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make_test
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make_test
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#!/bin/bash
############################################################################
## Argument scanning ##
############################################################################
ncpath=""
case_name=""
comp_mode="standard"
keep_config=0
restore=0
rm_logs=0
while [ $# -ge 1 ]
do
case $1 in
"--ncpath")
if [ $# -ge 2 ]
then
ncpath=$2
shift 2
else
echo ""
echo "Error: path required after option '--ncpath'. Option ignored."
shift 1
fi
;;
"--debug")
comp_mode="debug"
shift 1
;;
"--keep-config")
keep_config=1
shift 1
;;
"--restore"|'--restore-config')
restore=1
shift 1
;;
"--clean")
rm_logs=1
shift 1
;;
*)
if [ -z $case_name ]
then
case_name=$1
else
echo ""
echo "Warning: Ignore extra input argument \"$1\""
fi
shift 1
;;
esac
done
############################################################################
## Help text ##
############################################################################
test $restore -eq 1 -a "$case_name" == "" && case_name="_%STOP%_"
test $rm_logs -eq 1 -a "$case_name" == "" && case_name="_%STOP%_"
if [ "$case_name" == "" -o "$case_name" == "help" -o "$case_name" == "--help" ]
then
echo ""
echo "SYNOPSIS"
echo ""
echo " ./make_test case_name [--ncpath path] [--debug] [--keep-config] [--clean]"
echo " ./make_test --restore|--restore-config"
echo " ./make_test --clean"
echo ""
echo ""
echo "DESCRIPTION"
echo ""
echo " 'make_test' is a bash script that configured GEOCLIM for the given template"
echo " case, compile the code, execute the template run, and compare the outputs"
echo " (several COMBINE key variables) to a reference template run."
echo " It uses the script 'build_GEOCLIM', itself using the Makefile is \"source/\","
echo " and the Fortran codes + Makefile in postproc/template_comparison/ for the"
echo " comparison check."
echo ""
echo " For the sake of simplicity, you must have installed one of the known"
echo " Fortran compiler: gfortran, ifort or pgfortran"
echo ""
echo " You must also have installed a netCDF-Fortran library compatible with your"
echo " Fortran compiler. The compilation procedure gets the library path with"
echo " \`nc-config --prefix\` or use \"/usr\", if it fails."
echo " You can manually specify it with the option '--ncpath path'"
echo ""
echo " Use option '--debug' to compile GEOCLIM with debugging options"
echo ""
echo " When the run is completed, you can compare the outputs with the reference"
echo " one (with same *run* name) that is in 'OUTPUT/templates/'"
echo ""
echo " If you want the code not to restore the original configuration files, and"
echo " to let the ones used for the test, use the option \"--keep-config\". The"
echo " original files will be kept in the backup directory \".case_backup/\""
echo " WARNING: if you re-run \`make_test\` after, these \"test\" configuration"
echo " files will be considered as the original ones, and the true original ones"
echo " will be lost. To avoid that, use the option \"--restore-config\""
echo " (\"--restore\") to put back the eventual files stored in .case_backup/"
echo " This option can be used without running a case (\`./make_test --restore\`)"
echo ""
echo " The option \"--clean\" is for deleting the log files, and can also be used"
echo " without running a case (\`./make_test --clean\`)"
echo ""
echo ""
echo " TEMPLATE CASE NAMES:"
echo ""
echo " ERA5"
echo " Short Geoclim run (100 years) with DynSoil dynamic module, ERA5"
echo " boundary conditions (fixed 1PAL CO2, 0.5° of spatial resolution),"
echo " parametric oceanic temperature (fixed)."
echo " COMBINE resolution: 10 boxes, single coastal box"
echo " Parameterization: ERA5 (old) calibration"
echo " CO2 degassing = deduced from ERA5 calibration"
echo " COMBINE initial condition: restart/geoclim/output.calib_ERA5.equil"
echo " DynSoil initialization: startup:eq (analytical steady-state)"
echo " Oceanic boundary conditions: idealized"
echo " Seafloor sediment transport scheme: uniform"
echo " Input data format: netCDF (GCM outputs)"
echo " CO2 interpolation: logarithmic"
echo " Run name: .testrun_ERA5-DS-short"
echo " ----------"
echo " Reference for climate dataset:"
echo " Hersbach, H. et al., (2019): ERA5 monthly averaged data on single"
echo " levels from 1979 to present. Copernicus Climate Change Service (C3S)"
echo " Climate Data Store (CDS). (accessed on 19 Feb 2020)"
echo " https://doi.org/10.24381/cds.f17050d7"
echo " distributed under Copernicus Products license:"
echo " https://cds.climate.copernicus.eu/api/v2/terms/static/licence-to-use-copernicus-products.pdf"
echo ""
echo " IPSL"
echo " 10 kyr Geoclim run with DynSoil dynamic module, IPSL-CM5A2 pre-"
echo " industrial boundary conditions (res. 96x96), 1 CO2 level (280ppm)."
