updated codeql to silence warnings #2856
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| name: CI | |
| on: | |
| push: | |
| pull_request: | |
| env: | |
| # on CI, better dump stack trace in case there is an error | |
| PLUMED_STACK_TRACE: yes | |
| # use two threads for openMP tests | |
| PLUMED_NUM_THREADS: 2 | |
| # these are used to build required packages | |
| CC: gcc | |
| CXX: g++ | |
| jobs: | |
| linux: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| variant: | |
| - -doc-mpi- | |
| - -mpi- | |
| - -coverage-mpi- | |
| - -debug- | |
| - -debug-mpi- | |
| # temporarily commented out | |
| # see https://github.com/plumed/plumed2/issues/976 | |
| # - -intel- | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.ccache | |
| key: ccache-reset1-linux${{ matrix.variant }}hash-${{ github.sha }} | |
| restore-keys: ccache-reset1-linux${{ matrix.variant }}hash- | |
| - name: Removed unused stuff | |
| run: | | |
| df -h | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /usr/local/lib/android | |
| sudo rm -rf /opt/ghc | |
| df -h | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Set paths | |
| run: | | |
| echo "$HOME/opt/bin" >> $GITHUB_PATH | |
| # path required for pytest: | |
| echo "$HOME/.local/bin" >> $GITHUB_PATH | |
| echo "CPATH=$HOME/opt/include:$CPATH" >> $GITHUB_ENV | |
| echo "INCLUDE=$HOME/opt/include:$INCLUDE" >> $GITHUB_ENV | |
| echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV | |
| # this is to avoid errors on ubuntu 22. this is overridden in intel build | |
| echo "FC=gfortran -fallow-argument-mismatch" >> $GITHUB_ENV | |
| - name: Install generic packages | |
| run: | | |
| sudo apt-get update -qq | |
| sudo apt-get install -y libatlas-base-dev | |
| sudo apt-get install -y libfftw3-dev | |
| sudo apt-get install -y gsl-bin | |
| sudo apt-get install -y libgsl0-dev | |
| sudo apt-get install -y ccache | |
| - name: Install system boost | |
| if: ${{ ! contains( matrix.variant, '-debug-' ) }} | |
| run: | | |
| sudo apt-get install -y libboost-serialization-dev | |
| - name: Install boost with debug flags | |
| if: contains( matrix.variant, '-debug-' ) | |
| run: | | |
| .ci/install.boost | |
| - name: Install python packages needed for tests | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --user Cython | |
| pip install --user numpy | |
| pip install --user pytest | |
| pip install --user six ; | |
| pip install --user pandas ; | |
| pip install --user mdtraj ; | |
| pip install --user MDAnalysis ; | |
| python -c "import MDAnalysis" ; | |
| python -c "import mdtraj" ; | |
| - name: Install Libtorch | |
| if: ${{ ! contains( matrix.variant, '-debug-' ) }} # libtorch is not compiled with GLIBCXX_DEBUG | |
| run: | | |
| # added by luigibonati | |
| mkdir -p $HOME/opt/ | |
| cd $HOME/opt/ # GB: install in $HOME/opt/libtorch | |
| wget --no-check-certificate https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.13.1%2Bcpu.zip ; | |
| unzip libtorch-cxx11-abi-shared-with-deps-1.13.1+cpu.zip ; | |
| echo "LIBRARY_PATH=$PWD/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=$PWD/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| echo "CPATH=$PWD/libtorch/include/torch/csrc/api/include/:$PWD/libtorch/include/:$PWD/libtorch/include/torch:$CPATH" >> $GITHUB_ENV | |
| echo "INCLUDE=$PWD/libtorch/include/torch/csrc/api/include/:$PWD/libtorch/include/:$PWD/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV | |
| echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-libtorch" >> $GITHUB_ENV | |
| - name: Install Doxygen | |
| if: contains( matrix.variant, '-doc-' ) | |
| run: | | |
| sudo apt-get install -y graphviz | |
| sudo apt-get install -y doxygen-latex | |
| .ci/install.doxygen Release_1_8_17 | |
| echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-pdfdoc" >> $GITHUB_ENV | |
| # make sure all tests are run | |
| echo "PLUMED_ALL_TESTS=yes" >> $GITHUB_ENV | |
