Release 2.9-2 (#142) #116
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| # 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 | |