Prepare for PR to dev/gfdl

.codecov.yml

@@ -8,6 +8,6 @@ coverage:
             default:
                 threshold: 100%
                 base: parent
-comment:
-    # This must be set to the number of test cases (TCs)
-    after_n_builds: 8
+
+fixes:
+  - "MOM6/::"

.github/actions/macos-setup/action.yml

@@ -0,0 +1,33 @@
+name: 'install-macos-prerequisites'
+
+description: 'Install prerequisites for Mac OS compilation'
+
+runs:
+  using: 'composite'
+
+  steps:
+    - name: Install macOS packages
+      shell: bash
+      run: |
+        echo "::group::Install packages"
+        brew reinstall gcc
+        brew install automake
+        brew install netcdf
+        brew install netcdf-fortran
+        brew install mpich
+        echo "::endgroup::"
+
+    # NOTE: Floating point exceptions are currently disabled due to an error in
+    # HDF5 1.4.3.  They will be re-enabled when the default brew version has
+    # been updated to a working version.
+
+    - name: Set compiler flags
+      shell: bash
+      run: |
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"

.github/actions/testing-setup/action.yml

@@ -5,10 +5,6 @@ inputs:
     description: 'If true, will build the symmetric MOM6 executable'
     required: false
     default: 'true'
-  install_python:
-    description: 'If true, will install the local python env needed for .testing'
-    required: false
-    default: 'true'
 runs:
   using: 'composite'
   steps:
@@ -27,33 +23,12 @@ runs:
         env
         echo "::endgroup::"
 
-    - name: Install needed packages for compiling
-      shell: bash
-      run: |
-        echo "::group::Install linux packages"
-        sudo apt-get update
-        sudo apt-get install netcdf-bin libnetcdf-dev libnetcdff-dev mpich libmpich-dev
-        sudo apt-get install linux-tools-common
-        echo "::endgroup::"
-
     - name: Compile FMS library
       shell: bash
       run: |
         echo "::group::Compile FMS library"
         cd .testing
-        make deps/lib/libFMS.a -s -j
-        echo "::endgroup::"
-
-    - name: Store compiler flags used in Makefile
-      shell: bash
-      run: |
-        echo "::group::config.mk"
-        cd .testing
-        echo "FCFLAGS_DEBUG=-g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
-        echo "FCFLAGS_REPRO=-g -O2 -fbacktrace" >> config.mk
-        echo "FCFLAGS_INIT=-finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
-        echo "FCFLAGS_COVERAGE=--coverage" >> config.mk
-        cat config.mk
+        REPORT_ERROR_LOGS=true make build/deps/lib/libFMS.a -s -j
         echo "::endgroup::"
 
     - name: Compile MOM6 in symmetric memory mode
@@ -64,14 +39,6 @@ runs:
         test ${{ inputs.build_symmetric }} == true && make build/symmetric/MOM6 -j
         echo "::endgroup::"
 
-    - name: Install local python venv for generating input data
-      shell: bash
-      run: |
-        echo "::group::Create local python env for input data generation"
-        cd .testing
-        test ${{ inputs.install_python }} == true && make work/local-env
-        echo "::endgroup::"
-
     - name: Set flags
       shell: bash
       run: |

.github/actions/ubuntu-setup/action.yml

@@ -0,0 +1,31 @@
+name: 'install-ubuntu-prerequisites'
+
+description: 'Install prerequisites for Ubuntu Linux compilation'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Install Ubuntu Linux packages
+      shell: bash
+      run: |
+        echo "::group::Install linux packages"
+        sudo apt-get update
+        sudo apt-get install netcdf-bin
+        sudo apt-get install libnetcdf-dev
+        sudo apt-get install libnetcdff-dev
+        sudo apt-get install openmpi-bin
+        sudo apt-get install libopenmpi-dev
+        sudo apt-get install linux-tools-common
+        echo "::endgroup::"
+
+    - name: Store compiler flags used in Makefile
+      shell: bash
+      run: |
+        echo "::group::config.mk"
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -std=f2018 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"

.github/workflows/coupled-api.yml

@@ -11,14 +11,15 @@ jobs:
         working-directory: .testing
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
 
+    - uses: ./.github/actions/ubuntu-setup
+
     - uses: ./.github/actions/testing-setup
       with:
         build_symmetric: 'false'
-        install_python: 'false'
 
     - name: Compile MOM6 for the GFDL coupled driver
       shell: bash
@@ -27,7 +28,3 @@ jobs:
     - name: Compile MOM6 for the NUOPC driver
       shell: bash
       run: make check_mom6_api_nuopc -j
-
-    - name: Compile MOM6 for the MCT driver
-      shell: bash
-      run: make check_mom6_api_mct -j

.github/workflows/coverage.yml

@@ -3,22 +3,40 @@ name: Code coverage
 on: [push, pull_request]
 
 jobs:
-  build-test-nans:
+  build-coverage:
 
     runs-on: ubuntu-latest
     defaults:
       run:
         working-directory: .testing
 
-    env:
-      REPORT_COVERAGE: true
-
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
 