echo " COMBINE resolution: 10 boxes, single coastal box"
echo " Parameterization: IPSL-CM5A2 calibration"
echo " CO2 degassing = deduced from IPSL-CM5A2 calibration"
echo " COMBINE initial condition: restart/geoclim/output.ref"
echo " DynSoil initialization: startup:eq (analytical steady-state)"
echo " Oceanic boundary conditions: derived from IPSL simulation"
echo " Seafloor sediment transport scheme: neighbourg"
echo " Input data format: netCDF (GCM outputs)"
echo " CO2 interpolation: logarithmic"
echo " Run name: .testrun_IPSL"
echo ""
echo " CESM"
echo " 10 kyr Geoclim run with DynSoil dynamic module, boundary conditions"
echo " are CESM1.2 slab simulations, spatial resolution: 1.25° x 0.9°"
echo " (lon x lat), 2 CO2 levels (1 PAL and 2 PAL), parametric oceanic"
echo " temperature."
echo " COMBINE resolution: 10 boxes, single coastal box"
echo " Parameterization: IPSL-CM5A2 calibration"
echo " Lock Oxygen and Sulfur cycles"
echo " CO2 degassing = 4 times IPSL-CM5A2 calibration"
echo " COMBINE initial condition: restart/geoclim/output.calib_ERA5.equil"
echo " DynSoil initialization: startup:null (no regolith)"
echo " Oceanic boundary conditions: idealized + parametric temperature"
echo " Seafloor sediment transport scheme: uniform"
echo " Input data format: netCDF (GCM outputs)"
echo " CO2 interpolation: logarithmic"
echo " Run name: .testrun_CESM1.2-DSnull"
echo ""
echo " paleo"
echo " 50 kyr Geoclim run with DynSoil steady-state module, boundary"
echo " conditions are Thitonian (150Ma) ocean-atmosphere coupled FOAM"
echo " simulations, spatial resolution: 128x128 (~ 2.8° x 1.4°), 11 CO2"
echo " levels (560ppm -- 8960ppm)."
echo " COMBINE resolution: 10 boxes, single coastal box"
echo " Parameterization: IPSL-CM5A2 calibration"
echo " Oxygen and Sulfur cycles accelerated x33"
echo " CO2 degassing = 2 times pre-industrial IPSL degassing."
echo " Lithology mask: 6 class, uniform (modern values)"
echo " Slope field: \"crude\" linear regression of paleo-elevation."
echo " COMBINE initial condition: internally-generated ('coldstart')"
echo " Oceanic boundary conditions: oceanic temperature from FOAM,"
echo " all others from modern configuration"
echo " Seafloor sediment transport scheme: uniform"
echo " Input data format: netCDF (GCM outputs)"
echo " CO2 interpolation: logarithmic"
echo " Run name: .testrun_FOAM-paleo"
echo " ----------"
echo " Reference for GCM simulations:"
echo " Pohl, A et al., 2019,"
echo " https://doi.pangaea.de/10.1594/PANGAEA.904255"
echo " distributed under Creative Commons license (CC-BY-4.0)"
echo " https://creativecommons.org/licenses/by/4.0/"
echo ""
echo " ascii"
echo " 10 kyr Geoclim run with parametric weathering law (DynSoil module"
echo " not activated), boundary conditions are pre-industrial FOAM"
echo " simulations, spatial resolution: 7.5° x 4.5° (lon x lat), 6 CO2"
echo " levels (200ppm -- 560ppm), parametric oceanic temperature."
echo " COMBINE resolution: 10 boxes, single coastal box"
echo " Parameterization: IPSL-CM5A2 calibration"
echo " CO2 degassing = 2 times pre-industrial IPSL degassing."
echo " Lithology mask: 6 class, uniform."
echo " COMBINE initial condition: restart/geoclim/output.calib_ERA5.equil"
echo " Oceanic boundary conditions: historical (with parametric temp.)"
echo " Seafloor sediment transport scheme: uniform"
echo " Input data format: ascii"
echo " CO2 interpolation: linear"
echo " Run name: .testrun_FOAM-ascii"
echo ""
echo " orbit"
echo " 400 kyr Geoclim run with DynSoil steady-state module, idealized"
echo " orbital cycles (precession, eccentricity and obliquity), and"
echo " made-up boundary conditions (both climate and slope) on a \"fake\""
echo " 3x2 grid, with 1 CO2 level."
