dded GB/VI to Cuda platform

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers  = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail 

plugins/freeEnergy/platforms/cuda/cuda-cmake/make2cmake.cmake

+
+#  For more information, please see: http://software.sci.utah.edu
+#
+#  The MIT License
+#
+#  Copyright (c) 2007
+#  Scientific Computing and Imaging Institute, University of Utah
+#
+#  License for the specific language governing rights and limitations under
+#  Permission is hereby granted, free of charge, to any person obtaining a
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+#  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+#  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+#  DEALINGS IN THE SOFTWARE.
+
+# Make2cmake CMake Script
+# Abe Stephens and James Bigler
+# (c) 2007 Scientific Computing and Imaging Institute, University of Utah
+# Note that the REGEX expressions may need to be tweaked for different dependency generators.
+
+FILE(READ ${input_file} depend_text)
+
+IF (${depend_text} MATCHES ".+")
+
+  # MESSAGE("FOUND DEPENDS")
+
+  # Remember, four backslashes is escaped to one backslash in the string.
+  STRING(REGEX REPLACE "\\\\ " " " depend_text ${depend_text})
+  
+  # This works for the nvcc -M generated dependency files.
+  STRING(REGEX REPLACE "^.* : " "" depend_text ${depend_text})
+  STRING(REGEX REPLACE "[ \\\\]*\n" ";" depend_text ${depend_text})
+
+  FOREACH(file ${depend_text})
+
+    STRING(REGEX REPLACE "^ +" "" file ${file})
+
+    # IF (EXISTS ${file})
+	  #   MESSAGE("DEPEND = ${file}")    
+    # ELSE (EXISTS ${file})
+	  #   MESSAGE("ERROR = ${file}")
+    # ENDIF(EXISTS ${file})
+  
+    SET(cuda_nvcc_depend "${cuda_nvcc_depend} \"${file}\"\n")
+  
+  ENDFOREACH(file) 
+
+ELSE(${depend_text} MATCHES ".+") 
+  # MESSAGE("FOUND NO DEPENDS")
+ENDIF(${depend_text} MATCHES ".+")
+
+
+FILE(WRITE ${output_file} "# Generated by: make2cmake.cmake\nSET(CUDA_NVCC_DEPEND\n ${cuda_nvcc_depend})\n\n")

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

+#  For more information, please see: http://software.sci.utah.edu
+#
+#  The MIT License
+#
+#  Copyright (c) 2007
+#  Scientific Computing and Imaging Institute, University of Utah
+#
+#  License for the specific language governing rights and limitations under
+#  Permission is hereby granted, free of charge, to any person obtaining a
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+#  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+#  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+#  DEALINGS IN THE SOFTWARE.
+
+# .cubin Parsing CMake Script
+# Abe Stephens
+# (c) 2007 Scientific Computing and Imaging Institute, University of Utah
+
+FILE(READ ${input_file} file_text)
+
+IF (${file_text} MATCHES ".+")
+
+  # Remember, four backslashes is escaped to one backslash in the string.
+  STRING(REGEX REPLACE ";" "\\\\;" file_text ${file_text})
+  STRING(REGEX REPLACE "\ncode" ";code" file_text ${file_text})
+  
+  LIST(LENGTH file_text len)
+
+  FOREACH(line ${file_text})
+
+    # Only look at "code { }" blocks.
+    IF(line MATCHES "^code")
+      
+      # Break into individual lines.
+      STRING(REGEX REPLACE "\n" ";" line ${line})
+
+      FOREACH(entry ${line})
+
+        # Extract kernel names.
+        IF (${entry} MATCHES "[^g]name = ([^ ]+)")
+          STRING(REGEX REPLACE ".* = ([^ ]+)" "\\1" entry ${entry})
+
+          # Check to see if the kernel name starts with "_"
+          SET(skip FALSE)
+          # IF (${entry} MATCHES "^_")
+            # Skip the rest of this block.
+            # MESSAGE("Skipping ${entry}")
+            # SET(skip TRUE)
+          # ELSE (${entry} MATCHES "^_")
+            MESSAGE("Kernel:    ${entry}")  
+          # ENDIF (${entry} MATCHES "^_")
+
+        ENDIF(${entry} MATCHES "[^g]name = ([^ ]+)")
+
+        # Skip the rest of the block if necessary
+        IF(NOT skip)
+
+          # Registers
+          IF (${entry} MATCHES "reg = ([^ ]+)")
+            STRING(REGEX REPLACE ".* = ([^ ]+)" "\\1" entry ${entry})
+            MESSAGE("Registers: ${entry}")
+          ENDIF(${entry} MATCHES "reg = ([^ ]+)")
+          
+          # Local memory
+          IF (${entry} MATCHES "lmem = ([^ ]+)")
+            STRING(REGEX REPLACE ".* = ([^ ]+)" "\\1" entry ${entry})
+            MESSAGE("Local:     ${entry}")
+          ENDIF(${entry} MATCHES "lmem = ([^ ]+)")
+          
+          # Shared memory
+          IF (${entry} MATCHES "smem = ([^ ]+)")
+            STRING(REGEX REPLACE ".* = ([^ ]+)" "\\1" entry ${entry})
+            MESSAGE("Shared:    ${entry}")
+          ENDIF(${entry} MATCHES "smem = ([^ ]+)")
+                  
+          IF (${entry} MATCHES "^}")
+            MESSAGE("")
+          ENDIF(${entry} MATCHES "^}")
+
+        ENDIF(NOT skip)
+
+
+      ENDFOREACH(entry)
+
+    ENDIF(line MATCHES "^code")
+
+  ENDFOREACH(line) 
+
+ELSE(${file_text} MATCHES ".+") 
+  # MESSAGE("FOUND NO DEPENDS")
+ENDIF(${file_text} MATCHES ".+")
+
+

