ctsm5.3.071: b4b-dev merge 2025-08-22

.git-blame-ignore-revs

@@ -70,3 +70,8 @@ cdf40d265cc82775607a1bf25f5f527bacc97405
 4ad46f46de7dde753b4653c15f05326f55116b73
 75db098206b064b8b7b2a0604d3f0bf8fdb950cc
 84609494b54ea9732f64add43b2f1dd035632b4c
+7eb17f3ef0b9829fb55e0e3d7f02e157b0e41cfb
+62d7711506a0fb9a3ad138ceceffbac1b79a6caa
+49ad0f7ebe0b07459abc00a5c33c55a646f1e7e0
+ac03492012837799b7111607188acff9f739044a
+d858665d799690d73b56bcb961684382551193f4

cime_config/SystemTests/setparamfile.py

@@ -0,0 +1,95 @@
+"""
+CTSM-specific test that first runs the set_paramfile tool and then ensures that CTSM does not fail
+using the just-generated parameter file
+"""
+
+import os
+import sys
+import logging
+import re
+from CIME.SystemTests.system_tests_common import SystemTestsCommon
+
+# In case we need to import set_paramfile later
+_CTSM_PYTHON = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python"
+)
+sys.path.insert(1, _CTSM_PYTHON)
+
+logger = logging.getLogger(__name__)
+
+
+class SETPARAMFILE(SystemTestsCommon):
+    def __init__(self, case):
+        """
+        initialize an object interface to the SMS system test
+        """
+        SystemTestsCommon.__init__(self, case)
+
+        # Create out-of-the-box lnd_in to obtain paramfile
+        case.create_namelists(component="lnd")
+
+        # Find the paramfile to modify
+        lnd_in_path = os.path.join(self._get_caseroot(), "CaseDocs", "lnd_in")
+        self._paramfile_in = None
+        with open(lnd_in_path, "r", encoding="utf-8") as lnd_in:
+            for line in lnd_in:
+                paramfile_in = re.match(r" *paramfile *= *'(.*)'", line)
+                if paramfile_in:
+                    self._paramfile_in = paramfile_in.group(1)
+                    break
+        if not self._paramfile_in:
+            raise RuntimeError(f"paramfile not found in {lnd_in_path}")
+
+        # Get the output file
+        self.paramfile_out = os.path.join(self._get_caseroot(), "paramfile.nc")
+
+        # Define set_paramfile command
+        self.set_paramfile_cmd = [
+            "set_paramfile",
+            "-i",
+            self._paramfile_in,
+            "-o",
+            self.paramfile_out,
+            # Change two parameters for one PFT
+            "-p",
+            "needleleaf_deciduous_boreal_tree",
+            "rswf_min=0.35",
+            "rswf_max=0.7",
+        ]
+
+    def build_phase(self, sharedlib_only=False, model_only=False):
+        """
+        Run set_paramfile and then build the model
+        """
+
+        # Run set_paramfile.
+        # build_phase gets called twice:
+        # - once with sharedlib_only = True and
+        # - once with model_only = True
+        # Because we only need set_paramfile run once, we only do it for the sharedlib_only call.
+        # We could also check for the existence of the set_paramfile outputs, but that might lead to
+        # a situation where the user expects set_paramfile to be called but it's not. Better to run
+        # unnecessarily (e.g., if you fixed some FORTRAN code and just need to rebuild).
+        if sharedlib_only:
+            self._run_set_paramfile()
+
+        # Do the build
+        self.build_indv(sharedlib_only=sharedlib_only, model_only=model_only)
+
+    def _run_set_paramfile(self):
+        """
+        Run set_paramfile
+        """
+        # Import set_paramfile. Do it here rather than at top because otherwise the import will
+        # be attempted even during RUN phase.
+        # pylint: disable=wrong-import-position,import-outside-toplevel
+        from ctsm.param_utils.set_paramfile import main as set_paramfile
+
+        # Run set_paramfile
+        sys.argv = self.set_paramfile_cmd
+        set_paramfile()
+
+        # Append
+        user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
+        with open(user_nl_clm_path, "a", encoding="utf-8") as user_nl_clm:
+            user_nl_clm.write(f"paramfile = '{self.paramfile_out}'\n")

