check-linux-mpi.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: check-linux-mpi

jobs:
  check-linux-mpi:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }}_r-${{ matrix.config.r }}_${{ matrix.config.mpi }}

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: ubuntu-latest, r: 'release', mpi: 'openmpi'}
          - {os: ubuntu-latest, r: 'release', mpi: 'mpich'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/checkout@v4
        with:
          path: RNetCDF

      - uses: actions/checkout@v4
        with:
          repository: Unidata/netcdf-c
          path: netcdf-c

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: release
          use-public-rspm: true

      - name: Install system dependencies
        run: |
          case "${{ matrix.config.mpi }}" in
            openmpi) sudo apt-get install -y libhdf5-openmpi-dev openmpi-bin ;;
            mpich) sudo apt-get install -y libhdf5-mpich-dev mpich ;;
            *) echo "Unknown MPI variant"; exit 1 ;;
          esac
        shell: bash

      - name: Install netcdf with chosen MPI
        working-directory: netcdf-c
        run: |
          echo ::group::autoreconf
          autoreconf -if
          echo ::endgroup::
          echo ::group::configure
          inc_path="/usr/include/hdf5/${{ matrix.config.mpi }}"
          lib_path="/usr/lib/x86_64-linux-gnu/hdf5/${{ matrix.config.mpi }}"
          ./configure CC="mpicc.${{ matrix.config.mpi }}" \
            CPPFLAGS="-I${inc_path}" \
            LDFLAGS="-L${lib_path} -Wl,-rpath=${lib_path}"
          echo ::endgroup::
          echo ::group::make
          make
          echo ::endgroup::
          echo ::group::make install
          sudo make install
          echo ::endgroup::
        shell: bash

      - name: Install R dependencies with chosen MPI
        run: |
          cat("::group::bit64\n")
          install.packages("bit64")
          cat("::endgroup::\n")
          if ("${{ matrix.config.mpi }}" == "openmpi") {
            Rmpi_type <- "OPENMPI"
            pbdMPI_type <- "OPENMPI"
            mpi_include <- "/usr/lib/x86_64-linux-gnu/openmpi/include"
            mpi_lib <- "/usr/lib/x86_64-linux-gnu/openmpi/lib"
          } else if ("${{ matrix.config.mpi }}" == "mpich") {
            Rmpi_type <- "MPICH2"
            pbdMPI_type <- "MPICH3"
            mpi_include <- "/usr/include/x86_64-linux-gnu/mpich"
            mpi_lib <- "/usr/lib/x86_64-linux-gnu"
          } else {
            stop("Unknown MPI variant")
          }
          cat("::group::Rmpi\n")
          install.packages("parallel")
          install.packages("Rmpi", type="source",
            repos="https://cloud.r-project.org",
            configure.args=c(paste0("--with-Rmpi-type=", Rmpi_type),
                             paste0("--with-Rmpi-include=", mpi_include),
                             paste0("--with-Rmpi-libpath=", mpi_lib)))
          cat("::endgroup::\n")
          cat("::group::pbdMPI\n")
          install.packages(c("rlecuyer", "float"))
          install.packages("pbdMPI", type="source",
            repos="https://cloud.r-project.org",
            configure.args=c(paste0("--with-mpi-type=", pbdMPI_type),
                             paste0("--with-mpi-include=", mpi_include),
                             paste0("--with-mpi-libpath=", mpi_lib)))
          cat("::endgroup::\n")
        shell: Rscript {0}

      - name: Check RNetCDF with chosen MPI
        run: |
          echo ::group::Build RNetCDF
          R CMD build RNetCDF
          echo ::endgroup::
          echo ::group::Check RNetCDF
          Rscript -e "library(Rmpi); library(pbdMPI);"
          mpicc="mpicc.${{ matrix.config.mpi }}"
          mpiexec="mpiexec.${{ matrix.config.mpi }}"
          R CMD check --no-manual \
            --install-args="--configure-args='--without-nc-config \
              --with-mpiexec=$mpiexec --with-mpicc=$mpicc'" \
            RNetCDF_*.*-*.tar.gz
          echo ::endgroup::
        shell: bash

      - name: Upload check directory
        if: success() || failure()
        uses: actions/upload-artifact@v3
        with:
          name: ${{ matrix.config.os }}_r-${{ matrix.config.r }}_${{ matrix.config.mpi }}
          path: RNetCDF.Rcheck/
          retention-days: 5

      - name: Show RNetCDF install output
        run: |
          cat RNetCDF.Rcheck/00install.out
        shell: bash

      - name: Show RNetCDF test output
        run: |
          cat RNetCDF.Rcheck/tests/RNetCDF-test.Rout*
        shell: bash