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Unverified Commit 89d2ff0e authored by Anton Gorenko's avatar Anton Gorenko
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Add hipification of CUDA platform 

Port changes in CUDA backend to HIP

Fix a warning about arithmetic operations on void* in HipArray::uploadSubArray

Fix "Error Initializing context ROCm 5.3.0"

    https://github.com/StreamHPC/openmm-hip/issues/3


    hipDeviceSetCacheConfig returns hipErrorNotSupported on 5.3
Co-authored-by: default avatarNick Curtis <nicholas.curtis@amd.com>
parent 8defca2d
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platforms/hip/CMakeLists.txt 0 → 100644
View file @ 89d2ff0e
#---------------------------------------------------
# OpenMM HIP Platform
#
# Creates OpenMMHIP library.
#
# Windows:
# unsupported
# Unix:
# libOpenMMHIP.so
# libOpenMMHIP_static.a
#----------------------------------------------------
set(OPENMM_BUILD_HIP_TESTS TRUE CACHE BOOL "Whether to build HIP test cases")
if(BUILD_TESTING AND OPENMM_BUILD_HIP_TESTS)
SUBDIRS (tests)
endif(BUILD_TESTING AND OPENMM_BUILD_HIP_TESTS)
# 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(OPENMMHIP_LIBRARY_NAME OpenMMHIP)
SET(SHARED_TARGET ${OPENMMHIP_LIBRARY_NAME})
SET(STATIC_TARGET ${OPENMMHIP_LIBRARY_NAME}_static)
# 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
IF(MSVC)
FILE(GLOB_RECURSE kernel_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/kernels/*.hip)
SET(SOURCE_FILES ${SOURCE_FILES} ${kernel_files})
ENDIF(MSVC)
SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
ENDFOREACH(subdir)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
# Set variables needed for encoding kernel sources into a C++ class
SET(KERNEL_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
SET(KERNEL_SOURCE_CLASS HipKernelSources)
SET(KERNELS_CPP ${CMAKE_CURRENT_BINARY_DIR}/src/${KERNEL_SOURCE_CLASS}.cpp)
SET(KERNELS_H ${CMAKE_CURRENT_BINARY_DIR}/src/${KERNEL_SOURCE_CLASS}.h)
SET(COMMON_KERNELS_CPP ${CMAKE_CURRENT_BINARY_DIR}/../common/src/CommonKernelSources.cpp)
SET(SOURCE_FILES ${SOURCE_FILES} ${KERNELS_CPP} ${KERNELS_H} ${COMMON_KERNELS_CPP})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/../common/src)
# Install headers
FILE(GLOB CORE_HEADERS include/*.h)
INSTALL_FILES(/include/openmm/hip FILES ${CORE_HEADERS})
SUBDIRS (sharedTarget)
IF(OPENMM_BUILD_STATIC_LIB)
SUBDIRS (staticTarget)
ENDIF(OPENMM_BUILD_STATIC_LIB)
platforms/hip/include/HipArray.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPARRAY_H_
#define OPENMM_HIPARRAY_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) 2009-2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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/OpenMMException.h"
#include "openmm/common/windowsExportCommon.h"
#include "openmm/common/ArrayInterface.h"
#include <hip/hip_runtime.h>
#include <iostream>
#include <sstream>
#include <vector>
namespace OpenMM {
class HipContext;
/**
* This class encapsulates a block of HIP device memory. It provides a simplified API
* for working with it and for copying data to and from device memory.
*/
class OPENMM_EXPORT_COMMON HipArray : public ArrayInterface {
public:
/**
* Create a HipArray object. The object is allocated on the heap with the "new" operator.
* The template argument is the data type of each array element.
*
* @param context the context for which to create the array
* @param size the number of elements in the array
* @param name the name of the array
*/
template <class T>
static HipArray* create(HipContext& context, int size, const std::string& name) {
return new HipArray(context, size, sizeof(T), name);
}
/**
* Create an uninitialized HipArray object. It does not point to any device memory,
* and cannot be used until initialize() is called on it.
*/
HipArray();
/**
* Create a HipArray object.
*
* @param context the context for which to create the array
* @param size the number of elements in the array
* @param elementSize the size of each element in bytes
* @param name the name of the array
*/
HipArray(HipContext& context, int size, int elementSize, const std::string& name);
~HipArray();
/**
* Initialize this object.
*
* @param context the context for which to create the array
* @param size the number of elements in the array
* @param elementSize the size of each element in bytes
* @param name the name of the array
*/
void initialize(ComputeContext& context, int size, int elementSize, const std::string& name);
/**
* Initialize this object. The template argument is the data type of each array element.
*
* @param context the context for which to create the array
* @param size the number of elements in the array
* @param name the name of the array
*/
template <class T>
void initialize(ComputeContext& context, int size, const std::string& name) {
initialize(context, size, sizeof(T), name);
}
/**
* Recreate the internal storage to have a different size.
*/
void resize(int size);
/**
* Get whether this array has been initialized.
*/
bool isInitialized() const {
return (pointer != 0);
}
/**
* Get the number of elements in the array.
*/
int getSize() const {
return size;
}
/**
* Get the size of each element in bytes.
*/
int getElementSize() const {
return elementSize;
}
/**
* Get the name of the array.
*/
const std::string& getName() const {
return name;
}
/**
* Get the context this array belongs to.
*/
ComputeContext& getContext();
/**
* Get a pointer to the device memory.
*/
hipDeviceptr_t& getDevicePointer() {
return pointer;
}
/**
* Copy the values in a vector to the device memory.
*/
template <class T>
void upload(const std::vector<T>& data, bool convert=false) {
ArrayInterface::upload(data, convert);
}
/**
* Copy the values in the Buffer to a vector.
*/
template <class T>
void download(std::vector<T>& data) const {
ArrayInterface::download(data);
}
/**
* Copy the values from host memory to the array.
*
* @param data the data to copy
* @param blocking if true, this call will block until the transfer is complete. If false,
* the source array must be in page-locked memory.
*/
void upload(const void* data, bool blocking=true) {
uploadSubArray(data, 0, getSize(), blocking);
}
/**
* Copy values from host memory to a subset of the array.
*
* @param data the data to copy
* @param offset the index of the element within the array at which the copy should begin
* @param elements the number of elements to copy
* @param blocking if true, this call will block until the transfer is complete. If false,
* the source array must be in page-locked memory.
*/
void uploadSubArray(const void* data, int offset, int elements, bool blocking=true);
/**
* Copy the values in the device memory to an array.
*
* @param data the array to copy the memory to
* @param blocking if true, this call will block until the transfer is complete. If false,
* the destination array must be in page-locked memory.
*/
void download(void* data, bool blocking=true) const;
/**
* Copy the values in the device memory to a second array.
*
* @param dest the destination array to copy to
*/
void copyTo(ArrayInterface& dest) const;
private:
HipContext* context;
hipDeviceptr_t pointer;
int size, elementSize;
bool ownsMemory;
std::string name;
};
} // namespace OpenMM
#endif /*OPENMM_HIPARRAY_H_*/
platforms/hip/include/HipBondedUtilities.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPBONDEDUTILITIES_H_
#define OPENMM_HIPBONDEDUTILITIES_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) 2011-2018 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipArray.h"
#include "openmm/System.h"
#include "openmm/common/BondedUtilities.h"
#include <string>
#include <vector>
namespace OpenMM {
class HipContext;
/**
* This class provides a generic mechanism for evaluating bonded interactions. You write only
* the source code needed to compute one interaction, and this class takes care of creating
* and executing a complete kernel that loops over bonds, evaluates each one, and accumulates
* the resulting forces and energies. This offers two advantages. First, it simplifies the
* task of writing a new Force. Second, it allows multiple forces to be evaluated by a single
* kernel, which reduces overhead and improves performance.