+    - uses: ./.github/actions/ubuntu-setup
+
     - uses: ./.github/actions/testing-setup
 
-    - name: Run and post coverage
-      run: make run.symmetric -k -s
+    - name: Compile unit tests
+      run: make -j build.unit
+
+    - name: Run unit tests
+      run: make run.cov.unit
+
+    - name: Report unit test coverage to CI
+      run: make report.cov.unit
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Compile ocean-only MOM6 with code coverage
+      run: make -j build/cov/MOM6
+
+    - name: Run coverage tests
+      run: make -k run.cov
+
+    - name: Report coverage to CI
+      run: make report.cov
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/documentation-and-style.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
 

.github/workflows/expression.yml

@@ -11,10 +11,12 @@ jobs:
         working-directory: .testing
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
 
+    - uses: ./.github/actions/ubuntu-setup
+
     - uses: ./.github/actions/testing-setup
 
     - name: Compile MOM6 using repro optimization

.github/workflows/macos-regression.yml

@@ -0,0 +1,35 @@
+name: MacOS regression
+
+on: [pull_request]
+
+jobs:
+  test-macos-regression:
+
+    runs-on: macOS-latest
+
+    env:
+      CC: gcc
+      FC: gfortran
+      FMS_COMMIT: 2019.01.03
+
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/macos-setup
+
+    - uses: ./.github/actions/testing-setup
+
+    - name: Compile reference model
+      run: make build.regressions MOM_TARGET_SLUG=$GITHUB_REPOSITORY MOM_TARGET_LOCAL_BRANCH=$GITHUB_BASE_REF DO_REGRESSION_TESTS=true -j
+
+    - name: Create validation data
+      run: make run.symmetric -k -s
+
+    - name: Regression test
+      run: make test.regression DO_REGRESSION_TESTS=true -k -s

.github/workflows/macos-stencil.yml

@@ -0,0 +1,35 @@
+name: MacOS stencil tests
+
+on: [push, pull_request]
+
+jobs:
+  test-macos-stencil:
+
+    runs-on: macOS-latest
+
+    env:
+      CC: gcc
+      FC: gfortran
+      FMS_COMMIT: 2019.01.03
+
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/macos-setup
+
+    - uses: ./.github/actions/testing-setup
+
+    - name: Compile MOM6 in asymmetric memory mode
+      run: make build/asymmetric/MOM6 -j
+
+    - name: Create validation data
+      run: make run.symmetric -k -s
+
+    - name: Run tests
+      run: make test.grid test.layout test.rotate -k -s

.github/workflows/other.yml

@@ -11,10 +11,12 @@ jobs:
         working-directory: .testing
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
 
+    - uses: ./.github/actions/ubuntu-setup
+
     - uses: ./.github/actions/testing-setup
 
     - name: Compile with openMP

.github/workflows/perfmon.yml

@@ -1,6 +1,6 @@
 name: Performance Monitor
 
-on: [pull_request]
+on: [push, pull_request]
 
 jobs:
   build-test-perfmon:
@@ -11,26 +11,65 @@ jobs:
         working-directory: .testing
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
 
+    - uses: ./.github/actions/ubuntu-setup
+
     - uses: ./.github/actions/testing-setup
 
     - name: Compile optimized models
+      if: ${{ github.event_name == 'pull_request' }}
       run: >-
         make -j build.prof
         MOM_TARGET_SLUG=$GITHUB_REPOSITORY
         MOM_TARGET_LOCAL_BRANCH=$GITHUB_BASE_REF
         DO_REGRESSION_TESTS=true
 
     - name: Generate profile data
+      if: ${{ github.event_name == 'pull_request' }}
       run: >-
         pip install f90nml &&
         make profile
         DO_REGRESSION_TESTS=true
 
     - name: Generate perf data
+      if: ${{ github.event_name == 'pull_request' }}
       run: |
         sudo sysctl -w kernel.perf_event_paranoid=2
         make perf DO_REGRESSION_TESTS=true
+
+    # This job assumes that build/target_codebase was cloned above
+    - name: Compile timing tests for reference code
+      if: ${{ github.event_name == 'pull_request' }}
+      run: >-
+        make -j build.timing_target
+        MOM_TARGET_SLUG=$GITHUB_REPOSITORY
+        MOM_TARGET_LOCAL_BRANCH=$GITHUB_BASE_REF
+        DO_REGRESSION_TESTS=true
+
+    - name: Compile timing tests
+      run: |
+        make -j build.timing
+
+    # DO_REGERESSION_TESTS=true is needed here to set the internal macro TARGET_CODEBASE
+    - name: Run timing tests for reference code
+      if: ${{ github.event_name == 'pull_request' }}
+      run: >-
+        make -j run.timing_target
+        DO_REGRESSION_TESTS=true
+
+    - name: Run timing tests
+      run: |
+        make -j run.timing
+
+    - name: Display timing results
+      run: |
+        make -j show.timing
+
+    - name: Display comparison of timing results
+      if: ${{ github.event_name == 'pull_request' }}
+      run: >-
+        make -j compare.timing
+        DO_REGRESSION_TESTS=true