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Commit 73183c61 authored by ChayaSt's avatar ChayaSt
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resolved conflict

parents 0e218233 32e08b87
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Showing with 340 additions and 260 deletions
platforms/cuda/tests/TestCudaSort.cpp
View file @ 73183c61
......@@ -66,7 +66,7 @@ void verifySorting(vector<float> array) {
system.addParticle(0.0);
CudaPlatform::PlatformData platformData(NULL, system, "", "true", platform.getPropertyDefaultValue("CudaPrecision"), "false",
platform.getPropertyDefaultValue(CudaPlatform::CudaCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaTempDirectory()),
platform.getPropertyDefaultValue(CudaPlatform::CudaHostCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaDisablePmeStream()), 1);
platform.getPropertyDefaultValue(CudaPlatform::CudaHostCompiler()), platform.getPropertyDefaultValue(CudaPlatform::CudaDisablePmeStream()), "false", 1);
CudaContext& context = *platformData.contexts[0];
context.initialize();
CudaArray data(context, array.size(), 4, "sortData");
......
platforms/opencl/include/OpenCLContext.h
View file @ 73183c61
......@@ -408,6 +408,18 @@ public:
void setStepsSinceReorder(int steps) {
stepsSinceReorder = steps;
}
/**
* Get the flag that marks whether the current force evaluation is valid.
*/
bool getForcesValid() const {
return forcesValid;
}
/**
* Get the flag that marks whether the current force evaluation is valid.
*/
void setForcesValid(bool valid) {
forcesValid = valid;
}
/**
* Get the number of atoms.
*/
......@@ -684,7 +696,7 @@ private:
int numThreadBlocks;
int numForceBuffers;
int simdWidth;
bool supports64BitGlobalAtomics, supportsDoublePrecision, useDoublePrecision, useMixedPrecision, atomsWereReordered, boxIsTriclinic;
bool supports64BitGlobalAtomics, supportsDoublePrecision, useDoublePrecision, useMixedPrecision, atomsWereReordered, boxIsTriclinic, forcesValid;
mm_float4 periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ;
mm_double4 periodicBoxSizeDouble, invPeriodicBoxSizeDouble, periodicBoxVecXDouble, periodicBoxVecYDouble, periodicBoxVecZDouble;
std::string defaultOptimizationOptions;
......
platforms/opencl/include/OpenCLKernels.h
View file @ 73183c61
......@@ -156,7 +156,7 @@ public:
* @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) const;
void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
/**
* Create a checkpoint recording the current state of the Context.
*
......@@ -698,7 +698,7 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
void initInteractionGroups(const CustomNonbondedForce& force, const std::string& interactionSource);
void initInteractionGroups(const CustomNonbondedForce& force, const std::string& interactionSource, const std::vector<std::string>& tableTypes);
OpenCLContext& cl;
OpenCLParameterSet* params;
OpenCLArray* globals;
......
platforms/opencl/include/OpenCLNonbondedUtilities.h
View file @ 73183c61
......@@ -281,6 +281,9 @@ private:
OpenCLArray* oldPositions;
OpenCLArray* rebuildNeighborList;
OpenCLSort* blockSorter;
cl::Event downloadCountEvent;
cl::Buffer* pinnedCountBuffer;
int* pinnedCountMemory;
std::vector<std::vector<int> > atomExclusions;
std::vector<ParameterInfo> parameters;
std::vector<ParameterInfo> arguments;
......
platforms/opencl/include/OpenCLPlatform.h
View file @ 73183c61
......@@ -58,14 +58,14 @@ public:
* This is the name of the parameter for selecting which OpenCL device or devices to use.
*/
static const std::string& OpenCLDeviceIndex() {
static const std::string key = "OpenCLDeviceIndex";
static const std::string key = "DeviceIndex";
return key;
}
/**
* This is the name of the parameter that reports the OpenCL device or devices being used.
