Use system MPI in Dockerfile #3727
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI (with Spack) | |
| on: | |
| # Uncomment the below 'push' to trigger on push | |
| push: | |
| branches: | |
| - release | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| env: | |
| GITHUB_USER: ${{ github.actor }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| OMPI_ALLOW_RUN_AS_ROOT: 1 | |
| OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1 | |
| PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe | |
| jobs: | |
| ci-spack-build: | |
| name: ci-spack-build (${{ matrix.mpi }}${{ matrix.petsc && format(', petsc {0}/{1}', matrix.scalar, matrix.index) || ', no petsc' }}) | |
| runs-on: ubuntu-26.04 | |
| container: ubuntu:26.04 | |
| permissions: | |
| contents: read | |
| packages: write | |
| strategy: | |
| fail-fast: false | |
| # PETSc scalar/index combinations are covered on OpenMPI; MPICH | |
| # repeats the two most common ones, as it exercises the MPI layer | |
| # rather than the scalar type. The PETSc-free build tests the | |
| # optional-PETSc code paths and needs only one MPI. | |
| matrix: | |
| include: | |
| - {mpi: openmpi, petsc: true, scalar: float32, index: int32, | |
| petsc_dep: "^petsc+mpi+metis+mumps+ptscotch+scalapack+superlu-dist~hypre~suite-sparse~double~complex~int64"} | |
| - {mpi: openmpi, petsc: true, scalar: float64, index: int32, | |
| petsc_dep: "^petsc+mpi+hypre+metis+mumps+ptscotch+scalapack+suite-sparse+superlu-dist+double~complex~int64"} | |
| - {mpi: openmpi, petsc: true, scalar: complex64, index: int32, | |
| petsc_dep: "^petsc+mpi+metis+mumps+ptscotch+scalapack~hypre~suite-sparse~superlu-dist~double+complex~int64"} | |
| - {mpi: openmpi, petsc: true, scalar: complex128, index: int32, | |
| petsc_dep: "^petsc+mpi+hypre+metis+mumps+ptscotch+scalapack+suite-sparse+superlu-dist+double+complex~int64"} | |
| - {mpi: openmpi, petsc: true, scalar: float64, index: int64, | |
| petsc_dep: "^petsc+mpi+hypre+mumps+ptscotch+scalapack+suite-sparse+superlu-dist~metis+double~complex+int64"} | |
| - {mpi: openmpi, petsc: true, scalar: complex128, index: int64, | |
| petsc_dep: "^petsc+mpi+hypre+mumps+ptscotch+scalapack+suite-sparse+superlu-dist~metis+double+complex+int64"} | |
| - {mpi: mpich, petsc: true, scalar: float64, index: int32, | |
| petsc_dep: "^petsc+mpi+hypre+metis+mumps+ptscotch+scalapack+suite-sparse+superlu-dist+double~complex~int64"} | |
| - {mpi: mpich, petsc: true, scalar: complex128, index: int32, | |
| petsc_dep: "^petsc+mpi+hypre+metis+mumps+ptscotch+scalapack+suite-sparse+superlu-dist+double+complex~int64"} | |
| - {mpi: openmpi, petsc: false} | |
| steps: | |
| - name: Branch and commit SHA | |
| run: | | |
| echo "Branch and commit SHA: ${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }}, ${{ github.sha }}" | |
| - name: Install Spack requirements | |
| run: | | |
| apt-get -y update | |
| apt-get install -y --no-install-recommends file bzip2 ca-certificates g++ gcc gfortran git gzip \ | |
| libgl-dev libosmesa6-dev lsb-release patch python3 tar unzip xz-utils zstd | |
| - name: Set up Spack | |
| uses: spack/setup-spack@16b756799ede8b28951287f89bcd3fdb32ec1ca3 # v3.0.0 | |
| with: | |
| spack_ref: v1.2.2 | |
| packages_ref: d342cee94fb90fb020776c8bd8500b54a19c63cf | |
| # packages_ref: v2026.06.0 | |
| # Pinned, like spack itself and its packages repo above: an unpinned | |
| # 'main' changes what CI builds with no commit here, which makes a | |
| # failure impossible to attribute. Bump deliberately. | |
| - name: Get FEniCS Spack packages | |
| uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 | |
| with: | |
| repository: fenics/spack-fenics | |
| ref: 05ea6cd78f5fde9c580fe29cb6dbb040d05f74ee # main, 2026-08-12 | |
| path: spack-fenics | |
| # Add FEniCS Spack packages on top of the upstream Spack packages | |
| - name: Add FEniCS Spack packages repo | |
| run: | | |