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

+#ifndef OPENMM_FREE_ENERGY_CUDA_KERNEL_FACTORY_H_
+#define OPENMM_FREE_ENERGY_CUDA_KERNEL_FACTORY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * This program is free software: you can redistribute it and/or modify       *
+ * it under the terms of the GNU Lesser General Public License as published   *
+ * by the Free Software Foundation, either version 3 of the License, or       *
+ * (at your option) any later version.                                        *
+ *                                                                            *
+ * This program is distributed in the hope that it will be useful,            *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
+ * GNU Lesser General Public License for more details.                        *
+ *                                                                            *
+ * You should have received a copy of the GNU Lesser General Public License   *
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/KernelFactory.h"
+
+namespace OpenMM {
+
+/**
+ * This KernelFactory creates all kernels for CudaFreeEnergyPlatform.
+ */
+
+class CudaFreeEnergyKernelFactory : public KernelFactory {
+public:
+    KernelImpl* createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_FREE_ENERGY_CUDA_KERNEL_FACTORY_H_*/

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

+#
+# Include CUDA related files.
+#
+# ----------------------------------------------------------------------------
+# logging
+
+SET(LOG TRUE)
+   
+IF(LOG)
+   SET(LOG_FILE "CMakeLog.txt" )
+   FILE( WRITE ${LOG_FILE} "In freeEnergy/platforms/cuda/sharedTarget Cmake\n")
+#  FILE( APPEND ${LOG_FILE} "BROOK_LIB_PATH=${BROOK_LIB_PATH}\n")
+ENDIF(LOG)
+
+IF(LOG)
+   MACRO(LOG_DIR LOG_FILE DIR_LIST )
+   
+      FILE( APPEND ${LOG_FILE} "\n${DIR_LIST}\n")
+      FOREACH(currentFile ${ARGN})
+         FILE( APPEND ${LOG_FILE} "   ${currentFile}\n" )
+      ENDFOREACH(currentFile)
+   
+   ENDMACRO(LOG_DIR) 
+ENDIF(LOG)
+
+# ----------------------------------------------------------------------------
+
+SET(OPENMM_BUILD_FREE_ENERGY_PATH ${CMAKE_SOURCE_DIR}/plugins/freeEnergy) 
+
+# ----------------------------------------------------------------------------
+IF(LOG)
+   LOG_DIR( ${LOG_FILE} "Pre OPENMM_SOURCE_SUBDIRS" ${OPENMM_SOURCE_SUBDIRS} )
+   LOG_DIR( ${LOG_FILE} "Pre OPENMM_FREE_ENERGY_SOURCE_SUBDIRS " ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS} )
+   LOG_DIR( ${LOG_FILE} "Pre SOURCE_FILES" ${SOURCE_FILES} )
+ENDIF(LOG)
+## ----------------------------------------------------------------------------
+
+SET(CUDA_NVCC_BUILD_FLAGS) 
+INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake)
+INCLUDE_DIRECTORIES(${CUDA_INCLUDE})
+LINK_DIRECTORIES(${CUDA_TARGET_LINK})
+FOREACH(subdir ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS})
+    FILE(GLOB src_files ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/${subdir}/src/*.cu ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/src/*/*.cu)
+    FOREACH(file ${src_files})
+        FILE(RELATIVE_PATH file ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda ${file})
+        SET(SOURCE_FILES         ${SOURCE_FILES}         ${file})   #append
+    ENDFOREACH(file)
+    CUDA_INCLUDE_DIRECTORIES(BEFORE ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/../${subdir}/include)
+ENDFOREACH(subdir)
+
+# ----------------------------------------------------------------------------
+IF(LOG)
+   LOG_DIR( ${LOG_FILE} "OPENMM_BUILD_FREE_ENERGY_PATH" ${OPENMM_BUILD_FREE_ENERGY_PATH} )
+   FILE( APPEND ${LOG_FILE} "OPENMM_BUILD_FREE_ENERGY_PATH=${OPENMM_BUILD_FREE_ENERGY_PATH}\n")
+   LOG_DIR( ${LOG_FILE} "OPENMM_SOURCE_SUBDIRS" ${OPENMM_SOURCE_SUBDIRS} )
+   LOG_DIR( ${LOG_FILE} "CMAKE_SOURCE_DIR" ${CMAKE_SOURCE_DIR} )
