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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,51 @@ | ||
| name: OpenMM DMFF Plugin tests. | ||
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| on: | ||
| push: | ||
| pull_request: | ||
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| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: [3.9] | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Install Dependencies | ||
| run: | | ||
| source $CONDA/bin/activate | ||
| conda create -n dmff_omm -y python=${{ matrix.python-version }} numpy openmm=7.7 -c conda-forge | ||
| conda activate dmff_omm | ||
| conda install -y libtensorflow_cc=2.9.1 -c conda-forge | ||
| pip install setuptools==59.5.0 | ||
| mkdir /tmp/omm_dmff_working_dir | ||
| cd /tmp/omm_dmff_working_dir | ||
| wget https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.9.1.tar.gz | ||
| tar -xvf v2.9.1.tar.gz | ||
| cp -r tensorflow-2.9.1/tensorflow/c ${CONDA_PREFIX}/include/tensorflow/ | ||
| git clone https://github.com/serizba/cppflow.git | ||
| cd cppflow | ||
| git apply ${GITHUB_WORKSPACE}/backend/openmm_dmff_plugin/tests/cppflow_empty_constructor.patch | ||
| mkdir ${CONDA_PREFIX}/include/cppflow | ||
| cp -r include/cppflow ${CONDA_PREFIX}/include/ | ||
| - name: Install OpenMM DMFF Plugin | ||
| run: | | ||
| source $CONDA/bin/activate dmff_omm | ||
| cd ${GITHUB_WORKSPACE}/backend/openmm_dmff_plugin | ||
| mkdir build && cd build | ||
| export OPENMM_INSTALLED_DIR=$CONDA_PREFIX | ||
| export CPPFLOW_INSTALLED_DIR=$CONDA_PREFIX | ||
| export LIBTENSORFLOW_INSTALLED_DIR=$CONDA_PREFIX | ||
| cmake .. -DOPENMM_DIR=${OPENMM_INSTALLED_DIR} -DCPPFLOW_DIR=${CPPFLOW_INSTALLED_DIR} -DTENSORFLOW_DIR=${LIBTENSORFLOW_INSTALLED_DIR} -DUSE_HIGH_PRECISION=OFF | ||
| make && make install | ||
| make PythonInstall | ||
| - name: Run Tests | ||
| run: | | ||
| source $CONDA/bin/activate dmff_omm | ||
| cd ${GITHUB_WORKSPACE}/backend/ | ||
| python -m OpenMMDMFFPlugin.tests.test_dmff_plugin_nve -n 100 --pdb ../examples/water_fullpol/water_dimer.pdb --model ./openmm_dmff_plugin/python/OpenMMDMFFPlugin/data/admp_water_dimer_aux --has_aux True |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| **/build | ||
| **/.vscode | ||
| **/__pycache__ | ||
| *.dcd | ||
| **/output | ||
| **/.devcontainer |
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| Original file line number | Diff line number | Diff line change |
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| #--------------------------------------------------- | ||
| # OpenMM DMFF Plugin | ||
| #---------------------------------------------------- | ||
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| CMAKE_MINIMUM_REQUIRED(VERSION 3.5) | ||
| SET(CMAKE_VERBOSE_MAKEFILE OFF) | ||
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| project(OpenMMDMFF) | ||
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| # We need to know where OpenMM is installed so we can access the headers and libraries. | ||
| SET(OPENMM_DIR "/usr/local/openmm" CACHE PATH "Where OpenMM is installed") | ||
| INCLUDE_DIRECTORIES("${OPENMM_DIR}/include") | ||
| LINK_DIRECTORIES("${OPENMM_DIR}/lib" "${OPENMM_DIR}/lib/plugins") | ||
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| # Include the cppflow | ||
| SET(CPPFLOW_DIR "/usr/local/cppflow/" CACHE PATH "Where cppflow is installed") | ||
| INCLUDE_DIRECTORIES("${CPPFLOW_DIR}/include") | ||
| LINK_DIRECTORIES("${CPPFLOW_DIR}/lib") | ||
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| # Include the tensorflow | ||
| SET(TENSORFLOW_DIR "/usr/local/tensorflow/" CACHE PATH "Where libtensorflow is installed") | ||
| INCLUDE_DIRECTORIES("${TENSORFLOW_DIR}/include") | ||
| LINK_DIRECTORIES("${TENSORFLOW_DIR}/lib") | ||
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| # Specify the C++ version we are building for. | ||
| SET (CMAKE_CXX_STANDARD 17) | ||
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| set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-ignored-attributes -Wl,--allow-multiple-definition -Wl,--no-as-needed") | ||
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| # Set if high precision (double) is used. By default, it is off. | ||
| OPTION(USE_HIGH_PRECISION "Use high precision (double) for calculations" OFF) | ||
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| IF(USE_HIGH_PRECISION) | ||
| message(STATUS "USE_HIGH_PRECISION is enabled") | ||
| ADD_DEFINITIONS(-DUSE_HIGH_PRECISION) | ||
| endif () | ||
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| if (USE_HIGH_PRECISION) | ||
| set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHIGH_PRECISION") | ||
| else () | ||
| set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}") | ||
| endif () | ||
|
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| # Select where to install | ||
| IF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT}) | ||
| IF(WIN32) | ||
| SET(CMAKE_INSTALL_PREFIX "$ENV{ProgramFiles}/OpenMM" CACHE PATH "Where to install the plugin" FORCE) | ||
| ELSE(WIN32) | ||
| SET(CMAKE_INSTALL_PREFIX "${OPENMM_DIR}" CACHE PATH "Where to install the plugin" FORCE) | ||
| ENDIF(WIN32) | ||
| ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT}) | ||
