fix for hang in check_totals under MPI #1810
Workflow file for this run
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| # Run OpenMDAO Tests | |
| name: OpenMDAO Tests | |
| on: | |
| # Trigger on push or pull request events for the master branch | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| # Allow running the workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| tests: | |
| timeout-minutes: 120 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # test baseline versions on Ubuntu | |
| - NAME: Ubuntu Baseline | |
| OS: ubuntu-latest | |
| PY: '3.11' | |
| NUMPY: '1.24' | |
| SCIPY: '1.10' | |
| PETSc: '3.18' | |
| PYOPTSPARSE: 'v2.9.2' | |
| PAROPT: true | |
| SNOPT: '7.7' | |
| OPTIONAL: '[all]' | |
| JAX: '0.4.2' | |
| BANDIT: true | |
| TESTS: true | |
| # set DEBUG to create an interactive debugging session just before testflo is run. | |
| # Note that the workflow will run until you cancel the debugging session. | |
| # To access the terminal through the web-interface: | |
| # 1. Click on the web-browser link printed out in this action from the github | |
| # workflow terminal | |
| # 2. Press cntrl + c in the new tab that opens up to reveal the terminal | |
| # 3. To activate the conda environment run: | |
| # $ source $CONDA/etc/profile.d/conda.sh | |
| # $ conda activate test | |
| # See https://github.com/mxschmitt/action-tmate for more details | |
| # DEBUG: true | |
| # test baseline versions on MacOS | |
| - NAME: MacOS Baseline | |
| OS: macos-latest | |
| PY: '3.11' | |
| NUMPY: '1.24' | |
| SCIPY: '1.10' | |
| PETSc: '3.18' | |
| # PYOPTSPARSE: 'v2.9.2' | |
| # PAROPT: true | |
| # SNOPT: '7.7' | |
| OPTIONAL: '[all]' | |
| JAX: '0.4.2' | |
| TESTS: true | |
| # test minimal install | |
| - NAME: Ubuntu Minimal | |
| OS: ubuntu-latest | |
| PY: '3' | |
| NUMPY: '1.24' | |
| SCIPY: '1.10' | |
| OPTIONAL: '[test]' | |
| TESTS: true | |
| # test oldest supported versions | |
| - NAME: Ubuntu Oldest | |
| OS: ubuntu-latest | |
| PY: '3.7' | |
| NUMPY: '1.21' | |
| SCIPY: '1.7' | |
| OPENMPI: '4.0' | |
| MPI4PY: '3.0' | |
| PETSc: '3.13' | |
| PYOPTSPARSE: 'v1.2' | |
| SNOPT: '7.2' | |
| OPTIONAL: '[all]' | |
| TESTS: true | |
| # build docs (baseline versions) | |
| - NAME: Build Docs | |
| OS: ubuntu-latest | |
| PY: '3.11' | |
| NUMPY: '1.24' | |
| SCIPY: '1.10' | |
| PETSc: '3.18' | |
| PYOPTSPARSE: 'v2.9.2' | |
| SNOPT: '7.7' | |
| OPTIONAL: '[all]' | |
| JAX: '0.4.2' | |
| BUILD_DOCS: true | |
| runs-on: ${{ matrix.OS }} | |
| name: ${{ matrix.NAME }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Display run details | |
| run: | | |
| echo "=============================================================" | |
| echo "Run #${GITHUB_RUN_NUMBER}" | |
| echo "Run ID: ${GITHUB_RUN_ID}" | |
| echo "Testing: ${GITHUB_REPOSITORY}" | |
| echo "Triggered by: ${GITHUB_EVENT_NAME}" | |
| echo "Initiated by: ${GITHUB_ACTOR}" | |
| echo "=============================================================" | |
| - name: Create SSH key | |
| if: (matrix.SNOPT || matrix.BUILD_DOCS) | |
| env: | |
| SSH_PRIVATE_KEY: ${{ secrets.SSH_PRIVATE_KEY }} | |
| SSH_KNOWN_HOSTS: ${{ secrets.SSH_KNOWN_HOSTS }} | |
| run: | | |
| mkdir -p ~/.ssh/ | |
| echo "$SSH_PRIVATE_KEY" > ~/.ssh/id_rsa | |
| sudo chmod 600 ~/.ssh/id_rsa | |
| echo "$SSH_KNOWN_HOSTS" > ~/.ssh/known_hosts | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Fetch tags | |
| run: | | |
| git fetch --prune --unshallow --tags | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.PY }} | |
| conda-version: "*" | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| - name: Install OpenMDAO | |
| run: | | |
