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Merge pull request #3431 from samsrabin/b4b-dev-merge-20250822
ctsm5.3.071: b4b-dev merge 2025-08-22
2 parents a855d4e + 0f90c77 commit 72e8451

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‎.git-blame-ignore-revs‎

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ac03492012837799b7111607188acff9f739044a
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d858665d799690d73b56bcb961684382551193f4

‎cime_config/SystemTests/setparamfile.py‎

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"""
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CTSM-specific test that first runs the set_paramfile tool and then ensures that CTSM does not fail
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using the just-generated parameter file
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"""
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import os
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import sys
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import logging
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import re
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from CIME.SystemTests.system_tests_common import SystemTestsCommon
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# In case we need to import set_paramfile later
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_CTSM_PYTHON = os.path.join(
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os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python"
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)
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sys.path.insert(1, _CTSM_PYTHON)
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logger = logging.getLogger(__name__)
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class SETPARAMFILE(SystemTestsCommon):
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def __init__(self, case):
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"""
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initialize an object interface to the SMS system test
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"""
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SystemTestsCommon.__init__(self, case)
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# Create out-of-the-box lnd_in to obtain paramfile
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case.create_namelists(component="lnd")
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# Find the paramfile to modify
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lnd_in_path = os.path.join(self._get_caseroot(), "CaseDocs", "lnd_in")
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self._paramfile_in = None
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with open(lnd_in_path, "r", encoding="utf-8") as lnd_in:
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for line in lnd_in:
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paramfile_in = re.match(r" *paramfile *= *'(.*)'", line)
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if paramfile_in:
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self._paramfile_in = paramfile_in.group(1)
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break
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if not self._paramfile_in:
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raise RuntimeError(f"paramfile not found in {lnd_in_path}")
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# Get the output file
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self.paramfile_out = os.path.join(self._get_caseroot(), "paramfile.nc")
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# Define set_paramfile command
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self.set_paramfile_cmd = [
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"set_paramfile",
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"-i",
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self._paramfile_in,
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"-o",
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self.paramfile_out,
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# Change two parameters for one PFT
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"-p",
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"needleleaf_deciduous_boreal_tree",
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"rswf_min=0.35",
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"rswf_max=0.7",
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]
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def build_phase(self, sharedlib_only=False, model_only=False):
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"""
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Run set_paramfile and then build the model
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"""
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# Run set_paramfile.
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# build_phase gets called twice:
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# - once with sharedlib_only = True and
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# - once with model_only = True
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# Because we only need set_paramfile run once, we only do it for the sharedlib_only call.
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# We could also check for the existence of the set_paramfile outputs, but that might lead to
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# a situation where the user expects set_paramfile to be called but it's not. Better to run
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# unnecessarily (e.g., if you fixed some FORTRAN code and just need to rebuild).
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if sharedlib_only:
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self._run_set_paramfile()
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# Do the build
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self.build_indv(sharedlib_only=sharedlib_only, model_only=model_only)
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def _run_set_paramfile(self):
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"""
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Run set_paramfile
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"""
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# Import set_paramfile. Do it here rather than at top because otherwise the import will
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# be attempted even during RUN phase.
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# pylint: disable=wrong-import-position,import-outside-toplevel
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from ctsm.param_utils.set_paramfile import main as set_paramfile
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# Run set_paramfile
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sys.argv = self.set_paramfile_cmd
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set_paramfile()
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# Append
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user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
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with open(user_nl_clm_path, "a", encoding="utf-8") as user_nl_clm:
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user_nl_clm.write(f"paramfile = '{self.paramfile_out}'\n")

‎cime_config/config_pes.xml‎

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</rootpe>
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</pes>
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</mach>
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</grid>
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<grid name="l%mpasa3p75">
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<mach name="derecho">
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<pes pesize="any" compset="any">
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<comment>none</comment>
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<ntasks>
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<ntasks_atm>-80</ntasks_atm>
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<ntasks_lnd>-80</ntasks_lnd>
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<ntasks_rof>-80</ntasks_rof>
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<ntasks_ice>-80</ntasks_ice>
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<ntasks_ocn>-80</ntasks_ocn>
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<ntasks_glc>-80</ntasks_glc>
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<ntasks_wav>-80</ntasks_wav>
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<ntasks_cpl>-80</ntasks_cpl>
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<ntasks_lnd>-80</ntasks_lnd>
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</ntasks>
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<nthrds>
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<nthrds_atm>1</nthrds_atm>
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<nthrds_lnd>1</nthrds_lnd>
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<nthrds_rof>1</nthrds_rof>
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<nthrds_ice>1</nthrds_ice>
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<nthrds_ocn>1</nthrds_ocn>
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<nthrds_glc>1</nthrds_glc>
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<nthrds_wav>1</nthrds_wav>
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<nthrds_cpl>1</nthrds_cpl>
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</nthrds>
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<rootpe>
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<rootpe_atm>0</rootpe_atm>
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<rootpe_lnd>0</rootpe_lnd>
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<rootpe_rof>0</rootpe_rof>
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<rootpe_ice>0</rootpe_ice>
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<rootpe_ocn>0</rootpe_ocn>
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<rootpe_glc>0</rootpe_glc>
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<rootpe_wav>0</rootpe_wav>
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<rootpe_cpl>0</rootpe_cpl>
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</rootpe>
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</pes>
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</mach>
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</grid>
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<grid name="l%0.125nldas2">
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<mach name="any">