echo " COMBINE resolution: 10 boxes, single coastal box"
echo " Parameterization: IPSL-CM5A2 calibration"
echo " CO2 degassing = pre-industrial IPSL degassing."
echo " Lithology mask: 6 class, uniform"
echo " COMBINE initial condition: restart/geoclim/output.calib_ERA5.equil"
echo " Oceanic boundary conditions: historical (with parametric temp.)"
echo " Seafloor sediment transport scheme: uniform"
echo " Input data format: netCDF (GCM outputs)"
echo " CO2 interpolation: logarithmic"
echo " Climatic (orbital) parameters reading: every 1 kyr"
echo " Run ending: when reached end of climatic parameter time-series"
echo " Run name: .testrun_FakeOrbitParam"
echo ""
echo " 19box"
echo " 1 kyr Geoclim run with DynSoil dynamic module, IPSL-CM5A2 pre-"
echo " industrial boundary conditions (res. 96x96), 1 CO2 level (280ppm)."
echo " COMBINE resolution: 19 boxes (Arctic, Atlantic, Pacific, S oce.),"
echo " coastal boxes split per oceanic basin."
echo " Parameterization: IPSL-CM5A2 calibration"
echo " CO2 degassing = deduced from IPSL-CM5A2 calibration"
echo " COMBINE initial condition: internally-generated ('coldstart')"
echo " DynSoil initialization: startup:eq (analytical steady-state)"
echo " Oceanic boundary conditions: derived from IPSL simulation"
echo " Seafloor sediment transport scheme: neighbourg"
echo " Land-to-ocean flux routing: deduced from IPSL basinmap"
echo " Input data format: netCDF (GCM outputs)"
echo " CO2 interpolation: logarithmic"
echo " Run name: .testrun_IPSL"
exit 0
fi
############################################################################
## Template configuration ##
############################################################################
# If ask, restore eventual files stored in backup directory
if [ $restore -eq 1 ]
then
if [ -d .case_backup ]
then
mv -f .case_backup/IO_CONDITIONS config/IO_CONDITIONS
mv -f .case_backup/constante.f90 source/constante.f90
mv -f .case_backup/cont_weath.f source/cont_weath.f
mv -f .case_backup/shape.inc source/shape.inc
mv -f .case_backup/coupler.inc source/coupler.inc
rm -r -f .case_backup
else
echo ""
echo "NOTE: no backup files to restore."
fi
fi
if [ "$case_name" == "_%STOP%_" ]
then
test $rm_logs -eq 1 && rm -f GEOCLIM_environment build.log build.error postproc/template_comparison/build.log postproc/template_comparison/build.error
exit 0
fi
# Backup of files susceptible to be modified:
rm -r -f .case_backup
mkdir .case_backup
cp config/IO_CONDITIONS source/shape.inc source/coupler.inc source/constante.f90 source/cont_weath.f .case_backup/
case $case_name in
"ERA5")
# Copy main configuration file
test -e config/IO_CONDITIONS && rm -f config/IO_CONDITIONS
cp config/templates/IO_CONDITIONS.ERA5-short config/IO_CONDITIONS
config_iostat=$?
#
test -e 'source/constante.f90' && rm -f 'source/constante.f90'
cp 'source/templates/constante.f90.ERA5' 'source/constante.f90'
test $? -ne 0 && config_iostat=1
#
# Check that other configuration files exist
ls config/templates/GCM_input_conditions.ERA5 > /dev/null
test $? -ne 0 && config_iostat=1
#
ls config/templates/cond_p20.ERA5-short.dat > /dev/null
test $? -ne 0 && config_iostat=1
#
# Run configuration
resolution="1,720,360,6,10"
compset="COMBINE_WTH:DynSoil%dyn"
interpolation="log"
other_options=""
#
# executable name (as will be defined by 'build_GEOCLIM')
exec_name='geoclim_B-10_R-1x720x360x6_DS-10lev.exe'
;;
"IPSL")
# Copy main configuration file and model parameter file
test -e config/IO_CONDITIONS && rm -f config/IO_CONDITIONS
cp config/templates/IO_CONDITIONS.IPSL-test config/IO_CONDITIONS
config_iostat=$?