cime_config/config_pes.xml

@@ -2092,6 +2092,44 @@
 	</rootpe>
       </pes>
     </mach>
+  </grid>
+   <grid name="l%mpasa3p75">
+    <mach name="derecho">
+      <pes pesize="any" compset="any">
+	<comment>none</comment>
+	<ntasks>
+	  <ntasks_atm>-80</ntasks_atm>
+	  <ntasks_lnd>-80</ntasks_lnd>
+	  <ntasks_rof>-80</ntasks_rof>
+	  <ntasks_ice>-80</ntasks_ice>
+	  <ntasks_ocn>-80</ntasks_ocn>
+	  <ntasks_glc>-80</ntasks_glc>
+	  <ntasks_wav>-80</ntasks_wav>
+	  <ntasks_cpl>-80</ntasks_cpl>
+	  <ntasks_lnd>-80</ntasks_lnd>
+	</ntasks>
+	<nthrds>
+	  <nthrds_atm>1</nthrds_atm>
+	  <nthrds_lnd>1</nthrds_lnd>
+	  <nthrds_rof>1</nthrds_rof>
+	  <nthrds_ice>1</nthrds_ice>
+	  <nthrds_ocn>1</nthrds_ocn>
+	  <nthrds_glc>1</nthrds_glc>
+	  <nthrds_wav>1</nthrds_wav>
+	  <nthrds_cpl>1</nthrds_cpl>
+	</nthrds>
+	<rootpe>
+	  <rootpe_atm>0</rootpe_atm>
+	  <rootpe_lnd>0</rootpe_lnd>
+	  <rootpe_rof>0</rootpe_rof>
+	  <rootpe_ice>0</rootpe_ice>
+	  <rootpe_ocn>0</rootpe_ocn>
+	  <rootpe_glc>0</rootpe_glc>
+	  <rootpe_wav>0</rootpe_wav>
+	  <rootpe_cpl>0</rootpe_cpl>
+	</rootpe>
+      </pes>
+    </mach>
   </grid>
   <grid name="l%0.125nldas2">
     <mach name="any">

cime_config/config_tests.xml

@@ -175,6 +175,16 @@ This defines various CTSM-specific system tests
     <HIST_N>$STOP_N</HIST_N>
   </test>
 
+  <test NAME="SETPARAMFILE">
+    <DESC>Modify a copy of the paramfile and run with it.</DESC>
+    <INFO_DBUG>1</INFO_DBUG>
+    <DOUT_S>FALSE</DOUT_S>
+    <CONTINUE_RUN>FALSE</CONTINUE_RUN>
+    <REST_OPTION>never</REST_OPTION>
+    <HIST_OPTION>$STOP_OPTION</HIST_OPTION>
+    <HIST_N>$STOP_N</HIST_N>
+  </test>
+
 <!--
 SSP    smoke CLM spinup test (only valid for CLM compsets with CLM45)
        do an initial spin test (setting CLM_ACCELERATED_SPINUP to on)

cime_config/testdefs/testlist_clm.xml

@@ -15,6 +15,7 @@
         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.
         subset_data: Tests exercising the subset_data tool and running CTSM with its output
         decomp_init: Initialization tests specifically for examining the PE layout decomposition initialization
+        uhr_decomp_init: Initialization tests at Ultra High Resolution - specifically for examining the PE layout decomposition initialization
         interim_restart: Tests having to do with interim restart capability.
 -->
 <testlist version="2.0">
@@ -4203,7 +4204,28 @@
   </test>
 