*
* A "bonded interaction" means an interaction that affects a small, fixed set of particles.
* The interaction energy may depend on the positions of only those particles, and the list of
* particles forming a "bond" may not change with time. Examples of bonded interactions
* include HarmonicBondForce, HarmonicAngleForce, and PeriodicTorsionForce.
*
* To create a bonded interaction, call addInteraction(). You pass to it a block of source
* code for evaluating the interaction. The inputs and outputs for that source code are as
* follows:
*
* <ol>
* <li>The index of the bond being evaluated will have been stored in the unsigned int variable "index".</li>
* <li>The indices of the atoms forming that bond will have been stored in the unsigned int variables "atom1",
* "atom2", ....</li>
* <li>The positions of those atoms will have been stored in the real4 variables "pos1", "pos2", ....</li>
* <li>A real variable called "energy" will exist. Your code should add the potential energy of the
* bond to that variable.</li>
* <li>Your code should define real3 variables called "force1", "force2", ... that contain the force to
* apply to each atom.</li>
* </ol>
*
* As a simple example, the following source code would be used to implement a pairwise interaction of
* the form E=r^2:
*
* <tt><pre>
* real4 delta = pos2-pos1;
* energy += delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
* real3 force1 = 2.0f*delta;
* real3 force2 = -2.0f*delta;
* </pre></tt>
*
* Interactions will often depend on parameters or other data. Call addArgument() to provide the data
* to this class. It will be passed to the interaction kernel as an argument, and you can refer to it
* from your interaction code.
*/
class OPENMM_EXPORT_COMMON HipBondedUtilities : public BondedUtilities {
public:
HipBondedUtilities(HipContext& context);
/**
* Add a bonded interaction.
*
* @param atoms this should have one entry for each bond, and that entry should contain the list
* of atoms involved in the bond. Every entry must have the same number of atoms.
* @param source the code to evaluate the interaction
* @param group the force group in which the interaction should be calculated
*/
void addInteraction(const std::vector<std::vector<int> >& atoms, const std::string& source, int group);
/**
* Add an argument that should be passed to the interaction kernel.
*
* @param data the device memory containing the data to pass
* @param type the data type contained in the memory (e.g. "float4")
* @return the name that will be used for the argument. Any code you pass to addInteraction() should
* refer to it by this name.
*/
std::string addArgument(hipDeviceptr_t data, const std::string& type);
/**
* Add an argument that should be passed to the interaction kernel.
*
* @param data the array containing the data to pass
* @param type the data type contained in the memory (e.g. "float4")
* @return the name that will be used for the argument. Any code you pass to addInteraction() should
* refer to it by this name.
*/
std::string addArgument(ArrayInterface& data, const std::string& type);
/**
* Register that the interaction kernel will be computing the derivative of the potential energy
* with respect to a parameter.
*
* @param param the name of the parameter
* @return the variable that will be used to accumulate the derivative. Any code you pass to addInteraction() should
* add its contributions to this variable.
*/
std::string addEnergyParameterDerivative(const std::string& param);
/**
* Add some Hip code that should be included in the program, before the start of the kernel.
* This can be used, for example, to define functions that will be called by the kernel.
*
* @param source the code to include
*/
void addPrefixCode(const std::string& source);
/**
* Initialize this object in preparation for a simulation.
*/
void initialize(const System& system);
/**
* Compute the bonded interactions.
*
* @param groups a set of bit flags for which force groups to include
*/
void computeInteractions(int groups);
private:
std::string createForceSource(int forceIndex, int numBonds, int numAtoms, int group, const std::string& computeForce);
HipContext& context;
hipFunction_t kernel;
std::vector<std::vector<std::vector<int> > > forceAtoms;
std::vector<std::vector<int> > indexWidth;
std::vector<std::string> forceSource;
std::vector<int> forceGroup;
std::vector<hipDeviceptr_t> arguments;
std::vector<std::string> argTypes;
std::vector<std::vector<HipArray> > atomIndices;
std::vector<std::string> prefixCode;
std::vector<std::string> energyParameterDerivatives;
std::vector<void*> kernelArgs;
int numForceBuffers, maxBonds, allGroups;
bool hasInitializedKernels, hasInteractions;
};
} // namespace OpenMM
#endif /*OPENMM_HIPBONDEDUTILITIES_H_*/
platforms/hip/include/HipContext.h 0 → 100644
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platforms/hip/include/HipEvent.h 0 → 100644
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#ifndef OPENMM_HIPEVENT_H_
#define OPENMM_HIPEVENT_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) 2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipContext.h"
#include "openmm/common/ComputeEvent.h"
namespace OpenMM {
/**
* This is the HIP implementation of the ComputeKernelImpl interface.
*/
class HipEvent : public ComputeEventImpl {
public:
HipEvent(HipContext& context);
~HipEvent();
/**
* Place the event into the device's execution queue.
*/
void enqueue();
/**
* Block until all operations started before the call to enqueue() have completed.
*/
void wait();
private:
HipContext& context;
hipEvent_t event;
bool eventCreated;
};
} // namespace OpenMM
#endif /*OPENMM_HIPEVENT_H_*/
platforms/hip/include/HipExpressionUtilities.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPEXPRESSIONUTILITIES_H_
#define OPENMM_HIPEXPRESSIONUTILITIES_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) 2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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/common/ExpressionUtilities.h"
#include "openmm/common/windowsExportCommon.h"
namespace OpenMM {
/**
* This class exists only for backward compatibility. It adds no features beyond
* the base ExpressionUtilities class.
*/
class OPENMM_EXPORT_COMMON HipExpressionUtilities : public ExpressionUtilities {
public:
HipExpressionUtilities(ComputeContext& context) : ExpressionUtilities(context) {
}
};
} // namespace OpenMM
#endif /*OPENMM_HIPEXPRESSIONUTILITIES_H_*/
platforms/hip/include/HipFFT3D.h 0 → 100644
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#ifndef __OPENMM_HIPFFT3D_H__
#define __OPENMM_HIPFFT3D_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) 2009-2015 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipArray.h"
namespace OpenMM {
/**
* This class performs three dimensional Fast Fourier Transforms. It is based on the
* mixed radix algorithm described in
* <p>
* Takahashi, D. and Kanada, Y., "High-Performance Radix-2, 3 and 5 Parallel 1-D Complex
* FFT Algorithms for Distributed-Memory Parallel Computers." Journal of Supercomputing,
* 15, 207–228 (2000).
* <p>
* This class places certain restrictions on the allowed dimensions of the grid. First,
* the size of each dimension may have no prime factors other than 2, 3, 5, and 7. You
* can call findLegalDimension() to determine the smallest size that satisfies this
* requirement and is greater than or equal to a specified minimum size. Second, the size
* of each dimension must be small enough to compute each 1D transform entirely in local
* memory with one work unit per data point. This will vary between platforms, but is
* typically at least 512.
* <p>
* Note that this class performs an unnormalized transform. That means that if you perform
* a forward transform followed immediately by an inverse transform, the effect is to
* multiply every value of the original data set by the total number of data points.
*/
class OPENMM_EXPORT_COMMON HipFFT3D {
public:
/**
* Create an HipFFT3D object for performing transforms of a particular size.
*
* @param context the context in which to perform calculations
* @param xsize the first dimension of the data sets on which FFTs will be performed
* @param ysize the second dimension of the data sets on which FFTs will be performed
* @param zsize the third dimension of the data sets on which FFTs will be performed
* @param realToComplex if true, a real-to-complex transform will be done. Otherwise, it is complex-to-complex.