+   LOG_DIR( ${LOG_FILE} "CUDA_INCLUDE" ${CUDA_INCLUDE} )
+   LOG_DIR( ${LOG_FILE} "CUDA_TARGET_LINK" ${CUDA_TARGET_LINK} )
+   LOG_DIR( ${LOG_FILE} "SHARED_TARGET" ${SHARED_TARGET} )
+   LOG_DIR( ${LOG_FILE} "OPENMM_DIR" ${OPENMM_DIR} )
+   LOG_DIR( ${LOG_FILE} "SOURCE_FILES" ${SOURCE_FILES} )
+ENDIF(LOG)
+## ----------------------------------------------------------------------------
+
+# CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/jama/include)
+
+CUDA_INCLUDE_DIRECTORIES(${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/../src
+                         ${OPENMM_DIR}/platforms/cuda/src
+                         ${OPENMM_DIR}/platforms/cuda/src/kernels
+                         ${OPENMM_DIR}/openmmapi/include ) 
+
+CUDA_ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME} )
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
+
+INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernelFactory.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * This program is free software: you can redistribute it and/or modify       *
+ * it under the terms of the GNU Lesser General Public License as published   *
+ * by the Free Software Foundation, either version 3 of the License, or       *
+ * (at your option) any later version.                                        *
+ *                                                                            *
+ * This program is distributed in the hope that it will be useful,            *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
+ * GNU Lesser General Public License for more details.                        *
+ *                                                                            *
+ * You should have received a copy of the GNU Lesser General Public License   *
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
+ * -------------------------------------------------------------------------- */
+
+#include "CudaFreeEnergyKernelFactory.h"
+#include "CudaFreeEnergyKernels.h"
+#include "openmm/freeEnergyKernels.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/OpenMMException.h"
+
+#if defined(OPENMM_BUILDING_SHARED_LIBRARY)
+    #if defined(WIN32)
+      #include <windows.h>
+        extern "C" void initOpenMMCudaFreeEnergyPlugin();
+        BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
+            if (ul_reason_for_call == DLL_PROCESS_ATTACH)
+                initOpenMMCudaFreeEnergyPlugin();
+            return TRUE;
+        }   
+    #else
+        extern "C" void __attribute__((constructor)) initOpenMMCudaFreeEnergyPlugin();
+    #endif
+#endif
+
+using namespace OpenMM;
+
+extern "C" void initOpenMMCudaFreeEnergyPlugin() {
+
+    if ( gpuIsAvailable() ){
+        CudaPlatform* cudaPlatform            = new CudaPlatform();
+        CudaFreeEnergyKernelFactory* factory  = new CudaFreeEnergyKernelFactory();
+    
+        cudaPlatform->registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
+        cudaPlatform->registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
+        cudaPlatform->registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
+    
+        Platform::registerPlatform(cudaPlatform);
+    }
+}
+
+KernelImpl* CudaFreeEnergyKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
+
+    CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
+
+    if (name == CalcNonbondedSoftcoreForceKernel::Name())
+        return new CudaFreeEnergyCalcNonbondedSoftcoreForceKernel(name, platform, data, context.getSystem());
+
+    if (name == CalcGBSAOBCSoftcoreForceKernel::Name())
+        return new CudaFreeEnergyCalcGBSAOBCSoftcoreForceKernel(name, platform, data);
+
+    if (name == CalcGBVISoftcoreForceKernel::Name())
+        return new CudaFreeEnergyCalcGBVISoftcoreForceKernel(name, platform, data);
+
+    throw OpenMMException( (std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str() );
+}

