088939e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb index 2b75677f007..763b670f295 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iompi', 'version': '2017a'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['7911c0f777c4cb04225bf4518088939e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb index 35e5b716e18..68b6b7dee12 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2017.02-GCC-6.3.0-2.27'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['ef39a12dcbffe5f4a0ef141b8759208c'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb index 941c7c55065..8bbe27b5454 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'gompi', 'version': '2017b'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb index f75eb9307d3..6deca5796c7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iimpi', 'version': '2017b'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb index c41a34bd9a0..95c93a2cfff 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpic', 'version': '2017b'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb index 00757dc56fe..770bcf00248 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iompi', 'version': '2017b'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb index 0d77a694cf8..1c5e940f586 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iimpi', 'version': '2017.09'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['dcac591ed1e95bd72357fd778edba215a7eab9c6993236373231cc16c200c92a'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb index 118a71a3310..b9eaeff5154 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2018.00'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['c368baa40ca88057292512534d7fad59fa24aef06da038ea0248e7cd1e280cec'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb index 9e5eacd4164..b9936d332d3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2018.01'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb index 7096c233dd3..0c08b6a4a84 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb index 16c929d513a..362e1f6fd18 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iompi', 'version': '2018a'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb index 3a413da4629..783453db8eb 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iimpi', 'version': '2018.02'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['e28d12173bef9e615b0ded2f95f59a42b3e9ad0afa713a79f8801da2bfb31936'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb index cd34e04f641..c1541e5ba09 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'iompi', 'version': '2018.02'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['e28d12173bef9e615b0ded2f95f59a42b3e9ad0afa713a79f8801da2bfb31936'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb index ff57ee108c3..d22ff0708a8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb index 3bc1636a4ef..3101dc97775 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb index 723ae98d340..b766fd8f90f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb index 30483ffd745..9d1f876220a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb index 5c5dbea8426..fb5c8fa1a53 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb index ef88a33e497..dad9f08a557 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb index 524a75c4f95..aa6a03a6929 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb @@ -13,7 +13,7 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb index cae85e511ff..632c9947b20 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb index 181d8a13598..37b0f6cb860 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb @@ -13,7 +13,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb index 90685df7e9f..b8fb1ebef4c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb @@ -13,7 +13,7 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb index 9789dea30a6..6beef47051f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb index b6886b31353..830e9c0b35e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb index 7a2964df5e4..dea288fc36e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb index 5991582e53b..b902873dd52 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb @@ -15,7 +15,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb index 6124194c261..62cf27a5251 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb @@ -15,7 +15,7 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb index bd9f5456c4f..7ebb4dd310a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb @@ -15,7 +15,7 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mkl'] diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 39fce39091a..ae38382d9ef 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -14,14 +14,14 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['fc123875773816b7084a91e419d54d20'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb index 4dafa137caa..6f1bc13dbd6 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = ['l_mpi_%(version)s.tgz'] checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index a8fce42a538..bb8968983a5 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -14,14 +14,14 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 9f5485d56cf..1c10589bdad 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -14,14 +14,14 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb index fc921279503..eb371c39343 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -14,12 +14,12 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['b6c2e62c3fb9b1558ede72ccf72cf1d6'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb index 6f72d5d7da6..ea7fe3c6f55 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb @@ -12,12 +12,12 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb index 3db0955ff75..6e01470f251 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb @@ -14,14 +14,14 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index bd671dc9065..579f495a99b 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -12,12 +12,12 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb index a8d038a3751..a05fc7033ba 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb @@ -14,12 +14,12 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb index 10b947e07d0..d0835058637 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb @@ -12,12 +12,12 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['5a1048d284dce8bc75b45789471c83c94b3c59f8f159cab43d783fc44302510b'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb index 8d39255a0b9..1b829610732 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb @@ -12,12 +12,12 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['debaf2cf80df06db9633dfab6aa82213b84a665a55ee2b0178403906b5090209'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb index b316f07bf9a..1e9b050bbb9 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb @@ -12,12 +12,12 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 4b03e8c65ae..c2bd8a0f820 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -12,12 +12,12 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb index d47a1f07013..33bdf0b4638 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -12,12 +12,12 @@ sources = ['l_mpi_%(version)s.tgz'] checksums = ['0927f1bff90d10974433ba2892e3fd38e6fee5232ab056a9f9decf565e814460'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb index 592479f3090..bc24dfa6254 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb @@ -12,12 +12,12 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index a1a40d79585..bf654b96c79 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -12,12 +12,12 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb index f79f592dfb3..2781663645f 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -12,12 +12,12 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 9967c1471ae..e42262f10f4 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -10,12 +10,12 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb index 2559fcf0074..137bf491a27 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb @@ -10,12 +10,12 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb index b35eb020094..5f00a89b089 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb @@ -12,11 +12,11 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb index 5158df89d00..02e2ace8251 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb @@ -12,11 +12,11 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 8d01830ae25..1ca9ff449ea 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -12,11 +12,11 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 86a6d488d65..7e6b823b00d 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -12,11 +12,11 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 75e3a61ab85..d86765c209d 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -12,11 +12,11 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb index 79013de91f0..8e7f3adc53f 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -12,11 +12,11 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_mpi_%(version)s.tgz'] checksums = ['5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb index d5eea149d15..c4ca15ab10a 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166.eb @@ -12,11 +12,11 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['l_mpi_%(version)s.tgz'] checksums = ['119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index d845600ff46..7ee2e37b200 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -11,12 +11,12 @@ toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 5cd4f104035..098451a6972 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -12,7 +12,7 @@ toolchain = SYSTEM sources = ['l_mpi_pu_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' @@ -20,6 +20,6 @@ license_file = HOME + '/licenses/intel/license.lic' m32 = True # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index aac6f783f65..8fe47ac905e 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -11,12 +11,12 @@ toolchain = SYSTEM sources = ['l_mpi_pu_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 0d8622e1903..271af7c2b35 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -13,12 +13,12 @@ sources = ['l_mpi_p_%(version)s.tgz'] patches = ['impi_4.x_productsdb.patch'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index f9807bc5ab9..d48b3727cc1 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -11,12 +11,12 @@ toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 2d507e73d39..a5cfcbf78a5 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -11,12 +11,12 @@ toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index cf07a9c863a..1de1d380b4e 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -11,12 +11,12 @@ toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index d98ce241ba1..129b250a804 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -11,12 +11,12 @@ toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index bb0c047e177..16633ddb504 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -11,12 +11,12 @@ toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 8f1f78d2d20..5ca7aaeb97d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -11,12 +11,12 @@ toolchain = {'name': 'GCC', 'version': '4.8.3'} sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index a486e579876..155bdc0b4aa 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -11,12 +11,12 @@ toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb index a29fee7a767..7bd4e394550 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb @@ -11,12 +11,12 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = ['l_mpi_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index 5a1845ddb9b..62176375701 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -15,7 +15,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] checksums = ['aa4aaec41526aa5b244e531811877b01'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 137847dcf7c..7c60c805656 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -14,12 +14,12 @@ sources = ['l_mpi_p_%(version)s.tgz'] checksums = ['ec4db8f718c34f09fccf9d1c89454f0a'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 08aa97c8f61..d3215852c52 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -14,12 +14,12 @@ sources = ['l_mpi_p_%(version)s.tgz'] checksums = ['1c14656859d48bf8b90c71dace2a977b'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index a1e94bdfa1d..0ed2fcc2051 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -14,12 +14,12 @@ sources = ['l_mpi_p_%(version)s.tgz'] checksums = ['1c14656859d48bf8b90c71dace2a977b'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 3d597f449e2..c12c8385125 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -14,12 +14,12 @@ sources = ['l_mpi_p_%(version)s.tgz'] checksums = ['1c14656859d48bf8b90c71dace2a977b'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb index 121e9258f27..56fb0dfd5e1 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -14,12 +14,12 @@ sources = ['l_mpi_p_%(version)s.tgz'] checksums = ['1c14656859d48bf8b90c71dace2a977b'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index e74cd02b1bd..d51c76b986d 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -14,14 +14,14 @@ sources = ['l_mpi_p_%(version)s.tgz'] checksums = ['1c14656859d48bf8b90c71dace2a977b'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb index f3e312361a5..f84ce5000bf 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -14,14 +14,14 @@ sources = ['l_mpi_p_%(version)s.tgz'] checksums = ['1c14656859d48bf8b90c71dace2a977b'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True components = ['intel-mpi', 'intel-psxe', 'intel-imb'] license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers -# set_mpi_wrappers_all = 'True' +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb index 779092d0af4..b4d086765db 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb index 7128d121088..f52a6d981cc 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb @@ -15,7 +15,7 @@ patches = ['ipp_productsdb.patch'] moduleclass = 'perf' -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb index 21f023aced6..7ad0466d542 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb index 3b22735f1a5..6bd809d8bbc 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True # license file license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb index 07b50cccf1c..c3454d4eff7 100644 --- a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb +++ b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True preferredmpi = 'impi5' diff --git a/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb b/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb index da7e799b2df..d9785a995d5 100644 --- a/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb +++ b/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] checksums = ['c907d5883cfa965b8f5d625e927c24a9da2ff7bc25bb211dd5047ddffc69be01'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True preferredmpi = 'impi5' diff --git a/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb b/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb index a912ed96a0f..b32a7f75fdf 100644 --- a/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb +++ b/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] checksums = ['837b712ae2ef458868197a04068b710d76ee3037aceb8ab09b33392b92a97fe7'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True preferredmpi = 'impi5' diff --git a/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb b/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb index f69e8157eb7..7bf3fa17d9f 100644 --- a/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb +++ b/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] checksums = ['c66890beaf6e81da0f2ecb9695059a6686c95f6f01f467e32a076eb84ca8e40e'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True preferredmpi = 'impi5' diff --git a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb index fb681a8fe20..eff73ddc538 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['l_itac_p_%s.tgz' % version] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True preferredmpi = 'impi4' diff --git a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb index 9e6efed69a8..0e3dcfee35d 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True preferredmpi = 'impi4' diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb index c89e47a906a..efacaf21806 100644 --- a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -10,7 +10,7 @@ toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True preferredmpi = 'impi5' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb index 3fe9999b5e1..47311359541 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb @@ -15,7 +15,7 @@ toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb index 797a1f2402c..48efc64c3e0 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb @@ -17,7 +17,7 @@ sources = ['l_%(name)s_%(version)s.tgz'] patches = ['tbb-4.0_productsdb.patch'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb index 9d44b942cbb..cb968423fd9 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb @@ -17,7 +17,7 @@ sources = ['l_%(name)s_%(version)s.tgz'] patches = ['tbb-4.0_productsdb.patch'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb index 1edec2fba65..2f3c0189a26 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -15,7 +15,7 @@ toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb index 50156d7348c..765ba3a381d 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb @@ -15,7 +15,7 @@ toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] -dontcreateinstalldir = 'True' +dontcreateinstalldir = True license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index 877a28a1e75..30eee50474c 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -16,7 +16,7 @@ checksums = ['f0820a0f42dfc81ce3811af647bed777'] dependencies = [('netCDF-Fortran', '4.4.2')] -with_configure = 'True' +with_configure = True configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" --with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' From 5dceedab8c8fd9a515c0f18ed0f590be4d44cce0 Mon Sep 17 00:00:00 2001 From: Shahzeb Siddiqui Date: Sun, 12 Jan 2020 17:16:39 -0600 Subject: [PATCH 448/468] adding sha256 checksum and update syntax for source tarball --- easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb index 440f1dcda77..408e8e7c806 100644 --- a/easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2019.3.1.eb @@ -9,8 +9,9 @@ description = """PyCharm Community Edition: Python IDE for Professional Develope toolchain = SYSTEM source_urls = ['https://download-cf.jetbrains.com/python'] -sources = ['pycharm-community-%s.tar.gz' % version] -checksums = [] +sources = ['pycharm-community-%(version)s.tar.gz'] +checksums = ['bb243322951a2d195d9ab12a6990cdbf3d7cc284f17cd5f6ce3376f5ce16f0b2'] + sanity_check_paths = { 'files': ["bin/pycharm.sh"], 'dirs': [], From 54711ebf2489d5b8c8b0b4952dd5bc63272343af Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Mon, 13 Jan 2020 12:10:25 +1050 Subject: [PATCH 449/468] adding easyconfigs: Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb --- ...toconf-archive-2019.01.06-GCCcore-8.