Fast Matrix Assembly #2577
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| # This workflow will install Python dependencies and run tests with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Run tests | |
| on: | |
| push: | |
| branches: [ devel ] | |
| pull_request: | |
| branches: [ devel ] | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest ] | |
| python-version: [ 3.9, '3.10', '3.11', '3.12' ] | |
| isMerge: | |
| - ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }} | |
| exclude: | |
| - { isMerge: false, python-version: '3.10' } | |
| - { isMerge: false, python-version: '3.11' } | |
| include: | |
| - os: macos-latest | |
| python-version: '3.10' | |
| - os: macos-latest | |
| python-version: '3.11' | |
| name: ${{ matrix.os }} / Python ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| cache-dependency-path: | | |
| pyproject.toml | |
| requirements.txt | |
| requirements_extra.txt | |
| - name: Install non-Python dependencies on Ubuntu | |
| if: matrix.os == 'ubuntu-latest' | |
| uses: awalsh128/cache-apt-pkgs-action@latest | |
| with: | |
| packages: gfortran openmpi-bin libopenmpi-dev libhdf5-openmpi-dev | |
| version: 1.0 | |
| execute_install_scripts: true | |
| # When loading cached apt packages, the default MPI compiler isn't set. | |
| # Workaround is to 'reinstall' openmpi-bin, which doesn't actually perform | |
| # installation (since openmpi-bin already exists), but instead reruns | |
| # `update-alternatives` which fixes the symlinks to mpicc/mpif90. | |
| - name: Set default MPI and HDF5 C compilers on Ubuntu | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install --reinstall openmpi-bin libhdf5-openmpi-dev | |
| - name: Install non-Python dependencies on macOS | |
| if: matrix.os == 'macos-latest' | |
| run: | | |
| brew install open-mpi | |
| brew install hdf5-mpi | |
| brew install libomp | |
| GFORTRAN_HOME=$(which gfortran || true) | |
| echo "GFORTRAN_HOME : $GFORTRAN_HOME" | |
| if [[ ! -f "$GFORTRAN_HOME" ]]; then | |
| gfort=$(find ${PATH//:/\/ } -name 'gfortran-*' -exec basename {} \; | sort | tail -n 1 || true) | |
| echo "Found $gfort" | |
| gfort_path=$(which ${gfort}) | |
| folder=$(dirname ${gfort_path}) | |
| ln -s ${gfort_path} ${folder}/gfortran | |
| fi | |
| echo "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV | |
| - name: Print information on MPI and HDF5 libraries | |
| run: | | |
| ompi_info | |
| h5pcc -showconfig -echo || true | |
| - name: Upgrade pip | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Determine directory of parallel HDF5 library | |
| run: | | |
| if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then | |
| HDF5_DIR=$(dpkg -L libhdf5-openmpi-dev | grep libhdf5.so | xargs dirname) | |
| elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then | |
| HDF5_DIR=$(brew list hdf5-mpi | grep "libhdf5.dylib" | xargs dirname | xargs dirname) | |
| fi | |
| echo $HDF5_DIR | |
| echo "HDF5_DIR=$HDF5_DIR" >> $GITHUB_ENV | |
| - name: Cache PETSc | |
| uses: actions/cache@v4 | |
| id: cache-petsc | |
| env: | |
| cache-name: cache-PETSc | |
| with: | |
| path: "./petsc" | |
| key: cache-${{ matrix.os }}-${{ matrix.python-version }} | |
| - if: steps.cache-petsc.outputs.cache-hit != 'true' | |
| name: Download a specific release of PETSc | |
| run: | | |
| git clone --depth 1 --branch v3.21.4 https://gitlab.com/petsc/petsc.git | |
| - if: steps.cache-petsc.outputs.cache-hit != 'true' | |
| name: Install PETSc with complex support | |
| working-directory: ./petsc | |
| run: | | |
| export PETSC_DIR=$(pwd) | |
| export PETSC_ARCH=petsc-cmplx | |
| ./configure --with-scalar-type=complex --with-fortran-bindings=0 --have-numpy=1 | |
| make all | |
| echo "PETSC_DIR=$PETSC_DIR" > petsc.env | |
| echo "PETSC_ARCH=$PETSC_ARCH" >> petsc.env | |
| # This step is not really necessary and could be combined with PETSc install | |
| # step; however it's good to verify if the cached PETSc installation really works! | |
| - name: Test PETSc installation | |
| working-directory: ./petsc | |
| run: | | |
| source petsc.env | |
| make check | |
| echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV | |
| echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV | |
| - name: Install petsc4py | |
| working-directory: ./petsc | |
| run: | | |
| python -m pip install wheel Cython numpy | |
| python -m pip install src/binding/petsc4py | |
| - name: Install Python dependencies | |
| run: | | |
| export CC="mpicc" | |
| export HDF5_MPI="ON" | |
| python -m pip install -r requirements.txt | |
| python -m pip install -r requirements_extra.txt --no-build-isolation | |
| python -m pip list | |
| - name: Check parallel h5py installation | |
| run: | | |
| python -c " | |
| from mpi4py import MPI | |
| import h5py | |
| # This particular instantiation of h5py.File will fail if parallel h5py isn't installed | |
| f = h5py.File('parallel_test.hdf5', 'w', driver='mpio', comm=MPI.COMM_WORLD) | |
| print(f)" | |
| - name: Install project | |
| run: | | |
| python -m pip install . | |
| python -m pip freeze | |
| - name: Test Pyccel optimization flags | |
| run: | | |
| pytest --pyargs psydac -m pyccel --capture=no | |
| - name: Initialize test directory | |
| run: | | |
| mkdir pytest | |
| cp mpi_tester.py pytest | |
| - name: Run single-process tests with Pytest | |
| working-directory: ./pytest | |
| run: | | |
| export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh | |
| export OMP_NUM_THREADS=2 | |
| python -m pytest -n auto --pyargs psydac -m "not parallel and not petsc" | |
| #- name: Run MPI tests with Pytest | |
| # working-directory: ./pytest | |
| # run: | | |
| # export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh | |
| # export OMP_NUM_THREADS=2 | |
| # python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and not petsc" | |
| - name: Run single-process PETSc tests with Pytest | |
| working-directory: ./pytest | |
| run: | | |
| export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh | |
| export OMP_NUM_THREADS=2 | |
| python -m pytest -n auto --pyargs psydac -m "not parallel and petsc" | |
| #- name: Run MPI PETSc tests with Pytest | |
| # working-directory: ./pytest | |
| # run: | | |
| # export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh | |
| # export OMP_NUM_THREADS=2 | |
| # python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc" | |
| - name: Remove test directory | |
| if: ${{ always() }} | |
| run: | | |
| rm -rf pytest |