| conda install numpy=${{ matrix.NUMPY }} scipy=${{ matrix.SCIPY }} -q -y | |
| python -m pip install --upgrade pip | |
| echo "=============================================================" | |
| echo "Install OpenMDAO" | |
| echo "=============================================================" | |
| python -m pip install .${{ matrix.OPTIONAL }} | |
| - name: Install jax | |
| if: matrix.JAX | |
| run: | | |
| echo "=============================================================" | |
| echo "Install jax" | |
| echo "=============================================================" | |
| python -m pip install jaxlib=='${{ matrix.JAX }}' jax=='${{ matrix.JAX }}' | |
| - name: Install PETSc | |
| if: matrix.PETSc | |
| run: | | |
| echo "=============================================================" | |
| echo "Install compilers for PETSc" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.OPENMPI }}" ]]; then | |
| COMPILERS="cython compilers openmpi-mpicc=${{ matrix.OPENMPI }}" | |
| else | |
| COMPILERS="cython compilers openmpi-mpicc" | |
| fi | |
| conda install $COMPILERS -q -y | |
| echo "=============================================================" | |
| echo "Install PETSc" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.PETSc }}" == "3" ]]; then | |
| python -m pip install git+https://github.com/mpi4py/mpi4py | |
| python -m pip install petsc petsc4py | |
| else | |
| if [[ "${{ matrix.MPI4PY }}" ]]; then | |
| conda install mpi4py=${{ matrix.MPI4PY }} petsc4py=${{ matrix.PETSc }} -q -y | |
| else | |
| conda install mpi4py petsc4py=${{ matrix.PETSc }} -q -y | |
| fi | |
| fi | |
| echo "=============================================================" | |
| echo "Check MPI and PETSc installation" | |
| echo "=============================================================" | |
| export OMPI_MCA_rmaps_base_oversubscribe=1 | |
| echo "-----------------------" | |
| echo "Quick test of mpi4py:" | |
| mpirun -n 3 python -c "from mpi4py import MPI; print(f'Rank: {MPI.COMM_WORLD.rank}')" | |
| echo "-----------------------" | |
| echo "Quick test of petsc4py:" | |
| mpirun -n 3 python -c "import numpy; from mpi4py import MPI; comm = MPI.COMM_WORLD; \ | |
| import petsc4py; petsc4py.init(); \ | |
| x = petsc4py.PETSc.Vec().createWithArray(numpy.ones(5)*comm.rank, comm=comm); \ | |
| print(x.getArray())" | |
| echo "-----------------------" | |
| echo "OMPI_MCA_rmaps_base_oversubscribe=1" >> $GITHUB_ENV | |
| echo "Workaround for intermittent failures with OMPI https://github.com/open-mpi/ompi/issues/7393" | |
| echo "TMPDIR=/tmp" >> $GITHUB_ENV | |
| - name: Install pyOptSparse | |
| if: matrix.PYOPTSPARSE | |
| run: | | |
| echo "=============================================================" | |
| echo "Install pyoptsparse" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.PYOPTSPARSE }}" == "conda-forge" ]]; then | |
| if [[ "${{ matrix.SNOPT }}" ]]; then | |
| echo "SNOPT ${{ matrix.SNOPT }} was requested but is not available on conda-forge" | |
| fi | |
| conda install -c conda-forge pyoptsparse | |
| else | |
| python -m pip install git+https://github.com/OpenMDAO/build_pyoptsparse | |
| if [[ "${{ matrix.PYOPTSPARSE }}" == "latest" ]]; then | |
| function latest_version() { | |
| local REPO_URL=$1/releases/latest | |
| local LATEST_URL=`curl -fsSLI -o /dev/null -w %{url_effective} $REPO_URL` | |
| local LATEST_VER=`echo $LATEST_URL | awk '{split($0,a,"/tag/"); print a[2]}'` | |
| echo $LATEST_VER | |
| } | |
| BRANCH="-b $(latest_version https://github.com/mdolab/pyoptsparse)" | |
| else | |
| BRANCH="-b ${{ matrix.PYOPTSPARSE }}" | |
| fi | |
| if [[ "${{ matrix.PAROPT }}" ]]; then | |
| PAROPT="-a" | |
| fi | |