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..718abc599c5 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb @@ -0,0 +1,45 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2019.01.06' + +homepage = 'https://www.gnu.org/software/autoconf-archive' + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['17195c833098da79de5778ee90948f4c5d90ed1a0cf8391b4ab348e2ec511e3f'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' From c6fa82d243a7f7607059edd02d5a69f8a515d574 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Mon, 13 Jan 2020 12:41:45 +1050 Subject: [PATCH 450/468] toochain-update --- ...onf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..c06581323d4 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,45 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2019.01.06' + +homepage = 'https://www.gnu.org/software/autoconf-archive' + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['17195c833098da79de5778ee90948f4c5d90ed1a0cf8391b4ab348e2ec511e3f'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' From 50e88f80d8c4a787e5f49ff037d72404360ae601 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Mon, 13 Jan 2020 13:28:50 +1050 Subject: [PATCH 451/468] toochain_update-GCCcore2GCCbinutil --- ...toconf-archive-2019.01.06-GCCcore-8.2.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb deleted file mode 100644 index 718abc599c5..00000000000 --- a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCCcore-8.2.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: GNU Free Documentation License -# -# Notes:: -## - -easyblock = 'ConfigureMake' - -name = 'Autoconf-archive' -version = '2019.01.06' - -homepage = 'https://www.gnu.org/software/autoconf-archive' - -description = """ -The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf -that have been contributed as free software by friendly supporters of the cause from -all over the Internet. Every single one of those macros can be re-used without -imposing any restrictions whatsoever on the licensing of the generated configure script. -In particular, it is possible to use all those macros in configure scripts that -are meant for non-free software. This policy is unusual for a Free Software Foundation -project. The FSF firmly believes that software ought to be free, and software licenses -like the GPL are specifically designed to ensure that derivative work based on free -software must be free as well. In case of Autoconf, however, an exception has been made, -because Autoconf is at such a pivotal position in the software development tool chain -that the benefits from having this tool available as widely as possible outweigh the -disadvantage that some authors may choose to use it, too, for proprietary software. -""" - -toolchain = {'name': 'GCCcore', 'version': '8.2.0'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['17195c833098da79de5778ee90948f4c5d90ed1a0cf8391b4ab348e2ec511e3f'] - -sanity_check_paths = { - 'files': [], - 'dirs': ['share/%s' % x for x in - ['aclocal', 'doc', 'info']], -} - -moduleclass = 'devel' From 75b2c7ce9e18b6c7f4acc495ca26338324a4c13c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Mon, 13 Jan 2020 13:57:16 +1050 Subject: [PATCH 452/468] syntax fix --- .../Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb index c06581323d4..3c025ef307b 100644 --- a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2019.01.06-GCC-8.2.0-2.31.1.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'Autoconf-archive' version = '2019.01.06' -homepage = 'https://www.gnu.org/software/autoconf-archive' +homepage = "https://www.gnu.org/software/autoconf-archive" description = """ The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf @@ -37,9 +37,9 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['17195c833098da79de5778ee90948f4c5d90ed1a0cf8391b4ab348e2ec511e3f'] sanity_check_paths = { - 'files': [], - 'dirs': ['share/%s' % x for x in - ['aclocal', 'doc', 'info']], + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], } moduleclass = 'devel' From b720729629772207bec3fabbdfe5fe1d176c342e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Jan 2020 09:13:53 +0100 Subject: [PATCH 453/468] Use source distro for 10.5 and new URL for above --- easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb | 12 ++++++------ easybuild/easyconfigs/a/ant/ant-1.10.6-Java-1.8.eb | 2 +- easybuild/easyconfigs/a/ant/ant-1.10.7-Java-11.eb | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb b/easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb index 226d87849e4..8ab2e85ab4c 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb @@ -1,22 +1,22 @@ -easyblock = 'PackedBinary' - name = 'ant' version = '1.10.5' versionsuffix = '-Java-%(javaver)s' -homepage = 'http://ant.apache.org/' +homepage = 'https://ant.apache.org/' description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" toolchain = SYSTEM -source_urls = ['http://apache.cu.be//ant/binaries'] -sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] -checksums = ['cd52c6f77a0b1de7174addc94e5a512d86978ac9173a30cd11f4ab26f6d8deba'] +source_urls = ['https://archive.apache.org/dist/%(name)s/source/'] +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +checksums = ['5937cf11d74d75d6e8927402950b012e037e362f9f728262ce432ad289b9f6ca'] dependencies = [('Java', '1.8')] +builddependencies = [('JUnit', '4.12', versionsuffix)] + sanity_check_paths = { 'files': ['bin/ant', 'lib/ant.jar'], 'dirs': [], diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.6-Java-1.8.eb b/easybuild/easyconfigs/a/ant/ant-1.10.6-Java-1.8.eb index 4e54296f7e7..ef051169e57 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.6-Java-1.8.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.6-Java-1.8.eb @@ -11,7 +11,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio toolchain = SYSTEM -source_urls = ['https://apache.cu.be/ant/binaries'] +source_urls = ['https://apache.mirrors.cu.be/ant/binaries'] sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] checksums = ['ed87985be618d4be6c46ba2092a6c1fad60ef6ae0c8745c007ca9d5175c253fd'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.7-Java-11.eb b/easybuild/easyconfigs/a/ant/ant-1.10.7-Java-11.eb index 6f4b0a88ad3..c9a12a97947 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.7-Java-11.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.7-Java-11.eb @@ -11,7 +11,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio toolchain = SYSTEM -source_urls = ['https://apache.cu.be/ant/binaries'] +source_urls = ['https://apache.mirrors.cu.be/ant/binaries'] sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] checksums = ['2e0f2e0348e146b5a366de55bb97a1508c57544623f35f2432b7f6b844581341'] From 7ba00ccf8036e2bf5a1def63c3a571384b888deb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Jan 2020 13:47:52 +0100 Subject: [PATCH 454/468] Add patch to fix build caused by javadoc doclint failure --- .../a/ant/ant-1.10.2-fix-doclint-error.patch | 15 +++++++++++++++ .../easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb | 6 +++++- 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.2-fix-doclint-error.patch diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.2-fix-doclint-error.patch b/easybuild/easyconfigs/a/ant/ant-1.10.2-fix-doclint-error.patch new file mode 100644 index 00000000000..1794b9aa224 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.2-fix-doclint-error.patch @@ -0,0 +1,15 @@ +Author: Alexander Grund +Ant 1.10.2 removed the -Xdoclint:none option which leads to build failures +due to optional packages not beeing found during Javadoc generation +See https://bz.apache.org/bugzilla/show_bug.cgi?id=63438 +diff -aur a/build.xml b/build.xml +--- a/build.xml 2018-02-03 17:52:24.000000000 +0100 ++++ b/build.xml 2020-01-10 13:34:56.885004000 +0100 +@@ -1456,6 +1456,7 @@ + description="--> creates the API documentation" unless="javadoc.notrequired"> + + Date: Fri, 10 Jan 2020 10:01:27 +0100 Subject: [PATCH 455/468] adding easyconfigs: TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb, pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb and patches: TensorFlow-2.1.0_fix-build-tf-lite-avx512.patch, TensorFlow-2.1.0_fix-cuda-build.patch, scipy-1.4.1-fix-pthread.patch --- ...bind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb | 29 ++++ ...rFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb | 155 ++++++++++++++++++ ...rFlow-2.1.0_fix-build-tf-lite-avx512.patch | 38 +++++ .../TensorFlow-2.1.0_fix-cuda-build.patch | 47 ++++++ .../TensorFlow/scipy-1.4.1-fix-pthread.patch | 39 +++++ 5 files changed, 308 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-build-tf-lite-avx512.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-cuda-build.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/scipy-1.4.1-fix-pthread.patch diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..97e602e26aa --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'pybind11' +version = '2.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3'), + ('Eigen', '3.3.7', '', True), +] +dependencies = [('Python', '3.7.4')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/pybind11', 'share/cmake/pybind11'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..5e1cec12e75 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,155 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('Bazel', '0.29.1'), + ('protobuf', '3.10.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.23.0', '-nodocs'), + # For SciPy + ('pybind11', '2.4.3', versionsuffix), +] +dependencies = [ + ('Python', '3.7.4'), + ('h5py', '2.10.0', versionsuffix), + ('cuDNN', '7.6.4.38'), + ('NCCL', '2.4.8'), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +exts_list = [ + # TF 2.1 requires SciPy 1.4.1 due to potential crashes with other versions + # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d + ('scipy', '1.4.1', { + 'patches': ['scipy-1.4.1-fix-pthread.patch'], + 'checksums': [ + 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', + '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch + ], + }), + ('Markdown', '3.1.1', { + 'checksums': ['2e50876bcdd74517e7b71f3e7a76102050edec255b3983403f1a63e7c8a41e7a'], + }), + ('pyasn1-modules', '0.2.7', { + 'modulename': 'pyasn1_modules', + 'checksums': ['0c35a52e00b672f832e5846826f1fb7507907f7d52fba6faa9e3c4cbe874fe4b'], + }), + ('rsa', '4.0', { + 'checksums': ['1a836406405730121ae9823e19c6e806c62bbad73f890574fff50efa4122c487'], + }), + ('cachetools', '3.1.1', { + 'checksums': ['8ea2d3ce97850f31e4a08b0e2b5e6c34997d7216a9d2c98e0f3978630d4da69a'], + }), + ('google-auth', '1.7.1', { + 'modulename': 'google.auth', + 'checksums': ['baf1b3f8b29a5f96f66753ad848473699322b63f4d68964e510554b12d002443'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'modulename': 'requests_oauthlib', + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.1', { + 'modulename': 'google_auth_oauthlib', + 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], + }), + ('Werkzeug', '0.16.0', { + 'checksums': ['7280924747b5733b246fe23972186c6b348f9ae29724135a6dfc1e53cea433e7'], + }), + ('protobuf', '3.10.0', { + 'modulename': 'google.protobuf', + 'checksums': ['db83b5c12c0cd30150bb568e6feb2435c49ce4e68fe2d7b903113f0e221e58fe'], + }), + ('absl-py', '0.8.1', { + 'modulename': 'absl', + 'checksums': ['d9129186431e150d7fe455f1cb1ecbb92bb5dba9da9bc3ef7b012d98c4db2526'], + }), + ('grpcio', '1.25.0', { + 'modulename': 'grpc', + 'checksums': ['c948c034d8997526011960db54f512756fb0b4be1b81140a15b4ef094c6594a4'], + }), + ('tensorboard', '2.1.0', { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['e6e64ec1e1500cc963b300895258f9605032c3a18bb40f95f2b3b12be16ff2f2'], + }), + ('google-pasta', '0.1.8', { + 'modulename': 'pasta', + 'checksums': ['713813a9f7d6589e5defdaf21e80e4392eb124662f8bd829acd51a4f8735c0cb'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.1.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['e5c5f648a636f18d1be4cf7ed46132b108a2f0f3fd9f1c850eba924263dc6972'], + }), + ('astor', '0.8.0', { + 'checksums': ['37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862'], + }), + ('Keras-Applications', '1.0.8', { + 'modulename': 'keras_applications', + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('gast', '0.2.2', { + 'checksums': ['fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0'], + }), + ('opt-einsum', '3.1.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['edfada4b1d0b3b782ace8bc14e80618ff629abf53143e1e6bbf9bd00b11ece77'], + }), + ('wrapt', '1.11.2', { + 'checksums': ['565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1'], + }), + ('Keras-Preprocessing', '1.1.0', { + 'modulename': 'keras_preprocessing', + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['5a8debe01d840de93d49e05ccf1c9b81ae30e210d34dacbcc47aeb3049b528e5'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-1.14.0_swig-env.patch', + 'TensorFlow-1.15.0_lrt-flag.patch', + 'TensorFlow-1.14.0_remove_usrbin_from_linker_bin_path_flag.patch', + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.1.0_fix-build-tf-lite-avx512.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'checksums': [ + # v2.1.0.tar.gz + '638e541a4981f52c69da4a311815f1e7989bf1d67a41d204511966e1daed14f7', + # TensorFlow-1.14.0_swig-env.patch + 'b83cce6b91c7d19b8b320158ffc50fb4b2de454f5ac191c58d704234a1bf9005', + # TensorFlow-1.15.0_lrt-flag.patch + 'b0fd4c7902be45bba18bd04192800852b140a9cf312a44ac1efb7ee653d3d886', + # TensorFlow-1.14.0_remove_usrbin_from_linker_bin_path_flag.patch + 'bfa2701495dddfbbf4fbec808ea3c982b50043a16d28a8d1283f44df0b8aae7d', + # TensorFlow-2.1.0_fix-cuda-build.patch + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', + # TensorFlow-2.1.0_fix-build-tf-lite-avx512.patch + '022fde8f01deb08fc6d31a03ba693da7f684c6c150502ab2ace7ca02c4c0d4cf', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-build-tf-lite-avx512.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-build-tf-lite-avx512.patch new file mode 100644 index 00000000000..300cf1d63ba --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-build-tf-lite-avx512.patch @@ -0,0 +1,38 @@ +fix build on Skylake/Cannonlake by commenting out problematic define statements in tensorflow/lite +(this has no impact on performance since tensorflow/lite will not be used when built from source) + +see also https://github.com/tensorflow/tensorflow/issues/31187 and https://github.com/tensorflow/tensorflow/issues/32026 + +patch taken from https://github.com/Huawei-MRC-OSI/tensorflow/commit/c45d98ba2d92fcbf9ceb6baea13fbfc68ef1a1f7 + +From c45d98ba2d92fcbf9ceb6baea13fbfc68ef1a1f7 Mon Sep 17 00:00:00 2001 +From: Sergey Mironov +Date: Wed, 11 Sep 2019 16:13:06 +0300 +Subject: [PATCH] Workaround Skylake bug as suggested by TF #31187 + +Ref https://github.com/tensorflow/tensorflow/issues/31187#issuecomment-523673269 +--- + tensorflow/lite/experimental/ruy/platform.h | 12 +++++++----- + 1 file changed, 7 insertions(+), 5 deletions(-) + +diff --git a/tensorflow/lite/experimental/ruy/platform.h b/tensorflow/lite/experimental/ruy/platform.h +index 7a83173acb0b..90a08d9294dc 100644 +--- a/tensorflow/lite/experimental/ruy/platform.h ++++ b/tensorflow/lite/experimental/ruy/platform.h +@@ -103,13 +103,13 @@ + // TODO(b/138433137) Select x86 enhancements at runtime rather than via compile + // options. + // +-#if RUY_PLATFORM(X86_ENHANCEMENTS) && RUY_PLATFORM(X86) && \ ++/*#if RUY_PLATFORM(X86_ENHANCEMENTS) && RUY_PLATFORM(X86) && \ + defined(__AVX512F__) && defined(__AVX512DQ__) && defined(__AVX512CD__) && \ + defined(__AVX512BW__) && defined(__AVX512VL__) + #define RUY_DONOTUSEDIRECTLY_AVX512 1 +-#else ++#else*/ + #define RUY_DONOTUSEDIRECTLY_AVX512 0 +-#endif ++//#endif + + #if RUY_PLATFORM(X86_ENHANCEMENTS) && RUY_PLATFORM(X86) && defined(__AVX2__) + #define RUY_DONOTUSEDIRECTLY_AVX2 1 diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-cuda-build.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-cuda-build.patch new file mode 100644 index 00000000000..5873bdc5ed0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-cuda-build.patch @@ -0,0 +1,47 @@ +fix for "undeclared inclusion(s) in rule" errors when building TensorFlow 1.14.0 with CUDA support, +if the installation directory for GCC is hosted in a path that is a symlink to another path; +the symlinked path is resolved in several places (both by 'gcc' itself and by the TF build process), +which makes hard comparisons between paths fail +author: Alexander Grund based on original patch by Kenneth Hoste (HPC-UGent) +diff --git a/third_party/gpus/cuda_configure.bzl b/third_party/gpus/cuda_configure.bzl +index ba4bd8ad75..dab492ecda 100644 +--- a/third_party/gpus/cuda_configure.bzl ++++ b/third_party/gpus/cuda_configure.bzl +@@ -303,11 +303,36 @@ def _get_cxx_inc_directories_impl(repository_ctx, cc, lang_is_cpp): + else: + inc_dirs = result.stderr[index1 + 1:index2].strip() + +- return [ ++ compiler_includes = [ + _normalize_include_path(repository_ctx, _cxx_inc_convert(p)) + for p in inc_dirs.split("\n") + ] + ++ # fix include path by also including paths where resolved symlink is replaced by original path ++ # Try to find real path to CC installation to "see through" compiler wrappers ++ # GCC has the path to g++ ++ index1 = result.stderr.find("COLLECT_GCC=") ++ if index1 != -1: ++ index1 = result.stderr.find("=", index1) ++ index2 = result.stderr.find("\n", index1) ++ cc_topdir = repository_ctx.path(result.stderr[index1 + 1 : index2]).dirname.dirname ++ else: ++ # Clang has the directory ++ index1 = result.stderr.find("InstalledDir: ") ++ if index1 != -1: ++ index1 = result.stderr.find(" ", index1) ++ index2 = result.stderr.find("\n", index1) ++ cc_topdir = repository_ctx.path(result.stderr[index1 + 1 : index2]).dirname ++ else: ++ # Fallback to the CC path ++ cc_topdir = repository_ctx.path(cc).dirname.dirname ++ cc_topdir_resolved = str(cc_topdir.realpath).strip() ++ cc_topdir = str(cc_topdir).strip() ++ if cc_topdir_resolved != cc_topdir: ++ original_compiler_includes = [p.replace(cc_topdir_resolved, cc_topdir) for p in compiler_includes] ++ compiler_includes = compiler_includes + original_compiler_includes ++ return compiler_includes ++ + def get_cxx_inc_directories(repository_ctx, cc, tf_sysroot): + """Compute the list of default C and C++ include directories.""" + diff --git a/easybuild/easyconfigs/t/TensorFlow/scipy-1.4.1-fix-pthread.patch b/easybuild/easyconfigs/t/TensorFlow/scipy-1.4.1-fix-pthread.patch new file mode 100644 index 00000000000..d399b2ba412 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/scipy-1.4.1-fix-pthread.patch @@ -0,0 +1,39 @@ +From https://github.com/scipy/scipy/pull/11324 +Author: Peter Bell +diff --git a/scipy/fft/_pocketfft/setup.py b/scipy/fft/_pocketfft/setup.py +index a4411bdedb1..493387d9719 100644 +--- a/scipy/fft/_pocketfft/setup.py ++++ b/scipy/fft/_pocketfft/setup.py +@@ -5,20 +5,28 @@ def pre_build_hook(build_ext, ext): + cc = build_ext._cxx_compiler + args = ext.extra_compile_args + +- std_flag = get_cxx_std_flag(build_ext._cxx_compiler) ++ std_flag = get_cxx_std_flag(cc) + if std_flag is not None: + args.append(std_flag) + + if cc.compiler_type == 'msvc': + args.append('/EHsc') + else: +- try_add_flag(args, cc, '-fvisibility=hidden') +- ++ # Use pthreads if available + has_pthreads = try_compile(cc, code='#include \n' + 'int main(int argc, char **argv) {}') + if has_pthreads: + ext.define_macros.append(('POCKETFFT_PTHREADS', None)) +- ++ if has_flag(cc, '-pthread'): ++ args.append('-pthread') ++ ext.extra_link_args.append('-pthread') ++ else: ++ raise RuntimeError("Build failed: System has pthreads header " ++ "but could not compile with -pthread option") ++ ++ # Don't export library symbols ++ try_add_flag(args, cc, '-fvisibility=hidden') ++ # Set min macOS version + min_macos_flag = '-mmacosx-version-min=10.9' + import sys + if sys.platform == 'darwin' and has_flag(cc, min_macos_flag): From 5444ed1d1b1f4eb26feadea4bfd3039b411557b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jan 2020 18:24:53 +0100 Subject: [PATCH 456/468] add missing checksums in icc/ifort/impi/imkl/ipp/itac/tbb/Advisor/Inspector easyconfigs (+ a few more) --- easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb | 1 + easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb | 3 +-- easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb | 1 - easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb | 1 - .../b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb | 6 +++++- .../easyconfigs/i/Inspector/Inspector-2013_update6.eb | 1 + .../easyconfigs/i/Inspector/Inspector-2013_update7.eb | 1 + .../easyconfigs/i/Inspector/Inspector-2016_update3.eb | 1 + .../easyconfigs/i/Inspector/Inspector-2017_update1.eb | 1 + .../easyconfigs/i/Inspector/Inspector-2017_update2.eb | 2 +- .../easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 3 +-- .../easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 3 +-- .../easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 3 +-- .../easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb | 3 +-- .../easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb | 3 +-- .../easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb | 3 +-- .../easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb | 3 +-- .../easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb | 3 +-- .../easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb | 1 - .../easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb | 1 - .../easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb | 1 - .../easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb | 1 - .../easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb | 1 - easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb | 3 +-- .../i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 8 +++++--- easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 8 +++++--- .../i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 8 +++++--- .../i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 8 +++++--- .../i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 8 +++++--- .../i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb | 8 +++++--- .../i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 8 +++++--- .../i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb | 9 +++------ .../i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb | 8 +++++--- .../i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb | 8 +++++--- .../i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb | 8 +++++--- .../i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb | 8 +++++--- .../i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb | 9 +++------ .../i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb | 8 +++++--- .../i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb | 6 ++---- .../i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb | 6 ++---- .../i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb | 8 +++----- .../i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb | 2 +- .../i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb | 2 +- .../i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb | 2 +- .../i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb | 2 +- .../i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 2 +- .../i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb | 1 + .../imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb | 2 +- .../imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb | 1 + .../imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb | 2 +- .../imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb | 2 +- .../imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb | 2 +- .../imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 2 +- .../imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb | 2 +- .../imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb | 2 +- .../imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb | 2 +- .../imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb | 2 +- .../imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb | 2 +- .../easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb | 2 +- .../easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb | 2 +- .../imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb | 2 +- ...impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 3 +-- .../easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- ...impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 3 +-- ...impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 3 +-- ...impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 3 +-- .../easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb | 1 - .../easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb | 1 - ...impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 1 - ...-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb | 1 - ...impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb | 1 - ...impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb | 1 - .../easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb | 1 - ...impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb | 1 - easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 5 ++++- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 1 + easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 1 + easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb | 1 + .../impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- .../impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- .../impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 3 +-- .../impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 3 +-- .../impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 3 +-- .../impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 3 +-- .../impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 3 +-- .../i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb | 3 +-- easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb | 1 + easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb | 5 ++++- easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb | 1 + easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb | 1 + easybuild/easyconfigs/i/itac/itac-2017.1.024.eb | 1 + easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb | 1 + easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb | 1 + easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb | 1 + easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb | 1 + easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb | 5 ++++- easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb | 5 ++++- easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb | 1 + easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb | 1 + .../y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb | 4 ++-- 123 files changed, 181 insertions(+), 166 deletions(-) diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb index 86ea9f600b9..21672b12c98 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb @@ -11,6 +11,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM sources = ['advisor_xe_%(version)s.tar.gz'] +checksums = ['57ea721fb7d1c322a8b360ddc8de6834629dde9e7bc9dc2eb5c5c1c31aed7e90'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb index 17fa732bc46..d177dec792f 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -11,8 +11,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM sources = ['advisor_%(version)s.tar.gz'] - -checksums = ['af87b381394be3100507827a3461b3bc'] +checksums = ['5bb545d2d53dbc42a427e8aa34ab4060fa4a04812a6389849443ac19f72522de'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb index e4cbabd47a1..3e2ff237b89 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb @@ -11,7 +11,6 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM sources = ['advisor_%(version)s.tar.gz'] - checksums = ['611206c771a318fe23bebcf4058748229730821565a8e8c16afe86f240443f35'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb index 9366d079086..a2ff10db0ae 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb @@ -11,7 +11,6 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM sources = ['advisor_%(version)s.tar.gz'] - checksums = ['e8d42ffd478244cb168e4e8d8b3b15dd6e9245ed57a008d369337f0bba7d8f25'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb index 8a4e5b9debf..22ed6ef8ab1 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb @@ -11,9 +11,13 @@ description = """Blender is the free and open source 3D creation suite. It suppo toolchain = {'name': 'intel', 'version': '2016b'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://download.blender.org/source/'] +sources = [SOURCELOWER_TAR_GZ] patches = ['Blender-%(version)s_fix-ARRAY_SIZE-icc.patch'] +checksums = [ + '3770fa00f50a6654eb8b5fe625ca8942ab5672ac4685b7af24597251ace85c67', # blender-2.77a.tar.gz + 'b333219ca380b08bf167bfdea33c0d23a4ed5c2cd05c5f391ca3b529fdc72a73', # Blender-2.77a_fix-ARRAY_SIZE-icc.patch +] # disable SSE detection to give EasyBuild full control over optimization compiler flags being used configopts = '-DWITH_CPU_SSE=OFF -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE="-DNDEBUG" ' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index a11c2f33dc8..bcb823b40e2 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -8,6 +8,7 @@ description = """Intel Inspector XE 2013 is an easy to use memory error checker toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] +checksums = ['489a6f240609119b7f0452133ad8171c4ce5b5677e5cdef62bb85ce0a57f5fc2'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb index 8332389e547..558716e265d 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb @@ -8,6 +8,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] +checksums = ['336b9a5bbc0bdb1cf71ecac1e1b689dd92e7e811cf2c9a1ce1b4f030114bf531'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb index db3c91fa7f2..f30f9ae182a 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb @@ -8,6 +8,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] +checksums = ['de0bb34741e171601a1bf3eb190e4516374c3827e3a4b0ad25674c7abce1aa4d'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb index 180d0c494de..b8a53ee3316 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb @@ -8,6 +8,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] +checksums = ['0c5daaa0839a9a35fcaa7eb2762326a704917042e2f43b76954aa8ac1553a705'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb index 370dff01c5b..03f94be48ef 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb @@ -8,7 +8,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] -checksums = ['d85a3bbd699b0fc77967fcd5e923ad35'] +checksums = ['98475cca6aa919d001a2fada9f4e03f34aae66cdbf746b6448f796256a57118b'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index e818c19d778..c456cf318a5 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] - -checksums = ['f57a892fb494db3c80f20a88aa3e901f'] +checksums = ['d84518c368b4e4893eeaa0c81a1f5b5e24fec66d0561cf06ef92e9c5068d6499'] local_gccver = '4.9.3' local_binutilsver = '2.25' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index 75764dfd257..2674ffe3ecf 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] - -checksums = ['f57a892fb494db3c80f20a88aa3e901f'] +checksums = ['d84518c368b4e4893eeaa0c81a1f5b5e24fec66d0561cf06ef92e9c5068d6499'] # list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index fdf168d6afa..c876036cb35 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] - -checksums = ['4b93b0ff549e6bd8d1a8b9a441b235a8'] +checksums = ['8b6d11e7c31399ad48f24d08428b8b02a5f9cab20826cc03c2ea7425b54b716e'] local_gccver = '4.9.3' local_binutilsver = '2.25' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 8b786c858af..400b24e5c89 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] - -checksums = ['d6f8529a44231e427219c8e025dec3b2'] +checksums = ['8cfa3db0c9e8c16b2e301f573156a2ba58bc309646811b9f9557bef7336962b9'] local_gccver = '4.9.3' local_binutilsver = '2.25' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 47624b52a84..071f6eb577f 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] - -checksums = ['d6f8529a44231e427219c8e025dec3b2'] +checksums = ['8cfa3db0c9e8c16b2e301f573156a2ba58bc309646811b9f9557bef7336962b9'] local_gccver = '5.3.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb index ab126f02f2a..b5424afd98c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] - -checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] +checksums = ['4e9c151612a158e826078a47eb8b0e36df2aeb5321acfc2174c01a3027589404'] local_gccver = '4.9.3' local_binutilsver = '2.25' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index 9bd0c31ebbe..5c17c7a42c1 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] - -checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] +checksums = ['4e9c151612a158e826078a47eb8b0e36df2aeb5321acfc2174c01a3027589404'] local_gccver = '5.3.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb index 2addad927a3..0bc1f9980b6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] - -checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] +checksums = ['4e9c151612a158e826078a47eb8b0e36df2aeb5321acfc2174c01a3027589404'] local_gccver = '5.4.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb index 44d860d93ec..eede19845c3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] - -checksums = ['c8a2fdb1501fbc93bfaad93195677d86'] +checksums = ['47d537d0fbcea59693433c091935c4bd4a8c204b0484b8d888f74fc2e384a487'] local_gccver = '5.4.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb index 7ecbcf2303c..15e9dff9da1 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] - -checksums = ['41a0e8850ebb5f7169076c89be743ee2'] +checksums = ['0ecb2909c26cc8b3cba31fe5536e3a4dfc82ead56cb13d45cfd68862b918d0d9'] local_gccver = '5.4.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb index 13648b977df..27c9e3ac007 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] - -checksums = ['41a0e8850ebb5f7169076c89be743ee2'] +checksums = ['0ecb2909c26cc8b3cba31fe5536e3a4dfc82ead56cb13d45cfd68862b918d0d9'] local_gccver = '6.3.0' local_binutilsver = '2.27' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb index 84c25bc8196..9a4a5fe38dc 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -9,8 +9,7 @@ description = "C and C++ compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] - -checksums = ['1ed9e5176b30ed0f0917a7ea698021ee'] +checksums = ['d9ab12935669017e1867a116eaf3e12254e29e613bd3cc3f38023f6d8c0a9b40'] local_gccver = '6.3.0' local_binutilsver = '2.27' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb index 5801816c714..9c5977434c4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] - checksums = ['6b9b57dada0ec68e394866ec0a8b162c9233de18a7a6dd2dcc956d335e06acbc'] local_gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb index ba81f7038bc..938e55fa55d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] - checksums = ['96c60896e4cac1c5c65ee3a1f9fafd2eee43b3944465ea8591468e708a86d184'] local_gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb index ed12dffba99..e6564be6ab9 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] - checksums = ['299ab1702048802c1986bf031ee3f13e53555d55826f599e808564f1d9102455'] local_gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb index d124880f327..684e5631391 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] - checksums = ['3065e3ea0e489fe6d50aea725ac095422c13aa51b88d02f6380af06b708dbb98'] local_gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb index 2c8cd67bd9e..c71ac574cf0 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] - checksums = ['63fa158694c06ab3a1cac3ee54f978a45921079e302d185d4057c819f4ce99ea'] local_gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 1ab30938f60..70593480c69 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -12,8 +12,7 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/ sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ - # parallel_studio_xe_2020_composer_edition.tgz - '9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', + '9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', # parallel_studio_xe_2020_composer_edition.tgz # iccifort-2020.0.166_no_mpi_rt_dependency.patch 'b7a3d1934e8ffe1712ffb82747332e025355f9f5fbef62349d0c7b4cb7e636a5', ] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index ae6f5440f0a..5a1b6ed91c1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2016_no_mpi_mic_dependency.patch'] - -checksums = ['bce7f6a71f7e44f67956197501d00b7c'] +checksums = [ + # parallel_studio_xe_2016_composer_edition_for_fortran.tgz + '5ad986a01d2fa3f1c31bebb6ea7cd0cf4852528f2a510575bfdf9714bda35f05', + '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', # ifort_2016_no_mpi_mic_dependency.patch +] local_gccver = '4.9.3' local_binutilsver = '2.25' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index 52cf1ffbb22..dc27d744eba 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] - -checksums = ['bce7f6a71f7e44f67956197501d00b7c'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2016_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2016_composer_edition_for_fortran.tgz + '5ad986a01d2fa3f1c31bebb6ea7cd0cf4852528f2a510575bfdf9714bda35f05', + '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', # ifort_2016_no_mpi_mic_dependency.patch +] # list of regex for components to install # full list of components can be obtained from pset/mediaconfig.xml in unpacked sources diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index 5c57791f360..98777291255 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] - -checksums = ['1e848c8283cf6a0210bce1d35ecd748b'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2016_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2016_composer_edition_for_fortran_update1.tgz + 'f3a2903779b80c0e43e3da869c826587dcbae68749ba67d8ff73da3cffcbe992', + '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', # ifort_2016_no_mpi_mic_dependency.patch +] local_gccver = '4.9.3' local_binutilsver = '2.25' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 73e24caebf0..3443fe8309c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] - -checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2016_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2016_composer_edition_for_fortran_update2.tgz + '24a584344e16994a11848b804ac8f7839fc835e68390b84b7b6c04a9a093cd1e', + '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', # ifort_2016_no_mpi_mic_dependency.patch +] local_gccver = '4.9.3' local_binutilsver = '2.25' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 36599d9640b..79772d8356f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] - -checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2016_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2016_composer_edition_for_fortran_update2.tgz + '24a584344e16994a11848b804ac8f7839fc835e68390b84b7b6c04a9a093cd1e', + '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', # ifort_2016_no_mpi_mic_dependency.patch +] local_gccver = '5.3.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index 8c71e9e936e..ac8e6ac2a24 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] - -checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2016_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2016_composer_edition_for_fortran_update3.tgz + '2ae7d2b65c9c71e3192c072a1ae4c286950a4f81107608e7a18777b57f37efa0', + '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', # ifort_2016_no_mpi_mic_dependency.patch +] local_gccver = '4.9.3' local_binutilsver = '2.25' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index 481b31038d5..c12b08514bd 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] - -checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2016_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2016_composer_edition_for_fortran_update3.tgz + '2ae7d2b65c9c71e3192c072a1ae4c286950a4f81107608e7a18777b57f37efa0', + '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', # ifort_2016_no_mpi_mic_dependency.patch +] local_gccver = '5.3.