*/
HipFFT3D(HipContext& context, int xsize, int ysize, int zsize, bool realToComplex=false);
/**
* Perform a Fourier transform. The transform cannot be done in-place: the input and output
* arrays must be different. Also, the input array is used as workspace, so its contents
* are destroyed. This also means that both arrays must be large enough to hold complex values,
* even when performing a real-to-complex transform.
* <p>
* When performing a real-to-complex transform, the output data is of size xsize*ysize*(zsize/2+1)
* and contains only the non-redundant elements.
*
* @param in the data to transform, ordered such that in[x*ysize*zsize + y*zsize + z] contains element (x, y, z)
* @param out on exit, this contains the transformed data
* @param forward true to perform a forward transform, false to perform an inverse transform
*/
void execFFT(HipArray& in, HipArray& out, bool forward = true);
/**
* Get the smallest legal size for a dimension of the grid (that is, a size with no prime
* factors other than 2, 3, 5, and 7).
*
* @param minimum the minimum size the return value must be greater than or equal to
*/
static int findLegalDimension(int minimum);
private:
hipFunction_t createKernel(int xsize, int ysize, int zsize, int& threads, int axis, bool forward, bool inputIsReal);
int xsize, ysize, zsize;
int xthreads, ythreads, zthreads;
bool packRealAsComplex;
HipContext& context;
hipFunction_t xkernel, ykernel, zkernel;
hipFunction_t invxkernel, invykernel, invzkernel;
hipFunction_t packForwardKernel, unpackForwardKernel, packBackwardKernel, unpackBackwardKernel;
};
} // namespace OpenMM
#endif // __OPENMM_HIPFFT3D_H__
platforms/hip/include/HipForceInfo.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPFORCEINFO_H_
#define OPENMM_HIPFORCEINFO_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) 2009 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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/common/ComputeForceInfo.h"
#include "openmm/common/windowsExportCommon.h"
#include <vector>
namespace OpenMM {
/**
* This class exists solely for backward compatibility. It adds no features beyond the ones
* in ComputeForceInfo.
*/
class OPENMM_EXPORT_COMMON HipForceInfo : public ComputeForceInfo {
};
} // namespace OpenMM
#endif /*OPENMM_HIPFORCEINFO_H_*/
platforms/hip/include/HipIntegrationUtilities.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPINTEGRATIONUTILITIES_H_
#define OPENMM_HIPINTEGRATIONUTILITIES_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) 2009-2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipArray.h"
#include "openmm/System.h"
#include "openmm/common/IntegrationUtilities.h"
#include "openmm/common/windowsExportCommon.h"
#include <hip/hip_runtime.h>
namespace OpenMM {
class HipContext;
/**
* This class implements features that are used by many different integrators, including
* common workspace arrays, random number generation, and enforcing constraints.
*/
class OPENMM_EXPORT_COMMON HipIntegrationUtilities : public IntegrationUtilities {
public:
HipIntegrationUtilities(HipContext& context, const System& system);
~HipIntegrationUtilities();
/**
* Get the array which contains position deltas.
*/
HipArray& getPosDelta();
/**
* Get the array which contains random values. Each element is a float4, whose components
* are independent, normally distributed random numbers with mean 0 and variance 1.
*/
HipArray& getRandom();
/**
* Get the array which contains the current step size.
*/
HipArray& getStepSize();
/**
* Distribute forces from virtual sites to the atoms they are based on.
*/
void distributeForcesFromVirtualSites();
private:
void applyConstraintsImpl(bool constrainVelocities, double tol);
int* ccmaConvergedMemory;
hipDeviceptr_t ccmaConvergedDeviceMemory;
hipEvent_t ccmaEvent;
};
} // namespace OpenMM
#endif /*OPENMM_HIPINTEGRATIONUTILITIES_H_*/
platforms/hip/include/HipKernel.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPKERNEL_H_
#define OPENMM_HIPKERNEL_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) 2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipArray.h"
#include "HipContext.h"
#include <string>
#include <vector>
namespace OpenMM {
/**
* This is the HIP implementation of the ComputeKernelImpl interface.
*/
class HipKernel : public ComputeKernelImpl {
public:
/**
* Create a new HipKernel.
*
* @param context the context this kernel belongs to
* @param kernel the kernel to be invoked
* @param name the name of the kernel function
*/
HipKernel(HipContext& context, hipFunction_t kernel, const std::string& name);
/**
* Get the name of this kernel.
*/
std::string getName() const;
/**
* Get the maximum block size that can be used when executing this kernel.
*/
int getMaxBlockSize() const;
/**
* Execute this kernel.
*
* @param threads the maximum number of threads that should be used. Depending on the
* computing device, it may choose to use fewer threads than this number.
* @param blockSize the number of threads in each thread block. If this is omitted, a
* default size that is appropriate for the computing device is used.
*/
void execute(int threads, int blockSize=-1);
protected:
/**
* Add an argument to pass the kernel when it is invoked, where the value is a
* subclass of ArrayInterface.
*
* @param value the value to pass to the kernel
*/
void addArrayArg(ArrayInterface& value);
/**
* Add an argument to pass the kernel when it is invoked, where the value is a primitive type.
*
* @param value a pointer to the argument value
* @param size the size of the value in bytes
*/
void addPrimitiveArg(const void* value, int size);
/**
* Add a placeholder for an argument without specifying its value.
*/
void addEmptyArg();
/**
* Add an argument to pass the kernel when it is invoked, where the value is a
* subclass of ArrayInterface.
*
* @param index the index of the argument to set
* @param value the value to pass to the kernel
*/
void setArrayArg(int index, ArrayInterface& value);
/**
* Add an argument to pass the kernel when it is invoked, where the value is a primitive type.
*
* @param index the index of the argument to set
* @param value a pointer to the argument value
* @param size the size of the value in bytes
*/
void setPrimitiveArg(int index, const void* value, int size);
private:
HipContext& context;
hipFunction_t kernel;
std::string name;
std::vector<double4> primitiveArgs;
std::vector<HipArray*> arrayArgs;
std::vector<void*> argPointers;
};
} // namespace OpenMM
#endif /*OPENMM_HIPKERNEL_H_*/
platforms/hip/include/HipKernelFactory.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPKERNELFACTORY_H_
#define OPENMM_HIPKERNELFACTORY_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) 2012 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 HipPlatform.
*/
class HipKernelFactory : public KernelFactory {
public:
KernelImpl* createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const;
};
} // namespace OpenMM
#endif /*OPENMM_HIPKERNELFACTORY_H_*/
platforms/hip/include/HipKernels.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPKERNELS_H_
#define OPENMM_HIPKERNELS_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) 2008-2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipPlatform.h"
#include "HipArray.h"
#include "HipContext.h"
#include "HipFFT3D.h"
#include "HipSort.h"
#include "openmm/kernels.h"
#include "openmm/System.h"
#include "openmm/common/CommonKernels.h"
#include <hipfft.h>
namespace OpenMM {
/**
* This abstract class defines an interface for code that can compile CUDA kernels. This allows a plugin to take advantage of runtime compilation
* when running on recent versions of CUDA.
*/
class HipCompilerKernel : public KernelImpl {
public:
static std::string Name() {
return "HipCompilerKernel";
}
HipCompilerKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Compile a kernel to PTX.
*
* @param source the source code for the kernel
* @param options the flags to be passed to the compiler
* @param cu the HipContext for which the kernel is being compiled
*/
virtual std::string createModule(const std::string& source, const std::string& flags, HipContext& cu) = 0;
};
/**
* This kernel is invoked at the beginning and end of force and energy computations. It gives the
* Platform a chance to clear buffers and do other initialization at the beginning, and to do any
* necessary work at the end to determine the final results.
