Merge branch 'nessi.no-2023.06' of github-trz:NorESSI/software-layer …

…into nessi-2023.06-qt5-5.15.13-2023b

.github/workflows/scorecards.yml

@@ -40,7 +40,7 @@ jobs:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@99c53751e09b9529366343771cc321ec74e9bd3d # v2.0.6
+        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
         with:
           results_file: results.sarif
           results_format: sarif

.github/workflows/tests_scripts.yml

@@ -3,9 +3,9 @@ name: Tests for scripts
 on:
   push:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh
@@ -15,9 +15,9 @@ on:
 
   pull_request:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh

EESSI-determine-rebuilds.sh

@@ -0,0 +1,123 @@
+#!/bin/bash
+#
+# Script to determine which parts of the EESSI software stack (version set through init/eessi_defaults)
+# have to be rebuilt
+
+# see example parsing of command line arguments at
+#   https://wiki.bash-hackers.org/scripting/posparams#using_a_while_loop
+#   https://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash
+
+display_help() {
+  echo "usage: $0 [OPTIONS]"
+  echo "  -g | --generic         -  instructs script to build for generic architecture target"
+  echo "  -h | --help            -  display this usage information"
+}
+
+POSITIONAL_ARGS=()
+
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    -g|--generic)
+      DETECTION_PARAMETERS="--generic"
+      shift
+      ;;
+    -h|--help)
+      display_help  # Call your function
+      # no shifting needed here, we're done.
+      exit 0
+      ;;
+    -*|--*)
+      echo "Error: Unknown option: $1" >&2
+      exit 1
+      ;;
+    *)  # No more options
+      POSITIONAL_ARGS+=("$1") # save positional arg
+      shift
+      ;;
+  esac
+done
+
+set -- "${POSITIONAL_ARGS[@]}"
+
+TOPDIR=$(dirname $(realpath $0))
+
+export TMPDIR=$(mktemp -d /tmp/eessi-remove.XXXXXXXX)
+
+source $TOPDIR/scripts/utils.sh
+
+echo ">> Determining software subdirectory to use for current build host..."
+if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
+  export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
+  echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
+else
+  echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
+fi
+
+echo ">> Setting up environment..."
+
+source $TOPDIR/init/bash
+
+if [ -d $EESSI_CVMFS_REPO ]; then
+    echo_green "$EESSI_CVMFS_REPO available, OK!"
+else
+    fatal_error "$EESSI_CVMFS_REPO is not available!"
+fi
+
+if [[ -z ${EESSI_SOFTWARE_SUBDIR} ]]; then
+    fatal_error "Failed to determine software subdirectory?!"
+elif [[ "${EESSI_SOFTWARE_SUBDIR}" != "${EESSI_SOFTWARE_SUBDIR_OVERRIDE}" ]]; then
+    fatal_error "Values for EESSI_SOFTWARE_SUBDIR_OVERRIDE (${EESSI_SOFTWARE_SUBDIR_OVERRIDE}) and EESSI_SOFTWARE_SUBDIR (${EESSI_SOFTWARE_SUBDIR}) differ!"
+else
+    echo_green ">> Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory!"
+fi
+
+echo ">> Configuring EasyBuild..."
+EB="eb"
+source $TOPDIR/configure_easybuild
+
+echo ">> Setting up \$MODULEPATH..."
+# make sure no modules are loaded
+module --force purge
+# ignore current $MODULEPATH entirely
+module unuse $MODULEPATH
+module use $EASYBUILD_INSTALLPATH/modules/all
+if [[ -z ${MODULEPATH} ]]; then
+    fatal_error "Failed to set up \$MODULEPATH?!"
+else
+    echo_green ">> MODULEPATH set up: ${MODULEPATH}"
+fi
+
+# assume there's only one diff file that corresponds to the PR patch file
+pr_diff=$(ls [0-9]*.diff | head -1)
+
+# if this script is run as root, use PR patch file to determine if software needs to be removed first
+changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing' | grep "/rebuilds/")
+if [ -z ${changed_easystacks_rebuilds} ]; then
+    echo "No software needs to be removed."
+else
+    for easystack_file in ${changed_easystacks_rebuilds}; do
+        # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
+        eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+
+        # load EasyBuild module (will be installed if it's not available yet)
+        source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
+
+        if [ -f ${easystack_file} ]; then
+            echo_green "Software rebuild(s) requested in ${easystack_file}, so determining which existing installation have to be removed..."
+            # we need to remove existing installation directories first,
+            # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
+            #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
+            rebuild_apps=$(eb --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+            for app in ${rebuild_apps}; do
+                app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
+                app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
+                echo_yellow "Removing ${app_dir} and ${app_module}..."
+                find ${app_dir} -type d | sed -e 's/^/REMOVE_DIRECTORY /'
+                find ${app_dir} -type f | sed -e 's/^/REMOVE_FILE /'
+                echo "REMOVE_MODULE ${app_module}"
+            done
+        else
+            fatal_error "Easystack file ${easystack_file} not found!"
+        fi
+    done
+fi

