Fix mpi4py / MPI comms/checks overwriting local-comms environment #1611
Workflow file for this run
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| name: libEnsemble-CI | |
| on: | |
| pull_request: | |
| types: | |
| - ready_for_review | |
| - opened | |
| - reopened | |
| - synchronize | |
| jobs: | |
| test-libE: | |
| if: '! github.event.pull_request.draft' | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| mpi-version: [mpich] | |
| python-version: [3.8, 3.9, "3.10", "3.11"] | |
| comms-type: [m, l] | |
| include: | |
| - os: macos-latest | |
| python-version: 3.9 | |
| mpi-version: "mpich=4.0.3" | |
| comms-type: m | |
| - os: macos-latest | |
| python-version: 3.9 | |
| mpi-version: "mpich=4.0.3" | |
| comms-type: l | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| mpi-version: "mpich" | |
| comms-type: t | |
| env: | |
| HYDRA_LAUNCHER: "fork" | |
| TERM: xterm-256color | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup conda - Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: condaenv | |
| miniconda-version: "latest" | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge | |
| channel-priority: flexible | |
| auto-update-conda: true | |
| - uses: actions/cache/restore@v3 | |
| name: Restore cached dependencies | |
| id: cache | |
| if: matrix.os == 'ubuntu-latest' | |
| with: | |
| path: | | |
| /home/runner/work/libensemble/libensemble/heffte/build/ | |
| /home/runner/.local | |
| /usr/share/miniconda3/envs/condaenv | |
| /usr/share/miniconda3/bin | |
| /usr/share/miniconda3/lib | |
| /usr/share/miniconda3/include | |
| key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }} | |
| - name: Force-update certifi | |
| run: | | |
| python --version | |
| pip install -I --upgrade certifi | |
| # - name: Windows - Add clang path to $PATH env | |
| # shell: bash | |
| # if: matrix.os == 'windows-latest' | |
| # run: | | |
| # echo "PATH=$PATH:C:\msys64\mingw64\bin" >> $GITHUB_ENV | |
| # echo "PATH=$PATH:C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin\amd64" >> $GITHUB_ENV | |
| - name: Install Ubuntu compilers | |
| if: matrix.os == 'ubuntu-latest' | |
| run: conda install gcc_linux-64 | |
| # Roundabout solution on macos for proper linking with mpicc | |
| - name: Install macOS compilers and older SDK | |
| if: matrix.os == 'macos-latest' | |
| run: | | |
| wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.15.sdk.tar.xz | |
| mkdir ../sdk; tar xf MacOSX10.15.sdk.tar.xz -C ../sdk | |
| conda install clang_osx-64 | |
| # - name: Setup MPI (${{ matrix.mpi-version }}) | |
| # uses: mpi4py/setup-mpi@v1 | |
| # if: matrix.os == 'windows-latest' | |
| # with: | |
| # mpi: ${{ matrix.mpi-version }} | |
| # - name: Install mpi4py on Windows | |
| # if: matrix.os == 'windows-latest' | |
| # run: pip install mpi4py | |
| - name: Install mpi4py and MPI from conda | |
| if: matrix.python-version != '3.10' && matrix.os != 'windows-latest' | |
| run: | | |
| conda install ${{ matrix.mpi-version }} | |
| conda install mpi4py | |
| - name: Install mpi4py from pip, MPI from conda | |
| if: matrix.python-version == '3.10' && matrix.os != 'windows-latest' | |
| run: | | |
| conda install ${{ matrix.mpi-version }} | |
| pip install mpi4py | |
| - name: Install generator dependencies | |
| if: matrix.os != 'windows-latest' && steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| python -m pip install --upgrade pip | |
| conda env update --file install/gen_deps_environment.yml | |
| pip install ax-platform==0.2.8 | |
| - name: Install surmise | |
| if: matrix.os != 'macos-latest' && steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| pip install --upgrade git+https://github.com/surmising/surmise.git@develop | |
| - name: Build ytopt and dependencies | |
| if: matrix.python-version != '3.11' && matrix.os != 'windows-latest' && matrix.os != 'macos-latest' | |
| run: | | |
| pip install scikit-learn==1.1.2 | |
| pip install pandas==1.5.3 | |
| pip install ConfigSpace | |
| pip install "ray[default]" | |
| git clone https://github.com/ytopt-team/scikit-optimize.git | |
| cd scikit-optimize | |
| pip install . | |
| cd .. | |