*/
class HipCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
public:
HipCalcForcesAndEnergyKernel(std::string name, const Platform& platform, HipContext& cu) : CalcForcesAndEnergyKernel(name, platform), cu(cu) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
*/
void initialize(const System& system);
/**
* This is called at the beginning of each force/energy computation, before calcForcesAndEnergy() has been called on
* any ForceImpl.
*
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
* @param groups a set of bit flags for which force groups to include
*/
void beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups);
/**
* This is called at the end of each force/energy computation, after calcForcesAndEnergy() has been called on
* every ForceImpl.
*
* @param context the context in which to execute this kernel
* @param includeForce true if forces should be computed
* @param includeEnergy true if potential energy should be computed
* @param groups a set of bit flags for which force groups to include
* @param valid the method may set this to false to indicate the results are invalid and the force/energy
* calculation should be repeated
* @return the potential energy of the system. This value is added to all values returned by ForceImpls'
* calcForcesAndEnergy() methods. That is, each force kernel may <i>either</i> return its contribution to the
* energy directly, <i>or</i> add it to an internal buffer so that it will be included here.
*/
double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid);
private:
HipContext& cu;
};
/**
* This kernel provides methods for setting and retrieving various state data: time, positions,
* velocities, and forces.
*/
class HipUpdateStateDataKernel : public UpdateStateDataKernel {
public:
HipUpdateStateDataKernel(std::string name, const Platform& platform, HipContext& cu) : UpdateStateDataKernel(name, platform), cu(cu) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
*/
void initialize(const System& system);
/**
* Get the current time (in picoseconds).
*
* @param context the context in which to execute this kernel
*/
double getTime(const ContextImpl& context) const;
/**
* Set the current time (in picoseconds).
*
* @param context the context in which to execute this kernel
*/
void setTime(ContextImpl& context, double time);
/**
* Get the positions of all particles.
*
* @param positions on exit, this contains the particle positions
*/
void getPositions(ContextImpl& context, std::vector<Vec3>& positions);
/**
* Set the positions of all particles.
*
* @param positions a vector containg the particle positions
*/
void setPositions(ContextImpl& context, const std::vector<Vec3>& positions);
/**
* Get the velocities of all particles.
*
* @param velocities on exit, this contains the particle velocities
*/
void getVelocities(ContextImpl& context, std::vector<Vec3>& velocities);
/**
* Set the velocities of all particles.
*
* @param velocities a vector containg the particle velocities
*/
void setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities);
/**
* Get the current forces on all particles.
*
* @param forces on exit, this contains the forces
*/
void getForces(ContextImpl& context, std::vector<Vec3>& forces);
/**
* Get the current derivatives of the energy with respect to context parameters.
*
* @param derivs on exit, this contains the derivatives
*/
void getEnergyParameterDerivatives(ContextImpl& context, std::map<std::string, double>& derivs);
/**
* Get the current periodic box vectors.
*
* @param a on exit, this contains the vector defining the first edge of the periodic box
* @param b on exit, this contains the vector defining the second edge of the periodic box
* @param c on exit, this contains the vector defining the third edge of the periodic box
*/
void getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const;
/**
* Set the current periodic box vectors.
*
* @param a the vector defining the first edge of the periodic box
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
*/
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
/**
* Create a checkpoint recording the current state of the Context.
*
* @param stream an output stream the checkpoint data should be written to
*/
void createCheckpoint(ContextImpl& context, std::ostream& stream);
/**
* Load a checkpoint that was written by createCheckpoint().
*
* @param stream an input stream the checkpoint data should be read from
*/
void loadCheckpoint(ContextImpl& context, std::istream& stream);
private:
HipContext& cu;
};
/**
* This kernel is invoked by NonbondedForce to calculate the forces acting on the system.
*/
class HipCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
HipCalcNonbondedForceKernel(std::string name, const Platform& platform, HipContext& cu, const System& system) : CalcNonbondedForceKernel(name, platform),
cu(cu), hasInitializedFFT(false), sort(NULL), dispersionFft(NULL), fft(NULL), pmeio(NULL), usePmeStream(false) {
}
~HipCalcNonbondedForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the NonbondedForce this kernel will be used for
*/
void initialize(const System& system, const NonbondedForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @param includeDirect true if direct space interactions should be included
* @param includeReciprocal true if reciprocal space interactions should be included
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the NonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const NonbondedForce& force);
/**
* Get the parameters being used for PME.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*/
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
* Get the dispersion parameters being used for the dispersion term in LJPME.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*/
void getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
private:
class SortTrait : public HipSort::SortTrait {
int getDataSize() const {return 8;}
int getKeySize() const {return 4;}
const char* getDataType() const {return "int2";}
const char* getKeyType() const {return "int";}
const char* getMinKey() const {return "(-2147483647-1)";}
const char* getMaxKey() const {return "2147483647";}
const char* getMaxValue() const {return "make_int2(2147483647, 2147483647)";}
const char* getSortKey() const {return "value.y";}
};
class ForceInfo;
class PmeIO;
class PmePreComputation;
class PmePostComputation;
class SyncStreamPreComputation;
class SyncStreamPostComputation;
HipContext& cu;
ForceInfo* info;
bool hasInitializedFFT;
HipArray charges;
HipArray sigmaEpsilon;
HipArray exceptionParams;
HipArray exclusionAtoms;
HipArray exclusionParams;
HipArray baseParticleParams;
HipArray baseExceptionParams;
HipArray particleParamOffsets;
HipArray exceptionParamOffsets;
HipArray particleOffsetIndices;
HipArray exceptionOffsetIndices;
HipArray globalParams;
HipArray cosSinSums;
HipArray pmeGrid1;
HipArray pmeGrid2;
HipArray pmeBsplineModuliX;
HipArray pmeBsplineModuliY;
HipArray pmeBsplineModuliZ;
HipArray pmeDispersionBsplineModuliX;
HipArray pmeDispersionBsplineModuliY;
HipArray pmeDispersionBsplineModuliZ;
HipArray pmeAtomGridIndex;
HipArray pmeEnergyBuffer;
HipSort* sort;
Kernel cpuPme;
PmeIO* pmeio;
hipStream_t pmeStream;
hipEvent_t pmeSyncEvent, paramsSyncEvent;
HipFFT3D* fft;
hipfftHandle fftForward;
hipfftHandle fftBackward;
HipFFT3D* dispersionFft;
hipfftHandle dispersionFftForward;
hipfftHandle dispersionFftBackward;
hipFunction_t computeParamsKernel, computeExclusionParamsKernel;
hipFunction_t ewaldSumsKernel;
hipFunction_t ewaldForcesKernel;
hipFunction_t pmeGridIndexKernel;
hipFunction_t pmeDispersionGridIndexKernel;
hipFunction_t pmeSpreadChargeKernel;
hipFunction_t pmeDispersionSpreadChargeKernel;
hipFunction_t pmeFinishSpreadChargeKernel;
hipFunction_t pmeDispersionFinishSpreadChargeKernel;
hipFunction_t pmeEvalEnergyKernel;
hipFunction_t pmeEvalDispersionEnergyKernel;
hipFunction_t pmeConvolutionKernel;
hipFunction_t pmeDispersionConvolutionKernel;
hipFunction_t pmeInterpolateForceKernel;
hipFunction_t pmeInterpolateDispersionForceKernel;
std::vector<std::pair<int, int> > exceptionAtoms;
std::vector<std::string> paramNames;
std::vector<double> paramValues;
double ewaldSelfEnergy, dispersionCoefficient, alpha, dispersionAlpha;
int interpolateForceThreads;
int gridSizeX, gridSizeY, gridSizeZ;
int dispersionGridSizeX, dispersionGridSizeY, dispersionGridSizeZ;
bool hasCoulomb, hasLJ, usePmeStream, useHipFFT, doLJPME, usePosqCharges, recomputeParams, hasOffsets;
NonbondedMethod nonbondedMethod;
static const int PmeOrder = 5;
};
/**
* This kernel is invoked by CustomCVForce to calculate the forces acting on the system and the energy of the system.
