libsonatareport build and test #142
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| name: libsonatareport build and test | |
| on: | |
| schedule: | |
| # every evening at 20:00 UTC | |
| - cron: '0 20 * * *' | |
| pull_request: | |
| branches: | |
| - master | |
| push: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| inputs: | |
| NEURON_BRANCH: | |
| description: 'NEURON branch to use' | |
| required: false | |
| LIBSONATA_BRANCH: | |
| description: 'libsonata branch to use' | |
| required: false | |
| PY_NEURODAMUS_BRANCH: | |
| description: 'py-neurodamus branch to use' | |
| required: false | |
| NEURODAMUS_MODELS_BRANCH: | |
| description: 'neurodamus-models branch to use' | |
| required: false | |
| env: | |
| NEURON_COMMIT_ID: 'c48d7d5' | |
| RDMAV_FORK_SAFE: '1' | |
| jobs: | |
| simulation: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-22.04] | |
| python-version: ['3.9.20', '3.10.15', '3.11.10', '3.12.6'] | |
| steps: | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Checkout libsonatareport repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: 'recursive' | |
| - name: Get latest tags | |
| run: | | |
| echo "NEURON_BRANCH=${{ inputs.NEURON_BRANCH || github.event.inputs.NEURON_BRANCH || 'master' }}" >> $GITHUB_ENV | |
| LIBSONATA_LATEST=$(curl -s https://api.github.com/repos/BlueBrain/libsonata/releases/latest | grep -oP '"tag_name": "\K(.*)(?=")') | |
| echo "LIBSONATA_BRANCH=${{ inputs.LIBSONATA_BRANCH || github.event.inputs.LIBSONATA_BRANCH || '$LIBSONATA_LATEST' }}" >> $GITHUB_ENV | |
| PY_NEURODAMUS_LATEST=$(curl -s https://api.github.com/repos/BlueBrain/neurodamus/releases/latest | grep -oP '"tag_name": "\K(.*)(?=")') | |
| echo "PY_NEURODAMUS_BRANCH=${{ inputs.PY_NEURODAMUS_BRANCH || github.event.inputs.PY_NEURODAMUS_BRANCH || '$PY_NEURODAMUS_LATEST' }}" >> $GITHUB_ENV | |
| NEURODAMUS_MODELS_LATEST=$(curl -s https://api.github.com/repos/BlueBrain/neurodamus-models/releases/latest | grep -oP '"tag_name": "\K(.*)(?=")') | |
| echo "NEURODAMUS_MODELS_BRANCH=${{ inputs.NEURODAMUS_MODELS_BRANCH || github.event.inputs.NEURODAMUS_MODELS_BRANCH || '$NEURODAMUS_MODELS_LATEST' }}" >> $GITHUB_ENV | |
| - name: Get HEAD commit message and look for branches | |
| run: | | |
| COMMIT_MESSAGE=$(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" >> $GITHUB_ENV; fi | |
| LIBSONATA_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'LIBSONATA_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true) | |
| if [[ ! -z $LIBSONATA_BRANCH ]]; then echo "LIBSONATA_BRANCH=$LIBSONATA_BRANCH" >> $GITHUB_ENV; fi | |
| PY_NEURODAMUS_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'PY_NEURODAMUS_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true) | |
| if [[ ! -z $PY_NEURODAMUS_BRANCH ]]; then echo "PY_NEURODAMUS_BRANCH=$PY_NEURODAMUS_BRANCH" >> $GITHUB_ENV; fi | |
| NEURODAMUS_MODELS_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'NEURODAMUS_MODELS_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true) | |
| if [[ ! -z $NEURODAMUS_MODELS_BRANCH ]]; then echo "NEURODAMUS_MODELS_BRANCH=$NEURODAMUS_MODELS_BRANCH" >> $GITHUB_ENV; fi | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y mpich libmpich-dev libhdf5-mpich-dev hdf5-tools flex libfl-dev bison ninja-build | |
| - name: Cache python virtual env | |
| id: cache-venv | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: cache-venv | |
| with: | |
| path: venv | |
| key: ${{ matrix.os }}-libsonata-${{ env.LIBSONATA_BRANCH }}-py${{ matrix.python-version }} | |
| - name: Upgrade pip and install base Python packages | |
| if: steps.cache-venv.outputs.cache-hit != 'true' | |
| run: | | |
| python -m venv venv | |
| . ./venv/bin/activate | |
| python -m pip install --upgrade pip setuptools | |