plugins/freeEnergy/platforms/cuda/src/kernels/GpuGBVISoftcore.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Authors: Scott Le Grand, Peter Eastman                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * This program is free software: you can redistribute it and/or modify       *
+ * it under the terms of the GNU Lesser General Public License as published   *
+ * by the Free Software Foundation, either version 3 of the License, or       *
+ * (at your option) any later version.                                        *
+ *                                                                            *
+ * This program is distributed in the hope that it will be useful,            *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
+ * GNU Lesser General Public License for more details.                        *
+ *                                                                            *
+ * You should have received a copy of the GNU Lesser General Public License   *
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
+ * -------------------------------------------------------------------------- */
+
+using namespace std;
+
+#include "GpuGBVISoftcore.h"
+#include "GpuFreeEnergyCudaKernels.h"
+
+// GpuGBVISoftcore constructor
+
+GpuGBVISoftcore::GpuGBVISoftcore( ){
+    _bornRadiiScalingMethod   = 0;
+    _quinticLowerLimitFactor  = 0.8;
+    _quinticUpperLimit        = 0.008;
+    _psSwitchDerivative       = NULL;
+}
+
+// GpuGBVISoftcore destructor
+
+GpuGBVISoftcore::~GpuGBVISoftcore( ){
+    delete _psSwitchDerivative;
+}
+
+// set quintic lower limit factor value
+
+int GpuGBVISoftcore::setQuinticLowerLimitFactor( float inputQuinticLowerLimitFactor ){
+    _quinticLowerLimitFactor = inputQuinticLowerLimitFactor;
+    return 0;
+}
+
+// get quintic lower limit factor value
+
+float GpuGBVISoftcore::getQuinticLowerLimitFactor( void ) const {
+    return _quinticLowerLimitFactor;
+}
+
+// set quintic upper limit value
+
+int GpuGBVISoftcore::setQuinticUpperLimit( float inputQuinticUpperLimit ){
+    _quinticUpperLimit = inputQuinticUpperLimit;
+    return 0;
+}
+
+// get quintic upper limit value
+
+float GpuGBVISoftcore::getQuinticUpperLimit( void ) const {
+    return _quinticUpperLimit;
+}
+
+// get Born radii scaling method
+
+int GpuGBVISoftcore::getBornRadiiScalingMethod( void ) const {
+    return _bornRadiiScalingMethod;
+}
+
+// set Born radii scaling method
+
+int GpuGBVISoftcore::setBornRadiiScalingMethod( int inputBornRadiiScalingMethod ){
+    _bornRadiiScalingMethod = inputBornRadiiScalingMethod;
+    return 0;
+}
+
+// get address for SwitchDerivative array on board
+
+float* GpuGBVISoftcore::getGpuSwitchDerivative( void ) const {
+    return _psSwitchDerivative->_pDevStream[0];
+}
+
+// get SwitchDerivative array 
+
+CUDAStream<float>* GpuGBVISoftcore::getSwitchDerivative( void ) const {
+    return _psSwitchDerivative;
+}
+
+// initialize SwitchDerivative array
+
+int GpuGBVISoftcore::initializeGpuSwitchDerivative( unsigned int numberOfParticles ){
+    _psSwitchDerivative = new CUDAStream<float>( numberOfParticles, 1, "SwitchDerivative");
+    for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
+        (*_psSwitchDerivative)[ii] = 1.0f;
+    }   
+    return 0;
+}
+
+// upload SoftCoreLambda array
+
+int GpuGBVISoftcore::upload( gpuContext gpu ){
+    if( getBornRadiiScalingMethod() > 0 ){
+        SetCalculateGBVISoftcoreSupplementarySim( this );
+    }
+    return 0;
+}