| git clone -b version1 https://github.com/ytopt-team/autotune.git | |
| cd autotune | |
| pip install . | |
| cd .. | |
| git clone -b main https://github.com/ytopt-team/ytopt.git | |
| cd ytopt | |
| pip install . | |
| cd .. | |
| # - name: Install some generator dependencies on Windows | |
| # if: matrix.os == 'windows-latest' | |
| # run: | | |
| # python -m pip install --upgrade pip | |
| # conda install nlopt | |
| # conda install scipy | |
| # pip install mpmath | |
| - name: Install generator dependencies for Ubuntu tests | |
| if: matrix.os == 'ubuntu-latest' && steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| conda install octave | |
| sudo apt-get install bc | |
| # begin heffte build and dependencies | |
| sudo apt install libfftw3-dev | |
| git clone https://github.com/icl-utk-edu/heffte.git | |
| mkdir heffte/build | |
| cd heffte/build | |
| pwd | |
| cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS=ON -D CMAKE_INSTALL_PREFIX=./ -D Heffte_ENABLE_AVX=ON -D Heffte_ENABLE_FFTW=ON ../ | |
| make -j 4 | |
| make install | |
| cp ./benchmarks/speed3d_c2c ../../libensemble/tests/regression_tests/ | |
| # end heffte build and dependencies | |
| # pip install dragonfly-opt | |
| # pip install git+https://github.com/dragonfly/dragonfly.git | |
| pip install git+https://github.com/jlnav/dragonfly.git@fix/remove_npobject | |
| pip install scikit-build packaging Tasmanian --user | |
| - name: Copy heffte exe on cache-hit | |
| if: matrix.os == 'ubuntu-latest' && steps.cache.outputs.cache-hit != 'false' | |
| run: | | |
| cd /home/runner/work/libensemble/libensemble | |
| cp ./heffte/build/benchmarks/speed3d_c2c ./libensemble/tests/regression_tests/ | |
| - name: Install other testing dependencies | |
| run: | | |
| conda install pyzmq | |
| pip install -r install/testing_requirements.txt | |
| pip install -r install/misc_feature_requirements.txt | |
| git clone https://github.com/argonne-lcf/balsam.git | |
| sed -i -e "s/pyzmq>=22.1.0,<23.0.0/pyzmq>=23.0.0,<24.0.0/" ./balsam/setup.cfg | |
| cd balsam; pip install -e .; cd .. | |
| - uses: actions/cache/save@v3 | |
| name: Save dependencies to cache | |
| if: matrix.os == 'ubuntu-latest' | |
| with: | |
| path: | | |
| /home/runner/work/libensemble/libensemble/heffte/build/ | |
| /home/runner/.local | |
| /usr/share/miniconda3/envs/condaenv | |
| /usr/share/miniconda3/bin | |
| /usr/share/miniconda3/lib | |
| /usr/share/miniconda3/include | |
| key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }} | |
| - name: Install libEnsemble, flake8, lock environment | |
| run: | | |
| pip install -e . | |
| flake8 libensemble | |
| - name: Remove ytopt-heffte test on Python 3.11 (easy way) | |
| if: matrix.python-version == '3.11' | |
| run: | | |
| rm ./libensemble/tests/regression_tests/test_ytopt_heffte.py | |
| - name: Run extensive tests, Ubuntu | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| ./libensemble/tests/run-tests.sh -e -A "-W error" -z -${{ matrix.comms-type }} | |
| # - name: Run simple tests, Windows | |
| # if: matrix.os == 'windows-latest' | |
| # run: | | |
| # ./libensemble/tests/run-tests.sh -A "-W error" -z -${{ matrix.comms-type }} | |
| - name: Run extensive tests, macOS | |
| if: matrix.os == 'macos-latest' | |
| env: | |
| CONDA_BUILD_SYSROOT: /Users/runner/work/libensemble/sdk/MacOSX10.15.sdk | |
| run: | | |
| ./libensemble/tests/run-tests.sh -e -A "-W error" -z -${{ matrix.comms-type }} | |
| - name: Merge coverage, run Coveralls | |
| env: | |
| COVERALLS_PARALLEL: true | |
| run: | | |
| mv libensemble/tests/.cov* . | |
| coveralls --service=github | |
| coveralls: | |
| name: Notify coveralls of all jobs completing | |
| needs: [test-libE] | |
| if: '! github.event.pull_request.draft' | |
| runs-on: ubuntu-latest | |
| container: python:3-slim | |
| steps: | |
| - name: Finished | |
| run: | | |
| pip3 install --upgrade coveralls | |
| coveralls --finish | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| spellcheck: | |
| name: Spellcheck release branch | |
| if: contains(github.base_ref, 'main') | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: crate-ci/typos@v1.0.4 |