extraction_test.yml

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# Author J. Henrichs, Bureau of Meteorology
# Modified S. Siso, STFC Daresbury Lab


# This workflow will use a self-hosted runner to perform the more expensive
# integrations tests that are not run on GHA systems.

name: LFRic Extraction Tests

on:
  push

jobs:
  run_if_on_mirror:
    if: ${{ github.repository == 'stfc/PSyclone-mirror' }}
    runs-on: self-hosted
    env:
      LFRIC_APPS_REV: 7536
      LFRIC_CORE_REV: 52054
      PYTHON_VERSION: "3.13"

    steps:
    - uses: actions/checkout@v3
      with:
        submodules: recursive
        # This is required to get the commit history for merge commits for
        # the ci-skip check below.
        fetch-depth: '0'
    - name: Check for [skip ci] in commit message
      uses: mstachniuk/ci-skip@v1
      with:
        # This setting causes the tests to 'fail' if [skip ci] is specified
        fail-fast: true
        commit-filter: '[skip ci]'
    - name: Install dependencies
      run: |
        # Use a specific version of Python (rather than the system-wide one).
        module load python/${PYTHON_VERSION}
        python -m venv .runner_venv
        . .runner_venv/bin/activate
        python -m pip install --upgrade pip
        # Uncomment the below to use the submodule version of fparser rather
        # than the latest release from pypi.
        # pip install external/fparser
        pip install .[test]
        # Install BAF, and its version of Fab:
        # ------------------------------------
        git clone -b psyclone_ci_branch --recurse-submodules https://github.com/MetOffice/lfric-baf.git
        # First install Fab:
        pushd lfric-baf/fab
        pip install .
        popd

        # Now process the extraction library in PSyclone, and overwrite the
        # psydata files included in Fab:
        pushd lfric-baf/infrastructure/build/psyclone/psydata/extract
        rm *90   # Delete the old files (in case that the names are changed)
        popd

        # Create the new Fortran files, i.e. processing with Jinja2
        pushd lib/extract/netcdf/lfric
        make read_kernel_data_mod.f90 compare_variables_mod.F90 extract_netcdf_base.F90 \
             kernel_data_netcdf.f90 psy_data_base.f90 read_kernel_data_mod.f90
        popd

        # Copy the files into the LFRic Fab build system
        cp lib/extract/netcdf/lfric/*90 lfric-baf/infrastructure/build/psyclone/psydata/extract

        # Fetch the specified version of LFRic apps
        source /archive/psyclone-spack/psyclone-spack-Dec25/spack-repo/share/spack/setup-env.sh
        spack load fcm/zefe2ha
        cd /archive/psyclone-tests/latest-run
        rm -rf lfric_extraction
        mkdir lfric_extraction
        cd lfric_extraction
        fcm co --username ${{ secrets.UKMO_USER }} --password '${{ secrets.UKMO_PASSW }}' \
          -r ${LFRIC_APPS_REV} https://code.metoffice.gov.uk/svn/lfric_apps/main/trunk/ lfric_apps
        fcm co --username ${{ secrets.UKMO_USER }} --password '${{ secrets.UKMO_PASSW }}' \
          -r ${LFRIC_CORE_REV} https://code.metoffice.gov.uk/svn/lfric/LFRic/trunk/ lfric_core
        sed -i "s|lfric_core_rev=$LFRIC_CORE_REV|lfric_core_rev=|g" lfric_apps/dependencies.sh
        sed -i "s|lfric_core_sources=|lfric_core_sources=$PWD/lfric_core|g" lfric_apps/dependencies.sh
        sed -i "s|use_xios_io=.true.|use_xios_io=.false.|g" lfric_apps/applications/gungho_model/example/configuration.nml


    # Compile GungHo with extraction
    - name: GungHo Extraction Compilation
      run:  |
        # Set up environment
        source /archive/psyclone-spack/psyclone-spack-Dec25/spack-repo/share/spack/setup-env.sh
        spack load lfric-build-environment %gnu14_openmpi
        source .runner_venv/bin/activate
        export PSYCLONE_LFRIC_DIR=${GITHUB_WORKSPACE}/examples/lfric/scripts
        export PSYCLONE_CONFIG_FILE=${PSYCLONE_LFRIC_DIR}/KGOs/lfric_psyclone.cfg
        export COMPILER_PROFILE=fast-debug
        export NUM_PROCS=6
        export MAX_PROC=$((NUM_PROCS-1))