*/
class HipCalcCustomCVForceKernel : public CommonCalcCustomCVForceKernel {
public:
HipCalcCustomCVForceKernel(std::string name, const Platform& platform, ComputeContext& cc) : CommonCalcCustomCVForceKernel(name, platform, cc) {
}
ComputeContext& getInnerComputeContext(ContextImpl& innerContext) {
return *reinterpret_cast<HipPlatform::PlatformData*>(innerContext.getPlatformData())->contexts[0];
}
};
} // namespace OpenMM
#endif /*OPENMM_HIPKERNELS_H_*/
platforms/hip/include/HipNonbondedUtilities.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPNONBONDEDUTILITIES_H_
#define OPENMM_HIPNONBONDEDUTILITIES_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) 2009-2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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/System.h"
#include "HipArray.h"
#include "HipExpressionUtilities.h"
#include "openmm/common/NonbondedUtilities.h"
#include <hip/hip_runtime.h>
#include <sstream>
#include <string>
#include <vector>
namespace OpenMM {
class HipContext;
class HipSort;
/**
* This class provides a generic interface for calculating nonbonded interactions. It does this in two
* ways. First, it can be used to create kernels that evaluate nonbonded interactions. Clients
* only need to provide the code for evaluating a single interaction and the list of parameters it depends on.
* A complete kernel is then synthesized using an appropriate algorithm to evaluate all interactions on all
* atoms.
*
* Second, this class itself creates and invokes a single "default" interaction kernel, allowing several
* different forces to be evaluated at once for greater efficiency. Call addInteraction() and addParameter()
* to add interactions to this default kernel.
*
* During each force or energy evaluation, the following sequence of steps takes place:
*
* 1. Data structures (e.g. neighbor lists) are calculated to allow nonbonded interactions to be evaluated
* quickly.
*
* 2. calcForcesAndEnergy() is called on each ForceImpl in the System.
*
* 3. Finally, the default interaction kernel is invoked to calculate all interactions that were added
* to it.
*
* This sequence means that the default interaction kernel may depend on quantities that were calculated
* by ForceImpls during calcForcesAndEnergy().
*/
class OPENMM_EXPORT_COMMON HipNonbondedUtilities : public NonbondedUtilities {
public:
class ParameterInfo;
HipNonbondedUtilities(HipContext& context);
~HipNonbondedUtilities();
/**
* Add a nonbonded interaction to be evaluated by the default interaction kernel.
*
* @param usesCutoff specifies whether a cutoff should be applied to this interaction
* @param usesPeriodic specifies whether periodic boundary conditions should be applied to this interaction
* @param usesExclusions specifies whether this interaction uses exclusions. If this is true, it must have identical exclusions to every other interaction.
* @param cutoffDistance the cutoff distance for this interaction (ignored if usesCutoff is false)
* @param exclusionList for each atom, specifies the list of other atoms whose interactions should be excluded
* @param kernel the code to evaluate the interaction
* @param forceGroup the force group in which the interaction should be calculated
*/
void addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const std::vector<std::vector<int> >& exclusionList, const std::string& kernel, int forceGroup);
/**
* Add a nonbonded interaction to be evaluated by the default interaction kernel.
*
* @param usesCutoff specifies whether a cutoff should be applied to this interaction
* @param usesPeriodic specifies whether periodic boundary conditions should be applied to this interaction
* @param usesExclusions specifies whether this interaction uses exclusions. If this is true, it must have identical exclusions to every other interaction.
* @param cutoffDistance the cutoff distance for this interaction (ignored if usesCutoff is false)
* @param exclusionList for each atom, specifies the list of other atoms whose interactions should be excluded
* @param kernel the code to evaluate the interaction
* @param forceGroup the force group in which the interaction should be calculated
* @param supportsPairList specifies whether this interaction can work with a neighbor list that uses a separate pair list
*/
void addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const std::vector<std::vector<int> >& exclusionList, const std::string& kernel, int forceGroup, bool supportsPairList);
/**
* Add a per-atom parameter that the default interaction kernel may depend on.
*/
void addParameter(ComputeParameterInfo parameter);
/**
* Add a per-atom parameter that the default interaction kernel may depend on.
*
* @deprecated Use the version that takes a ComputeParameterInfo instead.
*/
void addParameter(const ParameterInfo& parameter);
/**
* Add an array (other than a per-atom parameter) that should be passed as an argument to the default interaction kernel.
*/
void addArgument(ComputeParameterInfo parameter);
/**
* Add an array (other than a per-atom parameter) that should be passed as an argument to the default interaction kernel.
*
* @deprecated Use the version that takes a ComputeParameterInfo instead.
*/
void addArgument(const ParameterInfo& parameter);
/**
* Register that the interaction kernel will be computing the derivative of the potential energy
* with respect to a parameter.
*
* @param param the name of the parameter
* @return the variable that will be used to accumulate the derivative. Any code you pass to addInteraction() should
* add its contributions to this variable.
*/
std::string addEnergyParameterDerivative(const std::string& param);
/**
* Specify the list of exclusions that an interaction outside the default kernel will depend on.
*
* @param exclusionList for each atom, specifies the list of other atoms whose interactions should be excluded
*/
void requestExclusions(const std::vector<std::vector<int> >& exclusionList);
/**
* Initialize this object in preparation for a simulation.
*/
void initialize(const System& system);
/**
* Get the number of force buffers required for nonbonded forces.
*/
int getNumForceBuffers() const {
return 0;
}
/**
* Get the number of energy buffers required for nonbonded forces.
*/
int getNumEnergyBuffers() {
return numForceThreadBlocks*forceThreadBlockSize;
}
/**
* Get whether a cutoff is being used.
*/
bool getUseCutoff() {
return useCutoff;
}
/**
* Get whether periodic boundary conditions are being used.
*/
bool getUsePeriodic() {
return usePeriodic;
}
/**
* Get the number of work groups used for computing nonbonded forces.
*/
int getNumForceThreadBlocks() {
return numForceThreadBlocks;
}
/**
* Get the size of each work group used for computing nonbonded forces.
*/
int getForceThreadBlockSize() {
return forceThreadBlockSize;
}
/**
* Get the maximum cutoff distance used by any force group.
*/
double getMaxCutoffDistance();
/**
* Given a nonbonded cutoff, get the padded cutoff distance used in computing
* the neighbor list.
*/
double padCutoff(double cutoff);
/**
* Prepare to compute interactions. This updates the neighbor list.
*/
void prepareInteractions(int forceGroups);
/**
* Compute the nonbonded interactions.
*
* @param forceGroups the flags specifying which force groups to include
* @param includeForces whether to compute forces
* @param includeEnergy whether to compute the potential energy
*/
void computeInteractions(int forceGroups, bool includeForces, bool includeEnergy);
/**
* Check to see if the neighbor list arrays are large enough, and make them bigger if necessary.
*
* @return true if the neighbor list needed to be enlarged.
*/
bool updateNeighborListSize();
/**
* Get the array containing the center of each atom block.
*/
HipArray& getBlockCenters() {
return blockCenter;
}
/**
* Get the array containing the dimensions of each atom block.
