Merge branch 'cesm3.0-alphabranch'

ESCOMP · Oct 1, 2024 · 60b024c · 60b024c
2 parents 51e6e06 + 1a27483
commit 60b024c
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Showing 28 changed files with 189 additions and 33 deletions.
diff --git a/.github/workflows/fleximod_test.yaml b/.github/workflows/fleximod_test.yaml
@@ -1,8 +1,8 @@
 on:
   push:
-    branches: [ master ]
+    branches: [ master, cesm3.0-alphabranch ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, cesm3.0-alphabranch ]
 jobs:
   fleximod-test:
     runs-on: ubuntu-latest
@@ -16,7 +16,12 @@ jobs:
       - id: run-fleximod
         run: |
           $GITHUB_WORKSPACE/bin/git-fleximod update
-          $GITHUB_WORKSPACE/bin/git-fleximod test
+          echo
+          echo "Update complete, checking status"
+          echo
+          $GITHUB_WORKSPACE/bin/git-fleximod status | tee status.out
+          grep testfails status.out || exit 0
+          exit 1
 #      - name: Setup tmate session
 #        if: ${{ failure() }}
 #        uses: mxschmitt/action-tmate@v3

diff --git a/.gitmodules b/.gitmodules
@@ -37,7 +37,7 @@
         path = cime
         url = https://github.com/ESMCI/cime
         fxDONOTUSEurl = https://github.com/ESMCI/cime
-        fxtag = cime6.1.25
+        fxtag = cime6.1.29
         fxrequired = ToplevelRequired
 
 [submodule "fms"]
@@ -66,7 +66,7 @@
         url = https://github.com/ESCOMP/CTSM
         fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
         fxrequired = ToplevelRequired
-        fxtag = ctsm5.2.027
+        fxtag = ctsm5.3.002
 
 [submodule "cice"]
         path = components/cice
@@ -80,7 +80,7 @@
         url = https://github.com/ESCOMP/MOM_interface
         fxDONOTUSEurl = https://github.com/ESCOMP/MOM_interface
         fxrequired = ToplevelRequired
-        fxtag = mi_240822
+        fxtag = mi_240923
 
 [submodule "cism"]
         path = components/cism
@@ -114,7 +114,7 @@
         path = components/ww3
         url = https://github.com/ESCOMP/WW3_interface
         fxDONOTUSEurl = https://github.com/ESCOMP/WW3_interface
-        fxtag = ww3i_0.0.3
+        fxtag = main_0.0.14
         fxrequired = ToplevelRequired
 
 [submodule "mizuroute"]
@@ -157,4 +157,4 @@
         url = https://github.com/NCAR/CUPiD.git
         fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git
         fxrequired = ToplevelRequired
-        fxtag = v0.1.0
+        fxtag = v0.1.1
diff --git a/.lib/git-fleximod/.github/workflows/pytest.yaml b/.lib/git-fleximod/.github/workflows/pytest.yaml
@@ -18,7 +18,7 @@ jobs:
       # reference the matrixe python version here.
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.12'
 
       # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
       # from installing Poetry every time, which can be slow. Note the use of the Poetry version
@@ -29,7 +29,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.local
-          key: poetry-1.7.1
+          key: poetry-1.8.2
 
       # Install Poetry. You could do this manually, or there are several actions that do this.
       # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
@@ -42,7 +42,7 @@ jobs:
       # cache it.
       - uses: snok/install-poetry@v1
         with:
-          version: 1.7.1
+          version: 1.8.2
           virtualenvs-create: true
           virtualenvs-in-project: true
 
@@ -74,4 +74,7 @@ jobs:
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
           poetry run pytest
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
 
diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py
@@ -2,7 +2,7 @@
 import argparse
 from git_fleximod import utils
 
-__version__ = "0.9.0"
+__version__ = "0.9.2"
 
 def find_root_dir(filename=".gitmodules"):
     """ finds the highest directory in tree

diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py
@@ -82,6 +82,8 @@ def config_get_value(self, section, name):
     def config_set_value(self, section, name, value):
         if self._use_module:
             with self.repo.config_writer() as writer:
+                if "." in section:  
+                    section = section.replace("."," \"")+'"'           
                 writer.set_value(section, name, value)
             writer.release()  # Ensure changes are saved
         else:

diff --git a/.lib/git-fleximod/git_fleximod/submodule.py b/.lib/git-fleximod/git_fleximod/submodule.py
@@ -186,7 +186,7 @@ def _add_remote(self, git):
                 return newremote
             else:
                 i = 0
-                while "newremote" in remotes:
+                while newremote in remotes:
                     i = i + 1
                     newremote = f"newremote.{i:02d}"
         else:
@@ -303,9 +303,9 @@ def sparse_checkout(self):
             print(f"Error checking out {self.name:>20} at {self.fxtag}")
         else:
             print(f"Successfully checked out {self.name:>20} at {self.fxtag}")
-        rgit.config_set_value(f'submodule "{self.name}"', "active", "true")
-        rgit.config_set_value(f'submodule "{self.name}"', "url", self.url)
-        rgit.config_set_value(f'submodule "{self.name}"', "path", self.path)
+        rgit.config_set_value('submodule.' + self.name, "active", "true")
+        rgit.config_set_value('submodule.' + self.name, "url", self.url)
+        rgit.config_set_value('submodule.' + self.name, "path", self.path)
 
     def update(self):
         """

diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py
@@ -312,10 +312,7 @@ def execute_subprocess(commands, status_to_caller=False, output_to_caller=False)
             "returned status {0}".format(error.returncode)
         )
         msg = failed_command_msg(msg_context, commands, output=error.output)
-        if return_to_caller:
-            logging.warning(error)
-            logging.warning(msg)
-        else:
+        if not return_to_caller:
             logging.error(error)
             logging.error(msg)
             log_process_output(error.output)

diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "git-fleximod"
-version = "0.9.0"
+version = "0.9.2"
 description = "Extended support for git-submodule and git-sparse-checkout"
 authors = ["Jim Edwards <[email protected]>"]
 maintainers = ["Jim Edwards <[email protected]>"]

diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml
@@ -2,7 +2,7 @@
 github_url = "https://github.com/jedwards4b/git-fleximod/"
 