| if [[ "${{ matrix.SNOPT }}" == "7.7" && "${{ secrets.SNOPT_LOCATION_77 }}" ]]; then | |
| echo " > Secure copying SNOPT 7.7 over SSH" | |
| mkdir SNOPT | |
| scp -qr ${{ secrets.SNOPT_LOCATION_77 }} SNOPT | |
| SNOPT="-s SNOPT/src" | |
| elif [[ "${{ matrix.SNOPT }}" == "7.2" && "${{ secrets.SNOPT_LOCATION_72 }}" ]]; then | |
| echo " > Secure copying SNOPT 7.2 over SSH" | |
| mkdir SNOPT | |
| scp -qr ${{ secrets.SNOPT_LOCATION_72 }} SNOPT | |
| SNOPT="-s SNOPT/source" | |
| elif [[ "${{ matrix.SNOPT }}" ]]; then | |
| echo "SNOPT version ${{ matrix.SNOPT }} was requested but source is not available" | |
| fi | |
| build_pyoptsparse $BRANCH $PAROPT $SNOPT | |
| fi | |
| - name: Install optional dependencies | |
| if: matrix.OPTIONAL == '[all]' | |
| run: | | |
| echo "=============================================================" | |
| echo "Install additional packages for testing/coverage" | |
| echo "=============================================================" | |
| python -m pip install pyparsing psutil objgraph pyxdsm | |
| - name: Display environment info | |
| run: | | |
| conda info | |
| conda list | |
| echo "=============================================================" | |
| echo "Check installed versions of Python, Numpy and Scipy" | |
| echo "=============================================================" | |
| python -c "import platform; assert platform.python_version().startswith(str(${{ matrix.PY }})), \ | |
| f'Python version {platform.python_version()} is not the requested version (${{ matrix.PY }})'" | |
| python -c "import numpy; assert str(numpy.__version__).startswith(str(${{ matrix.NUMPY }})), \ | |
| f'Numpy version {numpy.__version__} is not the requested version (${{ matrix.NUMPY }})'" | |
| python -c "import scipy; assert str(scipy.__version__).startswith(str(${{ matrix.SCIPY }})), \ | |
| f'Scipy version {scipy.__version__} is not the requested version (${{ matrix.SCIPY }})'" | |
| - name: Setup tmate session | |
| if: matrix.DEBUG | |
| uses: mxschmitt/action-tmate@v3 | |
| - name: Run tests | |
| if: matrix.TESTS | |
| env: | |
| OPENMDAO_CHECK_ALL_PARTIALS: true | |
| run: | | |
| echo "=============================================================" | |
| echo "Run tests with coverage (from directory other than repo root)" | |
| echo "=============================================================" | |
| echo "############ .coveragerc contents #################" | |
| cat .coveragerc | |
| echo "###################################################" | |
| cp .coveragerc $HOME | |
| cd $HOME | |
| testflo -n 2 openmdao --timeout=240 --show_skipped --coverage --coverpkg openmdao --durations=20 | |
| - name: Submit coverage | |
| if: matrix.TESTS | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_SERVICE_NAME: "github" | |
| COVERALLS_PARALLEL: true | |
| run: | | |
| echo "=============================================================" | |
| echo "Submit coverage" | |
| echo "=============================================================" | |
| cp $HOME/.coverage . | |
| python -m pip install coveralls | |
| SITE_DIR=`python -c 'import site; print(site.getsitepackages()[-1])'` | |
| coveralls --basedir $SITE_DIR | |
| - name: Build docs | |
| if: matrix.BUILD_DOCS | |
| id: build_docs | |
| run: | | |
| export OPENMDAO_REPORTS=0 | |
| export PYDEVD_DISABLE_FILE_VALIDATION=1 | |
| cd openmdao/docs | |
| if [[ "${{ secrets.SNOPT_LOCATION_72 }}" || "${{ secrets.SNOPT_LOCATION_77 }}" ]]; then | |
| echo "=============================================================" | |
| echo "Building docs with SNOPT examples." | |
| echo "=============================================================" | |
| else | |
