[BBPBGLIB-1135] Move CompartmentMapping to python #465
Workflow file for this run
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| name: neurodamus build and test | |
| on: | |
| schedule: | |
| # every evening at 20:00 UTC | |
| - cron: '0 20 * * *' | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| inputs: | |
| NEURON_BRANCH: | |
| description: 'NEURON branch to use' | |
| required: false | |
| LIBSONATA_REPORT_BRANCH: | |
| description: 'libsonatareport branch to use' | |
| required: false | |
| jobs: | |
| simulation: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout neurodamus repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| fetch-depth: 0 | |
| - name: Get HEAD commit message and look for branches | |
| run: | | |
| COMMIT_MESSAGE=$(git log -1 --pretty=%B) | |
| echo $COMMIT_MESSAGE | |
| NEURON_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'NEURON_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true) | |
| if [[ ! -z $NEURON_BRANCH ]]; then echo "NEURON_BRANCH=$NEURON_BRANCH" >> $GITHUB_ENV; fi | |
| LIBSONATA_REPORT_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'LIBSONATA_REPORT_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true) | |
| if [[ ! -z $LIBSONATA_REPORT_BRANCH ]]; then echo "LIBSONATA_REPORT_BRANCH=$LIBSONATA_REPORT_BRANCH" >> $GITHUB_ENV; fi | |
| - name: Install hdf5-mpich | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install mpich libmpich-dev libhdf5-mpich-dev hdf5-tools | |
| - name: Install libsonata | |
| run: | | |
| CC=mpicc CXX=mpic++ pip install git+https://github.com/BlueBrain/libsonata | |
| - name: Install libsonatareport | |
| run: | | |
| git clone --branch="${LIBSONATA_REPORT_BRANCH:-master}" https://github.com/BlueBrain/libsonatareport.git --recursive --depth=1 | |
| cd libsonatareport | |
| mkdir build && cd build | |
| cmake -DCMAKE_INSTALL_PREFIX=$(pwd)/install -DCMAKE_BUILD_TYPE=Release -DSONATA_REPORT_ENABLE_SUBMODULES=ON -DSONATA_REPORT_ENABLE_MPI=ON .. | |
| cmake --build . --parallel | |
| cmake --build . --target install | |
| - name: Install NEURON | |
| run: | | |
| sudo apt-get install flex libfl-dev bison ninja-build | |
| pip install -U pip setuptools | |
| pip install "cython<3" pytest sympy | |
| export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install | |
| git clone --branch="${NEURON_BRANCH:-master}" https://github.com/neuronsimulator/nrn.git --depth=1 | |
| cd nrn | |
| mkdir build && cd build | |
| cmake -G Ninja -DPYTHON_EXECUTABLE=$(which python) -DCMAKE_INSTALL_PREFIX=$(pwd)/install -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=OFF \ | |
| -DNRN_ENABLE_CORENEURON=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCORENRN_ENABLE_REPORTING=ON -DCMAKE_PREFIX_PATH=$SONATAREPORT_DIR .. | |
| cmake --build . --parallel | |
| cmake --build . --target install | |
| - name: Build h5py with the local hdf5 | |
| run: | | |
| pip install -U pip setuptools | |
| pip install cython numpy wheel pkgconfig | |
| MPICC="mpicc -shared" pip install --no-cache-dir --no-binary=mpi4py mpi4py | |
| CC="mpicc" HDF5_MPI="ON" HDF5_INCLUDEDIR=/usr/include/hdf5/mpich HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/mpich \ | |
| pip install --no-cache-dir --no-binary=h5py h5py --no-build-isolation | |
| - name: Install neurodamus | |
| run: | | |
| pip install . | |
| - name: Build models | |
| run: | | |
| export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install | |
| export PATH=$(pwd)/nrn/build/install/bin:$PATH | |
| # copy mod files from the Zenodo link | |
| wget --output-document="O1_mods.xz" --quiet "https://zenodo.org/record/8026353/files/O1_mods.xz?download=1" | |
| tar -xf O1_mods.xz | |
| cp -r mod tests/share/ | |
| cp core/mod/*.mod tests/share/mod/ | |
| ./docker/build_neurodamus.sh tests/share/mod | |
| - name: Example run | |
| run: | | |
| export PYTHONPATH=$(pwd)/nrn/build/lib/python:$PYTHONPATH | |
| cp core/hoc/* tests/share/hoc/ | |
| export HOC_LIBRARY_PATH=$(pwd)/tests/share/hoc | |
| # launch simulation with NEURON | |
| mpirun -np 2 ./x86_64/special -mpi -python init.py --configFile=tests/simulations/usecase3/simulation_sonata.json | |
| ls tests/simulations/usecase3/reporting/*.h5 | |
| # launch simulation with CORENEURON | |
| mpirun -np 2 ./x86_64/special -mpi -python init.py --configFile=tests/simulations/usecase3/simulation_sonata_coreneuron.json | |
| ls tests/simulations/usecase3/reporting_coreneuron/*.h5 | |
| # - name: live debug session, comment out | |
| # if: failure() | |
| # uses: mxschmitt/action-tmate@v3 |