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Commit 6ab42996 authored by Peter Eastman's avatar Peter Eastman
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Change suggested by Tony Tye to simplify debugging by including all... 

Change suggested by Tony Tye to simplify debugging by including all compilation options in the kernel source
parent c1f59f8e
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Showing with 562 additions and 560 deletions
platforms/opencl/src/OpenCLContext.cpp
View file @ 6ab42996
......@@ -91,12 +91,12 @@ OpenCLContext::OpenCLContext(int numParticles, int deviceIndex, OpenCLPlatform::
this->deviceIndex = deviceIndex;
if (device.getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>() < minThreadBlockSize)
throw OpenMMException("The specified OpenCL device is not compatible with OpenMM");
compilationOptions = "-DWORK_GROUP_SIZE="+OpenCLExpressionUtilities::intToString(ThreadBlockSize);
compilationDefines["WORK_GROUP_SIZE"] = OpenCLExpressionUtilities::intToString(ThreadBlockSize);
defaultOptimizationOptions = "-cl-fast-relaxed-math";
supports64BitGlobalAtomics = (device.getInfo<CL_DEVICE_EXTENSIONS>().find("cl_khr_int64_base_atomics") != string::npos);
string vendor = device.getInfo<CL_DEVICE_VENDOR>();
if (vendor.size() >= 6 && vendor.substr(0, 6) == "NVIDIA") {
compilationOptions += " -DWARPS_ARE_ATOMIC";
compilationDefines["WARPS_ARE_ATOMIC"] = "";
simdWidth = 32;
if (device.getInfo<CL_DEVICE_EXTENSIONS>().find("cl_nv_device_attribute_query") != string::npos) {
// Compute level 1.2 and later Nvidia GPUs support 64 bit atomics, even though they don't list the
......@@ -111,7 +111,7 @@ OpenCLContext::OpenCLContext(int numParticles, int deviceIndex, OpenCLPlatform::
}
else if (vendor.size() >= 28 && vendor.substr(0, 28) == "Advanced Micro Devices, Inc.") {
// AMD APP SDK 2.4 has a performance problem with atomics. Enable the work around.
compilationOptions += " -DAMD_ATOMIC_WORK_AROUND";
compilationDefines["AMD_ATOMIC_WORK_AROUND"] = "";
// AMD has both 32 and 64 width SIMDs. To determine need to create a kernel to query.
// For now default to 1 which will use the default kernels.
simdWidth = 1;
......@@ -119,7 +119,7 @@ OpenCLContext::OpenCLContext(int numParticles, int deviceIndex, OpenCLPlatform::
else
simdWidth = 1;
if (supports64BitGlobalAtomics)
compilationOptions += " -DSUPPORTS_64_BIT_ATOMICS";
compilationDefines["SUPPORTS_64_BIT_ATOMICS"] = "";
queue = cl::CommandQueue(context, device);
numAtoms = numParticles;
paddedNumAtoms = TileSize*((numParticles+TileSize-1)/TileSize);
......@@ -169,26 +169,11 @@ OpenCLContext::OpenCLContext(int numParticles, int deviceIndex, OpenCLPlatform::
maxExpError = max(maxExpError, fabs(exp(v)-values[i].s4)/values[i].s4);
maxLogError = max(maxLogError, fabs(log(v)-values[i].s5)/values[i].s5);
}
if (maxSqrtError < 1e-6)
compilationOptions += " -DSQRT=native_sqrt";
else
compilationOptions += " -DSQRT=sqrt";
if (maxRsqrtError < 1e-6)
compilationOptions += " -DRSQRT=native_rsqrt";
else
compilationOptions += " -DRSQRT=rsqrt";
if (maxRecipError < 1e-6)
compilationOptions += " -DRECIP=native_recip";
else
compilationOptions += " -DRECIP=1.0f/";
if (maxExpError < 1e-6)
compilationOptions += " -DEXP=native_exp";
else
compilationOptions += " -DEXP=exp";
if (maxLogError < 1e-6)
compilationOptions += " -DLOG=native_log";
else
compilationOptions += " -DLOG=log";
compilationDefines["SQRT"] = (maxSqrtError < 1e-6) ? "native_sqrt" : "sqrt";
compilationDefines["RSQRT"] = (maxRsqrtError < 1e-6) ? "native_rsqrt" : "rsqrt";
compilationDefines["RECIP"] = (maxRecipError < 1e-6) ? "native_recip" : "1.0f/";
compilationDefines["EXP"] = (maxExpError < 1e-6) ? "native_exp" : "exp";
compilationDefines["LOG"] = (maxLogError < 1e-6) ? "native_log" : "log";
// Create the work thread used for parallelization when running on multiple devices.
