Merge pull request #4632 from ex-rzr/make-hip-standard-platform

HIP platform

plugins/drude/platforms/hip/tests/TestHipDrudeSCFIntegrator.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2021 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * 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, CONTRIBUTORS 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "HipDrudeTests.h"
+#include "TestDrudeSCFIntegrator.h"
+
+void runPlatformTests() {}

plugins/rpmd/CMakeLists.txt

@@ -130,6 +130,15 @@ IF(OPENMM_BUILD_RPMD_CUDA_LIB)
     ADD_SUBDIRECTORY(platforms/cuda)
 ENDIF(OPENMM_BUILD_RPMD_CUDA_LIB)
 
+IF(OPENMM_BUILD_HIP_LIB)
+    SET(OPENMM_BUILD_RPMD_HIP_LIB ON CACHE BOOL "Build RPMD implementation for HIP")
+ELSE(OPENMM_BUILD_HIP_LIB)
+    SET(OPENMM_BUILD_RPMD_HIP_LIB OFF CACHE BOOL "Build RPMD implementation for HIP")
+ENDIF(OPENMM_BUILD_HIP_LIB)
+IF(OPENMM_BUILD_RPMD_HIP_LIB)
+    ADD_SUBDIRECTORY(platforms/hip)
+ENDIF(OPENMM_BUILD_RPMD_HIP_LIB)
+
 INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_RPMD_TARGET})
 IF( CREATE_SERIALIZABLE_OPENMM_RPMD )
     INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_RPMD_SERIALIZABLE_TARGET})

plugins/rpmd/platforms/hip/CMakeLists.txt

+#---------------------------------------------------
+# OpenMM HIP RPMD Integrator
+#
+# Creates OpenMMRPMDHIP library,.
+#
+# Windows:
+#   OpenMMRPMDHIP.dll
+#   OpenMMRPMDHIP.lib
+# Unix:
+#   libOpenMMRPMDHIP.so
+#----------------------------------------------------
+
+# The source is organized into subdirectories, but we handle them all from
+# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
+SET(OPENMM_SOURCE_SUBDIRS . ../common)
+
+
+# Collect up information about the version of the OpenMM library we're building
+# and make it available to the code so it can be built into the binaries.
+
+SET(OPENMMRPMDHIP_LIBRARY_NAME OpenMMRPMDHIP)
+
+SET(SHARED_TARGET ${OPENMMRPMDHIP_LIBRARY_NAME})
+
+# These are all the places to search for header files which are
+# to be part of the API.
+SET(API_INCLUDE_DIRS) # start empty
+FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
+    # append
+    SET(API_INCLUDE_DIRS ${API_INCLUDE_DIRS}
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
+ENDFOREACH(subdir)
+
+# We'll need both *relative* path names, starting with their API_INCLUDE_DIRS,
+# and absolute pathnames.
+SET(API_REL_INCLUDE_FILES)   # start these out empty
+SET(API_ABS_INCLUDE_FILES)
+
+FOREACH(dir ${API_INCLUDE_DIRS})
+    FILE(GLOB fullpaths ${dir}/*.h)	# returns full pathnames
+    SET(API_ABS_INCLUDE_FILES ${API_ABS_INCLUDE_FILES} ${fullpaths})
+
+    FOREACH(pathname ${fullpaths})
+        GET_FILENAME_COMPONENT(filename ${pathname} NAME)
+        SET(API_REL_INCLUDE_FILES ${API_REL_INCLUDE_FILES} ${dir}/${filename})
+    ENDFOREACH(pathname)
+ENDFOREACH(dir)
+
+# collect up source files
+SET(SOURCE_FILES) # empty
+SET(SOURCE_INCLUDE_FILES)
+
+FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
+    FILE(GLOB_RECURSE src_files  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.c)
+    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})
+    INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
+ENDFOREACH(subdir)
+
+SET(COMMON_KERNELS_CPP ${CMAKE_CURRENT_BINARY_DIR}/../common/src/CommonRpmdKernelSources.cpp)
+SET(SOURCE_FILES ${SOURCE_FILES} ${COMMON_KERNELS_CPP})
+
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../common/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/hip/include)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/hip/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_BINARY_DIR}/platforms/hip/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/platforms/common/include)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_BINARY_DIR}/platforms/common/src)
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/../common/src)
+
+# Create the library
+
+SET_SOURCE_FILES_PROPERTIES(${COMMON_KERNELS_CPP} PROPERTIES GENERATED TRUE)
+ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+ADD_DEPENDENCIES(${SHARED_TARGET} RpmdCommonKernels)
+
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}HIP)
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_RPMD_TARGET})
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
+
+INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
+
+IF(BUILD_TESTING AND OPENMM_BUILD_HIP_TESTS)
+    SUBDIRS(tests)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_HIP_TESTS)

plugins/rpmd/platforms/hip/include/HipRpmdKernelFactory.h

+#ifndef OPENMM_HIPRPMDKERNELFACTORY_H_
+#define OPENMM_HIPRPMDKERNELFACTORY_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) 2011-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2021 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * 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, CONTRIBUTORS 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/KernelFactory.h"
+
+namespace OpenMM {
+
+/**
+ * This KernelFactory creates kernels for the HIP implementation of RPMDIntegrator.
+ */
+
+class HipRpmdKernelFactory : public KernelFactory {
+public:
+    KernelImpl* createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_HIPRPMDKERNELFACTORY_H_*/