#
test -e 'source/constante.f90' && rm -f 'source/constante.f90'
cp 'source/templates/constante.f90.IPSL-CM5A2' 'source/constante.f90'
test $? -ne 0 && config_iostat=1
#
# Check that other configuration files exist
ls config/templates/GCM_input_conditions.IPSL-CM5A2 > /dev/null
test $? -ne 0 && config_iostat=1
#
ls config/templates/cond_p20.IPSL-test.dat > /dev/null
test $? -ne 0 && config_iostat=1
#
# Run configuration
resolution="1,96,96,6,10"
compset="COMBINE_WTH:DynSoil%dyn"
interpolation="log"
other_options=""
#
# executable name (as will be defined by 'build_GEOCLIM')
exec_name='geoclim_B-10_R-1x96x96x6_DS-10lev.exe'
;;
"CESM")
# Copy main configuration file
test -e config/IO_CONDITIONS && rm -f config/IO_CONDITIONS
cp config/templates/IO_CONDITIONS.CESM1.2-test config/IO_CONDITIONS
config_iostat=$?
#
test -e 'source/constante.f90' && rm -f 'source/constante.f90'
cp 'source/templates/constante.f90.ref' 'source/constante.f90'
test $? -ne 0 && config_iostat=1
#
# Check that other configuration files exist
ls config/templates/GCM_input_conditions.CESM1.2-test > /dev/null
test $? -ne 0 && config_iostat=1
#
ls config/templates/cond_p20.CESM1.2-test.dat > /dev/null
test $? -ne 0 && config_iostat=1
#
# Run configuration
resolution="2,288,192,6,10"
compset="COMBINE_WTH:DynSoil%dyn"
interpolation="log"
other_options="--lock OS"
#
# executable name (as will be defined by 'build_GEOCLIM')
exec_name='geoclim_B-10_R-2x288x192x6_DS-10lev_LCK-OS.exe'
;;
"paleo")
# Copy main configuration file
test -e config/IO_CONDITIONS && rm -f config/IO_CONDITIONS
cp config/templates/IO_CONDITIONS.FOAM-paleo config/IO_CONDITIONS
config_iostat=$?
#
test -e 'source/constante.f90' && rm -f 'source/constante.f90'
cp 'source/templates/constante.f90.ref' 'source/constante.f90'
test $? -ne 0 && config_iostat=1
#
# Check that other configuration files exist
ls config/templates/GCM_input_conditions.FOAM-paleo > /dev/null
test $? -ne 0 && config_iostat=1
#
ls config/templates/cond_p20.FOAM-paleo.dat > /dev/null
test $? -ne 0 && config_iostat=1
#
# Run configuration
resolution="11,128,128,6,10"
compset="COMBINE_WTH:DynSoil%steady"
interpolation="log"
other_options=""
#
# executable name (as will be defined by 'build_GEOCLIM')
exec_name='geoclim_B-10_R-11x128x128x6_DS-SS.exe'
;;
"ascii")
# Copy main configuration file
test -e config/IO_CONDITIONS && rm -f config/IO_CONDITIONS
cp config/templates/IO_CONDITIONS.FOAM-ascii config/IO_CONDITIONS
config_iostat=$?
#
test -e 'source/constante.f90' && rm -f 'source/constante.f90'
cp 'source/templates/constante.f90.ref' 'source/constante.f90'
test $? -ne 0 && config_iostat=1
#
# Check that other configuration files exist
ls config/templates/cond_p20.FOAM-ascii.dat > /dev/null
test $? -ne 0 && config_iostat=1
#
# Run configuration
resolution="6,48,40,6"
compset="COMBINE_WTH:old"
interpolation="linear"
other_options=""
#
# executable name (as will be defined by 'build_GEOCLIM')
exec_name='geoclim_B-10_R-6x48x40x6.exe'
;;
"orbit")
# Copy main configuration file
test -e config/IO_CONDITIONS && rm -f config/IO_CONDITIONS
cp config/templates/IO_CONDITIONS.FakOrbPar config/IO_CONDITIONS
config_iostat=$?
#
test -e 'source/constante.f90' && rm -f 'source/constante.f90'
cp 'source/templates/constante.f90.ref' 'source/constante.f90'
test $? -ne 0 && config_iostat=1
#
# Check that other configuration files exist
ls config/templates/GCM_input_conditions.FakOrbPar > /dev/null
test $? -ne 0 && config_iostat=1
#
ls config/templates/cond_p20.FakOrbPar.dat > /dev/null
test $? -ne 0 && config_iostat=1
#
# Run configuration
resolution="1,3,2,6,10"
compset="COMBINE_WTH:DynSoil%steady"
interpolation="log"
other_options="--clim-param 3,2,4 --clim-param-periods ,,360. --param-ending stoprun"
#
# executable name (as will be defined by 'build_GEOCLIM')
exec_name='geoclim_B-10_R-1x3x2x6_P-3x2x5x1x1_DS-SS.exe'
;;
"19box")
# Copy main configuration file and model parameter file
test -e config/IO_CONDITIONS && rm -f config/IO_CONDITIONS
cp config/templates/IO_CONDITIONS.IPSL-AAPS config/IO_CONDITIONS
config_iostat=$?