| - name: Install lcov | |
| if: contains( matrix.variant, '-coverage-' ) | |
| run: | | |
| .ci/install.lcov v1.16 | |
| echo "PLUMED_CONFIG=$PLUMED_CONFIG --disable-external-lapack --disable-external-blas --enable-gcov CXXFLAGS=-O" >> $GITHUB_ENV | |
| # make sure all tests are run | |
| echo "PLUMED_ALL_TESTS=yes" >> $GITHUB_ENV | |
| - name: Setup debug flags | |
| if: contains( matrix.variant, '-debug-' ) | |
| run: | | |
| echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-debug --enable-debug-glibcxx" >> $GITHUB_ENV | |
| - name: Install INTEL compiler | |
| # install INTEL at last since it modifies CC and CXX | |
| if: contains( matrix.variant, '-intel-' ) | |
| run: | | |
| wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | |
| sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | |
| rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | |
| echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list | |
| sudo apt-get update | |
| sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mkl intel-oneapi-mkl-devel intel-oneapi-compiler-fortran | |
| source /opt/intel/oneapi/setvars.sh | |
| printenv >> $GITHUB_ENV | |
| echo "CXX=icpc" >> $GITHUB_ENV | |
| echo "CC=icc" >> $GITHUB_ENV | |
| echo "FC=ifort" >> $GITHUB_ENV | |
| - name: Install MPI | |
| # install MPI at last since it modifies CC and CXX | |
| if: contains( matrix.variant, '-mpi-' ) | |
| run: | | |
| sudo apt-get install -y libopenmpi-dev openmpi-bin | |
| echo "CC=mpicc" >> $GITHUB_ENV | |
| echo "CXX=mpic++" >> $GITHUB_ENV | |
| echo "OMPI_MCA_btl_base_warn_component_unused=0" >> $GITHUB_ENV | |
| echo "OMPI_MCA_btl_base_verbose=0" >> $GITHUB_ENV | |
| echo "OMPI_MCA_plm=isolated" >> $GITHUB_ENV | |
| echo "OMPI_MCA_btl_vader_single_copy_mechanism=none" >> $GITHUB_ENV | |
| echo "OMPI_MCA_rmaps_base_oversubscribe=yes" >> $GITHUB_ENV | |
| pip install --user mpi4py | |
| python -c "import mpi4py" | |
| - name: Build PLUMED | |
| run: | | |
| ccache -s -M 100M | |
| ./configure CXX="ccache $CXX" --enable-boost_serialization --disable-dependency-tracking --enable-modules=all LDFLAGS=-Wl,-rpath,$LD_LIBRARY_PATH $PLUMED_CONFIG --prefix="$HOME/opt" | |
| make -j 4 | |
| make install | |
| # check for global symbols, see https://github.com/plumed/plumed2/issues/549 | |
| make nmcheck | |
| ccache -s -M 100M | |
| - name: Run tests | |
| if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) }} | |
| run: | | |
| (while true; do # see https://github.com/actions/virtual-environments/issues/1860 | |
| df -h | |
| sleep 15 | |
| done) & | |
| make --no-print-directory -C regtest testclean | |
| # these can fail for numerical reasons | |
| make -C regtest checkfail | |
| - name: Run python tests | |
| run: | | |
| cd python | |
| pytest -v | |
| - name: Build doc | |
| env: | |
| GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }} | |
| if: contains( matrix.variant, '-doc-' ) | |
| run: | | |
| make doc >/dev/null | |
| - name: Coverage | |
| env: | |
| GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }} | |
| if: contains( matrix.variant, '-coverage-' ) | |
| run: | | |
| make -C developer-doc coverage | |
| .ci/push coverage | |
| # this is hanging for some reason now (2024-04-03) - GB | |
| #bash <(curl -s https://codecov.io/bash) > /dev/null | |
| - name: Push doc | |
| if: contains( matrix.variant, '-doc-' ) | |
| env: | |
| GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }} | |
| run: | | |
| .ci/push doc | |
| codecheck: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set path | |
| run: | | |
| echo "$HOME/opt/bin" >> $GITHUB_PATH | |
| - name: Install requirements | |
| run: | | |
| .ci/install.cppcheck 2.10.3 | |
| # it is important that this is the same version used to generate the actual ./configure | |
| .ci/install.autoconf 2.69 | |
| - name: Build astyle | |
| run: | | |
