Merge tag 'mi_251024b' into update_MARBL_FeForcing

Author: mnlevy1981

.github/workflows/general-ci-tests.yml

@@ -94,6 +94,23 @@ jobs:
       - name: Run the check_default_params script
         run: python tests/check_default_params.py
 
+  # Job to check if duplicate parameters exist in param template files
+  check_duplicate_params:
+    
+    runs-on: ubuntu-latest
+    
+    steps:
+      # Checkout the repo
+      - uses: actions/checkout@v4
+      
+      # Run the test
+      - name: Run the check_duplicate_params script
+        run: |
+          python tests/check_duplicate_params.py param_templates/MOM_input.yaml
+          python tests/check_duplicate_params.py param_templates/input_data_list.yaml
+          python tests/check_duplicate_params.py param_templates/input_nml.yaml
+          python tests/check_duplicate_params.py param_templates/diag_table.yaml
+  
   # Job to run check_input_data_list script
   check_input_data_list:
 
@@ -118,10 +135,7 @@ jobs:
 
       # Run the test
       - name: Run the check_input_data_repo script
-        run: |
-          sudo apt-get update && sudo apt-get install -y subversion
-          pip install 'svn>=1,<1.1'
-          python tests/check_input_data_repo.py
+        run: python tests/check_input_data_repo.py
 
   # Job to run the black formatter for cime_config, see black documentation for more info
   check_black_format_for_cime_config:

.gitmodules

@@ -2,20 +2,20 @@
   path = MOM6
   url = https://github.com/NCAR/MOM6.git
   fxDONOTUSEurl = https://github.com/NCAR/MOM6.git
-    fxtag = dev/ncar_250428
+    fxtag = dev/ncar_251024b
     fxrequired = AlwaysRequired
 
 [submodule "stochastic_physics"]
   path = externals/stochastic_physics
   url = https://github.com/ESCOMP/stochastic_physics.git
   fxDONOTUSEurl = https://github.com/ESCOMP/stochastic_physics.git
-    fxtag = fcb_0.0.1
+    fxtag = sp_250827
     fxrequired = AlwaysRequired
 
 [submodule "MARBL"]
   path = externals/MARBL
   url = https://github.com/marbl-ecosys/MARBL.git
   fxDONOTUSEurl = https://github.com/marbl-ecosys/MARBL.git
-    fxtag = marbl0.48.2
+    fxtag = marbl0.48.3
     fxrequired = AlwaysRequired
 

MOM6

@@ -15,7 +15,7 @@ import logging
 CIMEROOT = os.environ.get("CIMEROOT")
 if CIMEROOT is None:
     raise SystemExit("ERROR: must set CIMEROOT environment variable")
-sys.path.append(os.path.join(CIMEROOT, "scripts", "Tools"))
+sys.path.append(os.path.join(CIMEROOT, "CIME", "Tools"))
 
 # The scope of the following path expansion is limited to this script only,
 # and is needed to import MOM6 input file classes:
@@ -399,10 +399,13 @@ def prechecks(case, inst_suffixes):
                 f"Missing rpointer files in rundir. Expected files with pattern {rpointer_pattern}.",
             )
 
-    # check if the restart file is present in rundir
+    # check if the restart file is present in rundir for fresh branch or hybrid runs
     if run_type in ["branch", "hybrid"] and not continue_run and not get_refcase:
-        restart_file = os.path.join(rundir, f'./{run_refcase}.mom6.r.{run_refdate}-{run_reftod}.nc')
-        assert os.path.exists(restart_file), f"Missing restart file {run_refcase}.mom6.r.{run_refdate}-{run_reftod}.nc in rundir."
+        restart_file_pattern = run_refcase + r".mom6.*.r." + run_refdate + "-" + run_reftod + r".*nc$"
+        restart_files = [
+            f for f in os.listdir(rundir) if re.match(restart_file_pattern, f)
+        ]
+        assert len(restart_files) > 0, f"Missing restart file in rundir. Expected file matching pattern {restart_file_pattern}."
 