#
test -e 'source/constante.f90' && rm -f 'source/constante.f90'
cp 'source/templates/constante.f90.IPSL-CM5A2' 'source/constante.f90'
test $? -ne 0 && config_iostat=1
#
# Check that other configuration files exist
ls config/templates/GCM_input_conditions.IPSL-CM5A2 > /dev/null
test $? -ne 0 && config_iostat=1
#
ls config/templates/cond_p20.IPSL-AAPS.dat > /dev/null
test $? -ne 0 && config_iostat=1
#
# Run configuration
resolution="1,96,96,6,10"
compset="COMBINE_WTH:DynSoil%dyn"
interpolation="log"
other_options="--nbasin 19"
#
# executable name (as will be defined by 'build_GEOCLIM')
exec_name='geoclim_B-19_R-1x96x96x6_DS-10lev.exe'
;;
*)
echo ""
echo "Error: unknown template name \"$case_name\""
exit -1
esac
if [ $config_iostat -ne 0 ]
then
echo ""
echo "ERROR: template configuration file(s) missing"
# put back original files
cp -f .case_backup/IO_CONDITIONS config/IO_CONDITIONS
cp -f .case_backup/constante.f90 source/constante.f90
cp -f .case_backup/cont_weath.f source/cont_weath.f
rm -r -f .case_backup
exit 1
fi
# Erase deathnote file
test -e deathnote.txt && rm -f deathnote.txt
touch deathnote.txt
############################################################################
## Compile and run template ##
############################################################################
# Complete configuration and compile (with 'build_GEOCLIM' command
test -z $ncpath && netcdf_option="" || netcdf_option="--ncpath $ncpath"
./build_GEOCLIM --resolution $resolution --compset $compset --co2-interp $interpolation --compilation-mode $comp_mode --reset $netcdf_option $other_options
# If successful: run template
test $? -eq 0 && executable/$exec_name 0 1 3 0 0
# If run succesfull: make template comparison
if [ $? -eq 0 ]
then
echo ""
echo ""
echo "Compare outputs to reference template output"
echo "============================================"
echo ""
source GEOCLIM_environment
cd postproc/template_comparison/
if [ $? -eq 0 ]
then
rm -f build.*
echo "Compile comparison code..."
echo ""
if [ "$FFLAGS" != "" ]
then
make FC=$FC MODE=$MODE FFLAGS="$FFLAGS" > build.log 2> build.error
elif [ "$main_fflags" != "" ]
then
if [ "$NETCDF_FLAGS" != "" ]
then
make FC=$FC MODE=$MODE main_flags="$main_fflags" NETCDF_FLAGS="$NETCDF_FLAGS" > build.log 2> build.error
else
make FC=$FC MODE=$MODE main_flags="$main_fflags" > build.log 2> build.error
fi
elif [ "$NETCDF_FLAGS" != "" ]
then
make FC=$FC MODE=$MODE NETCDF_FLAGS="$NETCDF_FLAGS" > build.log 2> build.error
else
make FC=$FC MODE=$MODE > build.log 2> build.error
fi
if [ $? -eq 0 ]
then
echo ""
echo "Execute comparison code..."
echo ""
./compare_template.exe
else
echo ""
echo "Compilation failed. Cannot conduct comparison check."
echo "See postproc/template_comparison/build.log and postproc/template_comparison/build.error"
echo "for more information"
fi
make clc > /dev/null 2>&1
cd ../../
fi
fi
# Put back original files
if [ $keep_config -eq 0 ]
then
cp -f .case_backup/IO_CONDITIONS config/IO_CONDITIONS
cp -f .case_backup/constante.f90 source/constante.f90
cp -f .case_backup/cont_weath.f source/cont_weath.f
cp -f .case_backup/shape.inc source/shape.inc
cp -f .case_backup/coupler.inc source/coupler.inc
rm -r -f .case_backup
fi
test $rm_logs -eq 1 && rm -f GEOCLIM_environment build.log build.error postproc/template_comparison/build.log postproc/template_comparison/build.error
cd source
make clean > /dev/null