......@@ -280,18 +265,34 @@ cl::Program OpenCLContext::createProgram(const string source, const char* optimi
}
cl::Program OpenCLContext::createProgram(const string source, const map<string, string>& defines, const char* optimizationFlags) {
cl::Program::Sources sources(1, make_pair(source.c_str(), source.size()));
string options = (optimizationFlags == NULL ? defaultOptimizationOptions : optimizationFlags);
stringstream src;
if (!options.empty())
src << "// Compilation Options: " << options << endl << endl;
for (map<string, string>::const_iterator iter = compilationDefines.begin(); iter != compilationDefines.end(); ++iter) {
src << "#define " << iter->first;
if (!iter->second.empty())
src << " " << iter->second;
src << endl;
}
if (!compilationDefines.empty())
src << endl;
for (map<string, string>::const_iterator iter = defines.begin(); iter != defines.end(); ++iter) {
src << "#define " << iter->first;
if (!iter->second.empty())
src << " " << iter->second;
src << endl;
}
if (!defines.empty())
src << endl;
src << source << endl;
// Get length before using c_str() to avoid length() call invalidating the c_str() value.
string src_string = src.str();
::size_t src_length = src_string.length();
cl::Program::Sources sources(1, make_pair(src_string.c_str(), src_length));
cl::Program program(context, sources);
stringstream options;
options << compilationOptions;
if (optimizationFlags == NULL)
options << " " << defaultOptimizationOptions;
else
options << " " << optimizationFlags;
for (map<string, string>::const_iterator iter = defines.begin(); iter != defines.end(); ++iter)
options << " -D" << iter->first << "=" << iter->second;
try {
program.build(vector<cl::Device>(1, device), options.str().c_str());
program.build(vector<cl::Device>(1, device), options.c_str());
} catch (cl::Error err) {
throw OpenMMException("Error compiling kernel: "+program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device));
}
......
platforms/opencl/src/OpenCLContext.h
View file @ 6ab42996
#ifndef OPENMM_OPENCLCONTEXT_H_
#define OPENMM_OPENCLCONTEXT_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. *
* 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 <map>
#include <queue>
#include <string>
#include <pthread.h>
#define __CL_ENABLE_EXCEPTIONS
#ifdef _MSC_VER
// Prevent Windows from defining macros that interfere with other code.
#define NOMINMAX
#endif
#include <cl.hpp>
#include "openmm/internal/windowsExport.h"
#include "OpenCLPlatform.h"
namespace OpenMM {
template <class T>
class OpenCLArray;
class OpenCLForceInfo;
class OpenCLIntegrationUtilities;
class OpenCLNonbondedUtilities;
class System;
/**
* We can't use predefined vector types like cl_float4, since different OpenCL implementations currently define
* them in incompatible ways. Hopefully that will be fixed in the future. In the mean time, we define our own
* types to represent them on the host.
*/
struct mm_float2 {
cl_float x, y;
mm_float2() {
}
mm_float2(cl_float x, cl_float y) : x(x), y(y) {
}
};
struct mm_float4 {
cl_float x, y, z, w;
mm_float4() {
}
mm_float4(cl_float x, cl_float y, cl_float z, cl_float w) : x(x), y(y), z(z), w(w) {
}
};
struct mm_float8 {
cl_float s0, s1, s2, s3, s4, s5, s6, s7;
mm_float8() {
}
mm_float8(cl_float s0, cl_float s1, cl_float s2, cl_float s3, cl_float s4, cl_float s5, cl_float s6, cl_float s7) :
s0(s0), s1(s1), s2(s2), s3(s3), s4(s4), s5(s5), s6(s6), s7(s7) {
}
};
struct mm_float16 {
cl_float s0, s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15;
mm_float16() {
}
mm_float16(cl_float s0, cl_float s1, cl_float s2, cl_float s3, cl_float s4, cl_float s5, cl_float s6, cl_float s7,
cl_float s8, cl_float s9, cl_float s10, cl_float s11, cl_float s12, cl_float s13, cl_float s14, cl_float s15) :
s0(s0), s1(s1), s2(s2), s3(s3), s4(s4), s5(s5), s6(s6), s7(s7),
s8(s8), s9(s9), s10(s10), s11(s11), s12(s12), s13(s13), s14(s14), s15(15) {
}
};
struct mm_ushort2 {
cl_ushort x, y;
mm_ushort2() {
}
mm_ushort2(cl_ushort x, cl_ushort y) : x(x), y(y) {
}
};
struct mm_int2 {
cl_int x, y;
mm_int2() {
}
mm_int2(cl_int x, cl_int y) : x(x), y(y) {
}
};
struct mm_int4 {
cl_int x, y, z, w;
mm_int4() {
}