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index 1dacd82ec38..838f12e87d1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -9,17 +9,14 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] - +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2016_composer_edition_for_fortran_update3.tgz '2ae7d2b65c9c71e3192c072a1ae4c286950a4f81107608e7a18777b57f37efa0', - # ifort_2016_no_mpi_mic_dependency.patch - '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', + '8f2ad5aa9036fc152438e977fe98d943965ff72bf0a5f88f65276f40f106064f', # ifort_2016_no_mpi_mic_dependency.patch ] -# remove dependency on intel-mpi-rt-mic -patches = ['ifort_2016_no_mpi_mic_dependency.patch'] - local_gccver = '5.4.0' local_binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (local_gccver, local_binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index e19a14b330d..d02bae93d85 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] - -checksums = ['8787795951fe10f90ce7dcdcec1b9341'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2017_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2017_composer_edition_for_fortran.tgz + '771eb2ef59daf036eab0c82166ede0d0605152a25659d37947d2777176a643e3', + '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch +] local_gccver = '5.4.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index af000c34d37..19349a16f38 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] - -checksums = ['612169f4b40cdded8e212bf097925e4f'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2017_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2017_update1_composer_edition_for_fortran.tgz + 'e8646c6a7ddef15929c5b818ceee2feef1581630d75745bfbc3d01f9c5701c01', + '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch +] local_gccver = '5.4.0' local_binutilsver = '2.26' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb index 86ea3beaab9..a9d29cadae3 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] - -checksums = ['612169f4b40cdded8e212bf097925e4f'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2017_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2017_update1_composer_edition_for_fortran.tgz + 'e8646c6a7ddef15929c5b818ceee2feef1581630d75745bfbc3d01f9c5701c01', + '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch +] local_gccver = '6.3.0' local_binutilsver = '2.27' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb index 2943a8b1b53..6f970664ac7 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -9,11 +9,13 @@ description = "Fortran compiler from Intel" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] - -checksums = ['9d5dfa36a36b7c9e877745f3e379248b'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2017_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2017_update2_composer_edition_for_fortran.tgz + '3817f242049a2f007b79617c982c9445bda12dfd3c3f97b92432b4c96ab3518f', + '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch +] local_gccver = '6.3.0' local_binutilsver = '2.27' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb index 236f035f753..2532277220e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -9,17 +9,14 @@ description = "Intel Fortran compiler" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] - +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2017_update4_composer_edition_for_fortran.tgz '0b6a222e015f776600b12b17c19506249c9e7691a8d287f44cd40a66ca9ac749', - # ifort_2017_no_mpi_mic_dependency.patch - '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', + '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch ] -# remove dependency on intel-mpi-rt-mic -patches = ['ifort_2017_no_mpi_mic_dependency.patch'] - local_gccver = '6.4.0' local_binutilsver = '2.28' versionsuffix = '-GCC-%s-%s' % (local_gccver, local_binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb index a99cf05cf65..1d5b824c294 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb @@ -9,11 +9,13 @@ description = "Intel Fortran compiler" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] - -checksums = ['671e08f50443272ab3885510766c38fc1da9aa109d37e435b2e663e5e46acf90'] - # remove dependency on intel-mpi-rt-mic patches = ['ifort_2017_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2017_update5_composer_edition_for_fortran.tgz + '671e08f50443272ab3885510766c38fc1da9aa109d37e435b2e663e5e46acf90', + '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch +] local_gccver = '6.4.0' local_binutilsver = '2.28' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb index df5323ed36a..97f9f150d3b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb @@ -9,16 +9,14 @@ description = "Intel Fortran compiler" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] - +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2017_update6_composer_edition_for_fortran.tgz 'd2f4427d07a70a895ff42e654d94cae8aa338e8813f79d902748cf3a4a7538ee', '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch ] -# remove dependency on intel-mpi-rt-mic -patches = ['ifort_2017_no_mpi_mic_dependency.patch'] - local_gccver = '6.4.0' local_binutilsver = '2.28' versionsuffix = '-GCC-%s-%s' % (local_gccver, local_binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb index 82c7e381f88..54fafa3a2a4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb @@ -9,16 +9,14 @@ description = "Intel Fortran compiler" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] - +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2017_update7_composer_edition_for_fortran.tgz 'b33908eacecdac12ddf30819349434c3982f4a2aea5614fe44e8cc879ced81e2', '7241e492a5f7ba4e62e8106c97f585c2fd931e32886d886f7bf0a9020e421325', # ifort_2017_no_mpi_mic_dependency.patch ] -# remove dependency on intel-mpi-rt-mic -patches = ['ifort_2017_no_mpi_mic_dependency.patch'] - local_gccver = '6.4.0' local_binutilsver = '2.28' versionsuffix = '-GCC-%s-%s' % (local_gccver, local_binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb index bf7e213d7c7..9a28bc26975 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb @@ -9,16 +9,14 @@ description = "Intel Fortran compiler" toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] - +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2018_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2018_composer_edition_for_fortran.tgz '597718bf752a52e043675102c6c03971be5dd3400a2e849bc295094395beef89', - '8e5e7312c3cc8063b3ee24119f8a6d8fc8453d8f0fd0dc6b4638ded964d15ea5', # ifort_2018_no_mpi_mic_dependency.patch + '8e5e7312c3cc8063b3ee24119f8a6d8fc8453d8f0fd0dc6b4638ded964d15ea5', # ifort_2018_no_mpi_mic_dependency.patch ] -# remove dependency on intel-mpi-rt-mic -patches = ['ifort_2018_no_mpi_mic_dependency.patch'] - local_gccver = '6.4.0' local_binutilsver = '2.28' versionsuffix = '-GCC-%s-%s' % (local_gccver, local_binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb index 0613a092d39..44229ab5574 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -14,7 +14,7 @@ patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2018_update1_composer_edition_for_fortran.tgz 'c9e7a3ecd89632e4a2babf3a483542edcfd7bc8646ee616f035a0caaf936dcd0', - 'fdc818390643e77b3dc7ae1d9ba4547e1f1792da8674ff47747c56d97be6fb99', # ifort_2018.1.163_no_mpi_mic_dependency.patch + 'fdc818390643e77b3dc7ae1d9ba4547e1f1792da8674ff47747c56d97be6fb99', # ifort_2018.1.163_no_mpi_mic_dependency.patch ] local_gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb index 8f7d47d7bd8..d4e0c9bcfd4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -13,7 +13,7 @@ patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2018_update2_composer_edition_for_fortran.tgz '8df5b765d8e231429dd84feea0c1b50f5927bc2369a3be16f43cc34a0e8b3aff', - 'f1ab2ec42723124e3ca5d38589c2d9b80fde4cc25119eee73df28354d8d3a9ac', # ifort_2018.2.199_no_mpi_mic_dependency.patch + 'f1ab2ec42723124e3ca5d38589c2d9b80fde4cc25119eee73df28354d8d3a9ac', # ifort_2018.2.199_no_mpi_mic_dependency.patch ] local_gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb index 4a00cc2b3bc..87ed3cd5747 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -14,7 +14,7 @@ patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2018_update3_composer_edition_for_fortran.tgz '9dc290ad2c95a5df041507bcad551c996a2aec04891d37f641f6db0776f96d89', - '2751935f922e975a85d8e6e8373d9d50e983af7b5017241c47249fcff2629b28', # ifort_2018.3.222_no_mpi_mic_dependency.patch + '2751935f922e975a85d8e6e8373d9d50e983af7b5017241c47249fcff2629b28', # ifort_2018.3.222_no_mpi_mic_dependency.patch ] local_gccver = '7.3.0' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb index de71a6af719..abde8a4a9c1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -14,7 +14,7 @@ patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2019_composer_edition_for_fortran.tgz 'a37334b38689af39c3a399b02624d3eb717cf23dbd2d18e4b01feb9831d57e03', - '21ccdad74a4371ddc91471c90a4278f8f87a12b9668b829c4569df8c2fe75253', # ifort_2019.0.117_no_mpi_mic_dependency.patch + '21ccdad74a4371ddc91471c90a4278f8f87a12b9668b829c4569df8c2fe75253', # ifort-2019.0.117_no_mpi_mic_dependency.patch ] local_gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 3f5302e51bd..8895ad0a58f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -14,7 +14,7 @@ patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2019_update1_composer_edition_for_fortran.tgz '55a5a3d1edb92faff76d7af5522803590247afef9dec6cc9b9f211ba385b0c23', - '12910d18c9f0560aeed80e6425903039d4b3198134155b47e99ff0c03a693ecd', # ifort_2019.1.144_no_mpi_mic_dependency.patch + '12910d18c9f0560aeed80e6425903039d4b3198134155b47e99ff0c03a693ecd', # ifort-2019.1.144_no_mpi_mic_dependency.patch ] local_gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 1a598dfa96b..16a184f66de 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -14,7 +14,7 @@ patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2019_update2_composer_edition_for_fortran.tgz '71e5c9bf055da9ccc50252064740febf506cdf9a560cefe88ba4ba18f84f885e', - 'dbc6496cb2adbf34e66b73d8d75da7dec2738c1026e736bb5bc8393e879f434f', # ifort_2019.2.187_no_mpi_mic_dependency.patch + 'dbc6496cb2adbf34e66b73d8d75da7dec2738c1026e736bb5bc8393e879f434f', # ifort-2019.2.187_no_mpi_mic_dependency.patch ] local_gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb index c704a2b2940..2af19418165 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -14,7 +14,7 @@ patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ # parallel_studio_xe_2019_update3_composer_edition_for_fortran.tgz '94b7d1c31e3b28ec1aa66c1ed1a6efc157f1776efb7544a0c326a58df9803572', - 'fb0bbb112a47b894ff3fbcc4a254ebcd33a76189c6a1814ecf6235472a51c2c5', # ifort_2019.3.199_no_mpi_mic_dependency.patch + 'fb0bbb112a47b894ff3fbcc4a254ebcd33a76189c6a1814ecf6235472a51c2c5', # ifort-2019.3.199_no_mpi_mic_dependency.patch ] local_gccver = '8.3.0' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb index ba37957de13..760ba279986 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb @@ -11,6 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gimpi', 'version': '2.11.5'} sources = ['l_mkl_%(version)s.tgz'] +checksums = ['0944c1192dd7df6f2d913536dbbeed7904a6ec5161f4d97da609a63afa256bdf'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index 196928d7d20..febc29aadab 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.00-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['47567e38801efe273b36b5250c759af7'] +checksums = ['728250dded28dfd012e5a004dd893a887df70385f945be793edb2789e90f4c85'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index ac97d66cbef..ceef81c285c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.01-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['b57ff502b5f97f2f783e4bbda7ce42b3'] +checksums = ['266fa20be4233caf8ddc7a126dda477f13f00cc0b04d16608df0428d8059e509'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb index 2125a67a9b6..01588b7e42f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -10,6 +10,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '8.1.5-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] +checksums = ['266fa20be4233caf8ddc7a126dda477f13f00cc0b04d16608df0428d8059e509'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 361f7384d38..61dfc760348 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['536dbd82896d6facc16de8f961d17d65'] +checksums = ['bac04a07a1fe2ae4996a67d1439ee90c54f31305e8663d1ccfce043bed84fc27'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index 9cfca7157f7..5141fbbb155 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.02-GCC-5.3.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['536dbd82896d6facc16de8f961d17d65'] +checksums = ['bac04a07a1fe2ae4996a67d1439ee90c54f31305e8663d1ccfce043bed84fc27'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb index a6bfaa4a443..a4fdffef5aa 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'pompi', 'version': '2016.03'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['536dbd82896d6facc16de8f961d17d65'] +checksums = ['bac04a07a1fe2ae4996a67d1439ee90c54f31305e8663d1ccfce043bed84fc27'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb index e0271a4e744..e57ba6e7580 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 1e54f7ae84e..2bd29452be3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.3.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb index 4afec3b59ec..c033a1e2817 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016.03-GCC-5.4.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb index e49356ff351..c9b1ed81bd5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2016b'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb index 358f3f14487..5ec068ad854 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2016.10'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb index 44678fcca48..f0a5a72bdbe 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb @@ -9,7 +9,7 @@ BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, a toolchain = {'name': 'iompi', 'version': '2016.07'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb index 6e514bb1142..df3197afca3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb @@ -10,7 +10,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2016.09-GCC-4.9.3-2.25'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb index cbceeb9fba8..de1f1191caf 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb @@ -10,7 +10,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2016.09-GCC-5.4.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb index 6374bfe60a3..f638b30d588 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'pompi', 'version': '2016.04'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb index 3cee04fdb17..9012a28b9dd 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'pompi', 'version': '2016.09'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] +checksums = ['ff858f0951fd698e9fb30147ea25a8a810c57f0126c8457b3b0cdf625ea43372'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb index 338bcaac09c..d344da79065 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2017.00-GCC-5.4.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['3cdcb739ab5ab1e047eb130b9ffdd8d0'] +checksums = ['f2233e8e011f461d9c15a853edf7ed0ae8849aa665a1ec765c1ff196fd70c4d9'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb index 1c0f6f31755..937c52b057a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb @@ -10,7 +10,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gimpi', 'version': '2017a'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['7911c0f777c4cb04225bf4518088939e'] +checksums = ['8c6bbeac99326d59ef3afdc2a95308c317067efdaae50240d2f4a61f37622e69'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb index 6ca575e0573..dbdcbf8cf6d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2017.01-GCC-5.4.0-2.26'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['7911c0f777c4cb04225bf4518088939e'] +checksums = ['8c6bbeac99326d59ef3afdc2a95308c317067efdaae50240d2f4a61f37622e69'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb index 7e96eb0727a..a9a770ee24f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2017a'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['7911c0f777c4cb04225bf4518088939e'] +checksums = ['8c6bbeac99326d59ef3afdc2a95308c317067efdaae50240d2f4a61f37622e69'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb index 29d4195cb4c..929cb77cba0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2017.01'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['7911c0f777c4cb04225bf4518088939e'] +checksums = ['8c6bbeac99326d59ef3afdc2a95308c317067efdaae50240d2f4a61f37622e69'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb index 763b670f295..fdac944e96a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2017a'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['7911c0f777c4cb04225bf4518088939e'] +checksums = ['8c6bbeac99326d59ef3afdc2a95308c317067efdaae50240d2f4a61f37622e69'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb index 68b6b7dee12..387a3eece20 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2017.02-GCC-6.3.0-2.27'} sources = ['l_mkl_%(version)s.tgz'] -checksums = ['ef39a12dcbffe5f4a0ef141b8759208c'] +checksums = ['0b8a3fd6bc254c3c3d9d51acf047468c7f32bf0baff22aa1e064d16d9fea389f'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb index ae38382d9ef..35adcb37b51 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2017.0.098-GCC-5.4.0-2.26'} sources = ['l_mpi_%(version)s.tgz'] - -checksums = ['fc123875773816b7084a91e419d54d20'] +checksums = ['82dd872844f492fbfe3bc49d4d54f32cf83ba6305cdd7d690e0ed1985a680bae'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb index 6f1bc13dbd6..ae75cbdecb1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb @@ -9,7 +9,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = ['l_mpi_%(version)s.tgz'] -checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] +checksums = ['8d30a63674fe05f17b0a908a9f7d54403018bfed2de03c208380b171ab99be82'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index bb8968983a5..687d0c94320 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-5.4.0-2.26'} sources = ['l_mpi_%(version)s.tgz'] - -checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] +checksums = ['8d30a63674fe05f17b0a908a9f7d54403018bfed2de03c208380b171ab99be82'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 1c10589bdad..c7c67635186 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} sources = ['l_mpi_%(version)s.tgz'] - -checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] +checksums = ['8d30a63674fe05f17b0a908a9f7d54403018bfed2de03c208380b171ab99be82'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb index eb371c39343..61742f3855f 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2017.2.174-GCC-6.3.0-2.27'} sources = ['l_mpi_%(version)s.tgz'] - -checksums = ['b6c2e62c3fb9b1558ede72ccf72cf1d6'] +checksums = ['106a4b362c13ddc6978715e50f5f81c58c1a4c70cd2d20a99e94947b7e733b88'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb index ea7fe3c6f55..67610b76731 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] - checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb index 6e01470f251..0955760d9d8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb @@ -11,7 +11,6 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'gcccuda', 'version': '2017b'} sources = ['l_mpi_%(version)s.tgz'] - checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 579f495a99b..8e0dd27f5ba 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] - checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb index a05fc7033ba..5708498b940 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb @@ -11,7 +11,6 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifortcuda', 'version': '2017.4.196-GCC-6.4.