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| # Put all the tests and libraries in a single output directory. | ||
| IF(NOT EXECUTABLE_OUTPUT_PATH) | ||
| SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR} | ||
| CACHE INTERNAL "Single output directory for building all executables.") | ||
| ENDIF() | ||
| IF(NOT LIBRARY_OUTPUT_PATH) | ||
| SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR} | ||
| CACHE INTERNAL "Single output directory for building all libraries.") | ||
| ENDIF() | ||
| SET(${PROJECT_NAME}_EXECUTABLE_DIR ${EXECUTABLE_OUTPUT_PATH}/${CMAKE_CFG_INTDIR}) | ||
| SET(${PROJECT_NAME}_LIBRARY_DIR ${LIBRARY_OUTPUT_PATH}/${CMAKE_CFG_INTDIR}) | ||
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| # The source is organized into subdirectories, but we handle them all from | ||
| # this CMakeLists file rather than letting CMake visit them as SUBDIRS. | ||
| SET(DMFF_PLUGIN_SOURCE_SUBDIRS openmmapi serialization) | ||
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| # Set the library name | ||
| SET(DMFF_LIBRARY_NAME OpenMMDMFF) | ||
| SET(SHARED_DMFF_TARGET ${DMFF_LIBRARY_NAME}) | ||
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| # These are all the places to search for header files that are to be part of the API. | ||
| SET(API_INCLUDE_DIRS "openmmapi/include" "openmmapi/include/internal") | ||
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| # Locate header files. | ||
| SET(API_INCLUDE_FILES) | ||
| FOREACH(dir ${API_INCLUDE_DIRS}) | ||
| FILE(GLOB fullpaths ${dir}/*.h) | ||
| SET(API_INCLUDE_FILES ${API_INCLUDE_FILES} ${fullpaths}) | ||
| ENDFOREACH(dir) | ||
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| # Collect source files | ||
| SET(SOURCE_FILES) # empty | ||
| SET(SOURCE_INCLUDE_FILES) | ||
| FOREACH(subdir ${DMFF_PLUGIN_SOURCE_SUBDIRS}) | ||
| FILE(GLOB src_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp) | ||
| FILE(GLOB incl_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h) | ||
| SET(SOURCE_FILES ${SOURCE_FILES} ${src_files}) #append | ||
| SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files}) | ||
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| ## Make sure we find these locally before looking in OpenMM/include if | ||
| ## OpenMM was previously installed there. | ||
| INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include) | ||
| ENDFOREACH(subdir) | ||
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| # Create the library. | ||
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| ADD_LIBRARY(${SHARED_DMFF_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES}) | ||
| SET_TARGET_PROPERTIES(${SHARED_DMFF_TARGET} | ||
| PROPERTIES COMPILE_FLAGS "-DDMFF_BUILDING_SHARED_LIBRARY ${EXTRA_COMPILE_FLAGS}" | ||
| LINK_FLAGS "${EXTRA_COMPILE_FLAGS}") | ||
| TARGET_LINK_LIBRARIES(${SHARED_DMFF_TARGET} OpenMM) | ||
| TARGET_LINK_LIBRARIES(${SHARED_DMFF_TARGET} tensorflow_cc) | ||
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| INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_DMFF_TARGET}) | ||
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| # install headers | ||
| FILE(GLOB API_ONLY_INCLUDE_FILES "openmmapi/include/*.h") | ||
| INSTALL (FILES ${API_ONLY_INCLUDE_FILES} DESTINATION include) | ||
| FILE(GLOB API_ONLY_INCLUDE_FILES_INTERNAL "openmmapi/include/internal/*.h") | ||
| INSTALL (FILES ${API_ONLY_INCLUDE_FILES_INTERNAL} DESTINATION include/internal) | ||
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| # Enable testing | ||
| # Set no testing here. | ||
| ENABLE_TESTING() | ||
| ADD_SUBDIRECTORY(serialization/tests) | ||
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| # Use reference platform default. | ||
| ADD_SUBDIRECTORY(platforms/reference) | ||
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| FIND_PACKAGE(CUDA QUIET) | ||
| IF(CUDA_FOUND) | ||
| message(STATUS "CUDA found, building CUDA implementation") | ||
| SET(PLUGIN_BUILD_CUDA_LIB ON CACHE BOOL "Build implementation for CUDA: ON") | ||
| ELSE(CUDA_FOUND) | ||
| message(STATUS "CUDA not found, not building CUDA implementation") | ||
| SET(PLUGIN_BUILD_CUDA_LIB OFF CACHE BOOL "Build implementation for CUDA: OFF") | ||
| ENDIF(CUDA_FOUND) | ||
| IF(PLUGIN_BUILD_CUDA_LIB) | ||
| ADD_SUBDIRECTORY(platforms/cuda) | ||
| ENDIF(PLUGIN_BUILD_CUDA_LIB) | ||
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| # Build the Python API | ||
| FIND_PROGRAM(PYTHON_EXECUTABLE python) | ||
| FIND_PROGRAM(SWIG_EXECUTABLE swig) | ||
| IF(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE) | ||
| message(STATUS "Python and SWIG found, building Python wrappers") | ||
| SET(PLUGIN_BUILD_PYTHON_WRAPPERS ON CACHE BOOL "Build wrappers for Python") | ||
| ELSE(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE) | ||
| message(FATAL_ERROR "Python or SWIG not found, not building Python wrappers") | ||
| SET(PLUGIN_BUILD_PYTHON_WRAPPERS OFF CACHE BOOL "Build wrappers for Python") | ||
| ENDIF(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE) | ||
| IF(PLUGIN_BUILD_PYTHON_WRAPPERS) | ||
| ADD_SUBDIRECTORY(python) | ||
| ENDIF(PLUGIN_BUILD_PYTHON_WRAPPERS) | ||
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