mm_int4(cl_int x, cl_int y, cl_int z, cl_int w) : x(x), y(y), z(z), w(w) {
}
};
struct mm_int8 {
cl_int s0, s1, s2, s3, s4, s5, s6, s7;
mm_int8() {
}
mm_int8(cl_int s0, cl_int s1, cl_int s2, cl_int s3, cl_int s4, cl_int s5, cl_int s6, cl_int s7) :
s0(s0), s1(s1), s2(s2), s3(s3), s4(s4), s5(s5), s6(s6), s7(s7) {
}
};
struct mm_int16 {
cl_int s0, s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15;
mm_int16() {
}
mm_int16(cl_int s0, cl_int s1, cl_int s2, cl_int s3, cl_int s4, cl_int s5, cl_int s6, cl_int s7,
cl_int s8, cl_int s9, cl_int s10, cl_int s11, cl_int s12, cl_int s13, cl_int s14, cl_int s15) :
s0(s0), s1(s1), s2(s2), s3(s3), s4(s4), s5(s5), s6(s6), s7(s7),
s8(s8), s9(s9), s10(s10), s11(s11), s12(s12), s13(s13), s14(s14), s15(15) {
}
};
/**
* This class contains the information associated with a Context by the OpenCL Platform. Each OpenCLContext is
* specific to a particular device, and manages data structures and kernels for that device. When running a simulation
* in parallel on multiple devices, there is a separate OpenCLContext for each one. The list of all contexts is
* stored in the OpenCLPlatform::PlatformData.
* <p>
* In addition, a worker thread is created for each OpenCLContext. This is used for parallel computations, so that
* blocking calls to one device will not block other devices. When only a single device is being used, the worker
* thread is not used and calculations are performed on the main application thread.
*/
class OPENMM_EXPORT OpenCLContext {
public:
class WorkTask;
class WorkThread;
static const int ThreadBlockSize;
static const int TileSize;
OpenCLContext(int numParticles, int deviceIndex, OpenCLPlatform::PlatformData& platformData);
~OpenCLContext();
/**
* This is called to initialize internal data structures after all Forces in the system
* have been initialized.
*/
void initialize(const System& system);
/**
* Add an OpenCLForce to this context.
*/
void addForce(OpenCLForceInfo* force);
/**
* Get the cl::Context associated with this object.
*/
cl::Context& getContext() {
return context;
}
/**
* Get the cl::Device associated with this object.
*/
cl::Device& getDevice() {
return device;
}
/**
* Get the index of the cl::Device associated with this object.
*/
int getDeviceIndex() {
return deviceIndex;
}
/**
* Get the PlatformData object this context is part of.
*/
OpenCLPlatform::PlatformData& getPlatformData() {
return platformData;
}
/**
* Get the index of this context in the list stored in the PlatformData.
*/
int getContextIndex() const {
return contextIndex;
}
/**
* Get the cl::CommandQueue associated with this object.
*/
cl::CommandQueue& getQueue() {
return queue;
}
/**
* Get the array which contains the position (the xyz components) and charge (the w component) of each atom.
*/
OpenCLArray<mm_float4>& getPosq() {
return *posq;
}
/**
* Get the array which contains the velocity (the xyz components) and inverse mass (the w component) of each atom.
*/
OpenCLArray<mm_float4>& getVelm() {
return *velm;
}
/**
* Get the array which contains the force on each atom.
*/
OpenCLArray<mm_float4>& getForce() {
return *force;
}
/**
* Get the array which contains the buffers in which forces are computed.
*/
OpenCLArray<mm_float4>& getForceBuffers() {
return *forceBuffers;
}
/**
* Get the array which contains the buffer in which energy is computed.
*/
OpenCLArray<cl_float>& getEnergyBuffer() {
return *energyBuffer;
}
/**
* Get the array which contains the index of each atom.
*/
OpenCLArray<cl_int>& getAtomIndex() {
return *atomIndex;
}
/**
* Get the number of cells by which the positions are offset.
*/
std::vector<mm_int4>& getPosCellOffsets() {
return posCellOffsets;
}
/**
* Load OpenCL source code from a file in the kernels directory.
*/
std::string loadSourceFromFile(const std::string& filename) const;
/**
* Load OpenCL source code from a file in the kernels directory.
*
* @param filename the file to load
* @param replacements a set of strings that should be replaced with new strings wherever they appear in the
*/
std::string loadSourceFromFile(const std::string& filename, const std::map<std::string, std::string>& replacements) const;
/**
* Replace all occurance of a list of substrings.
