Allow atommap rmsfit to proceed with partial atom maps #484
Workflow file for this run
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: 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 |