| spack repo add --name fenics $GITHUB_WORKSPACE/spack-fenics/spack_repo/fenics | |
| - name: Get DOLFINx code | |
| uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 | |
| with: | |
| path: dolfinx-src | |
| - name: Load dev branch environment variables | |
| run: cat dolfinx-src/.github/workflows/fenicsx-refs.env >> $GITHUB_ENV | |
| - name: Get UFL code | |
| uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 | |
| with: | |
| repository: ${{ env.ufl_repository }} | |
| ref: ${{ env.ufl_ref }} | |
| path: ufl-src | |
| - name: Get FFCx code | |
| uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 | |
| with: | |
| repository: ${{ env.ffcx_repository }} | |
| ref: ${{ env.ffcx_ref }} | |
| path: ffcx-src | |
| - name: Get Basix code | |
| uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 | |
| with: | |
| repository: ${{ env.basix_repository }} | |
| ref: ${{ env.basix_ref }} | |
| path: basix-src | |
| - name: Record source commit SHAs | |
| run: | | |
| echo "BASIX_SHA=$(git -C $GITHUB_WORKSPACE/basix-src rev-parse HEAD)" >> $GITHUB_ENV | |
| echo "UFL_SHA=$(git -C $GITHUB_WORKSPACE/ufl-src rev-parse HEAD)" >> $GITHUB_ENV | |
| echo "FFCX_SHA=$(git -C $GITHUB_WORKSPACE/ffcx-src rev-parse HEAD)" >> $GITHUB_ENV | |
| - name: Prepare Spack environment | |
| run: | | |
| spack env create ci dolfinx-src/.github/workflows/spack-config/gh-actions-env-test.yml | |
| spack -e ci config add "packages:mpi:require:${{ matrix.mpi }}" | |
| for pkg in fenics-basix:basix py-fenics-basix:basix py-fenics-ufl:ufl \ | |
| py-fenics-ffcx:ffcx fenics-ufcx:ffcx fenics-dolfinx:dolfinx py-fenics-dolfinx:dolfinx; do | |
| spack -e ci develop --no-clone --path $GITHUB_WORKSPACE/${pkg#*:}-src ${pkg%%:*}@main | |
| done | |
| # A single environment builds DOLFINx once for both the C++ and the | |
| # Python test steps. Separate environments resolve to an identical | |
| # runtime spec and differ only in build-time dependencies, so the | |
| # second build produces the same library at a different hash. | |
| - name: Build DOLFINx and test dependencies | |
| run: | | |
| # Ensure build provenance by adding manually and providing git sha | |
| spack -e ci add fenics-basix@main commit=$BASIX_SHA build_type=Developer | |
| spack -e ci add py-fenics-basix@main commit=$BASIX_SHA | |
| spack -e ci add py-fenics-ufl@main commit=$UFL_SHA | |
| spack -e ci add fenics-ufcx@main commit=$FFCX_SHA | |
| spack -e ci add py-fenics-ffcx@main commit=$FFCX_SHA | |
| # NOTE: adios2~sz drops the SZ2 compression dependency. 'sz' | |
| # installs its own unversioned libzstd.so, which interposes on the | |
| # real zstd once libdolfinx is loaded; a ZSTD_DCtx then gets | |
| # allocated in one zstd and freed in the other. This segfaults | |
| # Mesa's llvmpipe shader disk cache, so any PyVista render | |
| # following 'import dolfinx' crashes (see 'Run Python demos'). | |
| spack -e ci add fenics-dolfinx@main+adios2${{ matrix.petsc && '+petsc+slepc' || '~petsc~slepc+superlu-dist' }} commit=${{ github.sha }} build_type=Developer partitioners=parmetis \ | |
| ${{ matrix.petsc_dep }} ^adios2~libcatalyst~fortran~sz | |
| spack -e ci add py-fenics-dolfinx@main${{ matrix.petsc && '+petsc4py+slepc4py' || '~petsc4py~slepc4py' }} commit=${{ github.sha }} build_type=Developer | |
| spack -e ci add py-gmsh ^gmsh~med~fltk+external ^opencascade~draw py-pyamg py-matplotlib \ | |
| py-networkx \ | |
| py-numba ^llvm~clang~lldb~lld~offload~libomptarget~polly targets=x86 \ | |
| py-pytest py-pytest-xdist py-scipy \ | |
| "py-pyvista ^[virtuals=gl] osmesa" | |
| spack -e ci add catch2 ninja | |
| spack -e ci concretize -j $(nproc) | |
| spack -e ci install -j $(nproc) --use-buildcache auto | |
| # Pushed before the test steps so the artifacts are cached even if a | |
| # later step fails. The index is rebuilt by the final push. | |
| # | |
| # Both pushes are skipped for pull requests from forks: those run | |
| # with a read-only GITHUB_TOKEN whatever 'permissions' asks for, so | |