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] - checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb index d0835058637..1a3f0cc1f20 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2017.5.239-GCC-6.4.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] - checksums = ['5a1048d284dce8bc75b45789471c83c94b3c59f8f159cab43d783fc44302510b'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb index 1b829610732..6e06d737148 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.0.128-GCC-6.4.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] - checksums = ['debaf2cf80df06db9633dfab6aa82213b84a665a55ee2b0178403906b5090209'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb index 1e9b050bbb9..1f937d08e3e 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] - checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb index 33bdf0b4638..d1b315c9481 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -9,7 +9,6 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.2.199-GCC-6.4.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] - checksums = ['0927f1bff90d10974433ba2892e3fd38e6fee5232ab056a9f9decf565e814460'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 7ee2e37b200..b1aee75f2b5 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['5fd751bcd87d9842a2e4f2cd41c6091212d4bf9e39e77b62fd9dcee1ece5a378'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 098451a6972..db598d9b486 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -11,6 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_pu_%(version)s.tgz'] +checksums = ['ffb2d69e635ecbad124c4ce63541320e40a2809ae0cb1ae50a6cc833e90423c0'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index 8fe47ac905e..b7672b6741e 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_pu_%(version)s.tgz'] +checksums = ['ffb2d69e635ecbad124c4ce63541320e40a2809ae0cb1ae50a6cc833e90423c0'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 271af7c2b35..ea7c9406e1f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -10,8 +10,11 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] - patches = ['impi_4.x_productsdb.patch'] +checksums = [ + '671caa108f53760fe1b534f8055ebb062eaccedc667fe515be7c7b53f2289f22', # l_mpi_p_4.0.2.003.tgz + '65e5008188f1bf804fb264d1fd4990c8cc7016d32963a5633b6462faabc02e86', # impi_4.x_productsdb.patch +] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index d48b3727cc1..82d174e6a86 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['b7c3db8b027bcafe869af9432c938b3917e65c6a0e24173ed190a29b632648b9'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index a5cfcbf78a5..1c1dbd7a85c 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['cf37590d3ce0dce9c3b0285415f96952b8862cf8e1be74b1e210099987a1be79'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 1de1d380b4e..1aa267ad939 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['82f245bed5b3adaa3f437629f1c6f08d2eb0a1079f80783d6617a4c67b2da6f2'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 129b250a804..1bad164e830 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['3cab0d1622a4a814c29243042e89d3c32c7e5b002b56858de82429e2e31ad4c9'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index 16633ddb504..db4106bb2c8 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['3dd70186ce1be4bc843b2584a5d9fa84949d90eba4dd3957d1b8a57dac1fcc28'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 5ca7aaeb97d..5b302a40e7d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'GCC', 'version': '4.8.3'} sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['100f6a59ca0cb1c1d0906e6dd89517f8ddde1fa12edb81455544d3f761f5ae2d'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index 155bdc0b4aa..4bc1a45f122 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['100f6a59ca0cb1c1d0906e6dd89517f8ddde1fa12edb81455544d3f761f5ae2d'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb index 7bd4e394550..1b00f7c347b 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb @@ -10,6 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = ['l_mpi_p_%(version)s.tgz'] +checksums = ['54da77dc8463c258d1af502a7d334c6d63a0ddaec45d659eda0cee1a4ecd6bac'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index 62176375701..2b4885c12c6 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -12,8 +12,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2016.0.109-GCC-4.9.3-2.25'} sources = ['l_mpi_p_%(version)s.tgz'] - -checksums = ['aa4aaec41526aa5b244e531811877b01'] +checksums = ['64bd6f0d8fc1ea17fffe5b4cc0302d4b3b2decb9c1fdf4179f21d1b8b26c8894'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 7c60c805656..262fa702dc6 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2016.1.150-GCC-4.9.3-2.25'} sources = ['l_mpi_p_%(version)s.tgz'] - -checksums = ['ec4db8f718c34f09fccf9d1c89454f0a'] +checksums = ['b073b5fcd577b1fa115672eecdcf6dc55dbfa4ae390b903bb92307528168bb11'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index d3215852c52..c499c4b72c6 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.25'} sources = ['l_mpi_p_%(version)s.tgz'] - -checksums = ['1c14656859d48bf8b90c71dace2a977b'] +checksums = ['b41446685fdde5b7a82280a56e057742bb09c8619940d2328874928135e94e67'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index 0ed2fcc2051..20a63b66376 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-5.3.0-2.26'} sources = ['l_mpi_p_%(version)s.tgz'] - -checksums = ['1c14656859d48bf8b90c71dace2a977b'] +checksums = ['b41446685fdde5b7a82280a56e057742bb09c8619940d2328874928135e94e67'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index c12c8385125..fa8d359f383 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} sources = ['l_mpi_p_%(version)s.tgz'] - -checksums = ['1c14656859d48bf8b90c71dace2a977b'] +checksums = ['b41446685fdde5b7a82280a56e057742bb09c8619940d2328874928135e94e67'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb index 56fb0dfd5e1..75731d6bad9 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.3.0-2.26'} sources = ['l_mpi_p_%(version)s.tgz'] - -checksums = ['1c14656859d48bf8b90c71dace2a977b'] +checksums = ['b41446685fdde5b7a82280a56e057742bb09c8619940d2328874928135e94e67'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index d51c76b986d..efda10394a7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} sources = ['l_mpi_p_%(version)s.tgz'] - -checksums = ['1c14656859d48bf8b90c71dace2a977b'] +checksums = ['b41446685fdde5b7a82280a56e057742bb09c8619940d2328874928135e94e67'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb index f84ce5000bf..edd61f9e2c8 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -11,8 +11,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifortcuda', 'version': '2016.10'} sources = ['l_mpi_p_%(version)s.tgz'] - -checksums = ['1c14656859d48bf8b90c71dace2a977b'] +checksums = ['b41446685fdde5b7a82280a56e057742bb09c8619940d2328874928135e94e67'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb index b4d086765db..7105741cfd7 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb @@ -10,6 +10,7 @@ description = """Intel Integrated Performance Primitives (Intel IPP) is an exten toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] +checksums = ['2908bdeab3057d4ebcaa0b8ff5b00eb47425d35961a96f14780be68554d95376'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb index f52a6d981cc..019d8937d5d 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb @@ -10,8 +10,11 @@ description = """Intel Integrated Performance Primitives (Intel IPP) is an exten toolchain = SYSTEM sources = ['l_ipp_%s_intel64.tgz' % version] - patches = ['ipp_productsdb.patch'] +checksums = [ + '814ae67f49ba4e93e7492e5697cbf34b3aa1ee276368356e80fc862ff46d7a9b', # l_ipp_7.0.5.233_intel64.tgz + 'c73ef84f8a11b5b703cf94f2385ae5fc8b02e0408cdd64f874086d667ccaeb75', # ipp_productsdb.patch +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb index 7ad0466d542..8d0122c9c9c 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb @@ -10,6 +10,7 @@ description = """Intel Integrated Performance Primitives (Intel IPP) is an exten toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] +checksums = ['7e6c6d0341c73f70ecb1eb3b4649ba0ef1500b7cb4ae72ef477a82be0ba42939'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb index 6bd809d8bbc..b41d2bc55c4 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb @@ -10,6 +10,7 @@ description = """Intel Integrated Performance Primitives (Intel IPP) is an exten toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] +checksums = ['7fa41cc51ca5dfd36168fc226ff7fa4cb1b5ad0cac41b4d5192841cb6ee0cd88'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb index c3454d4eff7..8be93b5fa89 100644 --- a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb +++ b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb @@ -9,6 +9,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] +checksums = ['d0b2eee91809fe900c770fc265c639e5d9f8f744f4c35fb7310ea3617d807647'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb index eff73ddc538..2f10013bc53 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb @@ -9,6 +9,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM sources = ['l_itac_p_%s.tgz' % version] +checksums = ['0429c5791f532486be8644378bac224e4ad6c3229e7830a6f4a913a5512e4588'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb index 0e3dcfee35d..de0f0bf5a26 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb @@ -9,6 +9,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] +checksums = ['ad476201804d9e6788ccf3f24d2aac21f38087e7735d4ebe68798bef3fcde921'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb index efacaf21806..83d17f972de 100644 --- a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -9,6 +9,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] +checksums = ['4d0756b108c5f4d96602740e917d58698dd3307c6bd163e99bde40907a09d039'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb index 47311359541..a1ca61ae34a 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb @@ -14,6 +14,7 @@ description = """Intel Threading Building Blocks (Intel TBB) toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] +checksums = ['c9c99c269734587ab84031c8f8a69c1cc381879d023c8f6415c619711c171c0a'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb index 48efc64c3e0..d4015391be2 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb @@ -14,8 +14,11 @@ description = """Intel Threading Building Blocks (Intel TBB) toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] - patches = ['tbb-4.0_productsdb.patch'] +checksums = [ + '52d0aeaa08c6f44354f792655193b446cad81162c409506e738dc3910aa6cdc3', # l_tbb_4.0.0.233.tgz + 'af435d28316e8df4e0b29411f27521dc10c29765cc3d350b132f6f387dc28989', # tbb-4.0_productsdb.patch +] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb index cb968423fd9..23b8c0e8f99 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb @@ -14,8 +14,11 @@ description = """Intel Threading Building Blocks (Intel TBB) toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] - patches = ['tbb-4.0_productsdb.patch'] +checksums = [ + 'c3f16c50c35728343fc73ed194751428f6194ee41f81f2961867ac2f220a58db', # l_tbb_4.0.5.339.tgz + 'af435d28316e8df4e0b29411f27521dc10c29765cc3d350b132f6f387dc28989', # tbb-4.0_productsdb.patch +] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb index 2f3c0189a26..f55341ddc02 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -14,6 +14,7 @@ description = """Intel Threading Building Blocks (Intel TBB) toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] +checksums = ['3001afd6e3f5efdab4239fd319e18fcbf99ad525b7a2c160eabe1515efdd2e26'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb index 765ba3a381d..6e2feaf4e95 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb @@ -14,6 +14,7 @@ description = """Intel Threading Building Blocks (Intel TBB) toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] +checksums = ['dd014c2b105f3c5c140f85fbd90058a82b5a4d7121049ebec4f822be5ebbbf15'] dontcreateinstalldir = True diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index 30eee50474c..1c8b7cc7036 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -10,9 +10,9 @@ description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid s toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -sources = [SOURCELOWER_TGZ] source_urls = ['http://qe-forge.org/gf/download/frsrelease/208/932/'] -checksums = ['f0820a0f42dfc81ce3811af647bed777'] +sources = [SOURCELOWER_TGZ] +checksums = ['fec997bf31d177b5e910a8894b1a856cb363371cb0d5a160f5eb2fd63b502ea0'] dependencies = [('netCDF-Fortran', '4.4.2')] From 5a569945eb0eebaad855137ef562468ad7c7a9a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jan 2020 18:47:43 +0100 Subject: [PATCH 457/468] use https in source_urls and homepage for Intel tools & Blender --- easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb | 2 +- easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb | 2 +- .../b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb | 2 +- .../b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb | 2 +- .../b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb | 2 +- easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb | 4 ++-- .../easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb | 4 ++-- easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb | 4 ++-- easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb | 2 +- .../i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb | 2 +- .../easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb | 2 +- .../i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb | 2 +- .../i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb | 2 +- .../i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb | 4 ++-- easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb | 4 ++-- .../impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- .../impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb | 2 +- .../impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- .../impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- .../impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb | 2 +- .../impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb | 2 +- .../impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 4 ++-- .../impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb | 4 ++-- .../impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 4 ++-- .../impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb | 4 ++-- .../impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb | 4 ++-- .../impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb | 4 ++-- .../impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 4 ++-- .../impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 2 +- easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb | 2 +- .../impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- .../impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb | 2 +- easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb | 2 +- easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb | 2 +- easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb | 2 +- easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2017.1.024.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2018.1.017.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2018.3.022.eb | 2 +- easybuild/easyconfigs/i/itac/itac-2019.2.026.eb | 2 +- easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb | 2 +- easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb | 2 +- easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb | 2 +- 172 files changed, 210 insertions(+), 210 deletions(-) diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb index 19e9dc5f4d8..24ce3fe1c31 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb index fd5a6bbf429..a9f9a888154 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['6597f165dee3c6444eb0f38a9069327d10584b09555f5d2c4ed86b8f84d980bb'] diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb index 22ed6ef8ab1..0157e0d8969 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb @@ -11,7 +11,7 @@ description = """Blender is the free and open source 3D creation suite. It suppo toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://download.blender.org/source/'] +source_urls = ['https:/download.blender.org/source/'] sources = [SOURCELOWER_TAR_GZ] patches = ['Blender-%(version)s_fix-ARRAY_SIZE-icc.patch'] checksums = [ diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb index ce3af1d6036..9ef7a6e5c39 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb @@ -11,7 +11,7 @@ description = """Blender is the free and open source 3D creation suite. It suppo toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://download.blender.org/source/'] +source_urls = ['https:/download.blender.org/source/'] sources = [SOURCELOWER_TAR_GZ] patches = ['Blender-2.77a_fix-ARRAY_SIZE-icc.patch'] checksums = [ diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb index 2feec4137d6..5140ce0dbae 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb @@ -11,7 +11,7 @@ description = """Blender is the free and open source 3D creation suite. It suppo toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = ['http://download.blender.org/source/'] +source_urls = ['https:/download.blender.org/source/'] sources = [SOURCELOWER_TAR_GZ] patches = ['Blender-2.77a_fix-ARRAY_SIZE-icc.