Add cobalt CI (#3)

* fix cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * Update cobalt_ci.yml * add ref for auto rt
NOAA-CEFI-Regional-Ocean-Modeling · Dec 22, 2023 · 601eb9b · 601eb9b
1 parent 1f3d37b
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diff --git a/.github/ref/OM4.single_column.COBALT.p4/docker-linux-gnu/MOM.res.nc b/.github/ref/OM4.single_column.COBALT.p4/docker-linux-gnu/MOM.res.nc
diff --git a/.github/ref/OM4.single_column.COBALT.p4/docker-linux-gnu/ocean.stats b/.github/ref/OM4.single_column.COBALT.p4/docker-linux-gnu/ocean.stats
@@ -0,0 +1,11 @@
+  Step,       Day,  Truncs,      Energy/Mass,      Maximum CFL,  Mean Sea Level,  Total Mass,  Mean Salin, Mean Temp, Frac Mass Err,   Salin Err,    Temp Err
+            [days]                 [m2 s-2]           [Nondim]       [m]             [kg]         [PSU]      [degC]       [Nondim]        [PSU]        [degC]
+     0,  731595.000,     0, En 4.0531850015098383E-27, CFL  0.00000, SL -0.0000E+00, M 6.97073E+15, S 35.2427, T  6.2462, Me  0.00E+00, Se  0.00E+00, Te  0.00E+00
+    18,  731595.250,     0, En 2.3854654580464527E-06, CFL  0.00372, SL -3.6569E-06, M 6.97073E+15, S 35.2427, T  6.2460, Me -9.14E-10, Se -2.87E-07, Te -2.53E-06
+    36,  731595.500,     0, En 4.7618800034270000E-06, CFL  0.00348, SL -6.7408E-06, M 6.97073E+15, S 35.2427, T  6.2457, Me -7.71E-10, Se -7.18E-07, Te -7.00E-06
+    54,  731595.750,     0, En 1.1464049165959475E-05, CFL  0.00749, SL -9.5684E-06, M 6.97073E+15, S 35.2427, T  6.2459, Me -7.07E-10, Se -9.88E-07, Te -1.03E-05
+    72,  731596.000,     0, En 2.3222960705556885E-05, CFL  0.00881, SL -1.4119E-05, M 6.97073E+15, S 35.2427, T  6.2457, Me -1.14E-09, Se -1.40E-06, Te -1.41E-05
+    90,  731596.250,     0, En 2.9040534962143268E-05, CFL  0.00771, SL -1.8938E-05, M 6.97073E+15, S 35.2427, T  6.2454, Me -1.20E-09, Se -1.96E-06, Te -1.97E-05
+   108,  731596.500,     0, En 3.6391342252032763E-05, CFL  0.00790, SL -2.3731E-05, M 6.97073E+15, S 35.2427, T  6.2451, Me -1.20E-09, Se -2.38E-06, Te -2.44E-05
+   126,  731596.750,     0, En 4.2200585475070879E-05, CFL  0.00923, SL -2.8306E-05, M 6.97073E+15, S 35.2427, T  6.2453, Me -1.14E-09, Se -2.80E-06, Te -2.88E-05
+   144,  731597.000,     0, En 4.6813518525667337E-05, CFL  0.00922, SL -3.1872E-05, M 6.97073E+15, S 35.2427, T  6.2453, Me -8.91E-10, Se -3.11E-06, Te -3.18E-05
diff --git a/.github/workflows/cobalt_ci.yml b/.github/workflows/cobalt_ci.yml
@@ -19,18 +19,57 @@ jobs:
   build:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
+    # define container
+    container:
+       image: clouden90/1d_mom6_cobalt:base
+       options: --user root
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Checkout Repository
         uses: actions/checkout@v3
-
-      # Build and Test within Docker container
-      - name: Build and Test
-        uses: docker://clouden90/1d_mom6_cobalt:base:
         with:
-          args: |
-            ls -l -h
-            pwd
-            which wget
+          submodules: recursive
+
+      # Install wget and get data
+      - name: Install wget and get data
+        run: |
+          apt-get update
+          apt-get install -y wget
+          cd /opt
+          wget https://gfdl-med.s3.amazonaws.com/OceanBGC_dataset/1d_datasets.tar.gz
+          tar -zxvf 1d_datasets.tar.gz
+          rm -rf 1d_datasets.tar.gz
+
+      # git clone MOM6_OBGC_examples and replace ocean_BGC
+      - name: git clone MOM6_OBGC_examples and build mom6sis2-cobalt
+        run: |
+          cd ..
+          git clone https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6_OBGC_examples.git --recursive
+          rm -rf MOM6_OBGC_examples/src/ocean_BGC
+          cp -r ocean_BGC MOM6_OBGC_examples/src
+          cd MOM6_OBGC_examples/builds
+          ./linux-build.bash -m docker -p linux-gnu -t prod -f mom6sis2
+          
+
+      # run 1D mom6sis2-cobalt test
+      - name: 1D mom6sis2-cobalt test
+        run: |
+          cd ../MOM6_OBGC_examples/exps
+          ln -fs /opt/datasets ./
+          cd OM4.single_column.COBALT.p4
+          mkdir RESTART
+          mpirun --allow-run-as-root -np 1 ../../builds/build/docker-linux-gnu/ocean_ice/prod/MOM6SIS2
+
+      - name: baseline check
+        run: |      
+          cd ../MOM6_OBGC_examples/exps/OM4.single_column.COBALT.p4
+          mkdir -p ref
+          cp ../../src/ocean_BGC/.github/ref/OM4.single_column.COBALT.p4/docker-linux-gnu/* ./ref
+          # check ocean.stats 
+          diff -q ref/ocean.stats ./ocean.stats > /dev/null || { echo "Error: ocean.stats are different, check and update ref! Exiting now..."; exit 1; }
+          # check MOM.res.nc
+          ncdump ref/MOM.res.nc > org_ref.txt
+          ncdump RESTART/MOM.res.nc > new_ref.txt
+          diff -q ./org_ref.txt ./new_ref.txt > /dev/null || { echo "Error: MOM.res.nc are different, check and update ref! Exiting now..."; exit 1; }