| pip install cython numpy wheel pkgconfig | |
| - name: Add virtual environment to PATH | |
| run: echo "${{ github.workspace }}/venv/bin" >> $GITHUB_PATH | |
| - name: Install libsonata | |
| if: steps.cache-venv.outputs.cache-hit != 'true' | |
| run: | | |
| CC=mpicc CXX=mpic++ pip install git+https://github.com/BlueBrain/libsonata@${{ env.LIBSONATA_BRANCH }} | |
| - name: Install libsonatareport | |
| run: | | |
| mkdir build && cd build | |
| cmake -DCMAKE_INSTALL_PREFIX=$(pwd)/install -DCMAKE_BUILD_TYPE=Release -DSONATA_REPORT_ENABLE_SUBMODULES=ON -DSONATA_REPORT_ENABLE_MPI=ON .. | |
| cmake --build . --parallel | |
| cmake --build . --target install | |
| echo "SONATAREPORT_DIR=$(pwd)/install" >> $GITHUB_ENV | |
| - name: Cache NEURON | |
| id: cache-neuron | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: cache-neuron | |
| with: | |
| path: nrn | |
| key: ${{ matrix.os }}-neuron-${{ env.NEURON_BRANCH }}-${{ env.NEURON_COMMIT_ID }}-py${{ matrix.python-version }} | |
| - name: Install NEURON | |
| if: steps.cache-neuron.outputs.cache-hit != 'true' | |
| run: | | |
| sudo apt-get install flex libfl-dev bison ninja-build | |
| if [[ ${{ env.NEURON_BRANCH }} == 'master' ]]; then | |
| git clone --branch=${{ env.NEURON_BRANCH }} https://github.com/neuronsimulator/nrn.git | |
| cd nrn | |
| git checkout ${{ env.NEURON_COMMIT_ID }} | |
| cd .. | |
| else | |
| git clone --branch=${{ env.NEURON_BRANCH }} https://github.com/neuronsimulator/nrn.git --depth=1 | |
| fi | |
| python -m pip install --upgrade pip -r nrn/nrn_requirements.txt | |
| cmake -B nrn/build -S nrn -G Ninja \ | |
| -DPYTHON_EXECUTABLE=$(which python) \ | |
| -DCMAKE_INSTALL_PREFIX=$(pwd)/nrn/build/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=${{ env.SONATAREPORT_DIR }} | |
| cmake --build nrn/build --parallel | |
| cmake --build nrn/build --target install | |
| - name: Install h5py | |
| if: steps.cache-venv.outputs.cache-hit != 'true' | |
| run: | | |
| CC=mpicc CXX=mpic++ pip install --no-binary=h5py h5py | |
| - name: Install neurodamus | |
| run: | | |
| git clone --branch=${{ env.PY_NEURODAMUS_BRANCH }} https://github.com/BlueBrain/neurodamus.git | |
| cd neurodamus | |
| pip install .[full] | |
| - name: Build models | |
| run: | | |
| export PATH=$(pwd)/nrn/build/install/bin:$PATH | |
| # Clone neurodamus-models repository | |
| git clone --branch=${{ env.NEURODAMUS_MODELS_BRANCH }} https://github.com/BlueBrain/neurodamus-models.git | |
| mkdir -p neurodamus/tests/share/mod | |
| cp -L -r neurodamus-models/neocortex/mod/v5/* neurodamus/tests/share/mod | |
| cp -L -r neurodamus-models/neocortex/mod/v6/* neurodamus/tests/share/mod | |
| cp neurodamus/neurodamus/data/mod/*.mod neurodamus/tests/share/mod/ | |
| cd neurodamus | |
| ./docker/build_neurodamus.sh tests/share/mod | |
| - name: Example run | |
| run: | | |
| export PYTHONPATH=$(pwd)/nrn/build/lib/python:$PYTHONPATH | |
| cp neurodamus-models/neocortex/hoc/* neurodamus/neurodamus/data/hoc/ | |
| export HOC_LIBRARY_PATH=$(pwd)/neurodamus/neurodamus/data/hoc | |
| export NEURODAMUS_PYTHON=$(pwd)/neurodamus/neurodamus/data | |
| export CORENEURONLIB=$(pwd)/neurodamus/x86_64/libcorenrnmech.so | |
| export PATH=$(pwd)/neurodamus/x86_64:$PATH | |
| which special | |
| # launch simulation with NEURON | |
| cd neurodamus/tests/simulations/usecase3/ | |
| mpirun -np 2 special -mpi -python $NEURODAMUS_PYTHON/init.py --configFile=simulation_sonata.json | |
| ls reporting/*.h5 | |
| # launch simulation with CORENEURON | |
| mpirun -np 2 special -mpi -python $NEURODAMUS_PYTHON/init.py --configFile=simulation_sonata_coreneuron.json | |
| ls reporting_coreneuron/*.h5 | |
| # - name: live debug session, comment out | |
| # if: failure() | |
| # uses: mxschmitt/action-tmate@v3 |