Copy from https://github.com/openmm/openmm-nn/tree/c9a0e09cdb2c9449fc…

…a5cf02fe9e000c4757a721

.gitignore

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+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app

CMakeLists.txt

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+#---------------------------------------------------
+# OpenMM NeuralNetwork Plugin
+#----------------------------------------------------
+
+CMAKE_MINIMUM_REQUIRED(VERSION 3.5)
+
+# 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" "${OPENMM_DIR}/lib/plugins")
+
+# We need to know where TensorFlow is installed so we can access the headers and libraries.
+SET(TENSORFLOW_DIR "/usr/local" CACHE PATH "Where TensorFlow is installed")
+INCLUDE_DIRECTORIES("${TENSORFLOW_DIR}/include/tensorflow/c")
+LINK_DIRECTORIES("${TENSORFLOW_DIR}/lib")
+
+# Specify the C++ version we are building for.
+SET (CMAKE_CXX_STANDARD 11)
+
+# Set flags for linking on mac
+IF(APPLE)
+    SET (CMAKE_INSTALL_NAME_DIR "@rpath")
+    SET(EXTRA_COMPILE_FLAGS "-msse2 -stdlib=libc++")
+ENDIF(APPLE)
+
+# Select where to install
+IF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
+    IF(WIN32)
+        SET(CMAKE_INSTALL_PREFIX "$ENV{ProgramFiles}/OpenMM" CACHE PATH "Where to install the plugin" FORCE)
+    ELSE(WIN32)
+        SET(CMAKE_INSTALL_PREFIX "/usr/local/openmm" CACHE PATH "Where to install the plugin" FORCE)
+    ENDIF(WIN32)
+ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
+
+# 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})
+
+# The source is organized into subdirectories, but we handle them all from
+# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
+SET(NN_PLUGIN_SOURCE_SUBDIRS openmmapi serialization)
+
+# Set the library name
+SET(NN_LIBRARY_NAME OpenMMNN)
+SET(SHARED_NN_TARGET ${NN_LIBRARY_NAME})
+
+# These are all the places to search for header files which are to be part of the API.
+SET(API_INCLUDE_DIRS "openmmapi/include" "openmmapi/include/internal")
+
+# 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)
+
+# Collect up source files
+SET(SOURCE_FILES) # empty
+SET(SOURCE_INCLUDE_FILES)
+FOREACH(subdir ${NN_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})
+
+    ## 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)
+
+# Create the library.
+
+ADD_LIBRARY(${SHARED_NN_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
+SET_TARGET_PROPERTIES(${SHARED_NN_TARGET}
+    PROPERTIES COMPILE_FLAGS "-DNN_BUILDING_SHARED_LIBRARY ${EXTRA_COMPILE_FLAGS}"
+    LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+TARGET_LINK_LIBRARIES(${SHARED_NN_TARGET} OpenMM)
+TARGET_LINK_LIBRARIES(${SHARED_NN_TARGET} tensorflow)
+INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_NN_TARGET})
+
+# 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 ${API_ONLY_INCLUDE_FILES_INTERNAL} DESTINATION include/internal)
+
+# Enable testing
+
+ENABLE_TESTING()
+ADD_SUBDIRECTORY(serialization/tests)
+
+# Copy test files to the build directory.
+
+file(GLOB_RECURSE TEST_FILES RELATIVE "${CMAKE_SOURCE_DIR}"
+    "${CMAKE_SOURCE_DIR}/tests/*.pb"
+)
+file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/tests)
+set(COPIED_TEST_FILES)
+foreach(TEST_FILE ${TEST_FILES})
+    set(infile "${CMAKE_SOURCE_DIR}/${TEST_FILE}")
+    set(outfile "${CMAKE_BINARY_DIR}/${TEST_FILE}")
+    add_custom_command(
+        OUTPUT "${outfile}"
+        COMMAND "${CMAKE_COMMAND}" -E copy_if_different "${infile}" "${outfile}"
+        DEPENDS "${infile}"
+        COMMENT "CMake-copying file ${infile} to ${outfile}")
+    set(COPIED_TEST_FILES ${COPIED_TEST_FILES} "${outfile}")
+endforeach()
+add_custom_target(CopyTestFiles ALL DEPENDS ${COPIED_TEST_FILES})
+
+# Build the implementations for different platforms
+
+ADD_SUBDIRECTORY(platforms/reference)
+
+SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
+FIND_PACKAGE(OpenCL QUIET)
+IF(OPENCL_FOUND)
+    SET(NN_BUILD_OPENCL_LIB ON CACHE BOOL "Build implementation for OpenCL")
+ELSE(OPENCL_FOUND)
+    SET(NN_BUILD_OPENCL_LIB OFF CACHE BOOL "Build implementation for OpenCL")
+ENDIF(OPENCL_FOUND)
+IF(NN_BUILD_OPENCL_LIB)
+    ADD_SUBDIRECTORY(platforms/opencl)
+ENDIF(NN_BUILD_OPENCL_LIB)
+
+FIND_PACKAGE(CUDA QUIET)
+IF(CUDA_FOUND)
+    SET(NN_BUILD_CUDA_LIB ON CACHE BOOL "Build implementation for CUDA")
+ELSE(CUDA_FOUND)
+    SET(NN_BUILD_CUDA_LIB OFF CACHE BOOL "Build implementation for CUDA")
+ENDIF(CUDA_FOUND)
+IF(NN_BUILD_CUDA_LIB)
+    ADD_SUBDIRECTORY(platforms/cuda)
+ENDIF(NN_BUILD_CUDA_LIB)
+
+# Build the Python API
+
+FIND_PROGRAM(PYTHON_EXECUTABLE python)
+FIND_PROGRAM(SWIG_EXECUTABLE swig)
+IF(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE)
+    SET(NN_BUILD_PYTHON_WRAPPERS ON CACHE BOOL "Build wrappers for Python")
+ELSE(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE)
+    SET(NN_BUILD_PYTHON_WRAPPERS OFF CACHE BOOL "Build wrappers for Python")
+ENDIF(PYTHON_EXECUTABLE AND SWIG_EXECUTABLE)
+IF(NN_BUILD_PYTHON_WRAPPERS)
+    ADD_SUBDIRECTORY(python)
+ENDIF(NN_BUILD_PYTHON_WRAPPERS)
+