EESSI-extend-2023.06-easybuild.eb

@@ -0,0 +1,170 @@
+easyblock = 'Bundle'
+
+name = 'NESSI-extend'
+version = '2023.06'
+# May have different ways to extend NESSI in the future (manually, other tools,...)
+versionsuffix = '-easybuild'
+
+homepage = 'https://documentation.sigma2.no/software/nessi_eessi.html'
+
+description = """
+ NESSI is an innovative service to make optimized scientific software
+ installations available on any machine anywhere in the world in near
+ real-time - without the need to build or install the software. NESSI
+ works similarly to popular streaming services for videos and music.
+
+ NESSI is a sibling of EESSI, the European Environment for Scientific
+ Software Installations (see https://eessi.io/docs).
+
+ This module allows you to extend NESSI using the same configuration for
+ EasyBuild as NESSI itself uses. A number of environment variables control the
+ behaviour of the module:
+ - NESSI_USER_INSTALL can be set to a location to install modules for use by
+   the user only. The location must already exist on the filesystem.
+ - NESSI_PROJECT_INSTALL can be set to a location to install modules for use by
+   a project. The location must already exist on the filesystem and you should
+   ensure that the location has the correct Linux group and the SGID permission
+   is set on that directory (`chmod g+s $NESSI_PROJECT_INSTALL`) so that all
+   members of the group have permission to read and write installations.
+ - NESSI_SITE_INSTALL is either defined or not and cannot be used with another
+   environment variable. A site installation is done in a defined location and
+   any installations there are (by default) world readable.
+ - NESSI_CVMFS_INSTALL is either defined or not and cannot be used with another
+   environment variable. A CVMFS installation targets a defined location which
+   will be ingested into CVMFS and is only useful for CVMFS administrators.
+ - If none of the environment variables above are defined, a NESSI_USER_INSTALL
+   is assumed with a value of $HOME/NESSI
+ If both NESSI_USER_INSTALL and NESSI_PROJECT_INSTALL are defined, both sets of
+ installations are exposed, but new installations are created as user
+ installations.
+"""
+
+toolchain = SYSTEM
+
+# All the dependencies we filter in NESSI
+local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,M4,makeinfo,ncurses,util-linux,XZ,zlib,PSM2"
+local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
+local_deps_to_filter += local_arch_specific_deps_to_filter[ARCH]
+
+# Set the universal EasyBuild variables
+modextravars = {
+    'EASYBUILD_FILTER_DEPS': local_deps_to_filter,
+    'EASYBUILD_IGNORE_OSDEPS': '1',
+    'EASYBUILD_DEBUG': '1',
+    'EASYBUILD_TRACE': '1',
+    'EASYBUILD_ZIP_LOGS': 'bzip2',
+    'EASYBUILD_RPATH': '1',
+    'EASYBUILD_FILTER_ENV_VARS': 'LD_LIBRARY_PATH',
+    'EASYBUILD_READ_ONLY_INSTALLDIR': '1',
+    'EASYBUILD_MODULE_EXTENSIONS': '1',
+    'EASYBUILD_EXPERIMENTAL': '1',
+}
+
+# Need a few other variables, but they are more dynamic
+# EASYBUILD_SYSROOT=${EPREFIX}
+# EASYBUILD_PREFIX=${WORKDIR}/easybuild
+# EASYBUILD_HOOKS=${EESSI_PREFIX}/init/easybuild/eb_hooks.py
+# EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
+# EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
+#
+# And also some optional ones based on the kind of installation
+# EASYBUILD_SET_GID_BIT
+# EASYBUILD_GROUP_WRITABLE_INSTALLDIR
+# EASYBUILD_UMASK
+# EASYBUILD_STICKY_BIT
+modluafooter = """
+if (mode() == "load") then
+  -- Use a working directory for temporary build files
+  if (os.getenv("WORKING_DIR") == nil) then
+    LmodMessage("-- Using /tmp/$USER as a temporary working directory for installations, you can override this by setting the environment variable WORKING_DIR and reloading the module (e.g., /dev/shm is a common option)")
+  end
+end
+working_dir = os.getenv("WORKING_DIR") or pathJoin("/tmp", os.getenv("USER"))
+-- Gather the EPREFIX to use as a sysroot
+sysroot = os.getenv("EESSI_EPREFIX")
