Fix thread sanitizer leak when launching Python 3.13 and using from neuron import h, gui. #9040
Workflow file for this run
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| name: NEURON Code Coverage | |
| concurrency: | |
| # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow | |
| group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }} | |
| cancel-in-progress: true | |
| on: | |
| merge_group: | |
| push: | |
| branches: | |
| - master | |
| - release/** | |
| pull_request: | |
| branches: | |
| - master | |
| - release/** | |
| # TODO : https://github.com/neuronsimulator/nrn/issues/1063 | |
| # paths-ignore: | |
| # - '**.md' | |
| # - '**.rst' | |
| # - 'docs/**' | |
| env: | |
| PY_MIN_VERSION: '3.9' | |
| PY_MID_VERSION: '3.10' | |
| PY_MAX_VERSION: '3.12' | |
| jobs: | |
| coverage: | |
| runs-on: ubuntu-22.04 | |
| name: Code Coverage | |
| timeout-minutes: 60 | |
| env: | |
| DISPLAY: ${{ ':0' }} | |
| MUSIC_INSTALL_DIR: /opt/MUSIC | |
| MUSIC_VERSION: 1.2.0 | |
| steps: | |
| - name: Install apt packages | |
| run: | | |
| sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin gpg ninja-build flex bison libfl-dev | |
| shell: bash | |
| - name: Setup Caliper profiler | |
| run: | | |
| git clone https://github.com/LLNL/Caliper.git | |
| cd Caliper | |
| mkdir build && cd build | |
| cmake .. | |
| make && sudo make install | |
| - name: Setup MUSIC@${{ env.MUSIC_VERSION }} | |
| run: | | |
| python3 -m venv music-venv | |
| source music-venv/bin/activate | |
| python3 -m pip install 'mpi4py<4' cython numpy setuptools | |
| sudo mkdir -p $MUSIC_INSTALL_DIR | |
| sudo chown -R $USER $MUSIC_INSTALL_DIR | |
| curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip | |
| unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC | |
| ./autogen.sh | |
| ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource | |
| make -j install | |
| deactivate | |
| working-directory: ${{runner.temp}} | |
| - name: Setup Xvfb | |
| run: | | |
| sudo apt-get install xvfb | |
| sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem & # run in bg | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - name: Clone nmodl | |
| working-directory: ${{runner.workspace}}/nrn | |
| run: | | |
| git submodule update --init --recursive --force --depth 1 -- external/nmodl | |
| - name: Set up Python@${{ env.PY_MIN_VERSION }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PY_MIN_VERSION }} | |
| - name: Install Python@${{ env.PY_MIN_VERSION }} dependencies | |
| working-directory: ${{runner.workspace}}/nrn | |
| run: | | |
| python -m pip install --upgrade -r external/nmodl/requirements.txt | |
| python -m pip install --upgrade -r ci_requirements.txt | |
| python -m pip install --upgrade pip -r nrn_requirements.txt | |
| - name: Set up Python@${{ env.PY_MID_VERSION }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PY_MID_VERSION }} | |
| - name: Set up Python@${{ env.PY_MAX_VERSION }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PY_MAX_VERSION }} | |
| - name: Install Python@${{ env.PY_MAX_VERSION }} dependencies | |
| working-directory: ${{runner.workspace}}/nrn | |
| run: | | |
| python -m pip install --upgrade -r external/nmodl/requirements.txt | |
| python -m pip install --upgrade -r ci_requirements.txt | |
| python -m pip install --upgrade pip -r nrn_requirements.txt | |
| - name: Build & Test | |
| id: build-test | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/nrn | |
| run: | | |
| export SHELL="/bin/bash" | |
| # Compiler setup | |
| export CC=gcc | |
| export CXX=g++ | |
| # Python setup | |
| export PYTHON_MIN=$(which $PYTHON_MIN_NAME); | |
| export PYTHON_MID=$(which $PYTHON_MID_NAME); | |
| export PYTHON_MAX=$(which $PYTHON_MAX_NAME); | |
| mkdir build && cd build; | |
| # CMake options & flags | |
| cmake_args=(-G Ninja \ | |
| -DCMAKE_BUILD_TYPE=Debug \ | |
| -DCMAKE_C_COMPILER="$CC" \ | |
| -DCMAKE_CXX_COMPILER="$CXX" \ | |
| -DNRN_ENABLE_BACKTRACE=ON \ | |
| -DNRN_ENABLE_CORENEURON=ON \ | |
| -DNRN_ENABLE_COVERAGE=ON \ | |
| -DNRN_ENABLE_INTERVIEWS=ON \ | |
| -DNRN_ENABLE_MPI=ON \ | |
| -DNRN_ENABLE_PERFORMANCE_TESTS=OFF \ | |
| -DNRN_ENABLE_PROFILING=ON \ | |
| -DNRN_ENABLE_PYTHON=ON \ | |
| -DNRN_ENABLE_PYTHON_DYNAMIC=ON \ | |
| -DNRN_PYTHON_DYNAMIC="${PYTHON_MIN};${PYTHON_MAX}" \ | |
| -DNRN_PYTHON_EXTRA_FOR_TESTS=${PYTHON_MID} \ | |
| -DNRN_ENABLE_TESTS=ON \ | |
| -DNRN_ENABLE_MUSIC=ON \ | |
| -DCMAKE_PREFIX_PATH="${MUSIC_INSTALL_DIR}" \ | |
| -DMUSIC_ROOT="${MUSIC_INSTALL_DIR}") | |
| cmake .. "${cmake_args[@]}" | |
| # Coverage | |
| # The Linux runners apparently have 2 cores, but jobs were being killed when we did not specify this explicitly. | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
| # By default we get a modern version of CMake that understands --parallel. | |
| cmake --build . --parallel 2 | |
| cmake --build . --target cover_baseline | |
| xvfb-run ctest --rerun-failed --output-on-failure; | |
| for python in "${PYTHON_MIN}" "${PYTHON_MAX}" | |
| do | |
| echo "Using ${python}" | |
| NEURONHOME="${PWD}/share/nrn" \ | |
| PYTHONPATH="${PWD}/lib/python:${PYTHONPATH}" \ | |
| PATH="${PWD}/bin:${PATH}" \ | |
| LD_LIBRARY_PATH="${PWD}/lib:${LD_LIBRARY_PATH}" \ | |
| DYLD_LIBRARY_PATH="${PWD}/lib:${DYLD_LIBRARY_PATH}" \ | |
| "${python}" -c "from neuron import h; import neuron; neuron.test();neuron.test_rxd();" | |
| done | |
| cmake --build . --target cover_collect | |
| cmake --build . --target cover_combine | |
| env: | |
| MATRIX_EVAL: "CC=gcc CXX=g++" | |
| PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}" | |
| PYTHON_MID_NAME: "python${{ env.PY_MID_VERSION }}" | |
| PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}" | |
| # This step will set up an SSH connection on tmate.io for live debugging. | |
| # To enable it, you have to: | |
| # * add 'live-debug-coverage' to your PR title | |
| # * push something to your PR branch (note that just re-running the pipeline disregards the title update) | |
| - name: live debug session on failure (manual steps required, check `.github/coverage.yml`) | |
| if: failure() && contains(github.event.pull_request.title, 'live-debug-coverage') | |
| uses: mxschmitt/action-tmate@v3 | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| directory: ./build | |
| fail_ci_if_error: true | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} |