*/
static const std::string& OpenCLDeviceName() {
static const std::string key = "OpenCLDeviceName";
static const std::string key = "DeviceName";
return key;
}
/**
......@@ -86,21 +86,21 @@ public:
* This is the name of the parameter for selecting what numerical precision to use.
*/
static const std::string& OpenCLPrecision() {
static const std::string key = "OpenCLPrecision";
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& OpenCLUseCpuPme() {
static const std::string key = "OpenCLUseCpuPme";
static const std::string key = "UseCpuPme";
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& OpenCLDisablePmeStream() {
static const std::string key = "OpenCLDisablePmeStream";
static const std::string key = "DisablePmeStream";
return key;
}
};
......
platforms/opencl/src/OpenCLContext.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* 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) 2009-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -84,7 +84,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
useMixedPrecision = false;
}
else
throw OpenMMException("Illegal value for OpenCLPrecision: "+precision);
throw OpenMMException("Illegal value for Precision: "+precision);
try {
contextIndex = platformData.contexts.size();
std::vector<cl::Platform> platforms;
......@@ -105,7 +105,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
vector<cl::Device> devices;
platforms[j].getDevices(CL_DEVICE_TYPE_ALL, &devices);
if (deviceIndex < -1 || deviceIndex >= (int) devices.size())
throw OpenMMException("Illegal value for OpenCLDeviceIndex: "+intToString(deviceIndex));
throw OpenMMException("Illegal value for DeviceIndex: "+intToString(deviceIndex));
for (int i = 0; i < (int) devices.size(); i++) {
// If they supplied a valid deviceIndex, we only look through that one
......@@ -113,6 +113,11 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
continue;
if (platformVendor == "Apple" && (devices[i].getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU))
continue; // The CPU device on OS X won't work correctly.
if (useMixedPrecision || useDoublePrecision) {
bool supportsDouble = (devices[i].getInfo<CL_DEVICE_EXTENSIONS>().find("cl_khr_fp64") != string::npos);
if (!supportsDouble)
continue; // This device does not support double precision.
}
int maxSize = devices[i].getInfo<CL_DEVICE_MAX_WORK_ITEM_SIZES>()[0];
int processingElementsPerComputeUnit = 8;
if (devices[i].getInfo<CL_DEVICE_TYPE>() != CL_DEVICE_TYPE_GPU) {
......@@ -1047,7 +1052,6 @@ void OpenCLContext::reorderAtoms() {
reorderAtomsImpl<cl_float, mm_float4, cl_double, mm_double4>();
else
reorderAtomsImpl<cl_float, mm_float4, cl_float, mm_float4>();
nonbonded->updateNeighborListSize();
}
template <class Real, class Real4, class Mixed, class Mixed4>
......
platforms/opencl/src/OpenCLExpressionUtilities.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* 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) 2009-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -174,8 +174,8 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
out << "if (x >= " << paramsFloat[2] << " && x <= " << paramsFloat[3] << " && y >= " << paramsFloat[4] << " && y <= " << paramsFloat[5] << ") {\n";
out << "x = (x - " << paramsFloat[2] << ")*" << paramsFloat[6] << ";\n";
out << "y = (y - " << paramsFloat[4] << ")*" << paramsFloat[7] << ";\n";
out << "int s = min((int) floor(x), " << paramsInt[0] << ");\n";
out << "int t = min((int) floor(y), " << paramsInt[1] << ");\n";
out << "int s = min((int) floor(x), " << paramsInt[0] << "-1);\n";
out << "int t = min((int) floor(y), " << paramsInt[1] << "-1);\n";
out << "int coeffIndex = 4*(s+" << paramsInt[0] << "*t);\n";
out << "float4 c[4];\n";
for (int j = 0; j < 4; j++)
......@@ -217,9 +217,9 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
out << "x = (x - " << paramsFloat[3] << ")*" << paramsFloat[9] << ";\n";
out << "y = (y - " << paramsFloat[5] << ")*" << paramsFloat[10] << ";\n";
out << "z = (z - " << paramsFloat[7] << ")*" << paramsFloat[11] << ";\n";
out << "int s = min((int) floor(x), " << paramsInt[0] << ");\n";
out << "int t = min((int) floor(y), " << paramsInt[1] << ");\n";
out << "int u = min((int) floor(z), " << paramsInt[2] << ");\n";
out << "int s = min((int) floor(x), " << paramsInt[0] << "-1);\n";
out << "int t = min((int) floor(y), " << paramsInt[1] << "-1);\n";
out << "int u = min((int) floor(z), " << paramsInt[2] << "-1);\n";
out << "int coeffIndex = 16*(s+" << paramsInt[0] << "*(t+" << paramsInt[1] << "*u));\n";
out << "float4 c[16];\n";
for (int j = 0; j < 16; j++)
......@@ -254,7 +254,7 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
for (int k = 3; k >= 0; k--)
for (int m = 0; m < 4; m++) {
int base = 4*m;
string suffix = suffixes[m];
string suffix = suffixes[k];
out << "derivy[" << m << "] = da*derivy[" << m << "] + (3*c[" << (base+3) << "]" << suffix << "*db + 2*c[" << (base+2) << "]" << suffix << ")*db + c[" << (base+1) << "]" << suffix << ";\n";
}