| echo "=============================================================" | |
| echo "Disabling SNOPT cells in notebooks." | |
| echo "=============================================================" | |
| python openmdao_book/other/disable_snopt_cells.py | |
| fi | |
| # start ipcluster to run MPI under notebooks | |
| ./ipcluster_start.sh | |
| sleep 12 | |
| echo "=============================================================" | |
| echo "Build the docs" | |
| echo "=============================================================" | |
| python build_source_docs.py | |
| jupyter-book build openmdao_book | |
| python copy_build_artifacts.py | |
| - name: Display doc build reports | |
| if: failure() && matrix.BUILD_DOCS && steps.build_docs.outcome == 'failure' | |
| run: | | |
| for f in /home/runner/work/OpenMDAO/OpenMDAO/openmdao/docs/openmdao_book/_build/html/reports/*; do | |
| echo "=============================================================" | |
| echo $f | |
| echo "=============================================================" | |
| cat $f | |
| done | |
| - name: Publish docs | |
| if: ${{ github.event_name == 'push' && matrix.BUILD_DOCS }} | |
| env: | |
| DOCS_LOCATION: ${{ secrets.DOCS_LOCATION }} | |
| run: | | |
| if [[ "${#DOCS_LOCATION}" ]]; then | |
| echo "=============================================================" | |
| echo "Install version of openssl compatible with hosting service" | |
| echo "=============================================================" | |
| conda install -c conda-forge 'openssl=3.0' | |
| echo "=============================================================" | |
| echo "Publish docs" | |
| echo "=============================================================" | |
| cd openmdao/docs | |
| python upload_doc_version.py openmdao_book/_build/html/ ${{ secrets.DOCS_LOCATION }} | |
| else | |
| echo "Docs destination not available." | |
| fi | |
| - name: Scan for security issues | |
| if: matrix.BANDIT | |
| id: bandit | |
| run: | | |
| python -m pip install bandit | |
| echo "=============================================================" | |
| echo "Run bandit scan for high/medium severity issues" | |
| echo "=============================================================" | |
| cd $GITHUB_WORKSPACE | |
| python -m bandit -c bandit.yml -ll -r openmdao | |
| - name: Notify slack | |
| uses: act10ns/slack@v1.6.0 | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} | |
| with: | |
| status: ${{ job.status }} | |
| if: always() | |
| windows_tests: | |
| runs-on: windows-latest | |
| timeout-minutes: 60 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # baseline versions | |
| - NAME: Windows Baseline | |
| PY: '3.10' | |
| NUMPY: 1.22 | |
| SCIPY: 1.7 | |
| PYOPTSPARSE: '2.9.1' | |
| name: ${{ matrix.NAME }} | |
| defaults: | |
| run: | |
| shell: pwsh | |
| steps: | |
| - name: Display run details | |
| run: | | |
| echo "=============================================================" | |
| echo "Run #$env:GITHUB_RUN_NUMBER" | |
| echo "Run ID: $env:GITHUB_RUN_ID" | |
| echo "Testing: $env:GITHUB_REPOSITORY" | |
| echo "Triggered by: $env:GITHUB_EVENT_NAME" | |
| echo "Initiated by: $env:GITHUB_ACTOR" | |
| echo "=============================================================" | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Fetch tags | |
| run: | | |
| git fetch --prune --unshallow --tags | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.PY }} | |
| conda-version: "*" | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| - name: Install OpenDMAO | |
| run: | | |
| conda install numpy=${{ matrix.NUMPY }} scipy=${{ matrix.SCIPY }} -q -y | |
| python -m pip install --upgrade pip | |