 [version]
-current = "0.9.0"
+current = "0.9.2"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,112 @@
+==============================================================
+Tag name: cesm3_0_alpha03d
+Originator(s): CSEG
+Date: 25th September 2024
+One-line Summary: CLM answer changing tag
+
+components/cam          https://github.com/ESCOMP/CAM/cam6_4_032                              --
+components/cice         https://github.com/ESCOMP/CESM_CICE/tree/cesm_cice6_5_0_12             **
+cime                    https://github.com/ESMCI/cime/tree/cime6.1.29                         **
+share                   https://github.com/ESCOMP/CESM_share/tree/share1.1.2                  --
+ccs_config              https://github.com/ESMCI/ccs_config_cesm/tree/ccs_config_cesm1.0.7    --
+components/cmeps        https://github.com/ESCOMP/CMEPS/tree/cmeps1.0.16                      --
+components/cdeps        https://github.com/ESCOMP/CDEPS/tree/cdeps1.0.53                      --
+components/cism         https://github.com/ESCOMP/cism-wrapper/tree/cismwrap_2_2_002          --
+components/clm          https://github.com/ESCOMP/ctsm/tree/ctsm5.3.002                       **
+components/fms          https://github.com/ESCOMP/FMS_interface/tree/fi_240822                --
+components/mizuroute    https://github.com/ESCOMP/mizuRoute/tree/cesm-coupling.n02_v2.1.3     --
+components/mom          https://github.com/ESCOMP/MOM_interface/mi_240923                     **
+components/mosart       https://github.com/ESCOMP/mosart/tree/mosart1_1_02                    --
+components/rtm          https://github.com/ESCOMP/rtm/tree/rtm1_0_80                          --
+components/ww3          https://github.com/ESCOMP/WW3-CESM/tree/main_0.0.14                   **
+libraries/parallelio    https://github.com/NCAR/ParallilIO/tree/pio2_6_3                      --
+tools/CUPiD             https://github.com/NCAR/CUPiD/tree/v0.1.1                             **
+
+cime
+    Chris Fischer 2024-09-25 - cime6.1.29 - cime (cesm3_0_alpha03d)
+    https://github.com/ESMCI/cime/tags/cime6.1.29
+
+    cime6.1.29: Improve functionality of hidden workflow flag.
+    cime6.1.28: Avoid breaking Python environment by prepending CIME paths to PYTHONPATH.
+    cime6.1.27: Mark SETUP as FAIL if case.cmpgen_namelists fails.
+    cime6.1.26: Make the hidden status of batch jobs xml dependent.
+
+
+clm
+Erik Kluzek 2024-09-27 - ctsm5.3.002 - components/clm (cesm3_0_alpha03d)
+https://github.com/ESCOMP/ctsm/tags/ctsm5.3.002
+
+Duplicate tag of ctsm5.3.001
+
+
+Erik Kluzek 2024-09-27 - ctsm5.3.001 - components/clm (cesm3_0_alpha03d)
+https://github.com/ESCOMP/ctsm/tags/ctsm5.3.001
+
+Merge of b4b-dev to master. Some documentation updates.
+Some new namelist warnings for hillslope options.
+
+
+    Erik Kluzek 2024-09-24 - ctsm5.3.0 - components/clm (cesm3_0_alpha03d)
+    https://github.com/ESCOMP/ctsm/tags/ctsm5.3.0
+
+    Minor version update for CTSM:
+    - New surface datasets NOT backward compatible with ctsm5.2 ones
+    - New f09 1850 IC file
+    - New "hand tuned" parameter file
+    - New Li2024 fire turned on for clm6_0
+    - fire emissions factor file update
+
+
+    Erik Kluzek 2024-09-05 - ctsm5.2.028 - components/clm (cesm3_0_alpha03d)
+    https://github.com/ESCOMP/ctsm/tags/ctsm5.2.028
+
+    FATES update for history flushing
+
+
+CUPiD
+    Michael Levy 2024-09-16 - v0.1.1 - tools/CUPiD (cesm3_0_alpha03d)
+    https://github.com/NCAR/CUPiD/tags/v0.1.1
+
+    Remove manage_externals in favor of git submodules.
+    Also update the key_metrics example (and clean up documentation)
+
+
+mom
+    Alper Altuntas 2024-09-23 - mi_240923 - components/mom (cesm3_0_alpha03d)
+    https://github.com/ESCOMP/MOM_interface/tags/mi_2409??
+
+    Fix memory leak introduced with MARBL changes.
+
+
+    Michael Levy 2024-09-18 - mi_240920 - components/mom (cesm3_0_alpha03d)
+    https://github.com/ESCOMP/MOM_interface/tags/mi_2409??
+
+    Update externals:
+    1. Latest version of MARBL improves diag_table for fully coupled runs
+    2. Created an ESCOMP fork of stochastic_physics
+
+
+    Alper Altuntas 2024-09-09 - mi_240909b - components/mom (cesm3_0_alpha03d)
+    https://github.com/ESCOMP/MOM_interface/tags/mi_240909b
+
+    - MARBL: add STF_SALT_{tracer} diagnostics to diag_table.
+    - Check if fluxes%salt_flux is associated.
+
+
+    Alper Altuntas 2024-08-30 - mi_240909 - components/mom (cesm3_0_alpha03d)
+    https://github.com/ESCOMP/MOM_interface/tags/mi_2408??c
+
+    - Updates in FPMix and Stokes Most
+    - Modify NUOPC cap to accept separate glc runoff fluxes
+    - Re-tuning to bring MOM in line with CESM3 development runs:
+
+
+ww3
+    Alper Altuntas 2024-09-09 - main_0.0.14 - components/ww3 (cesm3_0_alpha03d)
+    https://github.com/ESCOMP/WW3_interface/tags/main_0.0.14
+
+    Merge latest dev/ufs-weather-model
+
 ==============================================================
 Tag name: cesm3_0_alpha03c
 Originator(s): CSEG

diff --git a/ccs_config b/ccs_config
diff --git a/cime b/cime
diff --git a/cime_config/testlist_allactive.xml b/cime_config/testlist_allactive.xml
@@ -8,6 +8,38 @@
       <option name="wallclock"> 01:00:00 </option>
     </options>
   </test>
+  <test name="ERS_Ld5" grid="ne30pg3_t232" compset="BLT1850" testmods="allactive/defaultio">
+    <machines>
+      <machine name="derecho" compiler="intel" category="prealpha"/>
+    </machines>
+    <options>
+      <option name="wallclock"> 01:00:00 </option>
+    </options>
+  </test>
+  <test name="ERS_Ld5" grid="ne30pg3_t232" compset="BLTHIST" testmods="allactive/defaultio">
+    <machines>
+      <machine name="derecho" compiler="intel" category="prealpha"/>
+    </machines>
+    <options>
+      <option name="wallclock"> 01:00:00 </option>
+    </options>
+  </test>
+  <test name="ERS_Ld5" grid="ne30pg3_t232" compset="BLT1850" testmods="allactive/decstart">
+    <machines>
+      <machine name="derecho" compiler="intel" category="prealpha"/>
+    </machines>
+    <options>
+      <option name="wallclock"> 01:00:00 </option>
+    </options>
+  </test>
+  <test name="ERS_Ld5" grid="ne30pg3_t232" compset="BLTHIST" testmods="allactive/decstart">
+    <machines>
+      <machine name="derecho" compiler="intel" category="prealpha"/>
+    </machines>
+    <options>
+      <option name="wallclock"> 01:00:00 </option>
+    </options>
+  </test>
 