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index bcb823b40e2..8b26f01fceb 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2013_update6' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb index 558716e265d..1acde219985 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2013_update7' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb index f30f9ae182a..ceb5410b255 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2016_update3' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb index b8a53ee3316..56c3676a2fb 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2017_update1' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb index 03f94be48ef..4a283554f8e 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2017_update2' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb index 183c174272d..4ae12220085 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2018_update1' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb index ce5b13969ca..09b1e206b7e 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2018_update2' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb index 8e36b2be2c5..dc0541c976e 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2018_update3' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb index 7469deb5650..88dfecf308a 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb @@ -1,7 +1,7 @@ name = 'Inspector' version = '2019_update2' -homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +homepage = 'https://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index c456cf318a5..1b644b846f4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2016.0.109' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index 2674ffe3ecf..6140d1d3f03 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2016.0.109' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index c876036cb35..d6934cd9ac2 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2016.1.150' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 400b24e5c89..0e97c65ac3b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2016.2.181' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 071f6eb577f..73720f0a334 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2016.2.181' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb index b5424afd98c..d7685cc7614 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2016.3.210' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index 5c17c7a42c1..5b8554ecf45 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2016.3.210' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb index 0bc1f9980b6..8564dc5fd74 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2016.3.210' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb index eede19845c3..c58c20eed32 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2017.0.098' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb index 15e9dff9da1..a30a931e02c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb index 27c9e3ac007..979a355ebf6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb index 9a4a5fe38dc..326f512d796 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2017.2.174' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb index 9c5977434c4..2b734455135 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2017.4.196' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb index 938e55fa55d..90f3472801d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2017.5.239' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb index e6564be6ab9..0bef6f368a5 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2017.6.256' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb index 684e5631391..7f826084d5d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2017.7.259' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb index c71ac574cf0..146a8d146cc 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2018.0.128' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb index 0d99f829232..ca49a084587 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb @@ -3,12 +3,12 @@ name = 'icc' version = '2018.1.163' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12382/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12382/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['ddbfdf88eed095817650ec0a226ef3b9c07c41c855d258e80eaade5173fedb6e'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb index c0219dc0cc4..fafb0bb7234 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'icc' version = '2018.2.199' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb index 2a19f4bcd21..9b3a071f005 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ name = 'icc' version = '2018.3.222' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13003/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13003/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['d8b7e6633faa2e0b7d4eebf3260cb3a200b951cb2cf7b5db957c5ae71508d34b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb index 7b5137cb18b..3918ba3f3f1 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ name = 'icc' version = '2018.5.274' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13723/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13723/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_cpp.tgz'] checksums = ['3850ab2a01fe8888af8fed65b7d24e0ddf45a84efe9635ff0f118c38dfc4544b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb index d10bd52f992..b78d2e8e11c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'icc' version = '2019.0.117' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13582/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13582/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['17932a54a76d04432de16e6db15a6ed80fa80ed20193f3b717fd391f623e23e1'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb index 19879f571af..7b37d3169dc 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'icc' version = '2019.1.144' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14865/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14865/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['4a156bbeac9bd8d67e74b33ad6f3ae02d4c24c8444365465db6dc50d3e891946'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb index bc12f6784b7..f192fd17472 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'icc' version = '2019.2.187' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['fc434a2e005af223f43d258c16f004134def726a8d2a225e830af85d553bee55'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb index 5d4b035a822..65821a417db 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb @@ -3,12 +3,12 @@ name = 'icc' version = '2019.3.199' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['969985e83ebf7bfe3c3ac3b771a7d16ba9b5dfbda84e7c2a60ef25fb827b58ae'] diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb index fae4e2171f8..5cefbfc2dee 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb @@ -3,12 +3,12 @@ name = 'iccifort' version = '2019.4.243' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb index 49fb563f11f..c080762f21d 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb @@ -3,12 +3,12 @@ name = 'iccifort' version = '2019.5.281' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index 5a1b6ed91c1..53d9359f181 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2016.0.109' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index dc27d744eba..b1ada8ea9fc 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2016.0.109' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index 98777291255..8128417b1f6 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2016.1.150' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 3443fe8309c..14d95352dee 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2016.2.181' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 79772d8356f..5bcf97033d9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2016.2.181' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index ac8e6ac2a24..76bd3539d00 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2016.3.210' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index c12b08514bd..3f2570c0bf9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2016.3.210' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index 838f12e87d1..1342ed6aeaf 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2016.3.210' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index d02bae93d85..dcda31d65e3 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2017.0.098' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index 19349a16f38..78765d1c852 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb index a9d29cadae3..97ef11dc69f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb index 6f970664ac7..f9fe7948e0a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2017.2.174' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb index 2532277220e..68547a5b813 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2017.4.196' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb index 1d5b824c294..1a0c9a9e040 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2017.5.239' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb index 97f9f150d3b..8039bd7c6e5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2017.6.256' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb index 54fafa3a2a4..02d9fce0f12 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2017.7.259' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb index 9a28bc26975..dc989e0ba5f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2018.0.128' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb index 44229ab5574..66cf55bd0c0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -3,12 +3,12 @@ name = 'ifort' version = '2018.1.163' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12383/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12383/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb index d4e0c9bcfd4..e347a1217ed 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'ifort' version = '2018.2.199' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb index 87ed3cd5747..8572f079dca 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ name = 'ifort' version = '2018.3.222' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13004/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13004/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb index 52960b79bfb..7668ec76749 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ name = 'ifort' version = '2018.5.274' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13724/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13724/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb index abde8a4a9c1..3457239087d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'ifort' version = '2019.0.117' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13583/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13583/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 8895ad0a58f..c47117b085b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'ifort' version = '2019.1.144' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14866/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14866/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 16a184f66de..924762c6de2 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'ifort' version = '2019.2.187' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb index 2af19418165..b8eb911adc2 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -3,12 +3,12 @@ name = 'ifort' version = '2019.3.199' -homepage = 'http://software.intel.com/en-us/intel-compilers/' +homepage = 'https://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb index 760ba279986..69ed2f98c81 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb @@ -2,7 +2,7 @@ name = 'imkl' version = '11.2.3.187' deprecated = "imkl versions older than 11.3.1.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index febc29aadab..a0a50712c66 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'imkl' version = '11.3.0.109' deprecated = "imkl versions older than 11.3.1.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index ceef81c285c..b613bc30a36 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.1.150' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb index 01588b7e42f..7aacf4fec45 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -1,7 +1,7 @@ name = 'imkl' version = '11.3.1.150' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 61dfc760348..5100b16b015 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.2.181' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index 5141fbbb155..4dd41c5001d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.2.181' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb index a4fdffef5aa..c8ddf58afca 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.2.181' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb index e57ba6e7580..c3730e746fb 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 2bd29452be3..aceeb91a8bb 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb index c033a1e2817..68f2afe5650 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb index c9b1ed81bd5..d5b258e8a4a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb index 5ec068ad854..3c6f1713da2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb index f0a5a72bdbe..8e3c414b98c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb @@ -1,7 +1,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb index df3197afca3..409a3ab0464 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb @@ -1,7 +1,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb index de1f1191caf..df84bb5955b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb @@ -1,7 +1,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb index f638b30d588..92c8c5f9ff3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb index 9012a28b9dd..ae9368f8bea 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '11.3.3.210' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb index d344da79065..32e5aa14f77 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.0.098' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb index 937c52b057a..7fee72b524e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb @@ -1,7 +1,7 @@ name = 'imkl' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb index dbdcbf8cf6d..2359e21c74c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb index a9a770ee24f..217cbe88035 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb index 929cb77cba0..7aea954707b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb index fdac944e96a..ce97a6c2138 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb index 387a3eece20..a1aad85ea17 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.2.174' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb index 8bbe27b5454..8824b168a33 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-gompi-2017b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.3.196' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb index 6deca5796c7..7a99eecb86b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.3.196' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library (MKL), a library of highly optimized, extensively threaded math functions, including BLAS, (Sca)LAPACK, Fast Fourier Transforms (FFT), etc.""" diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb index 95c93a2cfff..6284a94194d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpic-2017b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.3.196' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb index 770bcf00248..ab933abba99 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.3.196' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb index 1c5e940f586..6eae6e33d2d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.4.239-iimpi-2017.09.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2017.4.239' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library (MKL), a library of highly optimized, extensively threaded math functions, including BLAS, (Sca)LAPACK, Fast Fourier Transforms (FFT), etc.""" diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb index b9eaeff5154..8e8f518f98c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.0.128-iimpi-2018.00.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.0.128' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb index b9936d332d3..cc11fb4aea8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018.01.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.1.163' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb index 0c08b6a4a84..770acb76d87 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.1.163' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018a'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb index 362e1f6fd18..aa64b03e25d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iompi-2018a.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.1.163' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb index 783453db8eb..b723b27e95c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iimpi-2018.02.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.2.199' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb index c1541e5ba09..dd880cc0bb8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.2.199-iompi-2018.02.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.2.199' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb index d22ff0708a8..f340d755ee2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.3.222' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gimpi', 'version': '2018b'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb index 3101dc97775..6ead35efc9a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2018b'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb index b766fd8f90f..7f53145d6a3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.3.222' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018b'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb index 9d1f876220a..aeabee4d300 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.3.222' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2018b'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb index fb5c8fa1a53..02dba60737e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.4.274' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018.04'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb index dad9f08a557..a382ae20ac7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2019.0.117' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.00'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb index 632c9947b20..e63cc1a2695 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2019.1.144' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.01'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb index 37b0f6cb860..782473ec9fa 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb @@ -1,7 +1,7 @@ name = 'imkl' version = '2019.1.144' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019a'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb index 6beef47051f..3a5e6baedc4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2019.1.144' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019.01'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb index 830e9c0b35e..645ffaf31a7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2019.2.187' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.02'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb index dea288fc36e..2c06461ab97 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2019.3.199' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.03'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb index b902873dd52..d95d740ea28 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2019.5.281' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019b'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 35adcb37b51..c3a1d4c818d 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.0.098' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb index ae75cbdecb1..48776435858 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,7 +1,7 @@ name = 'impi' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 687d0c94320..55089ce7fd1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index c7c67635186..0067690c19e 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb index 61742f3855f..2a3667657eb 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.2.174' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb index 67610b76731..65908d60717 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.3.196' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb index 0955760d9d8..43372cd1434 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-gcccuda-2017b.