out << nodeNames[j] << " = derivy[0] + dc*(derivy[1] + dc*(derivy[2] + dc*derivy[3]));\n";
......@@ -271,7 +271,7 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
out << nodeNames[j] << " *= " << paramsFloat[11] << ";\n";
}
else
throw OpenMMException("Unsupported derivative order for Continuous2DFunction");
throw OpenMMException("Unsupported derivative order for Continuous3DFunction");
}
out << "}\n";
}
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 73183c61
......@@ -118,6 +118,7 @@ void OpenCLCalcForcesAndEnergyKernel::initialize(const System& system) {
}
void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
cl.setForcesValid(true);
cl.clearAutoclearBuffers();
for (vector<OpenCLContext::ForcePreComputation*>::iterator iter = cl.getPreComputations().begin(); iter != cl.getPreComputations().end(); ++iter)
(*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
......@@ -149,6 +150,8 @@ double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context,
sum += energy[i];
}
}
if (!cl.getForcesValid())
valid = false;
return sum;
}
......@@ -369,10 +372,27 @@ void OpenCLUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Ve
cl.getPeriodicBoxVectors(a, b, c);
}
void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const {
void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
// If any particles have been wrapped to the first periodic box, we need to unwrap them
// to avoid changing their positions.
vector<Vec3> positions;
for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++) {
mm_int4& offset = cl.getPosCellOffsets()[i];
if (offset.x != 0 || offset.y != 0 || offset.z != 0) {
getPositions(context, positions);
break;
}
}
// Update the vectors.
for (int i = 0; i < (int) contexts.size(); i++)
contexts[i]->setPeriodicBoxVectors(a, b, c);
if (positions.size() > 0)
setPositions(context, positions);
}
void OpenCLUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream& stream) {
......@@ -527,6 +547,7 @@ void OpenCLCalcHarmonicBondForceKernel::initialize(const System& system, const H
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicBondForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
......@@ -660,6 +681,7 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
vector<pair<string, string> > functionNames;
compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = compute.str();
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
}
......@@ -756,6 +778,7 @@ void OpenCLCalcHarmonicAngleForceKernel::initialize(const System& system, const
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicAngleForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
......@@ -890,6 +913,7 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
vector<pair<string, string> > functionNames;
compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = compute.str();
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
}
......@@ -987,6 +1011,7 @@ void OpenCLCalcPeriodicTorsionForceKernel::initialize(const System& system, cons
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::periodicTorsionForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float4");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
......@@ -1073,6 +1098,7 @@ void OpenCLCalcRBTorsionForceKernel::initialize(const System& system, const RBTo
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::rbTorsionForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float8");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
......@@ -1184,6 +1210,7 @@ void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CM
mapPositions->upload(mapPositionsVec);
torsionMaps->upload(torsionMapsVec);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COEFF"] = cl.getBondedUtilities().addArgument(coefficients->getDeviceBuffer(), "float4");
replacements["MAP_POS"] = cl.getBondedUtilities().addArgument(mapPositions->getDeviceBuffer(), "int2");
replacements["MAPS"] = cl.getBondedUtilities().addArgument(torsionMaps->getDeviceBuffer(), "int");
......@@ -1338,6 +1365,7 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
vector<pair<string, string> > functionNames;
compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = compute.str();
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
}
......@@ -1888,7 +1916,7 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
pmeInterpolateForceKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(1, cl.getForceBuffers().getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(2, pmeGrid->getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(7, pmeAtomGridIndex->getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(11, pmeAtomGridIndex->getDeviceBuffer());
if (cl.getSupports64BitGlobalAtomics()) {
pmeFinishSpreadChargeKernel = cl::Kernel(program, "finishSpreadCharge");
pmeFinishSpreadChargeKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
......@@ -1937,45 +1965,45 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
// Execute the reciprocal space kernels.