*
* @param input a string to process
* @param replacements a set of strings that should be replaced with new strings wherever they appear in the input string
* @return a new string produced by performing the replacements
*/
std::string replaceStrings(const std::string& input, const std::map<std::string, std::string>& replacements) const;
/**
* Create an OpenCL Program from source code.
*
* @param source the source code of the program
* @param optimizationFlags the optimization flags to pass to the OpenCL compiler. If this is
* omitted, a default set of options will be used
*/
cl::Program createProgram(const std::string source, const char* optimizationFlags = NULL);
/**
* Create an OpenCL Program from source code.
*
* @param source the source code of the program
* @param defines a set of preprocessor definitions (name, value) to define when compiling the program
* @param optimizationFlags the optimization flags to pass to the OpenCL compiler. If this is
* omitted, a default set of options will be used
*/
cl::Program createProgram(const std::string source, const std::map<std::string, std::string>& defines, const char* optimizationFlags = NULL);
/**
* Execute a kernel.
*
* @param kernel the kernel to execute
* @param workUnits the maximum number of work units that should be used
* @param blockSize the size of each thread block to use
*/
void executeKernel(cl::Kernel& kernel, int workUnits, int blockSize = -1);
/**
* Set all elements of an array to 0.
*/
void clearBuffer(OpenCLArray<float>& array);
/**
* Set all elements of an array to 0.
*/
void clearBuffer(OpenCLArray<mm_float4>& array);
/**
* Set all elements of an array to 0.
*
* @param memory the Memory to clear
* @param size the number of float elements in the buffer
*/
void clearBuffer(cl::Memory& memory, int size);
/**
* Register a buffer that should be automatically cleared (all elements set to 0) at the start of each force or energy computation.
*
* @param memory the Memory to clear
* @param size the number of float elements in the buffer
*/
void addAutoclearBuffer(cl::Memory& memory, int size);
/**
* Clear all buffers that have been registered with addAutoclearBuffer().
*/
void clearAutoclearBuffers();
/**
* Given a collection of buffers packed into an array, sum them and store
* the sum in the first buffer.
*
* @param array the array containing the buffers to reduce
* @param numBuffers the number of buffers packed into the array
*/
void reduceBuffer(OpenCLArray<mm_float4>& array, int numBuffers);
/**
* Get the current simulation time.
*/
double getTime() {
return time;
}
/**
* Set the current simulation time.
*/
void setTime(double t) {
time = t;
}
/**
* Get the number of integration steps that have been taken.
*/
int getStepCount() {
return stepCount;
}
/**
* Set the number of integration steps that have been taken.
*/
void setStepCount(int steps) {
stepCount = steps;
}
/**
* Get the number of times forces or energy has been computed.
*/
int getComputeForceCount() {
return computeForceCount;
}
/**
* Set the number of times forces or energy has been computed.
*/
void setComputeForceCount(int count) {
computeForceCount = count;
}
/**
* Get the number of atoms.
*/
int getNumAtoms() const {
return numAtoms;
}
/**
* Get the number of atoms, rounded up to a multiple of TileSize. This is the actual size of
* most arrays with one element per atom.
*/
int getPaddedNumAtoms() const {
return paddedNumAtoms;
}
/**
* Get the number of blocks of TileSize atoms.
*/
int getNumAtomBlocks() const {
return numAtomBlocks;
}
/**
* Get the standard number of thread blocks to use when executing kernels.
*/
int getNumThreadBlocks() const {
return numThreadBlocks;
}
/**
* Get the number of force buffers.
*/
int getNumForceBuffers() const {
return numForceBuffers;
}
/**
* Get the SIMD width of the device being used.
*/
int getSIMDWidth() const {
return simdWidth;
}
/**
* Get whether the device being used supports 64 bit atomic operations on global memory.
*/
bool getSupports64BitGlobalAtomics() {
return supports64BitGlobalAtomics;
}
/**
* Get the size of the periodic box.
*/
mm_float4 getPeriodicBoxSize() const {
return periodicBoxSize;
}
/**
* Set the size of the periodic box.
*/
void setPeriodicBoxSize(double xsize, double ysize, double zsize) {
periodicBoxSize = mm_float4((float) xsize, (float) ysize, (float) zsize, 0);
invPeriodicBoxSize = mm_float4((float) (1.0/xsize), (float) (1.0/ysize), (float) (1.0/zsize), 0);
}
/**
* Get the inverse of the size of the periodic box.
*/
mm_float4 getInvPeriodicBoxSize() const {
return invPeriodicBoxSize;
}
/**
* Get the OpenCLIntegrationUtilities for this context.
*/
OpenCLIntegrationUtilities& getIntegrationUtilities() {
return *integration;
}
/**
* Get the OpenCLNonbondedUtilities for this context.