+-- Use an installation prefix that we _should_ have write access to
+if (os.getenv("NESSI_CVMFS_INSTALL") ~= nil) then
+  -- Make sure no other NESSI install environment variables are set
+  if ((os.getenv("NESSI_SITE_INSTALL") ~= nil) or (os.getenv("NESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("NESSI_USER_INSTALL") ~= nil)) then
+    LmodError("You cannot use NESSI_CVMFS_INSTALL in combination with any other NESSI_*_INSTALL environment variables")
+  end
+  eessi_cvmfs_install = true
+  easybuild_installpath = os.getenv("EESSI_SOFTWARE_PATH")
+elseif (os.getenv("NESSI_SITE_INSTALL") ~= nil) then
+  -- Make sure no other NESSI install environment variables are set
+  if ((os.getenv("NESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("NESSI_USER_INSTALL") ~= nil)) then
+    LmodError("You cannot use NESSI_SITE_INSTALL in combination with any other NESSI_*_INSTALL environment variables")
+  end
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
+else
+  -- Deal with user and project installs
+  project_install = os.getenv("NESSI_PROJECT_INSTALL")
+  project_modulepath = nil
+  if (project_install ~= nil) then
+    -- Check the folder exists
+    if not isDir(project_install) then
+      LmodError("The location of NESSI_PROJECT_INSTALL (" .. project_install .. ") does not exist or is not a folder")
+    end
+    if (mode() == "load") then
+      LmodMessage("Configuring for use of NESSI_PROJECT_INSTALL under " .. project_install)
+    end
+    easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), project_install)
+    project_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
+  end
+  user_install = os.getenv("NESSI_USER_INSTALL")
+  user_modulepath = nil
+  if (user_install ~= nil) then
+    -- Check the folder exists
+    if not isDir(user_install) then
+      LmodError("The location of NESSI_USER_INSTALL (" .. user_install .. ") does not exist or is not a folder")
+    end
+  elseif (user_install == nil) and (project_install == nil) then
+    -- No need to check for existence when we use a HOME subdir
+    user_install = pathJoin(os.getenv("HOME"), "nessi")
+  end
+  if (user_install ~= nil) then
+    if (mode() == "load") then
+      LmodMessage("Configuring for use of NESSI_USER_INSTALL under " .. user_install)
+    end
+    easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), user_install)
+    user_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
+  end
+end
+if (mode() == "load") then
+  LmodMessage("-- To create installations for NESSI, you _must_ have write permissions to " .. easybuild_installpath)
+  -- Advise them to reuse sources
+  if (os.getenv("EASYBUILD_SOURCEPATH") == nil) then
+    LmodMessage("-- You may wish to configure a sources directory for EasyBuild (for example, via setting the environment variable EASYBUILD_SOURCEPATH) to allow you to reuse existing sources for packages.")
+  end
+end
+-- Set the relevant universal environment variables for EasyBuild
+setenv ("EASYBUILD_SYSROOT", sysroot)
+setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
+setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
+setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
+setenv ("EASYBUILD_UMASK", "002")
+
+-- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
+if (user_modulepath ~= nil) then
+  -- Use a more restrictive umask for this case
+  setenv ("EASYBUILD_UMASK", "022")
+  setenv ("EASYBUILD_STICKY_BIT", "1")
+  -- configure MODULEPATH
+  if (project_modulepath ~= nil) then
+    prepend_path("MODULEPATH", project_modulepath)
+  end
+  prepend_path("MODULEPATH", user_modulepath)
+elseif (project_modulepath ~= nil) then
+  setenv ("EASYBUILD_SET_GID_BIT", "1")
+  setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
+  setenv ("EASYBUILD_STICKY_BIT", "0")
+  -- configure MODULEPATH
+  prepend_path("MODULEPATH", project_modulepath)
+end
+-- Make sure EasyBuild itself is loaded
+if not ( isloaded("EasyBuild") ) then
+    load("EasyBuild")
+end
+"""
+
+moduleclass = 'devel'