   <!-- decomp_init tests -->
-  <test name="SMS_Ln1_P86x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
+  <test name="SMS_D_Ln1_Mmpi-serial" grid="1x1_brazil" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
+    <machines>
+      <machine name="derecho" compiler="intel" category="decomp_init"/>
+      <machine name="izumi" compiler="nag" category="decomp_init"/>
+    </machines>
+    <options>
+      <option name="wallclock">0:05:00</option>
+      <option name="comment">mpi-serial self tests with DEBUG</option>
+    </options>
+  </test>
+  <test name="SMS_D_Ln1" grid="f10_f10_mt232" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
+    <machines>
+      <machine name="derecho" compiler="intel" category="decomp_init"/>
+      <machine name="derecho" compiler="gnu" category="decomp_init"/>
+      <machine name="izumi" compiler="nag" category="decomp_init"/>
+    </machines>
+    <options>
+      <option name="wallclock">0:05:00</option>
+      <option name="comment">Self tests with DEBUG on for f10</option>
+    </options>
+  </test>
+  <test name="SMS_Ln1_P86x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
     <machines>
       <machine name="derecho" compiler="intel" category="decomp_init"/>
     </machines>
@@ -4212,7 +4234,7 @@
       <option name="comment">Initialization test for ne30pg3 with "Large" layout</option>
     </options>
   </test>
-  <test name="SMS_Ln1_P43x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
+  <test name="SMS_Ln1_P43x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
     <machines>
       <machine name="derecho" compiler="intel" category="decomp_init"/>
     </machines>
@@ -4221,7 +4243,7 @@
       <option name="comment">Initialization test for ne30pg3 with "Medium" layout</option>
     </options>
   </test>
-  <test name="SMS_Ln1_P22x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
+  <test name="SMS_Ln1_P22x1" grid="ne30pg3_ne30pg3_mt232" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
     <machines>
       <machine name="derecho" compiler="intel" category="decomp_init"/>
     </machines>
@@ -4230,7 +4252,7 @@
       <option name="comment">Initialization test for ne30pg3 with "Small" layout</option>
     </options>
   </test>
-  <test name="SMS_Ln1_PL" grid="ne120pg3_ne120pg3_mt13" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
+  <test name="SMS_Ln1_PL" grid="ne120pg3_ne120pg3_mt13" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
     <machines>
       <machine name="derecho" compiler="intel" category="decomp_init"/>
     </machines>
@@ -4239,7 +4261,7 @@
       <option name="comment">Initialization test for ne120pg3 with "Large" layout</option>
     </options>
   </test>
-  <test name="SMS_Ln1_PL" grid="mpasa15_mpasa15" compset="I2000Clm45Sp" testmods="clm-run_self_tests">
+  <test name="SMS_Ln1_PL" grid="mpasa15_mpasa15" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun">
     <machines>
       <machine name="derecho" compiler="intel" category="decomp_init"/>
     </machines>
@@ -4248,6 +4270,15 @@
       <option name="comment">Initialization test for mpasa15 with "Large" layout</option>
     </options>
   </test>
+  <test name="SMS_Ln1" grid="mpasa3p75_mpasa3p75_mt13" compset="I2000Clm45Sp" testmods="clm-for_testing_fastsetup_bypassrun--clm-mpasa3p75">
+    <machines>
+      <machine name="derecho" compiler="intel" category="uhr_decomp_init"/>
+    </machines>
+    <options>
+      <option name="wallclock">0:15:00</option>
+      <option name="comment">Initialization test for mpasa3p75 default layout</option>
+    </options>
+  </test>
 
   <test name="LGRAIN2_Ly1_P128x1" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/ciso--clm/cropMonthOutput">
     <machines>
@@ -4534,6 +4565,16 @@
     </options>
   </test>
 
+  <test name="SETPARAMFILE_Ld5" grid="f10_f10_mg37" compset="I1850Clm60BgcCrujra" testmods="clm/default">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="clm_pymods"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
+
   <test name="SMS_Ld5" grid="f10_f10_mg37" compset="IHistClm60BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="gnu" category="interim_restart"/>

cime_config/testdefs/testmods_dirs/clm/for_testing_fastsetup_bypassrun/README

@@ -0,0 +1,8 @@
+The purpose of this testmod directory is to setup for running fast testing
+of initialization. So it bypasses the run phase and exits early.
+
+We use cold start so that we can get through initialization faster,
+
+I/O is turned off as much as possible.
+
+And physics options that make the model run faster are used.

