Modified Cuda FreeEnergy plugin to use a different windows export macro than...

Modified Cuda FreeEnergy plugin to use a different windows export macro than main openmm library and cuda library.
Modified CUDA_NVCC_FLAGS to be consistent with Peter's latest version in all three locations they are defined.
Added "-Xcompiler '/MD'" to CUDA_NVCC_FLAGS on Windows to avoid link error in Cuda FreeEnergy plugin.

CMakeLists.txt

@@ -319,6 +319,24 @@ IF(NOT cmv EQUAL "2.4")
 ENDIF(NOT cmv EQUAL "2.4")
 IF(CUDA_FOUND)
     SET(OPENMM_BUILD_CUDA_LIB ON CACHE BOOL "Build OpenMMCuda library for Nvidia GPUs")
+
+    # I wish I was not hardcoding /MD here
+    # Avoid strange windows link error with cuda free energy 
+    # plugin by specifying /MD to CUDA_NVCC_FLAGS
+    MARK_AS_ADVANCED(CLEAR CUDA_NVCC_FLAGS)
+    IF(MSVC)
+        # Unfortunately the variables CUDA_NVCC_FLAGS_RELEASE and CUDA_NVCC_FLAGS_DEBUG
+        # appear to be unused, at least in CMake 2.6
+        # Release /MD linkage
+        IF(NOT (CUDA_NVCC_FLAGS MATCHES "-Xcompiler"))
+            set(new_flags "-Xcompiler \"/MD\"")
+            if(CUDA_NVCC_FLAGS)
+                set(new_flags "${CUDA_NVCC_FLAGS};${new_flags}")
+            endif(CUDA_NVCC_FLAGS)
+            SET(CUDA_NVCC_FLAGS "${new_flags}" 
+                CACHE STRING "Semicolon delimit multiple arguments" FORCE)
+        ENDIF(NOT (CUDA_NVCC_FLAGS MATCHES "-Xcompiler"))
+    ENDIF(MSVC)
 ELSE(CUDA_FOUND)
     SET(OPENMM_BUILD_CUDA_LIB OFF CACHE BOOL "Build OpenMMCuda library for Nvidia GPUs")
 ENDIF(CUDA_FOUND)

cmake_modules/FindCUDA.cmake

@@ -371,7 +371,8 @@ set(CUDA_GENERATED_OUTPUT_DIR "" CACHE PATH "Directory to put all the output fil
 option(CUDA_HOST_COMPILATION_CPP "Generated file extension" ON)
 
 # Extra user settable flags
-set(CUDA_NVCC_FLAGS "-maxrregcount=32;-use_fast_math;-O0;-arch=sm_11" CACHE STRING "Semi-colon delimit multiple arguments.")
+# set(CUDA_NVCC_FLAGS "-maxrregcount=32;-use_fast_math;-O0;-arch=sm_11" CACHE STRING "Semi-colon delimit multiple arguments.")
+SET(CUDA_NVCC_FLAGS "--maxrregcount=32;-gencode;arch=compute_11,code=sm_11;-gencode;arch=compute_13,code=sm_13;-use_fast_math;-O0" CACHE STRING "Semi-colon delimit multiple arguments.")
 
 # Propagate the host flags to the host compiler via -Xcompiler
 option(CUDA_PROPAGATE_HOST_FLAGS "Propage C/CXX_FLAGS and friends to the host compiler via -Xcompile" ON)

platforms/cuda/CMakeLists.txt

@@ -26,7 +26,7 @@ try_run(RUN_RESULT_VAR COMPILE_RESULT_VAR
     COMPILE_OUTPUT_VARIABLE COMPILE_OUTPUT_VAR
     RUN_OUTPUT_VARIABLE RUN_OUTPUT_VAR
 )
-message("${RUN_OUTPUT_VAR}") # Display number of GPUs found
+# message("${RUN_OUTPUT_VAR}") # Display number of GPUs found
 # COMPILE_RESULT_VAR is TRUE when compile succeeds
 # RUN_RESULT_VAR is zero when a GPU is found
 if(COMPILE_RESULT_VAR AND NOT RUN_RESULT_VAR)

plugins/freeEnergy/platforms/cuda/cuda-cmake/FindCuda.cmake

@@ -117,7 +117,7 @@ ELSE(CUDA_BUILD_TYPE MATCHES "Emulation")
 ENDIF(CUDA_BUILD_TYPE MATCHES "Emulation")
 
 SET(CUDA_BUILD_CUBIN TRUE CACHE BOOL "Generate and parse .cubin files in Device mode.")
-SET(CUDA_NVCC_FLAGS "-maxrregcount=32;-use_fast_math;-O0;-arch=sm_11" CACHE STRING "Semi-colon delimit multiple arguments.")
+SET(CUDA_NVCC_FLAGS "--maxrregcount=32;-gencode;arch=compute_11,code=sm_11;-gencode;arch=compute_13,code=sm_13;-use_fast_math;-O0" CACHE STRING "Semi-colon delimit multiple arguments.")
 
