continuous_integration.yml

# (c) British Crown Copyright 2020, the Met Office.
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# Workflow for continuous integration tests
name: CI
on: [push, pull_request]

jobs:
  # This workflow contains a single job called "test"
  test:
    # The type of runner that the job will run on
    runs-on: ubuntu-20.04
    strategy:
      matrix:
        fortran-compiler: [gfortran, gfortran-8, gfortran-7, ifort]
    env:
      F90: ${{ matrix.fortran-compiler }}
      FC: ${{ matrix.fortran-compiler }}
      F90FLAGS: "-O3 -ffree-line-length-none -fcheck=bounds -finit-real=nan"
      ATOL: 0.0
      RTOL: 0.0
      KGO_VERSION: v002
      NFHOME: /home/runner/netcdf-fortran
      LD_LIBRARY_PATH: /home/runner/netcdf-fortran/lib
    # Sequence of tasks that will be executed as part of the job
    steps:
    # Checks-out repository under $GITHUB_WORKSPACE
    - uses: actions/checkout@v2
    ###############################################################################
    # Initial steps
    ###############################################################################
    # Set up Python and install dependencies
    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: 3.7
    - name: Setup conda
      uses: s-weigand/setup-conda@v1
      with:
        python-version: 3.7
    - name: Install python packages
      run: conda install --yes cartopy matplotlib netcdf4
    # Update system packages
    - name: Update system packages
      run: sudo apt-get update
    # Non compiler-specific environment
    - name: Non compiler-specific environment
      run: export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${NFHOME}/lib
    ###############################################################################
    # FORTRAN compilers
    ###############################################################################
    #
    # Install gfortran compiler
    #
    - name: Install gfortran compiler
      if: contains(matrix.fortran-compiler, 'gfortran')
      run: sudo apt-get install ${{ matrix.fortran-compiler }}
    #
    # Intel compilers
    #
    - name: cache-intel-compilers
      id: cache-intel-compilers
      if: contains(matrix.fortran-compiler, 'ifort')
      uses: actions/cache@v2
      with:
        path: /opt/intel
        key: intel-${{ runner.os }}-compilers-b

    # https://software.intel.com/content/www/us/en/develop/articles/installing-intel-oneapi-toolkits-via-apt.html
    # List of packages from Docler file at
    #    https://github.com/intel/oneapi-containers/blob/master/images/docker/hpckit-devel-ubuntu18.04/Dockerfile
    - name: Install Intel compilers and libraries
      if: contains(matrix.fortran-compiler, 'ifort') && steps.cache-intel-compilers.outputs.cache-hit != 'true'
      run: |
        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
        sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
        sudo apt-get update
        sudo apt-get install intel-hpckit-getting-started intel-oneapi-clck intel-oneapi-common-licensing intel-oneapi-common-vars
        sudo apt-get install intel-oneapi-dev-utilities  intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-compiler-fortran intel-oneapi-itac

    #
    # Nvidia compilers
    #
    - name: cache-nvidia-compilers
      id: cache-nvidia-compilers
      if: contains(matrix.fortran-compiler, 'nvfortran')
      uses: actions/cache@v2
      with:
        path: /opt/nvidia/hpc_sdk/
        key: nvhpc-${{ runner.os }}-2020-20.7

    - name: Nvidia setup compilers
      if: contains(matrix.fortran-compiler, 'nvfortran') && steps.cache-nvidia-compilers.outputs.cache-hit != 'true'
      env:
        NVCOMPILERS: /opt/nvidia/hpc_sdk
      run: |
        wget -q https://developer.download.nvidia.com/hpc-sdk/nvhpc-20-7_20.7_amd64.deb https://developer.download.nvidia.com/hpc-sdk/nvhpc-2020_20.7_amd64.deb
        sudo apt-get install ./nvhpc-20-7_20.7_amd64.deb ./nvhpc-2020_20.7_amd64.deb
    ###############################################################################
    # Compiler-specific environment
    ###############################################################################
    # Environments for ifort and nvidia compilers
    - name: Environment for ifort compiler
      if: contains(matrix.fortran-compiler, 'ifort')
      run: |
        echo "CC=icx" > $GITHUB_ENV
        echo "FC=ifort" > $GITHUB_ENV
        echo "F90FLAGS=-O3 -heap-arrays" > $GITHUB_ENV
    - name: Environment for nvfortran compiler
      env:
        NVCOMPILERS: /opt/nvidia/hpc_sdk
      if: contains(matrix.fortran-compiler, 'nvfortran')
      run: |
        echo "CC=nvc" > $GITHUB_ENV
        echo "FC=nvfortran" > $GITHUB_ENV
        echo "F90FLAGS=-Mallocatable=03 -Mstandard -Mbounds -Mchkptr -Kieee -Mchkstk" > $GITHUB_ENV
        echo "${NVCOMPILERS}/Linux_x86_64/20.7/compilers/bin" >> $GITHUB_PATH
    ###############################################################################
    # NetCDF C and FORTRAN libraries
    ###############################################################################
    # NetCDF C library
    - name: Install NetCDF library
      run: sudo apt-get install libnetcdf-dev