*/
OpenCLNonbondedUtilities& getNonbondedUtilities() {
return *nonbonded;
}
/**
* Get the thread used by this context for executing parallel computations.
*/
WorkThread& getWorkThread() {
return *thread;
}
/**
* Reorder the internal arrays of atoms to try to keep spatially contiguous atoms close
* together in the arrays.
*/
void reorderAtoms();
private:
struct Molecule;
struct MoleculeGroup;
void findMoleculeGroups(const System& system);
static void tagAtomsInMolecule(int atom, int molecule, std::vector<int>& atomMolecule, std::vector<std::vector<int> >& atomBonds);
double time;
OpenCLPlatform::PlatformData& platformData;
int deviceIndex;
int contextIndex;
int stepCount;
int computeForceCount;
int numAtoms;
int paddedNumAtoms;
int numAtomBlocks;
int numThreadBlocks;
int numForceBuffers;
int simdWidth;
bool supports64BitGlobalAtomics;
mm_float4 periodicBoxSize;
mm_float4 invPeriodicBoxSize;
std::string compilationOptions, defaultOptimizationOptions;
cl::Context context;
cl::Device device;
cl::CommandQueue queue;
cl::Program utilities;
cl::Kernel clearBufferKernel;
cl::Kernel clearTwoBuffersKernel;
cl::Kernel clearThreeBuffersKernel;
cl::Kernel clearFourBuffersKernel;
cl::Kernel reduceFloat4Kernel;
std::vector<OpenCLForceInfo*> forces;
std::vector<MoleculeGroup> moleculeGroups;
std::vector<mm_int4> posCellOffsets;
OpenCLArray<mm_float4>* posq;
OpenCLArray<mm_float4>* velm;
OpenCLArray<mm_float4>* force;
OpenCLArray<mm_float4>* forceBuffers;
OpenCLArray<cl_float>* energyBuffer;
OpenCLArray<cl_int>* atomIndex;
std::vector<cl::Memory*> autoclearBuffers;
std::vector<int> autoclearBufferSizes;
OpenCLIntegrationUtilities* integration;
OpenCLNonbondedUtilities* nonbonded;
WorkThread* thread;
};
struct OpenCLContext::MoleculeGroup {
std::vector<int> atoms;
std::vector<int> instances;
};
/**
* This abstract class defines a task to be executed on the worker thread.
*/
class OpenCLContext::WorkTask {
public:
virtual void execute() = 0;
};
class OpenCLContext::WorkThread {
public:
struct ThreadData;
WorkThread();
~WorkThread();
/**
* Request that a task be executed on the worker thread. The argument should have been allocated on the
* heap with the "new" operator. After its execute() method finishes, the object will be deleted automatically.
*/
void addTask(OpenCLContext::WorkTask* task);
/**
* Get whether the worker thread is idle, waiting for a task to be added.
*/
bool isWaiting();
/**
* Get whether the worker thread has exited.
*/
bool isFinished();
/**
* Block until all tasks have finished executing and the worker thread is idle.
*/
void flush();
private:
std::queue<OpenCLContext::WorkTask*> tasks;
bool waiting, finished;
pthread_mutex_t queueLock;
pthread_cond_t waitForTaskCondition, queueEmptyCondition;
pthread_t thread;
};
} // namespace OpenMM
#endif /*OPENMM_OPENCLCONTEXT_H_*/
#ifndef OPENMM_OPENCLCONTEXT_H_
#define OPENMM_OPENCLCONTEXT_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. *
* 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 <map>
#include <queue>
#include <string>
#include <pthread.h>
#define __CL_ENABLE_EXCEPTIONS
#ifdef _MSC_VER
// Prevent Windows from defining macros that interfere with other code.
#define NOMINMAX
#endif
#include <cl.hpp>
#include "openmm/internal/windowsExport.h"
#include "OpenCLPlatform.h"
namespace OpenMM {
template <class T>
class OpenCLArray;
class OpenCLForceInfo;
class OpenCLIntegrationUtilities;
class OpenCLNonbondedUtilities;
class System;
/**
* We can't use predefined vector types like cl_float4, since different OpenCL implementations currently define
* them in incompatible ways. Hopefully that will be fixed in the future. In the mean time, we define our own
* types to represent them on the host.