 # Search for the cuda distribution.
 IF(NOT CUDA_INSTALL_PREFIX)

plugins/freeEnergy/platforms/cuda/include/windowsExportCudaFreeEnergy.h

+#ifndef OPENMM_WINDOWSEXPORTCUDAFREEENERGY_H_
+#define OPENMM_WINDOWSEXPORTCUDAFREEENERGY_H_
+
+/*
+ * Shared libraries are messy in Visual Studio. We have to distinguish three
+ * cases:
+ *   (1) this header is being used to build the OpenMM shared library
+ *       (dllexport)
+ *   (2) this header is being used by a *client* of the OpenMM shared
+ *       library (dllimport)
+ *   (3) we are building the OpenMM static library, or the client is
+ *       being compiled with the expectation of linking with the
+ *       OpenMM static library (nothing special needed)
+ * In the CMake script for building this library, we define one of the symbols
+ *     OpenMMCUDAFREEEERGY_BUILDING_{SHARED|STATIC}_LIBRARY
+ * Client code normally has no special symbol defined, in which case we'll
+ * assume it wants to use the shared library. However, if the client defines
+ * the symbol OPENMM_USE_STATIC_LIBRARIES we'll suppress the dllimport so
+ * that the client code can be linked with static libraries. Note that
+ * the client symbol is not library dependent, while the library symbols
+ * affect only the OpenMM library, meaning that other libraries can
+ * be clients of this one. However, we are assuming all-static or all-shared.
+ */
+
+#ifdef _MSC_VER
+    // We don't want to hear about how sprintf is "unsafe".
+    #pragma warning(disable:4996)
+    // Keep MS VC++ quiet about lack of dll export of private members.
+    #pragma warning(disable:4251)
+    #if defined(OPENMMCUDAFREEENERGY_BUILDING_SHARED_LIBRARY)
+        #define OPENMMCUDAFREEENERGY_EXPORT __declspec(dllexport)
+    #elif defined(OPENMMCUDAFREEENERGY_BUILDING_STATIC_LIBRARY) || defined(OPENMMCUDAFREEENERGY_USE_STATIC_LIBRARIES)
+		#define OPENMMCUDAFREEENERGY_EXPORT
+    #else
+		#define OPENMMCUDAFREEENERGY_EXPORT __declspec(dllimport)   // i.e., a client of a shared library
+    #endif
+#else
+    #define OPENMMCUDAFREEENERGY_EXPORT // Linux, Mac
+#endif
+
+#endif // OPENMM_WINDOWSEXPORTCUDAFREEENERGY_H_

plugins/freeEnergy/platforms/cuda/sharedTarget/CMakeLists.txt

@@ -35,8 +35,9 @@ IF(LOG)
 ENDIF(LOG)
 ## ----------------------------------------------------------------------------
 
-SET(CUDA_NVCC_BUILD_FLAGS) 
+# message("CUDA_NVCC_FLAGS = ${CUDA_NVCC_FLAGS}")
 INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake)
+# message("CUDA_NVCC_FLAGS = ${CUDA_NVCC_FLAGS}")
 INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
 LINK_DIRECTORIES(${CUDA_TARGET_LINK})
 FOREACH(subdir ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS})
@@ -65,6 +66,7 @@ ENDIF(LOG)
 # CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/jama/include)
 
 CUDA_INCLUDE_DIRECTORIES(${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/../src
+                         ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/include
                          ${OPENMM_DIR}/platforms/cuda/src
                          ${OPENMM_DIR}/platforms/cuda/include
                          ${OPENMM_DIR}/platforms/cuda/src/kernels
@@ -75,6 +77,6 @@ CUDA_ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES}
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME} )
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}Cuda_d optimized ${OPENMM_LIBRARY_NAME}Cuda )
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_FREE_ENERGY_LIBRARY_NAME}_d optimized ${OPENMM_FREE_ENERGY_LIBRARY_NAME} )
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMMCUDAFREEENERGY_BUILDING_SHARED_LIBRARY")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

plugins/freeEnergy/platforms/cuda/staticTarget/CMakeLists.txt

@@ -28,7 +28,7 @@ CUDA_ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES}
 # required for getting OPENMM_EXPORT to be set correctly in 'class OPENMM_EXPORT CudaStreamFactory', ...
 # see OpenMM/openmmapi/include/internal/windowsExport.h for details
 
-SET(CUDA_STATIC_COMPILE_FLAG "-DOPENMM_BUILDING_STATIC_LIBRARY -DOPENMM_USE_STATIC_LIBRARIES -DCUDPP_STATIC_LIB")
+SET(CUDA_STATIC_COMPILE_FLAG "-DOPENMMCUDAFREEENERGY_BUILDING_STATIC_LIBRARY -DOPENMMCUDAFREEENERGY_USE_STATIC_LIBRARIES -DCUDPP_STATIC_LIB")
 SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS ${CUDA_STATIC_COMPILE_FLAG})
 
 TARGET_LINK_LIBRARIES(${STATIC_TARGET} optimized ${OPENMM_LIBRARY_NAME}_static)