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fates parameter file auto-build for all tests #2336

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fates parameter file auto-build for all tests #2336

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3179627
adding fates parameter auto-build to all tests
rgknox Jan 25, 2024
5404a7c
Bring in changes to run_sys_tests from ctsm5.1.dev166.
samsrabin Feb 12, 2024
5e5d485
run_sys_tests now checks modules needed for FatesColdSeedDisp.
samsrabin Feb 12, 2024
fe5d12a
Remove code duplication in Fates*/shell_commands.
samsrabin Feb 15, 2024
ec6cd21
Fix check of modify_fates_paramfile module availability for run_sys_t…
samsrabin Feb 15, 2024
d82c7b5
Make dir for FATESPARAMFILE if needed.
samsrabin Feb 15, 2024
c1bd84d
Merge pull request #5 from samsrabin/fates-auto-params-ssr
rgknox Feb 22, 2024
ed41f90
Merge branch 'master' into fates-auto-params
samsrabin Feb 22, 2024
267fe14
added python to the call on modify_fates_paramfile.py, needed for izumi
rgknox Feb 26, 2024
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5 changes: 5 additions & 0 deletions cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands
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@@ -1,2 +1,7 @@
./xmlchange CLM_BLDNML_OPTS="-no-megan" --append
./xmlchange BFBFLAG="TRUE"

SRCROOT=`./xmlquery SRCROOT --value`
. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh

ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
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1 change: 1 addition & 0 deletions cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm
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Expand Up @@ -4,6 +4,7 @@ hist_nhtfrq = -24
hist_empty_htapes = .true.
hist_ndens = 1
fates_spitfire_mode = 1
fates_paramfile='${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc'
hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD',
'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF','FATES_DAYSINCE_COLDLEAFON',
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9 changes: 3 additions & 6 deletions cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands
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@@ -1,9 +1,6 @@
SRCDIR=`./xmlquery SRCROOT --value`
CASEDIR=`./xmlquery CASEROOT --value`
FATESDIR=$SRCDIR/src/fates/
FATESPARAMFILE=$SRCDIR/fates_params_seeddisp_4x5.nc

ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
SRCROOT=`./xmlquery SRCROOT --value`
. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
CASE=`./xmlquery CASE --value`

$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_fraction --val 0.2 --allpfts
$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_max_dist --val 2500000 --allpfts
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1 change: 0 additions & 1 deletion cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm
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@@ -1,3 +1,2 @@
fates_paramfile = '$SRCROOT/fates_params_seeddisp_4x5.nc'
fates_seeddisp_cadence = 1
hist_fincl1 = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF'
9 changes: 2 additions & 7 deletions cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands
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@@ -1,8 +1,3 @@
SRCDIR=`./xmlquery SRCROOT --value`
CASEDIR=`./xmlquery CASEROOT --value`
FATESDIR=$SRCDIR/src/fates
FATESPARAMFILE=$CASEDIR/fates_params_twostream.nc

ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl

SRCROOT=`./xmlquery SRCROOT --value`
. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_rad_model --val 2 --allpfts
2 changes: 1 addition & 1 deletion cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm
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fates_paramfile = '$CASEROOT/fates_params_twostream.nc'

9 changes: 2 additions & 7 deletions cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands
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@@ -1,8 +1,3 @@
SRCDIR=`./xmlquery SRCROOT --value`
CASEDIR=`./xmlquery CASEROOT --value`
FATESDIR=$SRCDIR/src/fates
FATESPARAMFILE=$CASEDIR/fates_params_twostream.nc

ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl

SRCROOT=`./xmlquery SRCROOT --value`
. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_rad_model --val 2 --allpfts
3 changes: 1 addition & 2 deletions cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm
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fates_paramfile = '$CASEROOT/fates_params_twostream.nc'
use_fates_fixed_biogeog=.true.
use_fates_fixed_biogeog=.true.
2 changes: 2 additions & 0 deletions cime_config/testdefs/testmods_dirs/clm/_scripts/README
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@@ -0,0 +1,2 @@
This directory contains scripts that can be called in
shell_commands of multiple testmods.
11 changes: 11 additions & 0 deletions cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
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# This script should be called in shell_commands with
# . "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh
# where the leading period ensures it's run in the same shell.

CASE=`./xmlquery CASE --value`
FATESDIR="${SRCROOT}/src/fates"
FATESPARAMDIR="${SRCROOT}/src/fates/parameter_files/binaries"
mkdir -p "${FATESPARAMDIR}"
FATESPARAMFILE="${FATESPARAMDIR}/${CASE}-params.nc"

# No exit status because it should be called in the same shell.
9 changes: 7 additions & 2 deletions python/ctsm/run_sys_tests.py
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Expand Up @@ -717,7 +717,8 @@ def _get_testmod_list(test_attributes, unique=False):
for test_attribute in test_attributes:
for dot_split in test_attribute.split("."):
slash_replaced = dot_split.replace("/", "-")
for ddash_split in slash_replaced.split("--"):
newline_replaced = slash_replaced.replace("\n", "")
for ddash_split in newline_replaced.split("--"):
if "clm-" in ddash_split and (ddash_split not in testmods or not unique):
testmods.append(ddash_split)

Expand All @@ -744,7 +745,11 @@ def _check_py_env(test_attributes):
raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err

# Check that list for any testmods that use modify_fates_paramfile.py
testmods_to_check = ["clm-FatesColdTwoStream", "clm-FatesColdTwoStreamNoCompFixedBioGeo"]
testmods_to_check = [
"clm-FatesColdSeedDisp",
"clm-FatesColdTwoStream",
"clm-FatesColdTwoStreamNoCompFixedBioGeo",
]
testmods = _get_testmod_list(test_attributes)
if any(t in testmods_to_check for t in testmods):
# This bit is needed because it's outside the top-level python/ directory.
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