Merge branch 'update_externals_alpha12c'

Update externals and minor fixes

Main change is to update externals to cesm2_3_alpha12c-ish.

Doing this exposed a few issues that are also fixed here.

Also, reduce GU_LULCC tests down to a single test.

- Resolves #1968 (Reduce the GULU tests down to one)
- Resolves #1971 (fsurdatmodifyctsm test should abort if it has trouble running the python script)

.config_files.xml

@@ -5,31 +5,31 @@
 <entry_id>
 
   <!-- This is the same as the default entry in
-       cime/config/cesm/config_files.xml except for the value for CTSM:
-       In a standalone CTSM checkout, COMP_ROOT_DIR_LND is $SRCROOT
+       cime/config/cesm/config_files.xml except for the value for CLM:
+       In a standalone CLM checkout, COMP_ROOT_DIR_LND is $SRCROOT
        rather than $SRCROOT/components/clm.
 
        However, because of the way overrides are handled, we need to
        re-specify the full information here rather than just overriding
-       the value for CTSM.
+       the value for CLM.
   -->
   <entry id="COMP_ROOT_DIR_LND">
     <type>char</type>
     <default_value>unset</default_value>
     <values>
-      <value component="clm"       >$SRCROOT</value>
-      <value component="ctsm"      >$SRCROOT</value>
-      <value component="dlnd" comp_interface="mct">$SRCROOT/components/cpl7/components/data_comps_mct/dlnd</value>
-      <value component="dlnd" comp_interface="nuopc">$SRCROOT/components/cdeps/dlnd</value>
-      <value component="slnd"  comp_interface="mct"     >$SRCROOT/components/cpl7/components/stub_comps_mct/slnd</value>
-      <value component="xlnd" comp_interface="mct"      >$SRCROOT/components/cpl7/components/xcpl_comps_mct/xlnd</value>
-      <value component="slnd"  comp_interface="nuopc"    >$CIMEROOT/src/components/stub_comps_nuopc/slnd</value>
-      <value component="xlnd"  comp_interface="nuopc"    >$CIMEROOT/src/components/xcpl_comps_nuopc/xlnd</value>
+      <value component="clm"                         >$SRCROOT</value>
+      <value component="slim"                        >$SRCROOT/components/slim/</value>
+      <value component="dlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/data_comps_$COMP_INTERFACE/dlnd</value>
+      <value component="dlnd" comp_interface="nuopc" >$SRCROOT/components/cdeps/dlnd</value>
+      <value component="slnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="slnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="xlnd" comp_interface="mct"   >$SRCROOT/components/cpl7/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
+      <value component="xlnd" comp_interface="nuopc" >$CIMEROOT/CIME/non_py/src/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
     </values>
     <group>case_comps</group>
     <file>env_case.xml</file>
     <desc>Root directory of the case land model component  </desc>
-    <schema>$CIMEROOT/config/xml_schemas/config_compsets.xsd</schema>
+    <schema>$CIMEROOT/CIME/data/config/xml_schemas/config_compsets.xsd</schema>
   </entry>
 
 </entry_id>

Externals.cfg

@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.38
+tag = ccs_config_cesm0.0.58
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,18 +44,18 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.45
+tag = cime6.0.100
 required = True
 
 [cmeps]
-tag = cmeps0.13.71
+tag = cmeps0.14.17
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.65
+tag = cdeps1.0.7
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -70,7 +70,7 @@ local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.13
+tag = share1.0.16
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
@@ -84,7 +84,7 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_7
+tag = pio2_5_10
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio

cime_config/SystemTests/fsurdatmodifyctsm.py

@@ -89,6 +89,7 @@ def _run_modify_fsurdat(self):
             print("getting an error within the fsurdat_modifier tool itself. ")
             print("Default error message: ")
             print(error.output)
+            raise
         except:
             print("ERROR trying to run fsurdat_modifier tool.")
             raise

cime_config/testdefs/ExpectedTestFails.xml

@@ -51,6 +51,13 @@
     </phase>
   </test>
 
+  <test name="FUNITCTSM_P1x1.f10_f10_mg37.I2000Clm50Sp.cheyenne_intel">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#1972</issue>
+    </phase>
+  </test>
+
   <!-- fates test suite failures -->
 