*/
HipArray& getBlockBoundingBoxes() {
return blockBoundingBox;
}
/**
* Get the array whose first element contains the number of tiles with interactions.
*/
HipArray& getInteractionCount() {
return interactionCount;
}
/**
* Get the array containing tiles with interactions.
*/
HipArray& getInteractingTiles() {
return interactingTiles;
}
/**
* Get the array containing the atoms in each tile with interactions.
*/
HipArray& getInteractingAtoms() {
return interactingAtoms;
}
/**
* Get the array containing single pairs in the neighbor list.
*/
HipArray& getSinglePairs() {
return singlePairs;
}
/**
* Get the array containing exclusion flags.
*/
HipArray& getExclusions() {
return exclusions;
}
/**
* Get the array containing tiles with exclusions.
*/
HipArray& getExclusionTiles() {
return exclusionTiles;
}
/**
* Get the array containing the index into the exclusion array for each tile.
*/
HipArray& getExclusionIndices() {
return exclusionIndices;
}
/**
* Get the array listing where the exclusion data starts for each row.
*/
HipArray& getExclusionRowIndices() {
return exclusionRowIndices;
}
/**
* Get the array containing a flag for whether the neighbor list was rebuilt
* on the most recent call to prepareInteractions().
*/
HipArray& getRebuildNeighborList() {
return rebuildNeighborList;
}
/**
* Get the index of the first tile this context is responsible for processing.
*/
int getStartTileIndex() const {
return startTileIndex;
}
/**
* Get the total number of tiles this context is responsible for processing.
*/
int getNumTiles() const {
return numTiles;
}
/**
* Set whether to add padding to the cutoff distance when building the neighbor list.
* This increases the size of the neighbor list (and thus the cost of computing interactions),
* but also means we don't need to rebuild it every time step. The default value is true,
* since usually this improves performance. For very expensive interactions, however,
* it may be better to set this to false.
*/
void setUsePadding(bool padding);
/**
* Set the range of atom blocks and tiles that should be processed by this context.
*/
void setAtomBlockRange(double startFraction, double endFraction);
/**
* Create a Kernel for evaluating a nonbonded interaction. Cutoffs and periodic boundary conditions
* are assumed to be the same as those for the default interaction Kernel, since this kernel will use
* the same neighbor list.
*
* @param source the source code for evaluating the force and energy
* @param params the per-atom parameters this kernel may depend on
* @param arguments arrays (other than per-atom parameters) that should be passed as arguments to the kernel
* @param useExclusions specifies whether exclusions are applied to this interaction
* @param isSymmetric specifies whether the interaction is symmetric
* @param groups the set of force groups this kernel is for
* @param includeForces whether this kernel should compute forces
* @param includeEnergy whether this kernel should compute potential energy
*/
hipFunction_t createInteractionKernel(const std::string& source, std::vector<ParameterInfo>& params, std::vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups, bool includeForces, bool includeEnergy);
/**
* Create the set of kernels that will be needed for a particular combination of force groups.
*
* @param groups the set of force groups
*/
void createKernelsForGroups(int groups);
/**
* Set the source code for the main kernel. This defaults to the content of nonbonded.hip. It only needs to be
* changed in very unusual circumstances.
*/
void setKernelSource(const std::string& source);
private:
class KernelSet;
class BlockSortTrait;
HipContext& context;
std::map<int, KernelSet> groupKernels;
HipArray exclusionTiles;
HipArray exclusions;
HipArray exclusionIndices;
HipArray exclusionRowIndices;
HipArray interactingTiles;
HipArray interactingAtoms;
HipArray interactionCount;
HipArray singlePairs;
HipArray singlePairCount;
HipArray blockCenter;
HipArray blockBoundingBox;
HipArray sortedBlocks;
HipArray sortedBlockCenter;
HipArray sortedBlockBoundingBox;
HipArray oldPositions;
HipArray rebuildNeighborList;
HipSort* blockSorter;
hipEvent_t downloadCountEvent;
int* pinnedCountBuffer;
std::vector<void*> forceArgs, findBlockBoundsArgs, sortBoxDataArgs, findInteractingBlocksArgs;
std::vector<std::vector<int> > atomExclusions;
std::vector<ParameterInfo> parameters;
std::vector<ParameterInfo> arguments;
std::vector<std::string> energyParameterDerivatives;
std::map<int, double> groupCutoff;
std::map<int, std::string> groupKernelSource;
double lastCutoff;
bool useCutoff, usePeriodic, anyExclusions, usePadding, forceRebuildNeighborList, canUsePairList;
int startTileIndex, startBlockIndex, numBlocks, maxTiles, maxSinglePairs, maxExclusions, numForceThreadBlocks, forceThreadBlockSize, numAtoms, groupFlags;
long long numTiles;
std::string kernelSource;
};
/**
* This class stores the kernels to execute for a set of force groups.
*/
class HipNonbondedUtilities::KernelSet {
public:
bool hasForces;
double cutoffDistance;
std::string source;
hipFunction_t forceKernel, energyKernel, forceEnergyKernel;
hipFunction_t findBlockBoundsKernel;
hipFunction_t sortBoxDataKernel;
hipFunction_t findInteractingBlocksKernel;
hipFunction_t findInteractionsWithinBlocksKernel;
};
/**
* This class stores information about a per-atom parameter that may be used in a nonbonded kernel.
*/
class HipNonbondedUtilities::ParameterInfo {
public:
/**
* Create a ParameterInfo object.
*
* @param name the name of the parameter
* @param type the data type of the parameter's components
* @param numComponents the number of components in the parameter
* @param size the size of the parameter in bytes
* @param memory the memory containing the parameter values
* @param constant whether the memory should be marked as constant
*/
ParameterInfo(const std::string& name, const std::string& componentType, int numComponents, int size, hipDeviceptr_t memory, bool constant=true) :
name(name), componentType(componentType), numComponents(numComponents), size(size), memory(memory), constant(constant) {
if (numComponents == 1)
type = componentType;
else {
std::stringstream s;
s << componentType << numComponents;
type = s.str();
}
}
const std::string& getName() const {
return name;
}
const std::string& getComponentType() const {
return componentType;
}
const std::string& getType() const {
return type;
}
int getNumComponents() const {
return numComponents;
}
int getSize() const {
return size;
}
hipDeviceptr_t& getMemory() {
return memory;
}
bool isConstant() const {
return constant;
}
private:
std::string name;
std::string componentType;
std::string type;
int size, numComponents;
hipDeviceptr_t memory;
bool constant;
};
} // namespace OpenMM
#endif /*OPENMM_HIPNONBONDEDUTILITIES_H_*/
platforms/hip/include/HipParallelKernels.h 0 → 100644
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platforms/hip/include/HipParameterSet.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPPARAMETERSET_H_
#define OPENMM_HIPPARAMETERSET_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) 2009-2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipContext.h"
#include "HipNonbondedUtilities.h"
#include "openmm/common/ComputeParameterSet.h"
namespace OpenMM {
class HipNonbondedUtilities;
/**
* This class exists for backward compatibility. For most purposes you can use
* ComputeParameterSet directly instead.
*/
class OPENMM_EXPORT_COMMON HipParameterSet : public ComputeParameterSet {
public:
/**
* Create an HipParameterSet.
*
* @param context the context for which to create the parameter set
* @param numParameters the number of parameters for each object
* @param numObjects the number of objects to store parameter values for
* @param name the name of the parameter set
* @param bufferPerParameter if true, a separate buffer is created for each parameter. If false,
* multiple parameters may be combined into a single buffer.
