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Github actions: use matrix to merge build options
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‎.github/workflows/main.yml‎

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name: Test PnetCDF-C master branch
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permissions:
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contents: read
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on:
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workflow_dispatch:
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inputs:
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reason:
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description: 'Enable manual run because PnetCDF is updated more frequently'
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required: false
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default: 'Manual trigger'
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push:
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branches:
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- main
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paths-ignore:
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- '**/*.md'
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- '**/*.txt'
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pull_request:
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branches:
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- main
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paths-ignore:
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- '**/*.md'
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- '**/*.txt'
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env:
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MPICH_VERSION: 4.3.2
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OPENMPI_VERSION: 5.0.9
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PNETCDF_VERSION: 1.14.1
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LIBTOOL_VERSION: 2.5.4
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MPI_DIR: ${{ github.workspace }}/MPI
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PNETCDF_DIR: ${{ github.workspace }}/PnetCDF-install
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jobs:
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build:
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strategy:
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fail-fast: false # This disables the default cancel-on-failure behavior
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matrix:
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mpi_vendor: [ MPICH, OpenMPI ]
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pnetcdf_ver: [ release, master ]
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runs-on: ubuntu-latest
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timeout-minutes: 60
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: 3.10
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- name: Install Ubuntu Dependencies
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run: |
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sudo apt-get update
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sudo apt-get install automake autoconf libtool libtool-bin m4
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- name: Install GNU autotools
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run: |
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sudo apt-get update
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sudo apt-get install autoconf
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sudo apt-get install automake
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sudo apt-get install m4
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wget -q https://ftp.gnu.org/gnu/libtool/libtool-${LIBTOOL_VERSION}.tar.gz
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gzip -dc libtool-${LIBTOOL_VERSION}.tar.gz | tar -xf -
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cd libtool-${LIBTOOL_VERSION}
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./configure --prefix=/usr --silent
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sudo make -s LIBTOOLFLAGS=--silent V=1 -j 8 install > qout 2>&1
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sudo make -s LIBTOOLFLAGS=--silent V=1 -j 8 distclean >> qout 2>&1
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- name: Install MPI compiler vendor - ${{ matrix.mpi_vendor }}
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run: |
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set -x
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if test "${{ matrix.mpi_vendor }}" = "MPICH" ; then
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# MPICH versions older than 4.2.2 do not support the MPI large
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# count feature.
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echo "Install MPICH ${MPICH_VERSION} in ${GITHUB_WORKSPACE}/MPI"
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wget -q https://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPICH_VERSION}.tar.gz
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gzip -dc mpich-${MPICH_VERSION}.tar.gz | tar -xf -
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cd mpich-${MPICH_VERSION}
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./configure --prefix=${MPI_DIR} \
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--silent \
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--enable-romio \
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--with-file-system=ufs \
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--with-device=ch3:sock \
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--disable-fortran \
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CC=gcc
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make -s LIBTOOLFLAGS=--silent V=1 -j 8 install
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make -s LIBTOOLFLAGS=--silent V=1 -j 8 distclean
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else # OpenMPI
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echo "Install OpenMPI ${OPENMPI_VERSION} in ${GITHUB_WORKSPACE}/MPI"
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VER_MAJOR=${OPENMPI_VERSION%.*}
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wget -q https://download.open-mpi.org/release/open-mpi/v${VER_MAJOR}/openmpi-${OPENMPI_VERSION}.tar.gz
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gzip -dc openmpi-${OPENMPI_VERSION}.tar.gz | tar -xf -
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cd openmpi-${OPENMPI_VERSION}
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./configure --prefix=${MPI_DIR} \
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--silent \
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--with-io-romio-flags="--with-file-system=ufs" \
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--disable-mpi-fortran \
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CC=gcc
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make -s LIBTOOLFLAGS=--silent V=1 -j 8 install
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make -s LIBTOOLFLAGS=--silent V=1 -j 8 distclean
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fi
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- name: Build PnetCDF-C from ${{ matrix.pnetcdf_ver }}
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run: |
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set -x
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cd ${GITHUB_WORKSPACE}
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export PATH="${MPI_DIR}/bin:${PATH}"
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export LD_LIBRARY_PATH="${MPI_DIR}/lib:${LD_LIBRARY_PATH}"
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m4 --version
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autoconf --version
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automake --version
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libtool --version
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if test "${{ matrix.pnetcdf_ver }}" = "master" ; then
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git clone -q https://github.com/Parallel-NetCDF/PnetCDF.git
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pushd PnetCDF
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autoreconf -i
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else
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wget -q https://parallel-netcdf.github.io/Release/pnetcdf-${PNETCDF_VERSION}.tar.gz
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tar -xzf pnetcdf-${PNETCDF_VERSION}.tar.gz
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pushd pnetcdf-${PNETCDF_VERSION}
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fi
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./configure --prefix=$PNETCDF_DIR \
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--silent \
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--enable-shared \
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--enable-debug \
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--disable-fortran \
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--disable-cxx \
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--with-mpi=$MPI_DIR
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make -s LIBTOOLFLAGS=--silent V=1 -j 4 install > qout 2>&1
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make -s -j 4 distclean >> qout 2>&1
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popd
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- name: Install python dependencies via pip
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run: |
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python -m pip install --upgrade pip setuptools wheel
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pip install numpy cython cftime pytest twine check-manifest
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export MPICC=$MPI_DIR/bin/mpicc
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export CC=$MPI_DIR/bin/mpicc
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pip install mpi4py
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pip install torch torchvision
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- name: Install PnetCDF-Python
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run: |
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export CC=$MPI_DIR/bin/mpicc
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pip install --verbose --no-build-isolation -e .
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- name: Test PnetCDF-Python
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run: |
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export PATH=${PNETCDF_DIR}/bin:${MPI_DIR}/bin:${PATH}
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export LD_LIBRARY_PATH="${PNETCDF_DIR}/lib:${MPI_DIR}/lib:${LD_LIBRARY_PATH}"
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if test "${{ matrix.mpi_vendor }}" = "OpenMPI" ; then
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make ptests TESTMPIRUN="${MPI_DIR}/bin/mpiexec --oversubscribe"
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else
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make ptests TESTMPIRUN="${MPI_DIR}/bin/mpiexec"
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fi
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- name: Re-install PnetCDF-Python from source distribution
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run: |
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pip uninstall -y pnetcdf
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make install-clean
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export CC=$MPI_DIR/bin/mpicc
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python setup.py sdist
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pip install --verbose dist/pnetcdf-*.tar.gz
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- name: Test PnetCDF-Python
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run: |
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export PATH=${PNETCDF_DIR}/bin:${MPI_DIR}/bin:${PATH}
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export LD_LIBRARY_PATH="${PNETCDF_DIR}/lib:${MPI_DIR}/lib:${LD_LIBRARY_PATH}"
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if test "${{ matrix.mpi_vendor }}" = "OpenMPI" ; then
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make ptests TESTMPIRUN="${MPI_DIR}/bin/mpiexec --oversubscribe"
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else
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make ptests TESTMPIRUN="${MPI_DIR}/bin/mpiexec"
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fi
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# - name: Tarball
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# run: |
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# export PATH=${NETCDF_DIR}/bin:${PATH}
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# python setup.py --version
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# check-manifest --version
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# check-manifest --verbose
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# pip wheel . -w dist --no-deps
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# twine check dist/*

‎.github/workflows/openmpi.yml‎

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