   <test name="ERS_Lm12.1x1_brazil.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesFireLightningPopDens">
@@ -88,7 +95,7 @@
     </phase>
   </test>
 
-  <test name="ERP_P144x2_Ld30.f45_f45_mg37.I2000Clm50FatesRs.cheyenne_intel.clm-mimicsFatesCold">
+  <test name="ERP_P72x2_Ld30.f45_f45_mg37.I2000Clm50FatesRs.cheyenne_intel.clm-mimicsFatesCold">
     <phase name="SHAREDLIB_BUILD">
       <status>PEND</status>
       <issue>#1045</issue>

cime_config/testdefs/testlist_clm.xml

@@ -327,7 +327,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">00:10:00</option>
+      <option name="wallclock">00:20:00</option>
       <option name="comment">Want one C96 test in the aux_clm test suite; just a short smoke test to make sure it can get off the ground. Use a PE layout that (1) has threading, because CAM uses threading at this resolution; and (2) has a smaller-than-standard task count in order to get through the queue faster.</option>
     </options>
   </test>
@@ -462,39 +462,18 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/ciso_decStart_GU_LULCC">
-    <machines>
-      <machine name="izumi" compiler="nag" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:40:00</option>
-      <option name="comment"  >Transient case with isotopes with a december start, and Gross Unrepresented Land Use and Land Cover change on, default dataset with GU_LULCC==0</option>
-    </options>
-  </test>
-  <test name="ERP_D_Ld10_P36x2" grid="f10_f10_mg37" compset="IHistClm50BgcCrop" testmods="clm/ciso_decStart_GU_LULCC">
+  <test name="ERP_D_Ld10_P36x2" grid="f10_f10_mg37" compset="IHistClm51BgcCrop" testmods="clm/ciso_decStart">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
-      <option name="comment"  >Transient case with isotopes with a december start, and Gross Unrepresented Land Use and Land Cover change on, default dataset with GU_LULCC==0</option>
+      <option name="comment"  >Transient case with isotopes with a December start</option>
     </options>
   </test>
-  <test name="ERP_D_Ld10" grid="f09_f09_mg17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
+  <test name="SMS_Ld3_PS" grid="f09_g17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
-      <machine name="izumi" compiler="nag" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:59:00</option>
-      <option name="comment"  >Transient case with a December 1990 start, and Gross Unrepresented Land Use and Land Cover change on, with f09 datasets with non-zero GU_LULCC values</option>
-    </options>
-  </test>
-  <test name="SMS_Ld10" grid="f09_f09_mg17" compset="IHistClm50BgcCrop" testmods="clm/f09_dec1990Start_GU_LULCC_monthly">
-    <machines>
-      <machine name="cheyenne" compiler="intel" category="aux_clm"/>
-      <machine name="cheyenne" compiler="gnu" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:40:00</option>
@@ -2037,7 +2016,7 @@
       <option name="comment">30 day exact restart test activating FATES size and age mortality mode on an f45 grid.</option>
     </options>
   </test>
-  <test name="ERP_P144x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/mimicsFatesCold">
+  <test name="ERP_P72x2_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/mimicsFatesCold">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
       <machine name="cheyenne" compiler="intel" category="fates"/>

cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands

@@ -1,3 +1,3 @@
-./xmlchange RUN_STARTDATE=1990-12-25
+./xmlchange RUN_STARTDATE=1990-12-30
 # Ignore warnings because we are using crop, but starting from a different date than the initial conditions were for
 ./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append

cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands

@@ -1,3 +1,5 @@
 #!/bin/bash
 ./xmlchange CLM_FORCE_COLDSTART="on"
 
+# We use this testmod in a _Ln1 test; this requires forcing the ROF coupling frequency to every time step
+./xmlchange ROF_NCPL=48

doc/.ChangeLog_template

@@ -121,10 +121,15 @@ infrastructure should be run when appropriate, as described below.
 