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.3.196' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 8e0dd27f5ba..dfd36999c70 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.3.196' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb index 5708498b940..4166e41efe6 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.3.196' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb index 1a3f0cc1f20..7ca3d79bbc4 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.4.239-iccifort-2017.5.239-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2017.4.239' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2017.5.239-GCC-6.4.0-2.28'} diff --git a/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb index 6e06d737148..6bf133382ad 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.0.128-iccifort-2018.0.128-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2018.0.128' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.0.128-GCC-6.4.0-2.28'} diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb index 1f937d08e3e..c7ea4f03aa3 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2018.1.163' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index c2bd8a0f820..21ad001e53c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2018.1.163' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12405/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12405/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb index d1b315c9481..ebe334a49d6 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.2.199-iccifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ name = 'impi' version = '2018.2.199' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.2.199-GCC-6.4.0-2.28'} diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb index bc24dfa6254..e39879ac218 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2018.3.222' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index bf654b96c79..f4e9e1a638f 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2018.3.222' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb index 2781663645f..060befc0a5a 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2018.4.274' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.5.274-GCC-7.3.0-2.30'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index e42262f10f4..e6c3602e1e3 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -1,12 +1,12 @@ name = 'impi' version = '2018.4.274' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb index 5f00a89b089..8f89b212fa4 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2018.5.288' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.5.281'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 1ca9ff449ea..2f60b422703 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2019.0.117' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.0.117-GCC-8.2.0-2.31.1'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 7e6b823b00d..8e2ed0b3980 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2019.1.144' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb index d86765c209d..7cdc6aca429 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2019.2.187' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.2.187-GCC-8.2.0-2.31.1'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb index 8e7f3adc53f..c0b1f565c0a 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -3,12 +3,12 @@ name = 'impi' version = '2019.3.199' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.3.199-GCC-8.3.0-2.32'} -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990'] diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index b1aee75f2b5..1f582213a92 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -2,7 +2,7 @@ name = 'impi' version = '3.2.2.006' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index db598d9b486..619e674440d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -3,7 +3,7 @@ version = '4.0.0.028' versionsuffix = '-32bit' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index b7672b6741e..50d30cb8546 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.0.0.028' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index ea7c9406e1f..7395bda9360 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.0.2.003' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 82d174e6a86..882e91e25de 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.1.0.027' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 1c1dbd7a85c..95e8281f375 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.1.0.030' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 1aa267ad939..d51fa3a43fd 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.1.1.036' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 1bad164e830..45646677d6b 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.1.2.040' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index db4106bb2c8..fcf30753164 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.1.3.045' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 5b302a40e7d..7eed439ca7f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.1.3.049' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index 4bc1a45f122..c78a70abd1d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -2,7 +2,7 @@ name = 'impi' version = '4.1.3.049' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb index 1b00f7c347b..57cd653c6d2 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb @@ -2,7 +2,7 @@ name = 'impi' version = '5.0.3.048' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index 2b4885c12c6..c2525e0abba 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'impi' version = '5.1.1.109' deprecated = "impi versions older than 5.1.2.150 are deprecated" -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 262fa702dc6..6ceccaf8396 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'impi' version = '5.1.2.150' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index c499c4b72c6..19ce621fa1a 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'impi' version = '5.1.3.181' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index 20a63b66376..df89d8f7863 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ name = 'impi' version = '5.1.3.181' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index fa8d359f383..ca9a84893c0 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ name = 'impi' version = '5.1.3.181' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb index 75731d6bad9..895ed26843b 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ name = 'impi' version = '5.1.3.181' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index efda10394a7..8588054725a 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ name = 'impi' version = '5.1.3.181' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb index edd61f9e2c8..4d99f54812e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -3,7 +3,7 @@ name = 'impi' version = '5.1.3.181' -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" diff --git a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb index 7105741cfd7..9c48807dd83 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb @@ -1,7 +1,7 @@ name = 'ipp' version = '2017.1.132' -homepage = 'http://software.intel.com/en-us/articles/intel-ipp/' +homepage = 'https://software.intel.com/en-us/articles/intel-ipp/' description = """Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions diff --git a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb index 019d8937d5d..821f8fa7ee5 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb @@ -1,7 +1,7 @@ name = 'ipp' version = '7.0.5.233' -homepage = 'http://software.intel.com/en-us/articles/intel-ipp/' +homepage = 'https://software.intel.com/en-us/articles/intel-ipp/' description = """Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions diff --git a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb index 8d0122c9c9c..4a0be92f1e4 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb @@ -1,7 +1,7 @@ name = 'ipp' version = '8.1.0.144' -homepage = 'http://software.intel.com/en-us/articles/intel-ipp/' +homepage = 'https://software.intel.com/en-us/articles/intel-ipp/' description = """Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions diff --git a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb index b41d2bc55c4..e41248e00f4 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb @@ -1,7 +1,7 @@ name = 'ipp' version = '9.0.1.150' -homepage = 'http://software.intel.com/en-us/articles/intel-ipp/' +homepage = 'https://software.intel.com/en-us/articles/intel-ipp/' description = """Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions diff --git a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb index 8be93b5fa89..317841b2b3b 100644 --- a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb +++ b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb @@ -1,7 +1,7 @@ name = 'itac' version = '2017.1.024' -homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' description = """The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ diff --git a/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb b/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb index d9785a995d5..ccdda419f0e 100644 --- a/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb +++ b/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb @@ -1,7 +1,7 @@ name = 'itac' version = '2018.1.017' -homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' description = """The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ diff --git a/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb b/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb index b32a7f75fdf..c1393f4a3df 100644 --- a/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb +++ b/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb @@ -1,7 +1,7 @@ name = 'itac' version = '2018.3.022' -homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' description = """The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ diff --git a/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb b/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb index 7bf3fa17d9f..91dcb5beb7c 100644 --- a/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb +++ b/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb @@ -1,7 +1,7 @@ name = 'itac' version = '2019.2.026' -homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' description = """The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ diff --git a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb index 2f10013bc53..32934e268f1 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb @@ -1,7 +1,7 @@ name = 'itac' version = '8.0.0.011' -homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' description = """The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ diff --git a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb index de0f0bf5a26..29afd015f99 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb @@ -1,7 +1,7 @@ name = 'itac' version = '8.1.4.045' -homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' description = """The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb index 83d17f972de..2536c3e6b91 100644 --- a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -1,7 +1,7 @@ name = 'itac' version = '9.0.3.051' -homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' description = """The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb index a1ca61ae34a..06e7fe79977 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb @@ -1,7 +1,7 @@ name = 'tbb' version = '2017.2.132' -homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +homepage = 'https://software.intel.com/en-us/articles/intel-tbb/' description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb index d4015391be2..08f73ad72a4 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb @@ -1,7 +1,7 @@ name = 'tbb' version = '4.0.0.233' -homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +homepage = 'https://software.intel.com/en-us/articles/intel-tbb/' description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb index 23b8c0e8f99..ba835398276 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb @@ -1,7 +1,7 @@ name = 'tbb' version = '4.0.5.339' -homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +homepage = 'https://software.intel.com/en-us/articles/intel-tbb/' description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb index f55341ddc02..c168492d3fc 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -1,7 +1,7 @@ name = 'tbb' version = '4.3.6.211' -homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +homepage = 'https://software.intel.com/en-us/articles/intel-tbb/' description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb index 6e2feaf4e95..406dcd81a93 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb @@ -1,7 +1,7 @@ name = 'tbb' version = '4.4.2.152' -homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +homepage = 'https://software.intel.com/en-us/articles/intel-tbb/' description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. From d987e3f3c8b0aad6898d06ad58480b0fc76f01bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jan 2020 21:32:19 +0100 Subject: [PATCH 458/468] add missing libGLU dependency + fix source URLs in Blender easyconfigs --- .../b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb | 3 ++- .../b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb | 3 ++- .../b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb index 0157e0d8969..6eadde95ca8 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb @@ -11,7 +11,7 @@ description = """Blender is the free and open source 3D creation suite. It suppo toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https:/download.blender.org/source/'] +source_urls = ['https://download.blender.org/source/'] sources = [SOURCELOWER_TAR_GZ] patches = ['Blender-%(version)s_fix-ARRAY_SIZE-icc.patch'] checksums = [ @@ -40,6 +40,7 @@ dependencies = [ ('zlib', '1.2.8'), ('X11', '20160819'), ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), ('OpenImageIO', '1.6.17'), # required for cycles render engine ] diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb index 9ef7a6e5c39..0c3d009c884 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79-intel-2017a-Python-3.6.1.eb @@ -11,7 +11,7 @@ description = """Blender is the free and open source 3D creation suite. It suppo toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['https:/download.blender.org/source/'] +source_urls = ['https://download.blender.org/source/'] sources = [SOURCELOWER_TAR_GZ] patches = ['Blender-2.77a_fix-ARRAY_SIZE-icc.patch'] checksums = [ @@ -40,6 +40,7 @@ dependencies = [ ('zlib', '1.2.11'), ('X11', '20170314'), ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), ('OpenImageIO', '1.7.17'), # required for cycles render engine ] diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb index 5140ce0dbae..baeac1390d5 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-intel-2018b-Python-3.6.6.eb @@ -11,7 +11,7 @@ description = """Blender is the free and open source 3D creation suite. It suppo toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = ['https:/download.blender.org/source/'] +source_urls = ['https://download.blender.org/source/'] sources = [SOURCELOWER_TAR_GZ] patches = ['Blender-2.77a_fix-ARRAY_SIZE-icc.patch'] checksums = [ From 6394ae7cb57382a697044889ac59b425aa909f3c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 14 Jan 2020 09:43:12 +0100 Subject: [PATCH 459/468] Build TF EC with fPIC Otherwise building a SciPy library fails due to missing fPIC, which is weird in itself, as python extensions are shared libraries and hence ought to be build with fPIC anyway. Hence no downside in using fPIC explicitely --- .../TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb index 5e1cec12e75..c6310928e33 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb @@ -8,7 +8,7 @@ homepage = 'https://www.tensorflow.org/' description = "An open-source software library for Machine Intelligence" toolchain = {'name': 'fosscuda', 'version': '2019b'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'pic': True} builddependencies = [ ('Bazel', '0.29.1'), From d4b1739094775d958d36544308a73eb75f60a005 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 14 Jan 2020 11:14:09 +0100 Subject: [PATCH 460/468] Add comment for gast --- .../t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb index c6310928e33..3ef9eff9052 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-fosscuda-2019b-Python-3.7.4.eb @@ -109,6 +109,7 @@ exts_list = [ 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], }), + # Tensorflow needs 0.2.2, see https://github.com/tensorflow/tensorflow/issues/32319 ('gast', '0.2.2', { 'checksums': ['fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0'], }), From 028568ddcb4645bed2fd228de4d235ceb6a250e1 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 14 Jan 2020 08:50:54 -0500 Subject: [PATCH 461/468] adding easyconfigs: SUNDIALS-5.1.0-intel-2019b.eb --- .../s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb new file mode 100644 index 00000000000..a8df7110417 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '5.1.0' + +homepage = 'https://computation.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fb22d14fad42203809dc46d046b001149ec4e901b23882bd4a80619157fd9b21'] + +builddependencies = [('CMake', '3.15.3')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in solvers] + ['include/%s' % s for s in solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From 06c8de87e06301e19b79f2fa1afc126745b6808c Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 14 Jan 2020 10:10:00 -0500 Subject: [PATCH 462/468] s/solvers/local_solvers/ --- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb index a8df7110417..a93b330a683 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb @@ -20,11 +20,12 @@ separate_build_dir = True configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" -solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + sanity_check_paths = { - 'files': ['lib/libsundials_%s.a' % s for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + - ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], - 'dirs': ['examples/%s' % s for s in solvers] + ['include/%s' % s for s in solvers] + + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + ['include/%s' % s for s in local_solvers] + ['examples/nvector', 'include/nvector', 'include/sundials'], } From e9212343114640c2131b72e46d525466542d3a8d Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 14 Jan 2020 10:53:16 -0500 Subject: [PATCH 463/468] fix line lengths... my bad... -check-contrib warned me --- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb index a93b330a683..153842bb2ad 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb @@ -23,9 +23,12 @@ configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] sanity_check_paths = { - 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + - ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], - 'dirs': ['examples/%s' % s for s in local_solvers] + ['include/%s' % s for s in local_solvers] + + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + ['examples/nvector', 'include/nvector', 'include/sundials'], } From 704c02d6f3eb7cd57d88b026587305b8364fbf05 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 15 Jan 2020 15:23:49 +0800 Subject: [PATCH 464/468] prepare release notes for eb411 --- RELEASE_NOTES | 68 ++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 67 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c711108a670..157e96cb5ac 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,75 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 8,748 easyconfig files, for 1,771 different software packages, +The latest version of easybuild-easyconfig provides 8,964 easyconfig files, for 1,798 different software packages, incl. 31 different (compiler) toolchains. +v4.1.1 (January 16th 2020) +-------------------------- + +update/bugfix release + +- added example easyconfig files for 27 new software packages: + - Autoconf-archive (#9658), breseq (#9603), CrossMap (#9483), CSBDeep (#9560), CNT-ILP (#9323), cytoolz (#9453), Faber (#9553), + Fiji (#8748), GARLI (#9404), Globus-CLI (#9565), GtkSourceView (#9526), gradunwarp (#9648), gsettings-desktop-schemas (#9529), + HyPhy (#9405), horton (#7449), IGMPlot (#9438), LEMON (#9323), Meld (#9530), mhcflurry (#9554), NCIPLOT (#9419), ncl (#9632), + OpenSlide (#9499), openslide-python (#9499), pythran (#9594), Qualimap (#9411), TinyDB (#9555), TreeShrink (#9381) +- added additional easyconfigs for various supported software packages, including: + - Anaconda2 2019.10, Anaconda3 2019.10, Autoconf archive, Autoconf 2.69, Automake 1.16.1, Autotools 20180311, arpack ng, Beast 1.10.4, Boost.Python 1.71.0, barrnap 