        # Set the directory names for the extraction runs:
        # -----------------------------------------------
        export RUNDIR=/archive/psyclone-tests/latest-run/extraction_test
        export LFRIC_CORE=${RUNDIR}/lfric_core
        export LFRIC_APPS=${RUNDIR}/lfric_apps

        # Copy the lfric source files (BAF copies files into the source tree)
        # -------------------------------------------------------------------
        rm -rf ${RUNDIR}
        mkdir -p ${LFRIC_CORE} ${LFRIC_APPS}
        cp -r /archive/psyclone-tests/latest-run/lfric_extraction/lfric_core/ ${RUNDIR}
        cp -r /archive/psyclone-tests/latest-run/lfric_extraction/lfric_apps/ ${RUNDIR}

        # Install the BAF scripts into the lfric directories:
        # ---------------------------------------------------
        cd lfric-baf
        ./install.sh ${LFRIC_CORE} ${LFRIC_APPS}

        # Copy the modified extraction script from PSyclone
        # -------------------------------------------------
        # This allows us to keep the extraction script working,
        # even if we are using new features/names.
        export EXTRACT_DIR=${LFRIC_APPS}/applications/gungho_model/optimisation/extract
        # Note that this directory exists after the BAF installation
        cp ${PSYCLONE_LFRIC_DIR}/extract_script.py ${EXTRACT_DIR}/global.py

        # Build GungHo with the BAF extraction script
        # -------------------------------------------
        cd ${LFRIC_APPS}/applications/gungho_model
        mkdir -p $PWD/fab_workspace
        export FAB_WORKSPACE=$PWD/fab_workspace
        # Run the Fab build script
        ${LFRIC_CORE}/build.sh ./fab_gungho_model_extract.py   \
          --profile ${COMPILER_PROFILE} --nproc 4 -fc $LDMPI -ld $LDMPI  -cc $CC

        # Run gungho (which will create the NetCDF kernel data files)
        # -----------------------------------------------------------
        # Modify number of timesteps to reduce impact on system
        cd example
        sed -i "s/timestep_end='10'/timestep_end='1'/" configuration.nml
        mpirun -n ${NUM_PROCS} ${FAB_WORKSPACE}/gungho_model_extract-${COMPILER_PROFILE}-mpif90-gfortran/gungho_model configuration.nml

        # Now compile a subset of the drivers
        # -----------------------------------

        cd ..

        compile_count=0

        # `name` is the 'basic' name. A driver file is then called driver-$FILE.F90, and
        # the kernel data files are called $FILE-$RANK.nc
        for name in sci_fem_constants_mod_psy-invoke_compute_w1_mass_matrix-compute_mass_matrix_w1_code-r0; do

          # We link with yaxt, since a few drivers inline a module that contains yaxt
          # functions (though these functions and therefore yaxt are not actually used
          # during the execution of the driver)
          mpif90 driver-${name}.F90 $FFLAGS $LDFLAGS -l yaxt_c -o driver-${name}
          compile_count=$((compile_count+1 ))
        done

        run_count=0
        all_files="sci_fem_constants_mod_psy-invoke_compute_w1_mass_matrix-compute_mass_matrix_w1_code-r0"
        for name in $all_files; do
          # Execute the driver for each kernel data file,
          # which will print results to the screen
          # ---------------------------------------------
          for proc in $(seq 0 $MAX_PROC); do
            echo "Executing driver-${name} for ${proc}"
            ./driver-${name} ./example/${name}-${proc}.nc
            run_count=$((run_count+1))
          done
        done

        NUM_NC_FILES=$(ls example/*-[0-${MAX_PROC}].nc|wc -w)
        KERNEL_DATA=$((NUM_NC_FILES / NUM_PROCS))
        echo "Drivers created:   $(ls driver*F90|wc -w)"
        echo "Kernel data files: $NUM_NC_FILES"
        echo "Unique Kernels:    $((NUM_NC_FILES/NUM_PROCS))"
        echo "Drivers compiled:  ${compile_count}"
        echo "Drivers executed:  ${run_count}"