* @param useDoublePrecision whether values should be stored as single or double precision
*/
HipParameterSet(HipContext& context, int numParameters, int numObjects, const std::string& name, bool bufferPerParameter=false, bool useDoublePrecision=false);
/**
* Get a set of HipNonbondedUtilities::ParameterInfo objects which describe the Buffers
* containing the data.
*/
std::vector<HipNonbondedUtilities::ParameterInfo>& getBuffers() {
return buffers;
}
private:
std::vector<HipNonbondedUtilities::ParameterInfo> buffers;
};
} // namespace OpenMM
#endif /*OPENMM_HIPPARAMETERSET_H_*/
platforms/hip/include/HipPlatform.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPPLATFORM_H_
#define OPENMM_HIPPLATFORM_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) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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/Platform.h"
#include "openmm/System.h"
#include "openmm/internal/ThreadPool.h"
#include "openmm/common/windowsExportCommon.h"
namespace OpenMM {
class HipContext;
/**
* This Platform subclass uses HIP implementations of the OpenMM kernels.
*/
class OPENMM_EXPORT_COMMON HipPlatform : public Platform {
public:
class PlatformData;
HipPlatform();
const std::string& getName() const {
static const std::string name = "HIP";
return name;
}
double getSpeed() const;
bool supportsDoublePrecision() const;
const std::string& getPropertyValue(const Context& context, const std::string& property) const;
void setPropertyValue(Context& context, const std::string& property, const std::string& value) const;
void contextCreated(ContextImpl& context, const std::map<std::string, std::string>& properties) const;
void linkedContextCreated(ContextImpl& context, ContextImpl& originalContext) const;
void contextDestroyed(ContextImpl& context) const;
/**
* This is the name of the parameter for selecting which HIP device or devices to use.
*/
static const std::string& HipDeviceIndex() {
static const std::string key = "DeviceIndex";
return key;
}
/**
* This is the name of the parameter that reports the HIP device or devices being used.
*/
static const std::string& HipDeviceName() {
static const std::string key = "DeviceName";
return key;
}
/**
* This is the name of the parameter for selecting whether HIP should sync or spin loop while waiting for results.
*/
static const std::string& HipUseBlockingSync() {
static const std::string key = "UseBlockingSync";
return key;
}
/**
* This is the name of the parameter for selecting what numerical precision to use.
*/
static const std::string& HipPrecision() {
static const std::string key = "Precision";
return key;
}
/**
* This is the name of the parameter for selecting whether to use the CPU based PME calculation.
*/
static const std::string& HipUseCpuPme() {
static const std::string key = "UseCpuPme";
return key;
}
/**
* This is the name of the parameter for specifying the path to the HIP compiler.
*/
static const std::string& HipCompiler() {
static const std::string key = "HipCompiler";
return key;
}
/**
* This is the name of the parameter for specifying the host compiler for the HIP compiler to use.
*/
static const std::string& HipHostCompiler() {
static const std::string key = "HipHostCompiler";
return key;
}
/**
* This is the name of the parameter for specifying the path to the directory for creating temporary files.
*/
static const std::string& HipTempDirectory() {
static const std::string key = "TempDirectory";
return key;
}
/**
* This is the name of the parameter for selecting whether to disable use of a separate stream for PME.
*/
static const std::string& HipDisablePmeStream() {
static const std::string key = "DisablePmeStream";
return key;
}
/**
* This is the name of the parameter for requesting that force computations be fully deterministic.
*/
static const std::string& HipDeterministicForces() {
static const std::string key = "DeterministicForces";
return key;
}
};
class OPENMM_EXPORT_COMMON HipPlatform::PlatformData {
public:
PlatformData(ContextImpl* context, const System& system, const std::string& deviceIndexProperty, const std::string& blockingProperty, const std::string& precisionProperty,
const std::string& cpuPmeProperty, const std::string& compilerProperty, const std::string& tempProperty, const std::string& hostCompilerProperty,
const std::string& pmeStreamProperty, const std::string& deterministicForcesProperty, int numThreads, ContextImpl* originalContext);
~PlatformData();
void initializeContexts(const System& system);
void syncContexts();
ContextImpl* context;
std::vector<HipContext*> contexts;
std::vector<double> contextEnergy;
bool hasInitializedContexts, removeCM, peerAccessSupported, useCpuPme, disablePmeStream, deterministicForces;
int cmMotionFrequency;
int stepCount, computeForceCount;
double time;
std::map<std::string, std::string> propertyValues;
ThreadPool threads;
};
} // namespace OpenMM
#endif /*OPENMM_HIPPLATFORM_H_*/
platforms/hip/include/HipProgram.h 0 → 100644
View file @ 89d2ff0e
#ifndef OPENMM_HIPPROGRAM_H_
#define OPENMM_HIPPROGRAM_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) 2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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/common/ComputeProgram.h"
#include "HipContext.h"
namespace OpenMM {
/**
* This is the HIP implementation of the ComputeProgramImpl interface.
*/
class HipProgram : public ComputeProgramImpl {
public:
/**
* Create a new HipProgram.
*
* @param context the context this kernel belongs to
* @param module the compiled module
*/
HipProgram(HipContext& context, hipModule_t module);
/**
* Create a ComputeKernel for one of the kernels in this program.
*
* @param name the name of the kernel to get
*/
ComputeKernel createKernel(const std::string& name);
private:
HipContext& context;
hipModule_t module;
};
} // namespace OpenMM
#endif /*OPENMM_HIPPROGRAM_H_*/
platforms/hip/include/HipSort.h 0 → 100644
View file @ 89d2ff0e
#ifndef __OPENMM_HIPSORT_H__
#define __OPENMM_HIPSORT_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) 2010-2018 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipArray.h"
#include "openmm/common/windowsExportCommon.h"
#include "HipContext.h"
namespace OpenMM {
/**
* This class sorts arrays of values. It supports any type of values, not just scalars,
* so long as an appropriate sorting key can be defined by which to sort them.
*
* The sorting behavior is specified by a "trait" class that defines the type of data to
* sort and the key for sorting it. Here is an example of a trait class for
* sorting floats:
*
* class FloatTrait : public HipSort::SortTrait {
* int getDataSize() const {return 4;}
* int getKeySize() const {return 4;}
* const char* getDataType() const {return "float";}
* const char* getKeyType() const {return "float";}
* const char* getMinKey() const {return "-3.40282e+38f";}
* const char* getMaxKey() const {return "3.40282e+38f";}
* const char* getMaxValue() const {return "3.40282e+38f";}
* const char* getSortKey() const {return "value";}
* };
*
* The algorithm used is a bucket sort, followed by a bitonic sort within each bucket
* (in local memory when possible, in global memory otherwise). This is similar to
* the algorithm described in
*
* Shifu Chen, Jing Qin, Yongming Xie, Junping Zhao, and Pheng-Ann Heng. "An Efficient
* Sorting Algorithm with CUDA" Journal of the Chinese Institute of Engineers, 32(7),
* pp. 915-921 (2009)
*
* but with many modifications and simplifications. In particular, this algorithm
* involves much less communication between host and device, which is critical to get
* good performance with the array sizes we typically work with (10,000 to 100,000
* elements).
*/
class OPENMM_EXPORT_COMMON HipSort {
public:
class SortTrait;
/**
* Create a HipSort object for sorting data of a particular type.
*
* @param context the context in which to perform calculations
* @param trait a SortTrait defining the type of data to sort. It should have been allocated
* on the heap with the "new" operator. This object takes over ownership of it,
* and deletes it when the HipSort is deleted.
* @param length the length of the arrays this object will be used to sort
*/
HipSort(HipContext& context, SortTrait* trait, unsigned int length);
~HipSort();
/**
* Sort an array.