0.9, breseq 0.35.0, bx python, CDO 1.9.8, CNT ILP, CRPropa 3.1.5, CSBDeep 0.4.1, CSBDeep 0.4.1, Clang 9.0.1, Clang 9.0.1, ConnectomeWorkbench 1.3.2, CrossMap 0.3.9, cairo 1.16.0, cuDNN 7.6.4.38, cytoolz 0.10.1, DCMTK 3.6.5, deepTools 3.3.1, EMBOSS 6.6.0, ESMF 8.0.0, EasyBuild 4.1.0, ecCodes 2.15.0, FFTW 3.3.8, FLTK 1.3.5, FSL 6.0.2, FSL 6.0.2, FSL 6.0.3, Faber 0.3, Fiji 20170530, Fiji 20191119, fastp 0.20.0, fastp 0.20.0, freeglut 3.2.1, GARLI 2.01, GDAL 3.0.0, GDAL 3.0.2, GEOS 3.7.2, GEOS 3.8.0, GLibmm 2.49.7, GLibmm 2.49.7, GROMACS 2019.3, GROMACS 2019.3, GROMACS 2019.4, GSL 2.6, GSL 2.6, GTS 0.7.6, Ghostscript 9.50, GitPython 3.0.3, Globus CLI, GtkSourceView 3.24.11, GtkSourceView 4.4.0, Guile 1.8.8, Gurobi 9.0.0, Gurobi 9.0.0, Gurobi 9.0.0, g2clib 1.6.0, g2clib 1.6.0, g2lib 3.1.0, g2lib 3.1.0, gc 7.6.12, gettext 0.20.1, gffread 0.11.6, glibc 2.30, gradunwarp 1.1.0, gradunwarp 1.1.0, gsettings desktop, HDF 4.2.14, HDF5 1.10.5, HPL 2.3, Horovod 0.18.2, HyPhy 2.5.1, horton 2.1.1, horton 2.1.1, hwloc 2.1.0, ICU 64.2, ICU 65.1, IGMPlot 2.4.2, IGMPlot 2.4.2, ITSTool 2.0.6, ImageMagick 7.0.9, iccifort 2020.0.166, iimpi 2020.00, imkl 2020.0.166, impi 2019.6.166, intel 2020.00, Java 1.8.0_231, Jellyfish 2.3.0, Julia 1.3.1, jemalloc 5.2.1, KMC 3.1.1, LEMON 1.3.1, LibTIFF 4.1.0, Libint 2.0.3, Libint 2.0.3, LittleCMS 2.9, libcerf 1.13, libgd 2.2.5, libgeotiff 1.5.1, libiconv 1.16, libiconv 1.16, libmatheval 1.1.11, libpciaccess 0.16, libsigc++ 2.10.2, libsndfile 1.0.28, libtool 2.4.6, libunistring 0.9.10, libxc 2.2.2, libxc 2.2.2, libxml++ 2.40.1, libxml++ 2.40.1, libxml2 python, libxml2 2.9.10, libxslt 1.1.34, lpsolve 5.5.2.5, lxml 4.4.2, MACS2 2.2.5, MDTraj 1.9.3, MRtrix 3.0, MRtrix 3.0, Meld 3.20.1, Mesquite 2.3.0, Mothur 1.43.0, make 4.2.1, makedepend 1.0.6, mayavi 4.7.1, mhcflurry 1.2.4, mhcflurry 1.2.4, molmod 1.4.5, NCIPLOT 4.0, NCL 6.6.2, NCL 6.6.2, NLopt 2.6.1, ncl 2.1.18, ncview 2.1.7, netCDF C++4, netCDF Fortran, netCDF 4.7.1, netCDF 4.7.1, netCDF 4.7.1, networkx 2.4, numactl 2.0.13, ORCA 4.2.1, OpenFOAM Extend, OpenFOAM 6, OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMM 7.4.1, OpenMPI 4.0.2, OpenSlide 3.4.1, openslide python, ownCloud 2.5.4, PLUMED 2.5.3, PROJ 6.2.1, ParMETIS 4.0.3, ParMGridGen 1.0, Pillow SIMD, PyCairo 1.18.0, PyCharm 2019.3.1, PyGObject 3.34.0, pixman 0.38.4, plotly.py 4.4.1, pocl 1.4, pocl 1.4, prokka 1.14.5, pyBigWig 0.3.17, pydicom 1.2.2, pythran 0.9.4.post1, QUAST 5.0.2, Qualimap 2.2.1, QuickFF 2.2.4, Qwt 6.1.4, Qwt 6.1.4, R 3.6.2, R 3.6.2, ReFrame 2.20, SAMtools 1.10, SCOTCH 6.0.9, SUNDIALS 5.1.0, SWIG 4.0.1, Salmon 1.0.0, Sambamba 0.7.1, SuiteSparse 5.6.0, scikit learn, seqtk 1.3, snakemake 5.7.1, TinyDB 3.15.2, TreeShrink 1.3.2, tbl2asn 25.8, tcsh 6.22.02, tcsh 6.22.02, texinfo 6.7, time 1.9, torchvision 0.4.2, UDUNITS 2.2.26, WPS 4.0.1, WPS 4.0.2, WPS 4.1, WRF 4.0.1, WRF 4.0.2, WRF 4.1.3, worker 1.6.11, XZ 5.2.4, xorg macros, xprop 1.2.4, xproto 7.0.31, YAXT 0.6.2, yaff 1.6.0 +- added easyconfigs for intel/2020.00 toolchain (#9575) +- minor enhancements, including: + - add POWER9 support to CUDA 10.1 easyconfigs (#9442) + - build CMake in parallel (#9543) + - use NCCL for GPU ops in Horovod 0.18.2 easyconfig (#9562) + - use alias to ensure the OpenBLAS library is used for pythran (#9594) +- various bug fixes, including: + - fix remote launch of broker and workers for SCOOP (#9366) + - fix failing sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using foss/2018b) (#9388) + - add missing 'wheel' extensions to Spark 2.4.0 easyconfig using intel/2018b toolchain (#9424) + - add missing OS dependencies in Java 1.8 easyconfig used on POWER systems (#9454) + - fix build of recent Bazel versions on Power9 + stick to Java/1.8 as dependency (#9455) + - fix CMake 3.15.3 build on Power (+ enable building in parallel) (#9469) + - fix source URLs in xorg-macros easyconfigs (#9477, #9578) + - add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs & enable 'pip check' in sanity check (#9479) + - disable running of 'sudo apt-get update' in GitHub CI config, since it's failing (and we don't really need it) (#9492) + - remove (wrong) GI_TYPELIB_PATH and XDG_DATA_DIRS (#9528) + - use xorg-macros as dependency in X11 easyconfigs (rather than installing it as a bundle component) (#9546) + - fix lpsymphony extension for R-bundle-Bioconductor (#9548) + - add correct 'old-versions' source URL to all Mesa easyconfigs (#9569) + - add missing checksums for Armadillo (#9572) + - only require sanity_pip_check if use_pip is enabled too (fixes #9563) (#9576) + - also define $AUGUSTUS_BIN_PATH and $AUGUSTUS_SCRIPTS_PATH in generated module file for AUGUSTUS (#9579) + - add SSL OS dependencies for GDAL 3.0.0 (#9586) + - add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension (#9587) + - patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long double in GCC (#9590) + - patch for GCCcore 8.2.0 to fix '__float128 is not supported on this target' on ppc64le (#9591) + - fix name for plotly extension in plotly.py v4.4.1 easyconfig (#9599) + - fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension (#9601) + - use absolute path for extraction to allow relocating the build dir for g2log-1.0 (#9604) + - update checksum for kallisto-0.43.1 (#9611) + - fix https// -> https:// in GConf, GST-plugins-base, GStreamer, Graphene, HarfBuzz, Pango easyconfigs (#9615) + - add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (#9621) + - update ctffind website (#9622) + - make sure we use easybuild Clang in pocl easyconfigs (#9624) + - make postinstallcmds independent of PWD in OpenCV 3.1.0 easyconfigs (#9628) + - update source_urls to include old releases folder in libsodium easyconfigs (#9632) + - fix source URLs for ant v1.10.5 - v1.10.7 (#9633) + - allow missing python versionsuffix for existing easyconfig files changed in PRs (#9634) + - update URLs to new location of libxc (#9635) + - use pip to install gradunwarp 1.1.0 (HCP fork) (#9637) + - use latest master as release candidate of MRtrix 3.0 (since 3.0_RC4 is not an official release) (#9638) + - add second checksum for rda_1.0.2-2.1.tar.gz in R 3.6.0 (#9644) + - update source URLs in QCA 2.1.0 easyconfigs (#9647) + - fix Python 3.5.1 easyconfig (bitstring 3.1.3 sources no longer available on PyPI) (#9649) + - fix tesseract 4.1.0 dependencies (#9650) + - make ICU 64.2 depend on Python3 instead of 2 (#9652) + - use True rather than 'True' for boolean easyconfig parameters (#9657) +- other changes: + - require that sanity_pip_check is enabled in new/changed easyconfigs (#9516) + - revert "WORKAROUND: Remove check for Python suffix to make CI pass for old ECs (#9577) + - update copyright statements for 2020 (#9598) + + v4.1.0 (December 4th 2019) -------------------------- From 024b56d0fcf2dc92b9de54147d4c177d7cb3fbb8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 15 Jan 2020 15:25:34 +0800 Subject: [PATCH 465/468] bump version to 4.1.1 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 171e24a96f6..7e951693042 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.1.1.dev0' +VERSION = '4.1.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 2d46218945ced4d25f080f188ecc7cd7cecba124 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 15 Jan 2020 13:18:16 +0000 Subject: [PATCH 466/468] Remove {bio}[foss/2019a] gradunwarp 1.1.0 w/ Python 3.7.2 until patch is accepted upstream --- ...nwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb deleted file mode 100644 index 3a23c88f10c..00000000000 --- a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.1.0-foss-2019a-HCP-Python-3.7.2.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = "gradunwarp" -version = "1.1.0" -versionsuffix = "-HCP-Python-%(pyver)s" - -homepage = "https://github.com/Washington-University/gradunwarp" -description = """Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original.""" - -toolchain = {'name': 'foss', 'version': '2019a'} - -source_urls = ['https://github.com/Washington-University/gradunwarp/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['4803b8055dbeedb0435246a525aa69f1f3425c55d57c973c045deb39bc95c955'] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -dependencies = [ - ('Python', '3.7.2'), - ('SciPy-bundle', '2019.03'), - ('NiBabel', '2.4.0') -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' From 64cbba960f24f730a53c5e3b5782ca82c2ecb186 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jan 2020 17:51:38 +0100 Subject: [PATCH 467/468] fix pyfits easyconfig by adding missing extension --- .../pyfits-3.5-intel-2018b-Python-2.7.15.eb | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pyfits/pyfits-3.5-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pyfits/pyfits-3.5-intel-2018b-Python-2.7.15.eb index d187ef123ef..8dd3a793050 100644 --- a/easybuild/easyconfigs/p/pyfits/pyfits-3.5-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pyfits/pyfits-3.5-intel-2018b-Python-2.7.15.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'pyfits' version = '3.5' @@ -9,21 +9,28 @@ description = """The PyFITS module is a Python library providing access to FITS toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -checksums = ['4e668622d5a3c140590bc6cf8222afcd4d133dde3d6beda3b9c3c9539c5acf18'] - dependencies = [ ('Python', '2.7.15') ] -download_dep_fail = True use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('d2to1', '0.2.12.post1', { + 'checksums': ['49ef2d16862b3efdc81fc5c32eac373b984945cde5fc02bb01a0a11ff03dd825'], + }), + (name, version, { + 'checksums': ['4e668622d5a3c140590bc6cf8222afcd4d133dde3d6beda3b9c3c9539c5acf18'], + }), +] + sanity_check_paths = { 'files': ['bin/fitscheck', 'bin/fitsdiff', 'bin/fitshead'], 'dirs': ['lib/python%(pyshortver)s/site-packages'] } +sanity_pip_check = True + moduleclass = 'astro' From 507f90199d1bef69fe8cd575abd7e65f70fcb70f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jan 2020 19:43:22 +0100 Subject: [PATCH 468/468] minor tweaks to v4.1.1 release notes --- RELEASE_NOTES | 43 ++++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 157e96cb5ac..70761eeb2c6 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -15,61 +15,62 @@ update/bugfix release - Autoconf-archive (#9658), breseq (#9603), CrossMap (#9483), CSBDeep (#9560), CNT-ILP (#9323), cytoolz (#9453), Faber (#9553), Fiji (#8748), GARLI (#9404), Globus-CLI (#9565), GtkSourceView (#9526), gradunwarp (#9648), gsettings-desktop-schemas (#9529), HyPhy (#9405), horton (#7449), IGMPlot (#9438), LEMON (#9323), Meld (#9530), mhcflurry (#9554), NCIPLOT (#9419), ncl (#9632), - OpenSlide (#9499), openslide-python (#9499), pythran (#9594), Qualimap (#9411), TinyDB (#9555), TreeShrink (#9381) + OpenSlide (#9499), openslide-python (#9499), pythran (#9488, #9594), Qualimap (#9411), TinyDB (#9555), TreeShrink (#9381) - added additional easyconfigs for various supported software packages, including: - - Anaconda2 2019.10, Anaconda3 2019.10, Autoconf archive, Autoconf 2.69, Automake 1.16.1, Autotools 20180311, arpack ng, Beast 1.10.4, Boost.Python 1.71.0, barrnap 0.9, breseq 0.35.0, bx python, CDO 1.9.8, CNT ILP, CRPropa 3.1.5, CSBDeep 0.4.1, CSBDeep 0.4.1, Clang 9.0.1, Clang 9.0.1, ConnectomeWorkbench 1.3.2, CrossMap 0.3.9, cairo 1.16.0, cuDNN 7.6.4.38, cytoolz 0.10.1, DCMTK 3.6.5, deepTools 3.3.1, EMBOSS 6.6.0, ESMF 8.0.0, EasyBuild 4.1.0, ecCodes 2.15.0, FFTW 3.3.8, FLTK 1.3.5, FSL 6.0.2, FSL 6.0.2, FSL 6.0.3, Faber 0.3, Fiji 20170530, Fiji 20191119, fastp 0.20.0, fastp 0.20.0, freeglut 3.2.1, GARLI 2.01, GDAL 3.0.0, GDAL 3.0.2, GEOS 3.7.2, GEOS 3.8.0, GLibmm 2.49.7, GLibmm 2.49.7, GROMACS 2019.3, GROMACS 2019.3, GROMACS 2019.4, GSL 2.6, GSL 2.6, GTS 0.7.6, Ghostscript 9.50, GitPython 3.0.3, Globus CLI, GtkSourceView 3.24.11, GtkSourceView 4.4.0, Guile 1.8.8, Gurobi 9.0.0, Gurobi 9.0.0, Gurobi 9.0.0, g2clib 1.6.0, g2clib 1.6.0, g2lib 3.1.0, g2lib 3.1.0, gc 7.6.12, gettext 0.20.1, gffread 0.11.6, glibc 2.30, gradunwarp 1.1.0, gradunwarp 1.1.0, gsettings desktop, HDF 4.2.14, HDF5 1.10.5, HPL 2.3, Horovod 0.18.2, HyPhy 2.5.1, horton 2.1.1, horton 2.1.1, hwloc 2.1.0, ICU 64.2, ICU 65.1, IGMPlot 2.4.2, IGMPlot 2.4.2, ITSTool 2.0.6, ImageMagick 7.0.9, iccifort 2020.0.166, iimpi 2020.00, imkl 2020.0.166, impi 2019.6.166, intel 2020.00, Java 1.8.0_231, Jellyfish 2.3.0, Julia 1.3.1, jemalloc 5.2.1, KMC 3.1.1, LEMON 1.3.1, LibTIFF 4.1.0, Libint 2.0.3, Libint 2.0.3, LittleCMS 2.9, libcerf 1.13, libgd 2.2.5, libgeotiff 1.5.1, libiconv 1.16, libiconv 1.16, libmatheval 1.1.11, libpciaccess 0.16, libsigc++ 2.10.2, libsndfile 1.0.28, libtool 2.4.6, libunistring 0.9.10, libxc 2.2.2, libxc 2.2.2, libxml++ 2.40.1, libxml++ 2.40.1, libxml2 python, libxml2 2.9.10, libxslt 1.1.34, lpsolve 5.5.2.5, lxml 4.4.2, MACS2 2.2.5, MDTraj 1.9.3, MRtrix 3.0, MRtrix 3.0, Meld 3.20.1, Mesquite 2.3.0, Mothur 1.43.0, make 4.2.1, makedepend 1.0.6, mayavi 4.7.1, mhcflurry 1.2.4, mhcflurry 1.2.4, molmod 1.4.5, NCIPLOT 4.0, NCL 6.6.2, NCL 6.6.2, NLopt 2.6.1, ncl 2.1.18, ncview 2.1.7, netCDF C++4, netCDF Fortran, netCDF 4.7.1, netCDF 4.7.1, netCDF 4.7.1, networkx 2.4, numactl 2.0.13, ORCA 4.2.1, OpenFOAM Extend, OpenFOAM 6, OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMM 7.4.1, OpenMPI 4.0.2, OpenSlide 3.4.1, openslide python, ownCloud 2.5.4, PLUMED 2.5.3, PROJ 6.2.1, ParMETIS 4.0.3, ParMGridGen 1.0, Pillow SIMD, PyCairo 1.18.0, PyCharm 2019.3.1, PyGObject 3.34.0, pixman 0.38.4, plotly.py 4.4.1, pocl 1.4, pocl 1.4, prokka 1.14.5, pyBigWig 0.3.17, pydicom 1.2.2, pythran 0.9.4.post1, QUAST 5.0.2, Qualimap 2.2.1, QuickFF 2.2.4, Qwt 6.1.4, Qwt 6.1.4, R 3.6.2, R 3.6.2, ReFrame 2.20, SAMtools 1.10, SCOTCH 6.0.9, SUNDIALS 5.1.0, SWIG 4.0.1, Salmon 1.0.0, Sambamba 0.7.1, SuiteSparse 5.6.0, scikit learn, seqtk 1.3, snakemake 5.7.1, TinyDB 3.15.2, TreeShrink 1.3.2, tbl2asn 25.8, tcsh 6.22.02, tcsh 6.22.02, texinfo 6.7, time 1.9, torchvision 0.4.2, UDUNITS 2.2.26, WPS 4.0.1, WPS 4.0.2, WPS 4.1, WRF 4.0.1, WRF 4.0.2, WRF 4.1.3, worker 1.6.11, XZ 5.2.4, xorg macros, xprop 1.2.4, xproto 7.0.31, YAXT 0.6.2, yaff 1.6.0 + - Beast 1.10.4, Boost.Python 1.71.0, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, fastp 0.20.0, freeglut 3.2.1, GDAL 3.0.2, + GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, hwloc 2.1.0, Jellyfish 2.3.0, Julia 1.3.1, LibTIFF 4.1.0, libxml2 2.9.10, + lxml 4.4.2, Mothur 1.43.0, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, numactl 2.0.13, + OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, plotly.py 4.4.1, + pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0, + SWIG 4.0.1, Salmon 1.0.0, SuiteSparse 5.6.0, snakemake 5.7.1, TensorFlow 2.1.0 w/ fosscuda/2019b, torchvision 0.4.2, + WPS 4.1, WRF 4.1.3 - added easyconfigs for intel/2020.00 toolchain (#9575) - minor enhancements, including: - add POWER9 support to CUDA 10.1 easyconfigs (#9442) - build CMake in parallel (#9543) - use NCCL for GPU ops in Horovod 0.18.2 easyconfig (#9562) - - use alias to ensure the OpenBLAS library is used for pythran (#9594) + - update Java/1.8 wrapper to Java/1.8.0_231 (for x86_64) (#9585) - various bug fixes, including: - fix remote launch of broker and workers for SCOOP (#9366) - - fix failing sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using foss/2018b) (#9388) + - fix failing RPATH sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using foss/2018b) (#9388) - add missing 'wheel' extensions to Spark 2.4.0 easyconfig using intel/2018b toolchain (#9424) - add missing OS dependencies in Java 1.8 easyconfig used on POWER systems (#9454) - fix build of recent Bazel versions on Power9 + stick to Java/1.8 as dependency (#9455) - fix CMake 3.15.3 build on Power (+ enable building in parallel) (#9469) - fix source URLs in xorg-macros easyconfigs (#9477, #9578) - add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs & enable 'pip check' in sanity check (#9479) - - disable running of 'sudo apt-get update' in GitHub CI config, since it's failing (and we don't really need it) (#9492) - - remove (wrong) GI_TYPELIB_PATH and XDG_DATA_DIRS (#9528) + - remove (wrong) GI_TYPELIB_PATH and XDG_DATA_DIRS in various easyconfigs (#9528, #9577, #9615) - use xorg-macros as dependency in X11 easyconfigs (rather than installing it as a bundle component) (#9546) - fix lpsymphony extension for R-bundle-Bioconductor (#9548) - add correct 'old-versions' source URL to all Mesa easyconfigs (#9569) - - add missing checksums for Armadillo (#9572) - - only require sanity_pip_check if use_pip is enabled too (fixes #9563) (#9576) + - add missing SHA256 checksums for Armadillo (#9572) - also define $AUGUSTUS_BIN_PATH and $AUGUSTUS_SCRIPTS_PATH in generated module file for AUGUSTUS (#9579) - add SSL OS dependencies for GDAL 3.0.0 (#9586) - add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension (#9587) - patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long double in GCC (#9590) - patch for GCCcore 8.2.0 to fix '__float128 is not supported on this target' on ppc64le (#9591) - - fix name for plotly extension in plotly.py v4.4.1 easyconfig (#9599) - fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension (#9601) - use absolute path for extraction to allow relocating the build dir for g2log-1.0 (#9604) - - update checksum for kallisto-0.43.1 (#9611) - - fix https// -> https:// in GConf, GST-plugins-base, GStreamer, Graphene, HarfBuzz, Pango easyconfigs (#9615) + - add alternate SHA256 checksum for kallisto-0.43.1 after re-release under same version without code changes (#9611) - add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (#9621) - update ctffind website (#9622) - make sure we use easybuild Clang in pocl easyconfigs (#9624) - - make postinstallcmds independent of PWD in OpenCV 3.1.0 easyconfigs (#9628) + - make postinstallcmds independent of current working directory in OpenCV 3.1.0 easyconfigs (#9628) - update source_urls to include old releases folder in libsodium easyconfigs (#9632) - fix source URLs for ant v1.10.5 - v1.10.7 (#9633) - - allow missing python versionsuffix for existing easyconfig files changed in PRs (#9634) - update URLs to new location of libxc (#9635) - - use pip to install gradunwarp 1.1.0 (HCP fork) (#9637) - - use latest master as release candidate of MRtrix 3.0 (since 3.0_RC4 is not an official release) (#9638) - - add second checksum for rda_1.0.2-2.1.tar.gz in R 3.6.0 (#9644) + - add alternate SHA256 checksum for rda_1.0.2-2.1 extension in R 3.6.0 (#9644) - update source URLs in QCA 2.1.0 easyconfigs (#9647) - - fix Python 3.5.1 easyconfig (bitstring 3.1.3 sources no longer available on PyPI) (#9649) + - fix Python 3.5.1 easyconfig: bitstring 3.1.3 sources no longer available on PyPI) (#9649) - fix tesseract 4.1.0 dependencies (#9650) - - make ICU 64.2 depend on Python3 instead of 2 (#9652) - - use True rather than 'True' for boolean easyconfig parameters (#9657) + - make ICU 64.2 depend on Python3 instead of Python 2, to avoid picking up system Python 3.x (#9652) + - use True (boolean value) rather than 'True' (string value) for boolean easyconfig parameters (#9657) + - fix pyfits easyconfig by adding missing d2to1 extension (#9687) - other changes: - - require that sanity_pip_check is enabled in new/changed easyconfigs (#9516) - - revert "WORKAROUND: Remove check for Python suffix to make CI pass for old ECs (#9577) + - disable running of 'sudo apt-get update' in GitHub CI config, since it's failing (and we don't really need it) (#9492) + - require that sanity_pip_check is enabled in new/changed easyconfigs (#9516, #9576) - update copyright statements for 2020 (#9598) + - allow missing '-Python-*' versionsuffix for existing easyconfig files changed in PRs (#9634) v4.1.0 (December 4th 2019)