*/
struct mm_float2 {
cl_float x, y;
mm_float2() {
}
mm_float2(cl_float x, cl_float y) : x(x), y(y) {
}
};
struct mm_float4 {
cl_float x, y, z, w;
mm_float4() {
}
mm_float4(cl_float x, cl_float y, cl_float z, cl_float w) : x(x), y(y), z(z), w(w) {
}
};
struct mm_float8 {
cl_float s0, s1, s2, s3, s4, s5, s6, s7;
mm_float8() {
}
mm_float8(cl_float s0, cl_float s1, cl_float s2, cl_float s3, cl_float s4, cl_float s5, cl_float s6, cl_float s7) :
s0(s0), s1(s1), s2(s2), s3(s3), s4(s4), s5(s5), s6(s6), s7(s7) {
}
};
struct mm_float16 {
cl_float s0, s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15;
mm_float16() {
}
mm_float16(cl_float s0, cl_float s1, cl_float s2, cl_float s3, cl_float s4, cl_float s5, cl_float s6, cl_float s7,
cl_float s8, cl_float s9, cl_float s10, cl_float s11, cl_float s12, cl_float s13, cl_float s14, cl_float s15) :
s0(s0), s1(s1), s2(s2), s3(s3), s4(s4), s5(s5), s6(s6), s7(s7),
s8(s8), s9(s9), s10(s10), s11(s11), s12(s12), s13(s13), s14(s14), s15(15) {
}
};
struct mm_ushort2 {
cl_ushort x, y;
mm_ushort2() {
}
mm_ushort2(cl_ushort x, cl_ushort y) : x(x), y(y) {
}
};
struct mm_int2 {
cl_int x, y;
mm_int2() {
}
mm_int2(cl_int x, cl_int y) : x(x), y(y) {
}
};
struct mm_int4 {
cl_int x, y, z, w;
mm_int4() {
}
mm_int4(cl_int x, cl_int y, cl_int z, cl_int w) : x(x), y(y), z(z), w(w) {
}
};
struct mm_int8 {
cl_int s0, s1, s2, s3, s4, s5, s6, s7;
mm_int8() {
}
mm_int8(cl_int s0, cl_int s1, cl_int s2, cl_int s3, cl_int s4, cl_int s5, cl_int s6, cl_int s7) :
s0(s0), s1(s1), s2(s2), s3(s3), s4(s4), s5(s5), s6(s6), s7(s7) {
}
};
struct mm_int16 {
cl_int s0, s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15;
mm_int16() {
}
mm_int16(cl_int s0, cl_int s1, cl_int s2, cl_int s3, cl_int s4, cl_int s5, cl_int s6, cl_int s7,
cl_int s8, cl_int s9, cl_int s10, cl_int s11, cl_int s12, cl_int s13, cl_int s14, cl_int s15) :
s0(s0), s1(s1), s2(s2), s3(s3), s4(s4), s5(s5), s6(s6), s7(s7),
s8(s8), s9(s9), s10(s10), s11(s11), s12(s12), s13(s13), s14(s14), s15(15) {
}
};
/**
* This class contains the information associated with a Context by the OpenCL Platform. Each OpenCLContext is
* specific to a particular device, and manages data structures and kernels for that device. When running a simulation
* in parallel on multiple devices, there is a separate OpenCLContext for each one. The list of all contexts is
* stored in the OpenCLPlatform::PlatformData.
* <p>
* In addition, a worker thread is created for each OpenCLContext. This is used for parallel computations, so that
* blocking calls to one device will not block other devices. When only a single device is being used, the worker
* thread is not used and calculations are performed on the main application thread.
*/
class OPENMM_EXPORT OpenCLContext {
public:
class WorkTask;
class WorkThread;
static const int ThreadBlockSize;
static const int TileSize;
OpenCLContext(int numParticles, int deviceIndex, OpenCLPlatform::PlatformData& platformData);
~OpenCLContext();
/**
* This is called to initialize internal data structures after all Forces in the system
* have been initialized.
*/
void initialize(const System& system);
/**
* Add an OpenCLForce to this context.
*/
void addForce(OpenCLForceInfo* force);
/**
* Get the cl::Context associated with this object.
*/
cl::Context& getContext() {
return context;
}
/**
* Get the cl::Device associated with this object.
*/
cl::Device& getDevice() {
return device;
}
/**
* Get the index of the cl::Device associated with this object.
*/
int getDeviceIndex() {
return deviceIndex;
}
/**
* Get the PlatformData object this context is part of.
*/
OpenCLPlatform::PlatformData& getPlatformData() {
return platformData;
}
/**
* Get the index of this context in the list stored in the PlatformData.
*/
int getContextIndex() const {
return contextIndex;
}
/**
* Get the cl::CommandQueue associated with this object.
*/
cl::CommandQueue& getQueue() {
return queue;
}
/**
* Get the array which contains the position (the xyz components) and charge (the w component) of each atom.
*/
OpenCLArray<mm_float4>& getPosq() {
return *posq;
}
/**
* Get the array which contains the velocity (the xyz components) and inverse mass (the w component) of each atom.
*/
OpenCLArray<mm_float4>& getVelm() {
return *velm;
}
/**
* Get the array which contains the force on each atom.