‎cime_config/config_tests.xml‎

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<HIST_N>$STOP_N</HIST_N>
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</test>
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<test NAME="SETPARAMFILE">
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<DESC>Modify a copy of the paramfile and run with it.</DESC>
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<INFO_DBUG>1</INFO_DBUG>
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<DOUT_S>FALSE</DOUT_S>
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<CONTINUE_RUN>FALSE</CONTINUE_RUN>
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<REST_OPTION>never</REST_OPTION>
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<HIST_OPTION>$STOP_OPTION</HIST_OPTION>
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<HIST_N>$STOP_N</HIST_N>
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</test>
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<!--
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SSP smoke CLM spinup test (only valid for CLM compsets with CLM45)
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do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

‎cime_config/testdefs/testlist_clm.xml‎

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aux_clm_mpi_serial: aux_clm tests using mpi-serial. Useful for redoing tests that failed due to https://github.com/ESCOMP/CTSM/issues/2916, after having replaced libraries/mpi-serial with a fresh copy.
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subset_data: Tests exercising the subset_data tool and running CTSM with its output
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decomp_init: Initialization tests specifically for examining the PE layout decomposition initialization
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uhr_decomp_init: Initialization tests at Ultra High Resolution - specifically for examining the PE layout decomposition initialization
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interim_restart: Tests having to do with interim restart capability.
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-->
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<testlist version="2.0">
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42034204
</test>
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42054206
<!-- decomp_init tests -->
4206-
<test name="SMS_Ln1_P86x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
4207+
<test name="SMS_D_Ln1_Mmpi-serial" grid="1x1_brazil" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
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<machines>
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<machine name="derecho" compiler="intel" category="decomp_init"/>
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<machine name="izumi" compiler="nag" category="decomp_init"/>
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</machines>
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<options>
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<option name="wallclock">0:05:00</option>
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<option name="comment">mpi-serial self tests with DEBUG</option>
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</options>
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</test>
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<test name="SMS_D_Ln1" grid="f10_f10_mt232" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
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<machines>
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<machine name="derecho" compiler="intel" category="decomp_init"/>
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<machine name="derecho" compiler="gnu" category="decomp_init"/>
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<machine name="izumi" compiler="nag" category="decomp_init"/>
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</machines>
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<options>
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<option name="wallclock">0:05:00</option>
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<option name="comment">Self tests with DEBUG on for f10</option>
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</options>
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</test>
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<test name="SMS_Ln1_P86x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
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<machines>
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<machine name="derecho" compiler="intel" category="decomp_init"/>
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</machines>
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42124234
<option name="comment">Initialization test for ne30pg3 with "Large" layout</option>
42134235
</options>
42144236
</test>
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<test name="SMS_Ln1_P43x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
4237+
<test name="SMS_Ln1_P43x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
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<machines>
42174239
<machine name="derecho" compiler="intel" category="decomp_init"/>
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</machines>
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42214243
<option name="comment">Initialization test for ne30pg3 with "Medium" layout</option>
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</options>
42234245
</test>
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<test name="SMS_Ln1_P22x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
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<test name="SMS_Ln1_P22x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
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<machines>
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<machine name="derecho" compiler="intel" category="decomp_init"/>
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</machines>
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42304252
<option name="comment">Initialization test for ne30pg3 with "Small" layout</option>
42314253
</options>
42324254
</test>
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<test name="SMS_Ln1_PL" grid="ne120pg3_ne120pg3_mt13" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
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<test name="SMS_Ln1_PL" grid="ne120pg3_ne120pg3_mt13" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
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<machines>
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<machine name="derecho" compiler="intel" category="decomp_init"/>
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</machines>
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42394261
<option name="comment">Initialization test for ne120pg3 with "Large" layout</option>
42404262
</options>
42414263
</test>
4242-
<test name="SMS_Ln1_PL" grid="mpasa15_mpasa15" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
4264+
<test name="SMS_Ln1_PL" grid="mpasa15_mpasa15" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
42434265
<machines>
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<machine name="derecho" compiler="intel" category="decomp_init"/>
42454267
</machines>
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42484270
<option name="comment">Initialization test for mpasa15 with "Large" layout</option>
42494271
</options>
42504272
</test>
4273+
<test name="SMS_Ln1" grid="mpasa3p75_mpasa3p75_mt13" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun--clm-mpasa3p75">
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<machines>
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<machine name="derecho" compiler="intel" category="uhr_decomp_init"/>
4276+
</machines>
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<options>
4278+
<option name="wallclock">0:15:00</option>
4279+
<option name="comment">Initialization test for mpasa3p75 default layout</option>
4280+
</options>
4281+
</test>
42514282