| # the push would 401 as soon as it had anything to upload, failing a | |
| # contributor's job on a step that tests nothing. Reads are | |
| # anonymous, so their builds still take from the cache. | |
| - name: Push packages to cache | |
| if: >- | |
| ${{ !cancelled() && (github.event_name != 'pull_request' | |
| || github.event.pull_request.head.repo.full_name == github.repository) }} | |
| run: | | |
| spack -e ci buildcache push --base-image ubuntu:26.04 --only dependencies \ | |
| --with-build-dependencies --allow-missing local-buildcache | |
| - name: Build and run C++ unit tests (serial and MPI) | |
| shell: spack-bash {0} | |
| run: | | |
| spack env activate ci | |
| spack load catch2 cmake ninja py-fenics-ffcx | |
| cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S dolfinx-src/cpp/test/ | |
| cmake --build build/test | |
| cd build/test | |
| ctest --output-on-failure -R unittests_np_1 | |
| ctest --output-on-failure -R unittests_np_3 | |
| # Skipped without PETSc: several demo CMakeLists reference | |
| # PETSC_INCLUDE_DIRS unconditionally, which --warn-uninitialized | |
| # turns into an error, and the top-level demo CMakeLists adds every | |
| # subdirectory, so configuration fails as a whole. | |
| - name: Build and run C++ demos (serial and MPI) | |
| if: ${{ matrix.petsc }} | |
| shell: spack-bash {0} | |
| run: | | |
| spack env activate ci | |
| spack load cmake ninja py-fenics-ffcx | |
| cmake -Werror=dev --warn-uninitialized -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/demo/ -S dolfinx-src/cpp/demo/ | |
| cmake --build build/demo | |
| cd build/demo | |
| ctest --output-on-failure -R "demo_.*_np_1" | |
| ctest --output-on-failure -R "demo_.*_np_2" | |
| # Guard against a mis-specified variant silently building PETSc into | |
| # the PETSc-free leg, which would make it test nothing new. | |
| - name: Check PETSc configuration matches the matrix | |
| shell: spack-bash {0} | |
| run: | | |
| spack env activate ci | |
| python -c "import dolfinx; assert dolfinx.has_petsc is ${{ matrix.petsc && 'True' || 'False' }}, dolfinx.has_petsc" | |
| - name: Set default DOLFINx JIT options | |
| run: | | |
| mkdir -p ~/.config/dolfinx | |
| echo '{ "cffi_extra_compile_args": ["-g0", "-O0" ] }' > ~/.config/dolfinx/dolfinx_jit_options.json | |
| - name: Run Python demos (serial and MPI) | |
| shell: spack-bash {0} | |
| run: | | |
| spack env activate ci | |
| spack load gcc | |
| python -m pytest -n=auto -m serial --durations=10 dolfinx-src/python/demo/test.py | |
| python -m pytest -m mpi --num-proc=3 dolfinx-src/python/demo/test.py | |
| # NOTE: the marker expression is written '!matrix.petsc && X || Y' | |
| # rather than 'matrix.petsc && Y || X'. GitHub expressions treat the | |
| # empty string as false, so the latter form falls through to X on | |
| # every leg and silently skips the petsc4py tests everywhere. | |
| - name: Run Python unit tests (serial and MPI) | |
| shell: spack-bash {0} | |
| run: | | |
| spack env activate ci | |
| spack load gcc | |
| python -m pytest -n=auto --durations=50 ${{ !matrix.petsc && '-m "not petsc4py"' || '' }} dolfinx-src/python/test/unit/ | |
| mpiexec -np 3 python -m pytest --durations=50 ${{ !matrix.petsc && '-m "not petsc4py"' || '' }} dolfinx-src/python/test/unit/ | |
| # The test tools are environment roots, so '--only dependencies' | |
| # skips them and they need naming explicitly. Only the final push | |
| # rebuilds the index, which is the expensive part. | |
| - name: Push test packages to cache and update index | |
| if: >- | |
| ${{ !cancelled() && (github.event_name != 'pull_request' | |
| || github.event.pull_request.head.repo.full_name == github.repository) }} | |
| run: | | |
| spack -e ci buildcache push --base-image ubuntu:26.04 --allow-missing --update-index local-buildcache \ | |
| py-gmsh py-matplotlib py-networkx py-numba py-pytest py-pytest-xdist py-scipy py-pyvista |