trying to install open-mpi 4.1.2 #169
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| name: Unit tests | |
| on: | |
| push: | |
| branches: ['**'] | |
| pull_request: | |
| branches: ['**'] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest,macos-latest] | |
| python-version: [3.8] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # - uses: conda-incubator/setup-miniconda@v3 | |
| # with: | |
| # activate-environment: test | |
| # python-version: ${{ matrix.python-version }} | |
| # fetch-depth: 2 | |
| - name: Install ubuntu dependencies | |
| shell: bash -el {0} | |
| run: | | |
| if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then | |
| sudo add-apt-repository ppa:ubuntu-toolchain-r/test | |
| sudo apt-get update | |
| sudo apt-get install libopenmpi-dev openmpi-bin | |
| fi; | |
| - name: Install MacOs dependencies | |
| shell: bash -el {0} | |
| run: | | |
| if [ "${{ matrix.os }}" == "macos-latest" ]; then | |
| brew install [email protected] | |
| fi; | |
| - name: Install dependencies | |
| shell: bash -el {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install mpi4py openmpi | |
| - name: Check MPI version | |
| shell: bash -el {0} | |
| run: | | |
| mpiexec --version | |
| - name: Install HNN-core | |
| shell: bash -el {0} | |
| run: | | |
| pip install --verbose '.[opt, parallel, test, gui]' | |
| - name: Set Env Variables | |
| shell: bash -el {0} | |
| run: | | |
| if [ "${{ matrix.os }}" == "macos-latest" ]; then | |
| echo "MPI_LIB_NRN_PATH=/opt/homebrew/lib" >> $GITHUB_ENV | |
| fi; | |
| - name: Run MPI application | |
| shell: bash -el {0} | |
| run: | | |
| mpiexec -np 2 python ./hnn_core/mpi_test.py | |
| - name: Verify NEURON installation | |
| shell: bash -el {0} | |
| run: | | |
| nrniv -python -nobanner -mpi -c "from neuron import h; print(h)" | |
| - name: Run MPI application with NEURON | |
| shell: bash -el {0} | |
| run: | | |
| mpiexec -np 2 -verbose nrniv -python -mpi -nobanner python ./hnn_core/mpi_test.py | |
| # - name: Lint with flake8 | |
| # shell: bash -el {0} | |
| # run: | | |
| # flake8 --count hnn_core | |
| - name: Test with pytest | |
| shell: bash -el {0} | |
| run: | | |
| python -m pytest ./hnn_core/tests/test_dipole.py --cov=hnn_core --cov-report=xml -s | |
| # - name: Upload coverage to Codecov | |
| # shell: bash -el {0} | |
| # run: | | |
| # bash <(curl -s https://codecov.io/bash) -f ./coverage.xml |