FindOpenCL.cmake

@@ -0,0 +1,95 @@
+
+### OPENCL_INCLUDE_DIR ###
+# Try OPENCL_DIR variable before looking elsewhere
+find_path(OPENCL_INCLUDE_DIR
+    NAMES OpenCL/opencl.h CL/opencl.h
+    PATHS $ENV{OPENCL_DIR}
+    PATH_SUFFIXES "include"
+    NO_DEFAULT_PATH
+)
+# Next look in environment variables set by OpenCL SDK installations
+find_path(OPENCL_INCLUDE_DIR
+    NAMES OpenCL/opencl.h CL/opencl.h
+    PATHS
+        $ENV{CUDA_PATH}
+        $ENV{AMDAPPSDKROOT}
+    PATH_SUFFIXES "include"
+    NO_DEFAULT_PATH
+)
+# On Macs, look inside the platform SDK
+if(DEFINED CMAKE_OSX_SYSROOT)
+    find_path(OPENCL_INCLUDE_DIR
+        NAMES opencl.h opencl.h
+        PATHS
+            "${CMAKE_OSX_SYSROOT}/System/Library/Frameworks/OpenCL.framework/Headers"
+        NO_DEFAULT_PATH
+    )
+endif(DEFINED CMAKE_OSX_SYSROOT)
+# As a last resort, look in default system areas followed by other possible locations
+find_path(OPENCL_INCLUDE_DIR
+    NAMES OpenCL/opencl.h CL/opencl.h
+    PATHS
+        "C:/CUDA"
+        "/usr/local/cuda"
+        "/usr/local/streamsdk"
+        "/usr"
+    PATH_SUFFIXES "include"
+)
+
+### OPENCL_LIBRARY ###
+if("${CMAKE_SYSTEM_NAME}" MATCHES "Linux")
+    if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
+      set(path_suffixes "lib/x86_64")
+    else("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
+      set(path_suffixes "lib/x86")
+    endif("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
+elseif(MSVC)
+    if(CMAKE_CL_64)
+      set(path_suffixes "lib/x64" "lib/x86_64")
+    else(CMAKE_CL_64)
+      set(path_suffixes "lib/Win32" "lib/x86")
+    endif(CMAKE_CL_64)
+else(MSVC)
+    set(path_suffixes "lib")
+endif("${CMAKE_SYSTEM_NAME}" MATCHES "Linux")
+# Try OPENCL_DIR variable before looking elsewhere
+find_library(OPENCL_LIBRARY
+    NAMES OpenCL
+    PATHS
+      $ENV{OPENCL_DIR}
+      ${OPENCL_LIB_SEARCH_PATH}
+    PATH_SUFFIXES ${path_suffixes}
+    NO_DEFAULT_PATH
+)
+# Next look in environment variables set by OpenCL SDK installations
+find_library(OPENCL_LIBRARY
+    NAMES OpenCL
+    PATHS
+      $ENV{CUDA_PATH}
+      $ENV{AMDAPPSDKROOT}
+    PATH_SUFFIXES ${path_suffixes}
+    NO_DEFAULT_PATH
+)
+# As a last resort, look in default system areas followed by other possible locations
+find_library(OPENCL_LIBRARY
+    NAMES OpenCL
+    PATHS
+        "C:/CUDA"
+        "/usr/local/cuda"
+        "/usr/local/streamsdk"
+        "/usr"
+    PATH_SUFFIXES ${path_suffixes} "lib"
+)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(OPENCL DEFAULT_MSG OPENCL_LIBRARY OPENCL_INCLUDE_DIR)
+
+if(OPENCL_FOUND)
+  set(OPENCL_LIBRARIES ${OPENCL_LIBRARY})
+  mark_as_advanced(CLEAR OPENCL_INCLUDE_DIR)
+  mark_as_advanced(CLEAR OPENCL_LIBRARY)
+else(OPENCL_FOUND)
+  set(OPENCL_LIBRARIES)
+  mark_as_advanced(OPENCL_INCLUDE_DIR)
+  mark_as_advanced(OPENCL_LIBRARY)
+endif(OPENCL_FOUND)