   <test name="ERI" grid="ne30pg3_t232" compset="BLT1850" testmods="allactive/defaultio">
     <machines>

diff --git a/cime_config/testmods_dirs/allactive/crossleap/include_user_mods b/cime_config/testmods_dirs/allactive/crossleap/include_user_mods
@@ -0,0 +1 @@
+../defaultio
diff --git a/cime_config/testmods_dirs/allactive/crossleap/shell_commands b/cime_config/testmods_dirs/allactive/crossleap/shell_commands
@@ -0,0 +1,2 @@
+./xmlchange RUN_STARTDATE=2004-02-28
+./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append
diff --git a/cime_config/testmods_dirs/allactive/crossleap_gregorian/include_user_mods b/cime_config/testmods_dirs/allactive/crossleap_gregorian/include_user_mods
@@ -0,0 +1 @@
+../crossleap
diff --git a/cime_config/testmods_dirs/allactive/crossleap_gregorian/shell_commands b/cime_config/testmods_dirs/allactive/crossleap_gregorian/shell_commands
@@ -0,0 +1 @@
+./xmlchange CALENDAR=GREGORIAN
diff --git a/cime_config/testmods_dirs/allactive/decstart/include_user_mods b/cime_config/testmods_dirs/allactive/decstart/include_user_mods
@@ -0,0 +1 @@
+../defaultio
diff --git a/cime_config/testmods_dirs/allactive/decstart/shell_commands b/cime_config/testmods_dirs/allactive/decstart/shell_commands
@@ -0,0 +1,2 @@
+./xmlchange RUN_STARTDATE=2001-12-30
+./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append
diff --git a/components/cam b/components/cam
diff --git a/components/cdeps b/components/cdeps
diff --git a/components/clm b/components/clm
diff --git a/components/cmeps b/components/cmeps
diff --git a/components/mom b/components/mom
diff --git a/components/ww3 b/components/ww3
diff --git a/libraries/FMS b/libraries/FMS
diff --git a/libraries/parallelio b/libraries/parallelio
diff --git a/tools/CUPiD b/tools/CUPiD
+3 −3		machines/derecho/config_batch.xml
+12 −12		machines/izumi/config_machines.xml
+26 −54		CIME/ParamGen/paramgen.py
+4 −4		CIME/Servers/__init__.py
+3 −14		CIME/SystemTests/ers.py
+2 −1		CIME/SystemTests/funit.py
+3 −4		CIME/SystemTests/hommebaseclass.py
+4 −4		CIME/SystemTests/mvk.py
+5 −5		CIME/SystemTests/pgn.py
+1 −1		CIME/SystemTests/restart_tests.py
+71 −2		CIME/SystemTests/system_tests_common.py
+4 −4		CIME/SystemTests/tsc.py
+49 −9		CIME/Tools/xmlchange
+65 −21		CIME/XML/env_batch.py
+12 −0		CIME/XML/env_workflow.py
+30 −7		CIME/XML/pes.py
+8 −3		CIME/build.py
+29 −9		CIME/case/case.py
+8 −4		CIME/case/case_cmpgen_namelists.py
+6 −2		CIME/case/case_run.py
+42 −2		CIME/case/case_setup.py
+6 −5		CIME/case/case_st_archive.py
+5 −1		CIME/case/case_submit.py
+2 −1		CIME/case/case_test.py
+9 −15		CIME/code_checker.py
+2 −1		CIME/compare_test_results.py
+0 −3		CIME/data/config/config_tests.xml
+2 −0		CIME/data/config/xml_schemas/config_workflow.xsd
+77 −0		CIME/data/templates/gitignore.template
+100 −0		CIME/gitinterface.py
+5 −2		CIME/hist_utils.py
+1 −1		CIME/non_py/cprnc
+10 −0		CIME/scripts/create_test.py
+132 −0		CIME/status.py
+30 −17		CIME/test_scheduler.py
+2 −2		CIME/test_status.py
+2 −1		CIME/tests/test_sys_cime_case.py
+1 −1		CIME/tests/test_sys_create_newcase.py
+19 −3		CIME/tests/test_sys_unittest.py
+1 −1		CIME/tests/test_unit_utils.py
+11 −97		CIME/utils.py
+0 −1		docker/Dockerfile
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		./xmlchange RUN_STARTDATE=2004-02-28
		./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		./xmlchange RUN_STARTDATE=2001-12-30