 def postchecks(case,  MOM_input_final):
     """Performs checks after input files are generated. To be called within prep_input() as a final step."""
@@ -433,7 +436,15 @@ def buildnml(case, caseroot, compname):
     # Build the component namelist
     if compname != "mom":
         raise AttributeError
-
+    # add the FMS library to the list of cesm support libraries for the case
+    # designed to be backward compatible in case cmeps does not define CASE_SUPPORT_LIBRARIES
+    try:
+        libs = case.get_values("CASE_SUPPORT_LIBRARIES")
+        if libs is not None and "FMS" not in libs:
+            libs.extend(["gptl","pio","csm_share","FMS"])
+            case.set_value("CASE_SUPPORT_LIBRARIES", ",".join(libs))
+    except:
+        pass
     ninst = case.get_value("NINST_OCN")
     inst_suffixes = (
         ["_{:04d}".format(i + 1) for i in range(ninst)] if ninst > 1 else [""]
@@ -460,7 +471,7 @@ def buildnml(case, caseroot, compname):
 def _main_func():
 
     caseroot = parse_input(sys.argv)
-    with Case(caseroot) as case:
+    with Case(caseroot, read_only=False) as case:
         buildnml(case, caseroot, "mom")
 
 

cime_config/buildnml

@@ -1,27 +1,30 @@
 <components version="2.0">
   <comp_archive_spec compname="mom" compclass="ocn">
     <rest_file_extension>r</rest_file_extension>
+    <rest_file_extension>r_stoch</rest_file_extension>
     <!-- match filenames of the form
          h[.optional stream name][._optional instance number].(date string).nc[.optional tile number] -->
-    <hist_file_extension>h(\.\w+)?(\._\d*)?\.[-\d+]+\.nc(\.\d*)?$</hist_file_extension>
+    <hist_file_extension>h(\.\w+)?(\._\d*)?\.[-\d+]+\.nc(\.\d*)?(\.gz)?$</hist_file_extension>
     <!-- match filenames of the form
          h.(static|ocean_geometry)[._optional instance number].nc[.optional tile number] -->
-    <hist_file_extension>h\.(static|ocean_geometry)(\._\d*)?\.nc(\.\d*)?$</hist_file_extension>
+    <hist_file_extension>h\.(static|ocean_geometry)(\._\d*)?\.nc(\.\d*)?(\.gz)?$</hist_file_extension>
     <!-- match filenames of the form
          h.bgc.*[._optional instance number].nc -->
-    <hist_file_extension>h\.bgc\..*?.?[_\d+]+.nc$</hist_file_extension>
+    <hist_file_extension>h\.bgc\..*(\._\d+)?\.nc$</hist_file_extension>
     <!-- match filenames of the form
-         ic.(date string[_optional id for splitting date over many files)[._optional instance number].nc[.optional tile number] -->
-    <hist_file_extension>ic.[-\d(_\d)?+]+(\._\d*)?\.nc(\.\d*)?$</hist_file_extension>
-    <hist_file_ext_regex>\w+\.\w+(\.\w+)?(\._\d*)?</hist_file_ext_regex>
+         ic.(date string)[._optional instance number].nc[.optional tile number] -->
+    <hist_file_extension>ic\.[-\d_]+(\._\d*(_\d)?)?\.nc(\.\d*)?$</hist_file_extension>
+    <hist_file_extension>e</hist_file_extension>
+    <hist_file_ext_regex>\w+\.\w+(\._\d*)?</hist_file_ext_regex>
     <rpointer>
-      <rpointer_file>rpointer.ocn$NINST_STRING.$DATENAME</rpointer_file>
+      <rpointer_file>rpointer.ocn$NINST_STRING</rpointer_file>
       <rpointer_content>$CASE.mom6$NINST_STRING.r.$DATENAME.nc</rpointer_content>
     </rpointer>
       <test_file_names>
         <tfile disposition="copy">rpointer.ocn.1976-01-01-00000</tfile>
         <tfile disposition="copy">casename.mom6.r.1976-01-01-00000.nc</tfile>
         <tfile disposition="copy">casename.mom6.r.1976-01-01-00000_1.nc</tfile>
+        <tfile disposition="copy">casename.mom6.r_stoch.1976-01-01-00000.nc</tfile>
         <tfile disposition="move">casename.mom6.h.bgc.native.1976-01-01.nc</tfile>
         <tfile disposition="move">casename.mom6.h.bgc.z.1976-01-01.nc</tfile>
         <tfile disposition="move">casename.mom6.h.native.1976-01-01-00000.nc</tfile>

cime_config/config_archive.xml

@@ -91,7 +91,7 @@
       <option name="wallclock">01:00:00</option>
     </options>
   </test>
-  <test name="SMS_Ld2" grid="ne30pg3_t232" compset="BLT1850">
+  <test name="SMS_Ld2" grid="ne30pg3_t232" compset="B1850C_LTso">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_mom"/>
       <machine name="derecho" compiler="intel" category="pr_mom"/>