42524283
<test name="LGRAIN2_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
42534284
<machines>
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45344565
</options>
45354566
</test>
45364567

4568+
<test name="SETPARAMFILE_Ld5" grid="f10_f10_mg37" compset="I1850Clm60BgcCrujra" testmods="clm/default">
4569+
<machines>
4570+
<machine name="derecho" compiler="gnu" category="aux_clm"/>
4571+
<machine name="derecho" compiler="gnu" category="clm_pymods"/>
4572+
</machines>
4573+
<options>
4574+
<option name="wallclock">00:20:00</option>
4575+
</options>
4576+
</test>
4577+
45374578
<test name="SMS_Ld5" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default">
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<machines>
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<machine name="derecho" compiler="gnu" category="interim_restart"/>

‎cime_config/testdefs/testmods_dirs/clm/for_testing_fastsetup_bypassrun/README‎

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The purpose of this testmod directory is to setup for running fast testing
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of initialization. So it bypasses the run phase and exits early.
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We use cold start so that we can get through initialization faster,
5+
6+
I/O is turned off as much as possible.
7+
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And physics options that make the model run faster are used.

‎cime_config/testdefs/testmods_dirs/clm/for_testing_fastsetup_bypassrun/shell_commands‎

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#!/bin/bash
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./xmlchange CLM_FORCE_COLDSTART="on"
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# We use this testmod in a _Ln1 test; this requires forcing the ROF coupling frequency to same frequency as DATM
5+
./xmlchange ROF_NCPL='$ATM_NCPL'
6+
7+
# Turn off ROF model when used with compsets that have them
8+
./xmlchange RTM_MODE='NULL'
9+
10+
# Turn MEGAN off to run faster
11+
./xmlchange CLM_BLDNML_OPTS='--no-megan' --append
12+
13+
# Use fast structure and NWP configuration for speed
14+
./xmlchange CLM_STRUCTURE="fast"
15+
./xmlchange CLM_CONFIGURATION="nwp"
16+
17+
# Restarts aren't allowed for these tests, and turn off CPL history
18+
# First change in env_test.xml, then in the standard one so it won't complain there
19+
./xmlchange --force REST_OPTION="never" --file env_test.xml
20+
./xmlchange --force HIST_OPTION="never" --file env_test.xml
21+
./xmlchange REST_OPTION="never"
22+
./xmlchange HIST_OPTION="never"
23+
24+
# Timer settings
25+
./xmlchange TIMER_DETAIL="2"
26+
./xmlchange SAVE_TIMING="TRUE"
27+
./xmlchange CHECK_TIMING="TRUE"
28+
./xmlchange ESMF_PROFILING_LEVEL="10"

‎cime_config/testdefs/testmods_dirs/clm/for_testing_fastsetup_bypassrun/user_nl_clm‎

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! Turn off history, restarts, and output
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hist_empty_htapes = .true.
3+
use_noio = .true.
4+
5+
! Turn off urban options, and only do urban in gridcells that are majority urban
6+
urban_hac = 'OFF'
7+
toosmall_urban = 98.0d00 ! Minimize urban in gridcells

‎cime_config/testdefs/testmods_dirs/clm/mpasa3p75/user_nl_clm‎

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! Settings currently required to run at the mpasa3p75 grid
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! urbantv files at that resolution and use a redistribution mapping
3+
4+
stream_fldfilename_urbantv = '$DIN_LOC_ROOT/lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_mpasa3p75_fromf09_simyr1849-2106_c20240502.nc'
5+
stream_meshfile_urbantv = '$DIN_LOC_ROOT/lnd/clm2/urbandata/CTSM52_tbuildmax_Oleson_2020_mpasa3p75_ESMFmesh_cdf5_c202405021.nc'
6+
urbantvmapalgo = 'redist'

‎cime_config/testdefs/testmods_dirs/clm/run_self_tests/README‎

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1-
The purpose of this testmod directory is to trigger the runtime
2-
self-tests. This runs a suite of unit/integration tests.
1+
The purpose of this testmod directory is to trigger runtime
2+
initialization self-tests. This runs a set of unit/integration tests
3+
that apply at initialization.
34

4-
We use cold start so that we can get through initialization faster,
5-
since how we initialize the model is unimportant for these self-tests.
5+
We inherit the test-mod that sets up for testing and bypassing as much as possible for speed.
6+
7+
There are other self_tests that need to be exercised in the model time stepping
8+
and are done outside of these.

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