		./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append
+0 −12		CMakeLists.txt
+18 −0		cime_config/stream_cdeps.py
+2 −1		cime_config/stream_definition_v2.0.xsd
+12 −5		datm/cime_config/buildnml
+9 −0		datm/cime_config/config_component.xml
+3 −0		datm/cime_config/namelist_definition_datm.xml
+48 −0		datm/cime_config/stream_definition_datm.xml
+4 −4		datm/cime_config/testdefs/testlist_datm.xml
+324 −38		dglc/dglc_datamode_noevolve_mod.F90
+32 −15		dglc/glc_comp_nuopc.F90
+2 −2		dice/cime_config/testdefs/testlist_dice.xml
+3 −0		doc/source/datm.rst
+2 −1		share/CMakeLists.txt
+778 −0		share/nuopc_shr_methods.F90
+2 −2		.github/workflows/extbuild.yml
+9 −8		.github/workflows/srt.yml
+12 −305		cesm/driver/esm_time_mod.F90
+0 −859		cesm/nuopc_cap_share/nuopc_shr_methods.F90
+19 −5		cime_config/buildnml
+1 −1		cime_config/config_component.xml
+2 −2		cime_config/config_component_cesm.xml
+13 −11		cime_config/namelist_definition_drv.xml
+2 −8		cime_config/runseq/driver_config.py
+1 −1		mediator/CMakeLists.txt
+3 −4		mediator/Makefile
+8 −10		mediator/esmFldsExchange_cesm_mod.F90
+4 −3		mediator/med.F90
+8 −19		mediator/med_diag_mod.F90
+3 −3		mediator/med_phases_aofluxes_mod.F90
+5 −6		mediator/med_phases_history_mod.F90
+3 −3		mediator/med_phases_prep_glc_mod.F90
+9 −5		mediator/med_phases_profile_mod.F90
+4 −8		mediator/med_phases_restart_mod.F90
+0 −302		mediator/med_time_mod.F90
+110 −0		.github/workflows/general-ci-tests.yml
+5 −5		.gitmodules
+0 −18		.travis.yml
+1 −1		MOM6
+1 −1		README.md
+11 −0		cime_config/MARBL_scripts/MOM_MARBL_diagnostics.py
+24 −15		cime_config/SystemTests/dimcs.py
+23 −14		cime_config/SystemTests/dimcsl.py
+27 −1		cime_config/buildnml
+5 −5		cime_config/config_archive.xml
+1 −0		cime_config/config_component.xml
+18 −1		cime_config/testdefs/testlist_mom.xml
+233 −0		cime_config/tools/lbe.py
+109 −0		cime_config/tools/plot_lbe.py
+117 −0		cime_config/tools/utils.py
+1 −1		externals/MARBL
+1 −1		externals/stochastic_physics
+66 −15		param_templates/MOM_input.yaml
+33 −11		param_templates/diag_table.yaml
+55 −14		param_templates/json/MOM_input.json
+44 −11		param_templates/json/diag_table.json
+0 −42		standalone/build/build_examples-darwin.sh
+52 −6		standalone/build/build_examples.sh
+1 −1		standalone/build/submit_casper_build
+2 −2		standalone/templates/ncar-gnu.mk
+170 −0		standalone/templates/ubuntu-gnu.mk
+4 −4		examples/basic/kinds_mod.F90
+2 −2		src/clib/pio_nc4.c
+1 −2		src/flib/piolib_mod.F90
+4 −4		src/gptl/perf_utils.F90
+1 −2		.gitignore
+6 −3		.gitmodules
+0 −16		Externals.cfg
+5 −6		README.md
+37 −0		contributors.md
+2 −2		cupid/clear.py
+54 −18		cupid/run.py
+26 −17		cupid/timeseries.py
+38 −1		cupid/util.py
+ −		docs/_static/images/config/config_1.png
+ −		docs/_static/images/config/config_2.png
+ −		docs/_static/images/config/config_3.png
+ −		docs/_static/images/config/config_4.png
+ −		docs/_static/images/config/config_5.png
+3 −2		docs/conf.py
+35 −0		docs/config.md
+2 −0		docs/contributors.rst
+2 −0		docs/index.rst
+4 −1		examples/coupled_model/config.yml
+28 −24		examples/key_metrics/config.yml
+189 −79		examples/nblibrary/atm/nmse_PSL.ipynb
+159 −26		examples/nblibrary/glc/LIWG_SMB_diagnostic.ipynb
+5 −3		examples/nblibrary/glc/utils.py
+1 −0		externals/ADF
+1 −0		externals/mom6-tools
+0 −1		manage_externals