     clm_pymods test suite on cheyenne - 
 
-  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+  regular tests:
+      - aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing
+      - Fortran unit tests on cheyenne (until https://github.com/ESCOMP/CTSM/issues/1972 is resolved): from src, run:
+          ../cime/scripts/fortran_unit_testing/run_tests.py --build-dir `mktemp -d --tmpdir=. unit_tests.XXXXXXXX`
+
+    aux_clm on cheyenne ------------
+    aux_clm on izumi ---------------
+    Fortran unit tests on cheyenne -
 
-    cheyenne ----
-    izumi -------
 
   fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
     cheyenne ----

doc/ChangeLog

@@ -1,4 +1,106 @@
 ===============================================================
+Tag name: ctsm5.1.dev120
+Originator(s): sacks (Bill Sacks)
+Date: Sat Mar 25 17:49:27 MDT 2023
+One-line Summary: Update externals and minor fixes
+
+Purpose and description of changes
+----------------------------------
+
+Main change is to update externals to cesm2_3_alpha12c-ish.
+
+Doing this exposed a few issues that are also fixed here.
+
+Also, reduce GU_LULCC tests down to a single test.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+CTSM issues fixed (include CTSM Issue #):
+- Resolves ESCOMP/CTSM#1968 (Reduce the GULU tests down to one)
+- Resolves ESCOMP/CTSM#1971 (fsurdatmodifyctsm test should abort if it has trouble running the python script)
+
+Known bugs introduced in this tag (include issue #):
+- ESCOMP/CTSM#1972 (FUNITCTSM test fails when run through run_sys_tests in upcoming ctsm5.1.dev120)
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:
+- Fortran unit tests now need to be run manually, since FUNITCTSM is
+  failing when run through run_sys_tests
+- Reduced GU_LULCC tests down to a single test
+
+
+Testing summary:
+----------------
+
+  regular tests:
+      - aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing
+      - Fortran unit tests on cheyenne (until https://github.com/ESCOMP/CTSM/issues/1972 is resolved): from src, run:
+          ../cime/scripts/fortran_unit_testing/run_tests.py --build-dir `mktemp -d --tmpdir=. unit_tests.XXXXXXXX`
+
+    aux_clm on cheyenne ------------ OK
+    aux_clm on izumi --------------- OK
+    Fortran unit tests on cheyenne - PASS
+
+    For the two new tests (with BFAILs), ran them from dev119 with
+    comparison against this branch:
+    - ERP_D_Ld10_P36x2.f10_f10_mg37.IHistClm51BgcCrop.cheyenne_intel.clm-ciso_decStart
+    - SMS_Ld3_PS.f09_g17.IHistClm50BgcCrop.cheyenne_intel.clm-f09_dec1990Start_GU_LULCC
+      (with start date in the test mod changed to match the new version)
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES, but just for certain compilers
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: all on certain compilers
+    - what platforms/compilers:
+      - nvhpc on cheyenne in non-debug cases (can be explained from
+        differences in compilation flags for non-debug cases, and also
+        some module differences)
+      - intel on izumi in debug cases (there were updates in ESMF
+        modules, though that's the same for other izumi compilers; I'm not
+        seeing other relevant diffs in ccs_config, so I'm not sure why we're
+        getting diffs here. I tried investigating, but ran into trouble trying
+        to get things to compile with the old ccs_config, so gave up on
+        tracking down the source of this difference)
+
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+      not investigated
+
+Other details
+-------------
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+- ccs_config: ccs_config_cesm0.0.38 -> ccs_config_cesm0.0.58
+- cime: cime6.0.45 -> cime6.0.100
+- cmeps: cmeps0.13.71 -> cmeps0.14.17
+- cdeps: cdeps0.12.65 -> cdeps1.0.7
+- share: share1.0.13 -> share1.0.16
+- pio: pio2_5_7 -> pio2_5_10
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev119
 Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310), ekluzek Erik Kluzek), lawrencepj1 (Peter Lawrence)
 Date: Thu Mar 16 14:13:37 MDT 2023

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev120    sacks 03/25/2023 Update externals and minor fixes
     ctsm5.1.dev119   slevis 03/16/2023 Allow gross unrepresented land use transition (PR #309)
     ctsm5.1.dev118   slevis 02/05/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test
     ctsm5.1.dev117  afoster 02/02/2023 Updates to facilitate running FATES at NEON sites