plugins/rpmd/platforms/hip/src/HipRpmdKernelFactory.cpp

+/* -------------------------------------------------------------------------- *
+ *                              OpenMMAmoeba                                  *
+ * -------------------------------------------------------------------------- *
+ * 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) 2011-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2021 Advanced Micro Devices, Inc.                   *
+ * 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 <exception>
+
+#include "HipRpmdKernelFactory.h"
+#include "CommonRpmdKernels.h"
+#include "HipContext.h"
+#include "openmm/internal/windowsExport.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/OpenMMException.h"
+
+using namespace OpenMM;
+
+extern "C" OPENMM_EXPORT void registerPlatforms() {
+}
+
+extern "C" OPENMM_EXPORT void registerKernelFactories() {
+    try {
+        Platform& platform = Platform::getPlatformByName("HIP");
+        HipRpmdKernelFactory* factory = new HipRpmdKernelFactory();
+        platform.registerKernelFactory(IntegrateRPMDStepKernel::Name(), factory);
+    }
+    catch (std::exception ex) {
+        // Ignore
+    }
+}
+
+extern "C" OPENMM_EXPORT void registerRPMDHipKernelFactories() {
+    try {
+        Platform::getPlatformByName("HIP");
+    }
+    catch (...) {
+        Platform::registerPlatform(new HipPlatform());
+    }
+    registerKernelFactories();
+}
+
+KernelImpl* HipRpmdKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
+    HipContext& cl = *static_cast<HipPlatform::PlatformData*>(context.getPlatformData())->contexts[0];
+    if (name == IntegrateRPMDStepKernel::Name())
+        return new CommonIntegrateRPMDStepKernel(name, platform, cl);
+    throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '")+name+"'").c_str());
+}

plugins/rpmd/platforms/hip/tests/CMakeLists.txt

+#
+# Testing
+#
+
+ENABLE_TESTING()
+
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/plugins/rpmd/tests)
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/hip/tests)
+
+# Automatically create tests using files named "Test*.cpp"
+FILE(GLOB TEST_PROGS "*Test*.cpp")
+FOREACH(TEST_PROG ${TEST_PROGS})
+    GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
+
+    # Link with shared library
+    ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
+    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_RPMD_TARGET} ${SHARED_TARGET})
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
+    IF(OPENMM_BUILD_HIP_DOUBLE_PRECISION_TESTS)
+        ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed)
+        ADD_TEST(${TEST_ROOT}Double ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} double)
+    ENDIF(OPENMM_BUILD_HIP_DOUBLE_PRECISION_TESTS)
+
+ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/rpmd/platforms/hip/tests/TestHipRpmd.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) 2011-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2021 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * 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, CONTRIBUTORS 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "HipTests.h"
+#include "TestRpmd.h"
+
+extern "C" void registerRPMDHipKernelFactories();
+
+using namespace OpenMM;
+
+void runPlatformTests() {
+    testParaHydrogen();
+}
+
+void setupKernels (int argc, char* argv[]) {
+    registerRPMDHipKernelFactories();
+    platform = dynamic_cast<HipPlatform&>(Platform::getPlatformByName("HIP"));
+    initializeTests(argc, argv);
+}

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -43,21 +43,18 @@ SKIP_METHODS = [('State', 'getPositions'),
                 ('CalcGBSAOBCForceKernel',),
                 ('CalcHarmonicAngleForceKernel',),
                 ('CalcHarmonicBondForceKernel',),
-                ('CalcKineticEnergyKernel',),
                 ('CalcNonbondedForceKernel',),
                 ('CalcPeriodicTorsionForceKernel',),
                 ('CalcRBTorsionForceKernel',),
                 ('ComputationInfo',),
                 ('ConstraintInfo',),
                 ('CudaKernelFactory',),
-                ('CudaStreamFactory',),
+                ('HipKernelFactory',),
                 ('ExceptionInfo',),
                 ('ExclusionInfo',),
                 ('FunctionInfo',),
                 ('GlobalParameterInfo',),
-                ('InitializeForcesKernel',),
                 ('IntegrateBrownianStepKernel',),
-                ('IntegrateLangevinStepKernel',),
                 ('IntegrateNoseHooverStepKernel',),
                 ('IntegrateVariableLangevinStepKernel',),
                 ('IntegrateVariableVerletStepKernel',),
@@ -75,23 +72,19 @@ SKIP_METHODS = [('State', 'getPositions'),
                 ('RBTorsionInfo',),
                 ('RemoveCMMotionKernel',),
                 ('SplineFitter',),
-                ('StreamFactory',),
                 ('TorsionInfo',),
                 ('TorsionTorsionGridInfo',),
                 ('TorsionTorsionInfo',),
                 ('UpdateStateDataKernel',),
-                ('UpdateTimeKernel',),
                 ('VdwInfo',),
                 ('WcaDispersionInfo',),
                 ('Context',  'getIntegrator'),
                 ('Context',  'createCheckpoint'),
                 ('Context',  'loadCheckpoint'),
                 ('CudaPlatform',),
+                ('HipPlatform',),
                 ('Force',    'Force'),
                 ('ParticleParameterInfo',),
-                ('Platform', 'createStream'),
-                ('Platform', 'getDefaultStreamFactory'),
-                ('Platform', 'registerStreamFactory'),
                 ('Platform', 'contextCreated'),
                 ('Platform', 'contextDestroyed'),
                 ('Platform', 'createKernel'),
@@ -113,7 +106,7 @@ SKIP_METHODS = [('State', 'getPositions'),
 
 
 # The build script assumes method args that are non-const references are
-# used to output values. This list gives excpetions to this rule.
+# used to output values. This list gives exceptions to this rule.
 NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
                   ('Platform', 'setPropertyValue', 'context'),
                   ('AmoebaTorsionTorsionForce', 'setTorsionTorsionGrid', 'grid'),