Improve several mod files for coreneuron in memory transfer. #48
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| name: Test model compilation | |
| on: | |
| push: | |
| branches: ['main'] | |
| pull_request: | |
| env: | |
| SONATA_REPORT_VERSION: '1.2.3' | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| model: ['hippocampus', 'neocortex', 'thalamus'] | |
| coreneuron: ['ON'] | |
| metabolism: ['OFF'] | |
| ngv: ['OFF'] | |
| plasticity: ['OFF'] | |
| v5: ['OFF'] | |
| include: | |
| - model: 'neocortex' | |
| coreneuron: 'OFF' | |
| metabolism: 'ON' | |
| ngv: 'ON' | |
| plasticity: 'OFF' | |
| v5: 'OFF' | |
| - model: 'neocortex' | |
| coreneuron: 'ON' | |
| metabolism: 'OFF' | |
| ngv: 'OFF' | |
| plasticity: 'ON' | |
| v5: 'OFF' | |
| - model: 'neocortex' | |
| coreneuron: 'ON' | |
| metabolism: 'OFF' | |
| ngv: 'OFF' | |
| plasticity: 'OFF' | |
| v5: 'ON' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.12' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install libopenmpi-dev libhdf5-dev | |
| python -m pip install --upgrade pip | |
| python -m pip install NEURON-nightly neurodamus | |
| - name: Cache SONATA™ reporting library build | |
| id: cache-libsonatareport | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: cache-libsonatareport | |
| with: | |
| path: ~/reports | |
| key: build-reports-${{ env.SONATA_REPORT_VERSION}} | |
| - name: Install SONATA™ reporting library | |
| if: steps.cache-libsonatareport.outputs.cache-hit != 'true' | |
| run: | | |
| gh repo clone BlueBrain/libsonatareport $HOME/reports/src -- --recursive --shallow-submodules --branch ${{ env.SONATA_REPORT_VERSION }} | |
| cmake \ | |
| -B $HOME/reports/build \ | |
| -S $HOME/reports/src \ | |
| -DCMAKE_INSTALL_PREFIX=$HOME/reports/install \ | |
| -DSONATA_REPORT_ENABLE_SUBMODULES=ON \ | |
| -DSONATA_REPORT_ENABLE_TEST=OFF | |
| cmake --build $HOME/reports/build | |
| cmake --install $HOME/reports/build | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| - name: Configure models | |
| run: | | |
| export CC=$(which mpicc) | |
| export CXX=$(which mpicxx) | |
| DATADIR=$(python -c "import neurodamus; from pathlib import Path; print(Path(neurodamus.__file__).parent / 'data')") | |
| cmake -B build -S . \ | |
| -DCMAKE_INSTALL_PREFIX=$PWD/install \ | |
| -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON \ | |
| -DCMAKE_PREFIX_PATH=$HOME/reports/install \ | |
| -DNEURODAMUS_CORE_DIR=${DATADIR} \ | |
| -DNEURODAMUS_ENABLE_CORENEURON=${{ matrix.coreneuron }} \ | |
| -DNEURODAMUS_MECHANISMS=${{ matrix.model }} \ | |
| -DNEURODAMUS_NCX_METABOLISM=${{ matrix.metabolism }} \ | |
| -DNEURODAMUS_NCX_NGV=${{ matrix.ngv }} \ | |
| -DNEURODAMUS_NCX_PLASTICITY=${{ matrix.plasticity }} \ | |
| -DNEURODAMUS_NCX_V5=${{ matrix.v5 }} | |
| - name: Build and install models | |
| run: | | |
| export CC=$(which mpicc) | |
| export CXX=$(which mpicxx) | |
| cmake --build build | |
| cmake --install build | |
| ls -R install | |
| - name: Quick test to load models | |
| run: | | |
| ./install/bin/special -python -c "from neuron import h; from neurodamus import Neurodamus; h.quit()" |