    # Cache netcdf FORTRAN library
    - name: cache-netcdf-fortran
      id: cache-netcdf-fortran
      uses: actions/cache@v2
      with:
        path: /home/runner/netcdf-fortran
        key: netcdf-fortran-4.4.4a-${{ runner.os }}-${{ matrix.fortran-compiler }}-v02

    # Build NetCDF FORTRAN library for current compiler
    - name: Build NetCDF FORTRAN library
      env:
        FCFLAGS: -fPIC
      if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
      run: |
        source /opt/intel/oneapi/setvars.sh || true
        ${F90} --version
        git clone https://github.com/Unidata/netcdf-fortran.git --branch v4.4.4
        cd netcdf-fortran
        ./configure --prefix=${NFHOME}
        make -j
        sudo make install
    ###############################################################################
    # Build COSP and retrieve input and test files
    ###############################################################################
    # Build COSP2 driver. Intel Fortran stores automatic arrays in the stack
    # by default, whereas GNU Fortran stores them in the heap. This can cause
    # segmentation faults with ifort, especially in memory-intensive applications
    # like COSP. We tell ifort to use heap arrays.
    - name: Build driver
      run: |
        source /opt/intel/oneapi/setvars.sh || true
        ${F90} --version
        cd build
        make -j driver
    # Retrieve and expand large data files
    - name: Retrieve data files
      run: |
        GDFILE='https://docs.google.com/uc?export=download&id=17eK4_DVEvFOE9Uf6siXJDpWZJKT1aqkU'
        OUTPATH=driver/data/inputs/UKMO/cosp_input.um_global.nc.gz
        wget --no-check-certificate $GDFILE -O $OUTPATH
        gunzip ${OUTPATH}
        cd driver/data/inputs/UKMO
        md5sum -c cosp_input.um_global.nc.md5
        cd ${GITHUB_WORKSPACE}
        GDFILE='https://docs.google.com/uc?export=download&id=1s5Ha6Hqnv_hWbRUs8KQpJ4Lxy8uvJDar'
        OUTPATH=driver/data/outputs/UKMO/cosp2_output.um_global.gfortran.kgo.$KGO_VERSION.nc.gz
        wget --no-check-certificate $GDFILE -O $OUTPATH
        gunzip ${OUTPATH}
        cd driver/data/outputs/UKMO
        md5sum -c cosp2_output.um_global.gfortran.kgo.$KGO_VERSION.nc.md5
        cd ${GITHUB_WORKSPACE}
        GDFILE='https://docs.google.com/uc?export=download&id=11dKcIL3EQr7s6jbo4f9GsoW0SufesGbq'
        OUTPATH=driver/data/outputs/UKMO/cosp2_output_um.gfortran.kgo.$KGO_VERSION.nc.gz
        wget --no-check-certificate $GDFILE -O $OUTPATH
        gunzip ${OUTPATH}
        cd driver/data/outputs/UKMO
        md5sum -c cosp2_output_um.gfortran.kgo.$KGO_VERSION.nc.md5
        cd ${GITHUB_WORKSPACE}
        GDFILE='https://docs.google.com/uc?export=download&id=1kY1lRgzd0UhDiQef2u-VgTQql_iut3U2'
        OUTPATH=driver/data/outputs/UKMO/cosp2_output.um_global_model_levels.gfortran.kgo.$KGO_VERSION.nc.gz
        wget --no-check-certificate $GDFILE -O $OUTPATH
        gunzip ${OUTPATH}
        cd driver/data/outputs/UKMO
        md5sum -c cosp2_output.um_global_model_levels.gfortran.kgo.$KGO_VERSION.nc.md5
    ###############################################################################
    # Run COSP2 tests. We could run both tests in one step, but
    # doing it this way the output is easier to interpret.
    ###############################################################################
    # 1. Basic test
    - name: Basic test
      run: |
        source /opt/intel/oneapi/setvars.sh || true
        cd driver/run
        ./cosp2_test cosp2_input_nl.txt
    # 2. UM global snapshot
    - name: UM global snapshot
      run: |
        source /opt/intel/oneapi/setvars.sh || true
        cd driver/run
        ./cosp2_test cosp2_input_nl.um_global.txt
    # 3. UM global snapshot. Diagnostics on model levels.
    - name: UM global snapshot. Diagnostics on model levels.