| make -j 4 -C astyle | |
| - name: Checking code | |
| run: | | |
| # this is required so as to have all the include files in place | |
| # notice that this is done automatically in build | |
| # first make sure that dirslinks are generated for all modules | |
| ./configure --enable-modules=all | |
| # then generate the links | |
| make -C src/lib/ dirslinks | |
| make codecheck | |
| # We test on centos7 to make sure we have compatibility with older compilers (gcc 4.8) | |
| centos7: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build and run tests | |
| run: | | |
| make -C docker centos7 | |
| # We test on fedora37 to make sure we have compatibility with newer compilers (gcc 12) | |
| fedora37: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build and run tests | |
| run: | | |
| make -C docker fedora37 | |
| # We test on rockylinux8 as well | |
| rocky8: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build and run tests | |
| run: | | |
| make -C docker rocky8 | |
| macports: | |
| runs-on: macos-12 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| variant: [ "" , "+allmodules" ] | |
| # see https://github.community/t/how-to-conditionally-include-exclude-items-in-matrix-eg-based-on-branch/16853/6 for possible exclusions | |
| env: | |
| PYVERS: "py39 py310" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.macports-ci-ccache | |
| key: ccache-macports-${{ matrix.variant }}-${{ github.sha }} | |
| restore-keys: ccache-macports-${{ matrix.variant }}- | |
| - name: Install MacPorts | |
| run: | | |
| wget https://raw.githubusercontent.com/GiovanniBussi/macports-ci/master/macports-ci | |
| source ./macports-ci install | |
| source ./macports-ci ccache | |
| - name: Build local Portfile | |
| run: | | |
| make macports | |
| source ./macports-ci localports macports | |
| - name: Build PLUMED | |
| run: | | |
| sudo port -N -k install plumed ${{ matrix.variant }} | |
| plumed config show | |
| for p in $PYVERS ; do | |
| sudo port -N install $p-plumed | |
| done | |
| source ./macports-ci ccache --save | |
| - name: Run tests | |
| run: | | |
| sudo port -N -d test plumed ${{ matrix.variant }} | |
| - name: Run python tests | |
| run: | | |
| for p in $PYVERS ; do | |
| sudo port test $p-plumed | |
| done | |
| macsimple: | |
| runs-on: macos-12 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set paths | |
| run: | | |
| echo "$HOME/opt/bin" >> $GITHUB_PATH | |
| echo "CPATH=$HOME/opt/include:$CPATH" >> $GITHUB_ENV | |
| echo "INCLUDE=$HOME/opt/include:$INCLUDE" >> $GITHUB_ENV | |
| echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| - name: Build PLUMED | |
| run: | | |
| # it seems brew update is screwing up something | |
| # GB on Mar 8, 2024 | |
| #brew update > /dev/null | |
| brew install gawk | |
| ./configure --disable-dependency-tracking --prefix="$HOME/opt" | |
| make -j 4 | |
| make install | |
| - name: Run tests | |
| run: | | |
| make --no-print-directory -C regtest | |
| # these can fail for numerical reasons | |
| make -C regtest checkfail | |
| conda: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04 , macos-12, macos-14 ] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install conda | |
| run: | | |
| curl -LO https://raw.githubusercontent.com/GiovanniBussi/conda-ci/master/conda-ci | |
| source ./conda-ci install | |
| source ./conda-ci install-conda-build | |
| - name: Build PLUMED | |
| run: | | |
| source activate base | |
| export VERSION=none | |
| if [[ $GITHUB_REF == "refs/tags/"* ]]; then | |
| VERSION=${GITHUB_REF#refs/tags/} | |
| VERSION=${VERSION//-/_} | |
| VERSION=${VERSION#v} | |
| fi | |
| make -C conda | |
| - name: Deploy | |
| env: | |
| CONDA_UPLOAD_TOKEN: ${{ secrets.CONDA_UPLOAD_TOKEN }} | |
| if: ${{ startsWith( github.ref , 'refs/tags/' ) }} | |
| run: | | |
| source activate base | |
| export CONDA_LABEL=tag | |
| make -C conda upload |