*/
OpenCLArray<mm_float4>& getForce() {
return *force;
}
/**
* Get the array which contains the buffers in which forces are computed.
*/
OpenCLArray<mm_float4>& getForceBuffers() {
return *forceBuffers;
}
/**
* Get the array which contains the buffer in which energy is computed.
*/
OpenCLArray<cl_float>& getEnergyBuffer() {
return *energyBuffer;
}
/**
* Get the array which contains the index of each atom.
*/
OpenCLArray<cl_int>& getAtomIndex() {
return *atomIndex;
}
/**
* Get the number of cells by which the positions are offset.
*/
std::vector<mm_int4>& getPosCellOffsets() {
return posCellOffsets;
}
/**
* Load OpenCL source code from a file in the kernels directory.
*/
std::string loadSourceFromFile(const std::string& filename) const;
/**
* Load OpenCL source code from a file in the kernels directory.
*
* @param filename the file to load
* @param replacements a set of strings that should be replaced with new strings wherever they appear in the
*/
std::string loadSourceFromFile(const std::string& filename, const std::map<std::string, std::string>& replacements) const;
/**
* Replace all occurance of a list of substrings.
*
* @param input a string to process
* @param replacements a set of strings that should be replaced with new strings wherever they appear in the input string
* @return a new string produced by performing the replacements
*/
std::string replaceStrings(const std::string& input, const std::map<std::string, std::string>& replacements) const;
/**
* Create an OpenCL Program from source code.
*
* @param source the source code of the program
* @param optimizationFlags the optimization flags to pass to the OpenCL compiler. If this is
* omitted, a default set of options will be used
*/
cl::Program createProgram(const std::string source, const char* optimizationFlags = NULL);
/**
* Create an OpenCL Program from source code.
*
* @param source the source code of the program
* @param defines a set of preprocessor definitions (name, value) to define when compiling the program
* @param optimizationFlags the optimization flags to pass to the OpenCL compiler. If this is
* omitted, a default set of options will be used
*/
cl::Program createProgram(const std::string source, const std::map<std::string, std::string>& defines, const char* optimizationFlags = NULL);
/**
* Execute a kernel.
*
* @param kernel the kernel to execute
* @param workUnits the maximum number of work units that should be used
* @param blockSize the size of each thread block to use
*/
void executeKernel(cl::Kernel& kernel, int workUnits, int blockSize = -1);
/**
* Set all elements of an array to 0.
*/
void clearBuffer(OpenCLArray<float>& array);
/**
* Set all elements of an array to 0.
*/
void clearBuffer(OpenCLArray<mm_float4>& array);
/**
* Set all elements of an array to 0.
*
* @param memory the Memory to clear
* @param size the number of float elements in the buffer
*/
void clearBuffer(cl::Memory& memory, int size);
/**
* Register a buffer that should be automatically cleared (all elements set to 0) at the start of each force or energy computation.
*
* @param memory the Memory to clear
* @param size the number of float elements in the buffer
*/
void addAutoclearBuffer(cl::Memory& memory, int size);
/**
* Clear all buffers that have been registered with addAutoclearBuffer().
*/
void clearAutoclearBuffers();
/**
* Given a collection of buffers packed into an array, sum them and store
* the sum in the first buffer.
*
* @param array the array containing the buffers to reduce
* @param numBuffers the number of buffers packed into the array
*/
void reduceBuffer(OpenCLArray<mm_float4>& array, int numBuffers);
/**
* Get the current simulation time.
*/
double getTime() {
return time;
}
/**
* Set the current simulation time.
*/
void setTime(double t) {
time = t;
}
/**
* Get the number of integration steps that have been taken.
*/
int getStepCount() {
return stepCount;
}
/**
* Set the number of integration steps that have been taken.
*/
void setStepCount(int steps) {
stepCount = steps;
}
/**
* Get the number of times forces or energy has been computed.
*/
int getComputeForceCount() {
return computeForceCount;
}
/**
* Set the number of times forces or energy has been computed.
*/
void setComputeForceCount(int count) {
computeForceCount = count;
}
/**
* Get the number of atoms.
*/
int getNumAtoms() const {
return numAtoms;
}
/**
* Get the number of atoms, rounded up to a multiple of TileSize. This is the actual size of
* most arrays with one element per atom.
*/
int getPaddedNumAtoms() const {
return paddedNumAtoms;
}
/**
* Get the number of blocks of TileSize atoms.
*/
int getNumAtomBlocks() const {
return numAtomBlocks;
}
/**
* Get the standard number of thread blocks to use when executing kernels.
*/
int getNumThreadBlocks() const {
return numThreadBlocks;
}
/**
* Get the number of force buffers.