      run: |
        if [[ "${F90}" = 'gfortran' ]]; then
          cd driver/run
          ./cosp2_test cosp2_input_nl.um_global_model_levels.txt cosp2_output_nl.um_global_model_levels.txt
        else
          echo "Test is only run for gfortran compiler."
        fi
    ###############################################################################
    # Compare results against known good outputs. As above,
    # we split it in as many steps as tests.
    ###############################################################################
    # 1. Basic test
    - name: Basic against known good output (KGO)
      run: |
        if [[ "${F90}" != 'gfortran' ]]; then
          ATOL=1.0e-20
          RTOL=0.0006
        fi
        cd driver
        KGO=data/outputs/UKMO/cosp2_output_um.gfortran.kgo.$KGO_VERSION.nc
        TST=data/outputs/UKMO/cosp2_output_um.nc
        python compare_to_kgo.py ${KGO} ${TST} --atol=${ATOL} --rtol=${RTOL}
    # 2. UM global snapshot. The approach used for the basic test would needed
    # large tolerances for the ifort compiler. We keep tolerances small for ifort,
    # and then we test against the output table.
    - name: UM global against known good output (KGO)
      run: |
        cd driver
        KGO=data/outputs/UKMO/cosp2_output.um_global.gfortran.kgo.$KGO_VERSION.nc
        TST=data/outputs/UKMO/cosp2_output.um_global.nc
        if [[ "${F90}" = 'gfortran' ]]; then
          python compare_to_kgo.py ${KGO} ${TST} --atol=${ATOL} --rtol=${RTOL}
        else
          ATOL=1.0e-20
          RTOL=0.0006
          OUTTST=data/outputs/UKMO/cosp2_output.um_global.out
          OUTKGO=data/outputs/UKMO/cosp2_output.um_global.${F90}.kgo.${KGO_VERSION}.out
          python compare_to_kgo.py ${KGO} ${TST} --atol=${ATOL} --rtol=${RTOL} \
            --noerror=True --stats_file=${OUTTST}
          diff ${OUTKGO} ${OUTTST}
        fi
    # 3. UM global snapshot. Diagnostics on model levels. Only gfortran.
    - name: UM global on model levels against known good output (KGO)
      run: |
        cd driver
        KGO=data/outputs/UKMO/cosp2_output.um_global_model_levels.gfortran.kgo.$KGO_VERSION.nc
        TST=data/outputs/UKMO/cosp2_output.um_global_model_levels.nc
        if [[ "${F90}" = 'gfortran' ]]; then
          python compare_to_kgo.py ${KGO} ${TST} --atol=${ATOL} --rtol=${RTOL}
        else
          echo "Test only run for gfortran compiler."
        fi
    ###############################################################################
    # Produce plots when it fails during global snapshot tests,
    # and create a tarball with outputs.
    ###############################################################################
    - name: Produce plots and create tarball
      if: failure()
      run: |
        TST_MLEV=data/outputs/UKMO/cosp2_output.um_global_model_levels.nc
        cd driver
        if [[ -e data/outputs/UKMO/cosp2_output.um_global.nc ]]; then
          python plot_test_outputs.py
        fi
        if [[ -e data/outputs/UKMO/cosp2_output.um_global_model_levels.nc ]]; then
          python plot_test_outputs.py --tst_file=$TST_MLEV
        fi
        cd data/outputs/UKMO
        tar --ignore-failed-read -czf outputs.UKMO.tgz cosp2_output.um_global.nc \
          cosp2_output_um.nc cosp2_output.um_global_model_levels.nc *.png \
          cosp2_output.um_global.out
        ls -lh
    ###############################################################################
    # Make output files available if any test fails
    ###############################################################################
    - name: Upload output file if test fails
      if: failure()
      uses: actions/upload-artifact@v1.0.0
      with:
        name: outputs.UKMO.tgz
        path: driver/data/outputs/UKMO/outputs.UKMO.tgz