cime_config/testdefs/testmods_dirs/clm/for_testing_fastsetup_bypassrun/shell_commands

@@ -0,0 +1,28 @@
+#!/bin/bash
+./xmlchange CLM_FORCE_COLDSTART="on"
+
+# We use this testmod in a _Ln1 test; this requires forcing the ROF coupling frequency to same frequency as DATM
+./xmlchange ROF_NCPL='$ATM_NCPL'
+
+# Turn off ROF model when used with compsets that have them
+./xmlchange RTM_MODE='NULL'
+
+# Turn MEGAN off to run faster
+./xmlchange CLM_BLDNML_OPTS='--no-megan' --append
+
+# Use fast structure and NWP configuration for speed
+./xmlchange CLM_STRUCTURE="fast"
+./xmlchange CLM_CONFIGURATION="nwp"
+
+# Restarts aren't allowed for these tests, and turn off CPL history
+# First change in env_test.xml, then in the standard one so it won't complain there
+./xmlchange --force REST_OPTION="never" --file env_test.xml
+./xmlchange --force HIST_OPTION="never" --file env_test.xml
+./xmlchange REST_OPTION="never"
+./xmlchange HIST_OPTION="never"
+
+# Timer settings
+./xmlchange TIMER_DETAIL="2"
+./xmlchange SAVE_TIMING="TRUE"
+./xmlchange CHECK_TIMING="TRUE"
+./xmlchange ESMF_PROFILING_LEVEL="10"

cime_config/testdefs/testmods_dirs/clm/for_testing_fastsetup_bypassrun/user_nl_clm

@@ -0,0 +1,7 @@
+! Turn off history, restarts, and output
+hist_empty_htapes = .true.
+use_noio = .true.
+
+! Turn off urban options, and only do urban in gridcells that are majority urban
+urban_hac = 'OFF'
+toosmall_urban =  98.0d00  ! Minimize urban in gridcells

cime_config/testdefs/testmods_dirs/clm/mpasa3p75/user_nl_clm

@@ -0,0 +1,6 @@
+! Settings currently required to run at the mpasa3p75 grid
+! urbantv files at that resolution and use a redistribution mapping
+
+stream_fldfilename_urbantv = '$DIN_LOC_ROOT/lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_mpasa3p75_fromf09_simyr1849-2106_c20240502.nc'
+stream_meshfile_urbantv = '$DIN_LOC_ROOT/lnd/clm2/urbandata/CTSM52_tbuildmax_Oleson_2020_mpasa3p75_ESMFmesh_cdf5_c202405021.nc'
+urbantvmapalgo = 'redist'

cime_config/testdefs/testmods_dirs/clm/run_self_tests/README

@@ -1,5 +1,8 @@
-The purpose of this testmod directory is to trigger the runtime
-self-tests. This runs a suite of unit/integration tests.
+The purpose of this testmod directory is to trigger runtime
+initialization self-tests. This runs a set of unit/integration tests
+that apply at initialization.
 
-We use cold start so that we can get through initialization faster,
-since how we initialize the model is unimportant for these self-tests.
+We inherit the test-mod that sets up for testing and bypassing as much as possible for speed.
+
+There are other self_tests that need to be exercised in the model time stepping
+and are done outside of these.

cime_config/testdefs/testmods_dirs/clm/run_self_tests/include_user_mods

@@ -0,0 +1 @@
+../for_testing_fastsetup_bypassrun

cime_config/testdefs/testmods_dirs/clm/run_self_tests/user_nl_clm

@@ -1 +1,5 @@
 for_testing_run_ncdiopio_tests = .true.
+
+! Turn off history, restarts, and output
+hist_empty_htapes = .true.
+use_noio = .true.