Add 'rescut' and 'bondoffset' keywords to 'prepareforleap' #469
Workflow file for this run
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| name: Cpptraj Tests | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| jobs: | |
| linux_build: | |
| runs-on: ubuntu-latest | |
| name: Build ${{ matrix.compiler }} with CMake ${{ matrix.use_cmake }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| compiler: ["gnu", "clang"] | |
| use_cmake: ["0", "1"] | |
| use_openmp: ["no"] | |
| use_mpi: ["no"] | |
| include: | |
| - use_openmp: "yes" | |
| compiler: "gnu" | |
| use_mpi: "no" | |
| use_cmake: "0" | |
| - use_openmp: "no" | |
| compiler: "gnu" | |
| use_mpi: "yes" | |
| use_cmake: "0" | |
| - use_openmp: "yes" | |
| compiler: "gnu" | |
| use_mpi: "yes" | |
| use_cmake: "0" | |
| - use_openmp: "no" | |
| compiler: "gnu" | |
| use_mpi: "yes" | |
| use_cmake: "1" | |
| env: | |
| COMPILER: ${{ matrix.compiler }} | |
| USE_CMAKE: ${{ matrix.use_cmake }} | |
| BUILD_TYPE: "install" | |
| TEST_TYPE: "test.showerrors" | |
| USE_MPI: ${{ matrix.use_mpi }} | |
| USE_OPENMP: ${{ matrix.use_openmp }} | |
| steps: | |
| - name: Install prerequisite packages | |
| run: | | |
| sudo apt-get install gfortran | |
| sudo apt-get install libbz2-dev | |
| sudo apt-get install libblas-dev liblapack-dev | |
| sudo apt-get install libfftw3-dev | |
| sudo apt-get install clang | |
| sudo apt-get install cmake-data cmake | |
| - name: Checkout source code | |
| uses: actions/checkout@v4 | |
| - name: Compile and test cpptraj | |
| shell: bash -lex {0} | |
| run: | | |
| curl -OL https://anaconda.org/AmberMD/amber_phenix/0.9.6/download/linux-64/amber_phenix-0.9.6-0.tar.bz2 | |
| tar jxf amber_phenix-0.9.6-0.tar.bz2 lib/libsander.so AmberTools/src/sander/sander.h | |
| mkdir -p include && mv AmberTools/src/sander/sander.h include | |
| mv lib include $HOME | |
| if [ $USE_OPENMP = "yes" ]; then | |
| export OPT="openmp" | |
| export OMP_NUM_THREADS=4 | |
| if [ "$USE_CMAKE" = "1" ]; then | |
| export BUILD_FLAGS="-DOPENMP=TRUE" | |
| else | |
| export BUILD_FLAGS="-openmp" | |
| fi | |
| fi | |
| if [ $USE_MPI = "yes" ]; then | |
| curl -OL http://www.mpich.org/static/downloads/3.4.2/mpich-3.4.2.tar.gz | |
| tar -zxf mpich-3.4.2.tar.gz | |
| cd mpich-3.4.2 | |
| export FFLAGS=-fallow-argument-mismatch | |
| ./configure --with-device=ch3 --prefix=$HOME | |
| make -j2 | |
| make install | |
| cd .. | |
| export PATH=$HOME/bin:$PATH | |
| export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH | |
| export DO_PARALLEL="mpirun -n 2" | |
| if [ $USE_OPENMP = "yes" ]; then | |
| export OMP_NUM_THREADS=1 | |
| fi | |
| if [ "$USE_CMAKE" = "1" ]; then | |
| export BUILD_FLAGS="-DMPI=TRUE ${BUILD_FLAGS}" | |
| else | |
| export BUILD_FLAGS="-mpi ${BUILD_FLAGS}" | |
| fi | |
| fi | |
| if [ "$USE_CMAKE" = "1" ]; then | |
| curl -OL https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz | |
| tar -zxf v4.9.2.tar.gz | |
| cd netcdf-c-4.9.2 | |
| ./configure --disable-byterange --disable-libxml2 --disable-netcdf-4 --disable-dap --disable-doxygen --prefix=$HOME | |
| make -j2 | |
| make install | |
| cd .. | |
| export PATH=$HOME/bin:$PATH | |
| export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH} | |
| mkdir build install | |
| installdir=$(pwd) | |
| cd build | |
| cmake .. $BUILD_FLAGS -DCOMPILER=${COMPILER^^} -DINSTALL_HEADERS=FALSE \ | |
| -DCMAKE_INSTALL_PREFIX=$installdir -DCMAKE_LIBRARY_PATH=$HOME/lib \ | |
| -DPRINT_PACKAGING_REPORT=TRUE -DNetCDF_LIBRARIES_C=$HOME/lib/libnetcdf.so \ | |
| -DNetCDF_INCLUDES=$HOME/include | |
| make -j2 install | |
| cd .. | |
| export PATH=$installdir/bin:$PATH | |
| else | |
| export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH} | |
| ./configure --buildlibs ${BUILD_FLAGS} ${COMPILER} | |
| source cpptraj.sh | |
| make -j2 install | |
| fi | |
| cd test && make $TEST_TYPE | |
| build-pytraj: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - name: Install prerequisite packages | |
| run: | | |
| sudo apt-get install gfortran | |
| sudo apt-get install libbz2-dev | |
| sudo apt-get install libblas-dev liblapack-dev | |
| sudo apt-get install libfftw3-dev | |
| sudo apt-get install clang | |
| sudo apt-get install cmake-data cmake | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install conda packages | |
| run: | | |
| which conda | |
| conda install conda=23.11.0 python=3.10 | |
| conda --version | |
| conda env update --file devtools/ci/environment.yml --name base | |
| - name: Install cpptraj | |
| run: | | |
| export PATH=$HOME/bin:${PATH} | |
| export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH} | |
| export MAKE_COMMAND="make -j2" | |
| ./configure --buildlibs -openmp -shared gnu | |
| source cpptraj.sh | |
| make -j2 libcpptraj | |
| - name: Install pytraj | |
| run: | | |
| git clone https://github.com/Amber-MD/pytraj.git | |
| source cpptraj.sh | |
| cd pytraj | |
| python setup.py install | |
| cd .. | |
| - name: Test with pytest | |
| run: | | |
| source cpptraj.sh && cd pytraj/tests && pytest -vs --ignore=test_parallel_pmap |