Add NEP10-COBALT RT, refactor CI workflows, and add stable nightly re…

…lease workflow (#33)

* Add NEP10.COBALT test case

* change NWA xml to make a prefect reproduce

* add stable_weekly release workflow

.github/workflows/CEFI_MOM6-ci.yaml

@@ -60,7 +60,7 @@ jobs:
     strategy:
       max-parallel: 2
       matrix:
-        case: ["NWA12.COBALT"] #, "NWA12.CFC"]
+        case: ["NWA12.COBALT", "NEP10.COBALT"]
     steps:
       - name: Run Experiment ${{ matrix.case }}
         run: |

.github/workflows/mom6_cobalt_1D.yaml

@@ -5,6 +5,7 @@ on:
     branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
+  workflow_dispatch:    
 
 jobs:
   build:

.github/workflows/nightly_update._yaml

@@ -0,0 +1,27 @@
+name: Update and Push Ocean BGC Submodule
+
+on:
+  schedule:
+    - cron: '0 4 * * 2'  # Run at 12:00 am EDT every Tuesday
+
+jobs:
+  nightly_update:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set Git user name and email
+        run: |
+          git config --global user.email ${{ secrets.GHA_EMAIL }} 
+          git config --global user.name ${{ secrets.GHA_ID }} 
+
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }} 
+          fetch-depth: 0
+          submodules: 'recursive'
+
+      - name: Update Ocean BGC Submodule
+        run: |
+          git submodule update --remote --merge src/ocean_BGC
+          git add src/ocean_BGC
+          git commit -m "Update ocean_BGC submodule nightly"

.github/workflows/stable_weekly_release.yaml

@@ -0,0 +1,30 @@
+on:
+  schedule:
+    - cron: '0 0 * * 3'  # Run at midnight (00:00) every Wednesday
+
+jobs:
+  stable_release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.PAT }}
+
+      - name: Show diff between stable/weekly_release and main
+        if: github.ref == 'refs/heads/main'
+        run: |
+          echo "Showing diff between stable/weekly_release and main"
+          git fetch origin stable/weekly_release:stable/weekly_release
+          git diff stable/weekly_release..origin/main
+
+      - name: Merge develop into main
+        if: github.ref == 'refs/heads/feature/main'
+        run: |
+          echo ${{ github.ref }}
+          git checkout stable/weekly_release
+          git pull origin stable/weekly_release
+          git merge origin/main --no-edit
+          git push --force origin stable/weekly_release

builds/ci_build_driver.sh

@@ -10,15 +10,56 @@
 #SBATCH --account=cefi
 
 #
+[ -d "build" ] && rm -rf build
 
 #
-[ -d "build" ] && rm -rf build
+echo "Build MOM6SIS2-COBALT for CI testing started:  " `date`
+
+#
+machine_name="gaea" 
+platform="ncrc5.intel23"
+target="repro"
+flavor="fms1_mom6sis2"
+
+FMSlib_PATH="/gpfs/f5/cefi/scratch/Yi-cheng.Teng/github/FMS/2023.04_FMS1"
+rootdir=$(pwd)
+abs_rootdir=$rootdir
+
+echo $abs_rootdir
+
+#load modules              
+source $MODULESHOME/init/bash
+source $rootdir/$machine_name/$platform.env
+. $rootdir/$machine_name/$platform.env
+
+makeflags="NETCDF=3"
+
+if [[ $target =~ "repro" ]] ; then
+   makeflags="$makeflags REPRO=1"
+fi
+
+srcdir=$abs_rootdir/../src
 
 #
-echo "Build started:  " `date`
+sed -i 's/static pid_t gettid(void)/pid_t gettid(void)/g' $srcdir/FMS/affinity/affinity.c
 
 #
-./linux-build.bash -m gaea -p ncrc5.intel23 -t repro -f fms1_mom6sis2
+if [[ $flavor == "fms1_mom6sis2" ]] ; then
+    echo "build mom6sis2 with FMS1 cap" 	
+
+    mkdir -p build/$machine_name-$platform/ocean_ice/$target
+    pushd build/$machine_name-$platform/ocean_ice/$target
+    rm -f path_names
+    $srcdir/mkmf/bin/list_paths $srcdir/MOM6/{config_src/infra/FMS1,config_src/memory/dynamic_symmetric,config_src/drivers/FMS_cap,config_src/external/ODA_hooks,config_src/external/database_comms,config_src/external/drifters,config_src/external/stochastic_physics,pkg/GSW-Fortran/{modules,toolbox}/,src/{*,*/*}/} $srcdir/SIS2/{config_src/dynamic_symmetric,config_src/external/Icepack_interfaces,src} $srcdir/icebergs/src $srcdir/FMS/{coupler,include}/ $srcdir/{ocean_BGC/generic_tracers,ocean_BGC/mocsy/src}/ $srcdir/{atmos_null,ice_param,land_null,coupler/shared/,coupler/full/}/
+
+   compiler_options='-DINTERNAL_FILE_NML -DMAX_FIELDS_=600 -DNOT_SET_AFFINITY -D_USE_MOM6_DIAG -D_USE_GENERIC_TRACER -DUSE_PRECISION=2 -D_USE_LEGACY_LAND_ -Duse_AM3_physics'
+
+   $srcdir/mkmf/bin/mkmf -t $abs_rootdir/$machine_name/$platform.mk -o "-I${FMSlib_PATH}/shared/$target" -p MOM6SIS2 -l "-L${FMSlib_PATH}/shared/$target -lfms" -c "$compiler_options" path_names
+
+   make $makeflags MOM6SIS2 
+
+fi
+
 
 #
-echo "Build ended:  " `date`
+echo "Build MOM6SIS2-COBALT for CI testing ended:  " `date`

exps/NEP10.COBALT/INPUT/ERA5_lp_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_lp_1993_padded.nc

exps/NEP10.COBALT/INPUT/ERA5_msl_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_msl_1993_padded.nc

exps/NEP10.COBALT/INPUT/ERA5_sf_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_sf_1993_padded.nc

exps/NEP10.COBALT/INPUT/ERA5_sphum_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_sphum_1993_padded.nc

exps/NEP10.COBALT/INPUT/ERA5_ssrd_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_ssrd_1993_padded.nc

exps/NEP10.COBALT/INPUT/ERA5_strd_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_strd_1993_padded.nc

exps/NEP10.COBALT/INPUT/ERA5_t2m_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_t2m_1993_padded.nc

exps/NEP10.COBALT/INPUT/ERA5_u10_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_u10_1993_padded.nc

exps/NEP10.COBALT/INPUT/ERA5_v10_1993_padded.nc

@@ -0,0 +1 @@
+../../datasets/nep_input/ERA5_v10_1993_padded.nc