*/
int getNumForceBuffers() const {
return numForceBuffers;
}
/**
* Get the SIMD width of the device being used.
*/
int getSIMDWidth() const {
return simdWidth;
}
/**
* Get whether the device being used supports 64 bit atomic operations on global memory.
*/
bool getSupports64BitGlobalAtomics() {
return supports64BitGlobalAtomics;
}
/**
* Get the size of the periodic box.
*/
mm_float4 getPeriodicBoxSize() const {
return periodicBoxSize;
}
/**
* Set the size of the periodic box.
*/
void setPeriodicBoxSize(double xsize, double ysize, double zsize) {
periodicBoxSize = mm_float4((float) xsize, (float) ysize, (float) zsize, 0);
invPeriodicBoxSize = mm_float4((float) (1.0/xsize), (float) (1.0/ysize), (float) (1.0/zsize), 0);
}
/**
* Get the inverse of the size of the periodic box.
*/
mm_float4 getInvPeriodicBoxSize() const {
return invPeriodicBoxSize;
}
/**
* Get the OpenCLIntegrationUtilities for this context.
*/
OpenCLIntegrationUtilities& getIntegrationUtilities() {
return *integration;
}
/**
* Get the OpenCLNonbondedUtilities for this context.
*/
OpenCLNonbondedUtilities& getNonbondedUtilities() {
return *nonbonded;
}
/**
* Get the thread used by this context for executing parallel computations.
*/
WorkThread& getWorkThread() {
return *thread;
}
/**
* Reorder the internal arrays of atoms to try to keep spatially contiguous atoms close
* together in the arrays.
*/
void reorderAtoms();
private:
struct Molecule;
struct MoleculeGroup;
void findMoleculeGroups(const System& system);
static void tagAtomsInMolecule(int atom, int molecule, std::vector<int>& atomMolecule, std::vector<std::vector<int> >& atomBonds);
double time;
OpenCLPlatform::PlatformData& platformData;
int deviceIndex;
int contextIndex;
int stepCount;
int computeForceCount;
int numAtoms;
int paddedNumAtoms;
int numAtomBlocks;
int numThreadBlocks;
int numForceBuffers;
int simdWidth;
bool supports64BitGlobalAtomics;
mm_float4 periodicBoxSize;
mm_float4 invPeriodicBoxSize;
std::string defaultOptimizationOptions;
std::map<std::string, std::string> compilationDefines;
cl::Context context;
cl::Device device;
cl::CommandQueue queue;
cl::Program utilities;
cl::Kernel clearBufferKernel;
cl::Kernel clearTwoBuffersKernel;
cl::Kernel clearThreeBuffersKernel;
cl::Kernel clearFourBuffersKernel;
cl::Kernel reduceFloat4Kernel;
std::vector<OpenCLForceInfo*> forces;
std::vector<MoleculeGroup> moleculeGroups;
std::vector<mm_int4> posCellOffsets;
OpenCLArray<mm_float4>* posq;
OpenCLArray<mm_float4>* velm;
OpenCLArray<mm_float4>* force;
OpenCLArray<mm_float4>* forceBuffers;
OpenCLArray<cl_float>* energyBuffer;
OpenCLArray<cl_int>* atomIndex;
std::vector<cl::Memory*> autoclearBuffers;
std::vector<int> autoclearBufferSizes;
OpenCLIntegrationUtilities* integration;
OpenCLNonbondedUtilities* nonbonded;
WorkThread* thread;
};
struct OpenCLContext::MoleculeGroup {
std::vector<int> atoms;
std::vector<int> instances;
};
/**
* This abstract class defines a task to be executed on the worker thread.
*/
class OpenCLContext::WorkTask {
public:
virtual void execute() = 0;
};
class OpenCLContext::WorkThread {
public:
struct ThreadData;
WorkThread();
~WorkThread();
/**
* Request that a task be executed on the worker thread. The argument should have been allocated on the
* heap with the "new" operator. After its execute() method finishes, the object will be deleted automatically.
*/
void addTask(OpenCLContext::WorkTask* task);
/**
* Get whether the worker thread is idle, waiting for a task to be added.
*/
bool isWaiting();
/**
* Get whether the worker thread has exited.
*/
bool isFinished();
/**
* Block until all tasks have finished executing and the worker thread is idle.
*/
void flush();
private:
std::queue<OpenCLContext::WorkTask*> tasks;
bool waiting, finished;
pthread_mutex_t queueLock;
pthread_cond_t waitForTaskCondition, queueEmptyCondition;
pthread_t thread;
};
} // namespace OpenMM
#endif /*OPENMM_OPENCLCONTEXT_H_*/
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