| echo "=============================================================" | |
| echo "Install lxml for Windows (No Python 3.11 version on pypi)" | |
| echo "=============================================================" | |
| conda install lxml | |
| echo "=============================================================" | |
| echo "Install OpenMDAO" | |
| echo "=============================================================" | |
| python -m pip install .[all] | |
| - name: Install pyOptSparse | |
| if: matrix.PYOPTSPARSE | |
| run: | | |
| echo "=============================================================" | |
| echo "Install pyoptsparse from conda-forge" | |
| echo "=============================================================" | |
| conda install -c conda-forge pyoptsparse=${{ matrix.PYOPTSPARSE }} -q -y | |
| - name: Install optional dependencies | |
| run: | | |
| echo "=============================================================" | |
| echo "Install additional packages for testing/coverage" | |
| echo "=============================================================" | |
| python -m pip install psutil objgraph git+https://github.com/mdolab/pyxdsm | |
| - name: Display environment info | |
| run: | | |
| conda info | |
| conda list | |
| echo "=============================================================" | |
| echo "Check installed versions of Python, Numpy and Scipy" | |
| echo "=============================================================" | |
| python -c "import sys; assert str(sys.version).startswith(str(${{ matrix.PY }})), \ | |
| f'Python version {sys.version} is not the requested version (${{ matrix.PY }})'" | |
| python -c "import numpy; assert str(numpy.__version__).startswith(str(${{ matrix.NUMPY }})), \ | |
| f'Numpy version {numpy.__version__} is not the requested version (${{ matrix.NUMPY }})'" | |
| python -c "import scipy; assert str(scipy.__version__).startswith(str(${{ matrix.SCIPY }})), \ | |
| f'Scipy version {scipy.__version__} is not the requested version (${{ matrix.SCIPY }})'" | |
| - name: Run tests | |
| env: | |
| OPENMDAO_CHECK_ALL_PARTIALS: true | |
| run: | | |
| echo "=============================================================" | |
| echo "Run tests with coverage (from directory other than repo root)" | |
| echo "=============================================================" | |
| copy .coveragerc $HOME | |
| cd $HOME | |
| testflo -n 2 openmdao --timeout=240 --show_skipped --coverage --coverpkg openmdao --durations=20 | |
| - name: Submit coverage | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_SERVICE_NAME: "github" | |
| COVERALLS_PARALLEL: true | |
| run: | | |
| echo "=============================================================" | |
| echo "Submit coverage" | |
| echo "=============================================================" | |
| copy $HOME\.coverage . | |
| python -m pip install coveralls | |
| $SITE_DIR=python -c "import site; print(site.getsitepackages()[-1].replace('lib\\site-', 'Lib\\site-'))" | |
| coveralls --basedir $SITE_DIR | |
| - name: Notify slack | |
| uses: act10ns/slack@v2.0.0 | |
| with: | |
| webhook-url: ${{ secrets.SLACK_WEBHOOK_URL }} | |
| status: ${{ job.status }} | |
| if: always() | |
| coveralls: | |
| name: Finish coverage | |
| needs: [tests, windows_tests] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel-finished: true | |
| dymos_tests: | |
| name: Run Dymos Tests | |
| needs: [tests, windows_tests] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: benc-uk/workflow-dispatch@v1 | |
| with: | |
| workflow: Dymos Tests | |
| repo: ${{ github.repository_owner }}/dymos | |
| token: ${{ secrets.ACCESS_TOKEN }} | |
| if: github.event_name == 'push' |