Rebased #968 to a single commit #2111
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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- | |
| - -intel- | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.ccache | |
| key: ccache-reset1-linux${{ matrix.variant }}hash-${{ github.sha }} | |
| restore-keys: ccache-reset1-linux${{ matrix.variant }}hash- | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Set paths | |
| run: | | |
| echo "$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 | |
| bash <(curl -s https://codecov.io/bash) > /dev/null | |
| - name: Push doc | |
| if: contains( matrix.variant, '-doc-' ) | |
| env: | |
| GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }} | |
| run: | | |
| .ci/push doc | |
| codecheck: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set path | |
| run: | | |
| echo "$HOME/opt/bin" >> $GITHUB_PATH | |
| - name: Install requirements | |
| run: | | |
| .ci/install.cppcheck 2.10.3 | |
| # it is important that this is the same version used to generate the actual ./configure | |
| .ci/install.autoconf 2.69 | |
| - name: Build astyle | |
| run: | | |
| make -j 4 -C astyle | |
| - name: Checking code | |
| run: | | |
| # this is required so as to have all the include files in place | |
| # notice that this is done automatically in build | |
| # first make sure that dirslinks are generated for all modules | |
| ./configure --enable-modules=all | |
| # then generate the links | |
| make -C src/lib/ dirslinks | |
| make codecheck | |
| # We test on centos7 to make sure we have compatibility with older compilers (gcc 4.8) | |
| centos7: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build and run tests | |
| run: | | |
| make -C docker centos7 | |
| # We test on fedora37 to make sure we have compatibility with newer compilers (gcc 12) | |
| fedora37: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build and run tests | |
| run: | | |
| make -C docker fedora37 | |
| # We test on rockylinux8 as well | |
| rocky8: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build and run tests | |
| run: | | |
| make -C docker rocky8 | |
| macports: | |
| runs-on: macos-11 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| variant: [ "" , "+allmodules" ] | |
| # see https://github.community/t/how-to-conditionally-include-exclude-items-in-matrix-eg-based-on-branch/16853/6 for possible exclusions | |
| env: | |
| PYVERS: "py37 py38 py39 py310" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.macports-ci-ccache | |
| key: ccache-macports-${{ 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 $p-plumed | |
| done | |
| macsimple: | |
| runs-on: macos-11 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set paths | |
| run: | | |
| echo "$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" >> $GITHUB_ENV | |
| - name: Build PLUMED | |
| run: | | |
| brew update > /dev/null | |
| brew install gawk | |
| ./configure --disable-dependency-tracking --prefix="$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-11] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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 |