*/
void sort(HipArray& data);
private:
HipContext& context;
SortTrait* trait;
HipArray dataRange;
HipArray bucketOfElement;
HipArray offsetInBucket;
HipArray bucketOffset;
HipArray buckets;
hipFunction_t shortListKernel, shortList2Kernel, computeRangeKernel, assignElementsKernel, computeBucketPositionsKernel, copyToBucketsKernel, sortBucketsKernel;
unsigned int dataLength, rangeKernelSize, positionsKernelSize, sortKernelSize;
bool isShortList;
};
/**
* A subclass of SortTrait defines the type of value to sort, and the key for sorting them.
*/
class HipSort::SortTrait {
public:
virtual ~SortTrait() {
}
/**
* Get the size of each data value in bytes.
*/
virtual int getDataSize() const = 0;
/**
* Get the size of each key value in bytes.
*/
virtual int getKeySize() const = 0;
/**
* Get the data type of the values to sort.
*/
virtual const char* getDataType() const = 0;
/**
* Get the data type of the sorting key.
*/
virtual const char* getKeyType() const = 0;
/**
* Get the minimum value a key can take.
*/
virtual const char* getMinKey() const = 0;
/**
* Get the maximum value a key can take.
*/
virtual const char* getMaxKey() const = 0;
/**
* Get a value whose key is guaranteed to equal getMaxKey().
*/
virtual const char* getMaxValue() const = 0;
/**
* Get the HIP code to select the key from the data value.
*/
virtual const char* getSortKey() const = 0;
};
} // namespace OpenMM
#endif // __OPENMM_HIPSORT_H__
platforms/hip/sharedTarget/CMakeLists.txt 0 → 100644
View file @ 89d2ff0e
#
# Include HIP related files.
#
# add include / link dirs
INCLUDE_DIRECTORIES(${MMHIP_INCLUDE_DIRS})
LINK_DIRECTORIES(${MMHIP_LINK_DIRS})
FILE(GLOB HIP_KERNELS ${KERNEL_SOURCE_DIR}/kernels/*.hip)
ADD_CUSTOM_COMMAND(OUTPUT ${KERNELS_CPP} ${KERNELS_H}
COMMAND ${CMAKE_COMMAND}
ARGS -D KERNEL_SOURCE_DIR=${KERNEL_SOURCE_DIR} -D KERNELS_CPP=${KERNELS_CPP} -D KERNELS_H=${KERNELS_H} -D KERNEL_SOURCE_CLASS=${KERNEL_SOURCE_CLASS} -D KERNEL_FILE_EXTENSION=hip -P ${CMAKE_SOURCE_DIR}/cmake_modules/EncodeKernelFiles.cmake
DEPENDS ${HIP_KERNELS}
)
# set HIP compile flags
SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "${HIPCXXFLAGS}")
SET_SOURCE_FILES_PROPERTIES(${KERNELS_CPP} ${KERNELS_H} ${COMMON_KERNELS_CPP} PROPERTIES GENERATED TRUE)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
ADD_DEPENDENCIES(${SHARED_TARGET} CommonKernels)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} PUBLIC ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB} ${MMHIP_LIBS})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_COMMON_BUILDING_SHARED_LIBRARY")
IF (APPLE)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework HIP")
ELSE (APPLE)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
ENDIF (APPLE)
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
platforms/hip/src/HipArray.cpp 0 → 100644
View file @ 89d2ff0e
/* -------------------------------------------------------------------------- *
* 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) 2012-2019 Stanford University and the Authors. *
* Portions copyright (c) 2020 Advanced Micro Devices, Inc. *
* Authors: Peter Eastman, Nicholas Curtis *
* 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 "HipArray.h"
#include "HipContext.h"
#include <iostream>
#include <sstream>
#include <vector>
using namespace OpenMM;
HipArray::HipArray() : pointer(0), ownsMemory(false) {
}
HipArray::HipArray(HipContext& context, int size, int elementSize, const std::string& name) : pointer(0) {
initialize(context, size, elementSize, name);
}
HipArray::~HipArray() {
if (pointer != 0 && ownsMemory && context->getContextIsValid()) {
context->setAsCurrent();
hipError_t result = hipFree(pointer);
if (result != hipSuccess) {
std::stringstream str;
str<<"Error deleting array "<<name<<": "<<HipContext::getErrorString(result)<<" ("<<result<<")";
throw OpenMMException(str.str());
}
}
}
void HipArray::initialize(ComputeContext& context, int size, int elementSize, const std::string& name) {
if (this->pointer != 0)
throw OpenMMException("HipArray has already been initialized");
this->context = &dynamic_cast<HipContext&>(context);
this->size = size;
this->elementSize = elementSize;
this->name = name;
ownsMemory = true;
hipError_t result = hipMalloc(&pointer, size*elementSize);
if (result != hipSuccess) {
std::stringstream str;
str<<"Error creating array "<<name<<": "<<HipContext::getErrorString(result)<<" ("<<result<<")";
throw OpenMMException(str.str());
}
}
void HipArray::resize(int size) {
if (pointer == 0)
throw OpenMMException("HipArray has not been initialized");
if (!ownsMemory)
throw OpenMMException("Cannot resize an array that does not own its storage");
hipError_t result = hipFree(pointer);
if (result != hipSuccess) {
std::stringstream str;
str<<"Error deleting array "<<name<<": "<<HipContext::getErrorString(result)<<" ("<<result<<")";
throw OpenMMException(str.str());
}
pointer = 0;
initialize(*context, size, elementSize, name);
}
ComputeContext& HipArray::getContext() {
return *context;
}
void HipArray::uploadSubArray(const void* data, int offset, int elements, bool blocking) {
if (pointer == 0)
throw OpenMMException("HipArray has not been initialized");
if (offset < 0 || offset+elements > getSize())
throw OpenMMException("uploadSubArray: data exceeds range of array");
hipError_t result;
if (blocking)
result = hipMemcpyHtoD(reinterpret_cast<char*>(pointer)+offset*elementSize, const_cast<void*>(data), elements*elementSize);
else
result = hipMemcpyHtoDAsync(reinterpret_cast<char*>(pointer)+offset*elementSize, const_cast<void*>(data), elements*elementSize, context->getCurrentStream());
if (result != hipSuccess) {
std::stringstream str;
str<<"Error uploading array "<<name<<": "<<HipContext::getErrorString(result)<<" ("<<result<<")";
throw OpenMMException(str.str());
}
}
void HipArray::download(void* data, bool blocking) const {
if (pointer == 0)
throw OpenMMException("HipArray has not been initialized");
hipError_t result;
if (blocking)
result = hipMemcpyDtoH(data, pointer, size*elementSize);
else
result = hipMemcpyDtoHAsync(data, pointer, size*elementSize, context->getCurrentStream());
if (result != hipSuccess) {
std::stringstream str;
str<<"Error downloading array "<<name<<": "<<HipContext::getErrorString(result)<<" ("<<result<<")";
throw OpenMMException(str.str());
}
}
void HipArray::copyTo(ArrayInterface& dest) const {
if (pointer == 0)
throw OpenMMException("HipArray has not been initialized");
if (dest.getSize() != size || dest.getElementSize() != elementSize)
throw OpenMMException("Error copying array "+name+" to "+dest.getName()+": The destination array does not match the size of the array");
HipArray& cuDest = context->unwrap(dest);
hipError_t result = hipMemcpyDtoDAsync(cuDest.getDevicePointer(), pointer, size*elementSize, context->getCurrentStream());
if (result != hipSuccess) {
std::stringstream str;
str<<"Error copying array "<<name<<" to "<<dest.getName()<<": "<<HipContext::getErrorString(result)<<" ("<<result<<")";
throw OpenMMException(str.str());
}
}
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