Fixed a MPI bug with MultiCompartmentReaction which produce membrane … #32
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| name: Template for building NEURON Python wheels | ||
|
Check failure on line 1 in .github/workflows/wheels-template.yml
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| on: | ||
| workflow_call: | ||
| inputs: | ||
| platform: | ||
| description: The platform (OS) for which to build the wheel | ||
| required: true | ||
| type: string | ||
| python_version: | ||
| description: The Python version for which to build the wheel | ||
| required: true | ||
| type: string | ||
| commit: | ||
| description: The commit of NEURON for which to build the wheel | ||
| required: true | ||
| type: string | ||
| version: | ||
| description: Override version (tag name), in format major.minor.patch | ||
| default: '' | ||
| type: string | ||
| build_type: | ||
| description: The type of build (release or nightly) | ||
| default: 'nightly' | ||
| type: string | ||
| clone_depth: | ||
| description: The depth to clone the repo | ||
| default: '1' | ||
| type: string | ||
| optimize_rxd: | ||
| description: Whether to optimize the RX3D Python module | ||
| default: false | ||
| type: boolean | ||
| jobs: | ||
| build-test: | ||
| name: Build and test Python ${{ inputs.python_version }} wheel on ${{ inputs.platform }} | ||
| runs-on: ${{ inputs.platform }} | ||
| timeout-minutes: 60 | ||
| steps: | ||
| - name: Check out code at branch/commit ${{ inputs.commit }} | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| ref: ${{ inputs.commit }} | ||
| submodules: recursive | ||
| fetch-depth: ${{ inputs.clone_depth }} | ||
| fetch-tags: true # Ensures tags are available for git describe | ||
| - name: Install Python from python.org | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| # I would've preferred the versions to be in their own YAML file for | ||
| # readability, but alas, GitHub Actions does not support expanding | ||
| # nested expressions, so we do this the brute-force way with Bash | ||
| case "${{ inputs.python_version }}" in | ||
| 3.9) version="3.9.13" ;; | ||
| 3.10) version="3.10.11" ;; | ||
| 3.11) version="3.11.7" ;; | ||
| 3.12) version="3.12.0" ;; | ||
| 3.13) version="3.13.0" ;; | ||
| 3.14) version="3.14.0" ;; | ||
| *) echo "Unknown Python version"; exit 1 ;; | ||
| esac | ||
| installer_name="macos11.pkg" | ||
| installer_filename="python-${version}-${installer_name}" | ||
| url="https://www.python.org/ftp/python/${version}/${installer_filename}" | ||
| curl $url -o $installer_filename | ||
| sudo installer -pkg $installer_filename -target / | ||
| - name: Install system dependencies | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| brew install --cask xquartz | ||
| brew uninstall cmake || echo "CMake was not pre-installed" | ||
| brew install flex bison cmake mpich ninja | ||
| brew unlink mpich && brew install openmpi | ||
| # Install newer version of Bash on MacOS | ||
| brew install bash | ||
| # For debugging | ||
| bash --version | ||
| cmake --version | ||
| # Uninstall libomp for compatibility with issue #817 | ||
| brew uninstall --ignore-dependencies libomp || echo "libomp doesn't exist" | ||
| echo "$(brew --prefix)/opt/cmake/bin:$(brew --prefix)/opt/flex/bin:$(brew --prefix)/opt/bison/bin" >> $GITHUB_PATH | ||
| - name: Install readline | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| sudo mkdir -p /opt/nrnwheel/$(uname -m) | ||
| sudo bash packaging/python/build_static_readline_osx.bash | ||
| - name: Change name of package for release | ||
| if: inputs.build_type == 'release' | ||
| run: | | ||
| python3 -m venv venv | ||
| source venv/bin/activate | ||
| python3 -m pip install tomli tomli-w | ||
| python3 packaging/python/change_name.py ./pyproject.toml neuron | ||
| - name: Optimize RX3D Python module | ||
| if: inputs.optimize_rxd == true | ||
| run: | | ||
| echo "NRN_RX3D_OPT_LEVEL=1" >> $GITHUB_ENV | ||
| - name: Set custom version | ||
| if: inputs.version != '' | ||
| run: | | ||
| echo SETUPTOOLS_SCM_PRETEND_VERSION=${{ inputs.version }} >> $GITHUB_ENV | ||
| - name: Build wheel | ||
| run: | | ||
| bash packaging/python/build_wheels.bash $(uname -s) ${{ inputs.python_version }} | ||
| - name: Upload wheel files | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: wheels-${{ inputs.python_version }}-${{ inputs.platform }} | ||
| path: wheelhouse/*.whl | ||
| - name: Setup Python ${{ inputs.python_version }} for testing | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ inputs.python_version }} | ||
| - name: Install test dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt update | ||
| sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev ninja-build | ||
| - name: "Apply workaround for MPICH on Ubuntu 24.04" | ||
| if: inputs.platform == 'ubuntu-24.04' | ||
| run: | | ||
| # mpich is fundamentally broken on Ubuntu 24.04 LTS, for more details see: | ||
| # https://bugs.launchpad.net/ubuntu/+source/mpich/+bug/2072338 | ||
| # This is fixed in version 4.2.0-5.1, but this version has not been | ||
| # backported, so as a workaround, we install that version manually | ||
| sudo apt install -y mpich | ||
| wget 'https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/mpich_4.2.0-5.1_amd64.deb' | ||
| wget 'https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/libmpich12_4.2.0-5.1_amd64.deb' | ||
| sudo dpkg --install mpich_4.2.0-5.1_amd64.deb libmpich12_4.2.0-5.1_amd64.deb | ||
| - name: Set env vars for testing (Linux) | ||
| if: startsWith(inputs.platform, "ubuntu") | ||
| run: | | ||
| echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV | ||
| echo CMAKE_GENERATOR=Ninja >> $GITHUB_ENV | ||
| - name: Set env vars for testing (MacOS) | ||
| if: startsWith(runner.os, "macOS") | ||
| run: | | ||
| if [[ "${{runner.os}}" == "macOS-15-intel" ]]; then | ||
| echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV | ||
| else | ||
| echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV | ||
| fi | ||
| echo CMAKE_GENERATOR=Ninja >> $GITHUB_ENV | ||
| - name: Test wheel with ${{ inputs.python_version }} | ||
| run: | | ||
| minor_version="$(python${{ inputs.python_version }} -c 'import sys;print(sys.version_info.minor)')" | ||
| bash packaging/python/test_wheels.sh $(command -v python${{ inputs.python_version }}) wheelhouse/*cp3${minor_version}*.whl | ||