setPeriodicBoxSizeArg(cl, pmeUpdateBsplinesKernel, 4);
setPeriodicBoxArgs(cl, pmeUpdateBsplinesKernel, 4);
if (cl.getUseDoublePrecision()) {
pmeUpdateBsplinesKernel.setArg<mm_double4>(5, recipBoxVectors[0]);
pmeUpdateBsplinesKernel.setArg<mm_double4>(6, recipBoxVectors[1]);
pmeUpdateBsplinesKernel.setArg<mm_double4>(7, recipBoxVectors[2]);
pmeUpdateBsplinesKernel.setArg<mm_double4>(9, recipBoxVectors[0]);
pmeUpdateBsplinesKernel.setArg<mm_double4>(10, recipBoxVectors[1]);
pmeUpdateBsplinesKernel.setArg<mm_double4>(11, recipBoxVectors[2]);
}
else {
pmeUpdateBsplinesKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[0]);
pmeUpdateBsplinesKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[1]);
pmeUpdateBsplinesKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[2]);
pmeUpdateBsplinesKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[0]);
pmeUpdateBsplinesKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[1]);
pmeUpdateBsplinesKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[2]);
}
cl.executeKernel(pmeUpdateBsplinesKernel, cl.getNumAtoms());
if (deviceIsCpu && !cl.getSupports64BitGlobalAtomics()) {
setPeriodicBoxSizeArg(cl, pmeSpreadChargeKernel, 5);
setPeriodicBoxArgs(cl, pmeSpreadChargeKernel, 5);
if (cl.getUseDoublePrecision()) {
pmeSpreadChargeKernel.setArg<mm_double4>(6, recipBoxVectors[0]);
pmeSpreadChargeKernel.setArg<mm_double4>(7, recipBoxVectors[1]);
pmeSpreadChargeKernel.setArg<mm_double4>(8, recipBoxVectors[2]);
pmeSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
pmeSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
pmeSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
}
else {
pmeSpreadChargeKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[0]);
pmeSpreadChargeKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[1]);
pmeSpreadChargeKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[2]);
pmeSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
pmeSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
pmeSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
}
cl.executeKernel(pmeSpreadChargeKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
}
else {
sort->sort(*pmeAtomGridIndex);
if (cl.getSupports64BitGlobalAtomics()) {
setPeriodicBoxSizeArg(cl, pmeSpreadChargeKernel, 5);
setPeriodicBoxArgs(cl, pmeSpreadChargeKernel, 5);
if (cl.getUseDoublePrecision()) {
pmeSpreadChargeKernel.setArg<mm_double4>(6, recipBoxVectors[0]);
pmeSpreadChargeKernel.setArg<mm_double4>(7, recipBoxVectors[1]);
pmeSpreadChargeKernel.setArg<mm_double4>(8, recipBoxVectors[2]);
pmeSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
pmeSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
pmeSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
}
else {
pmeSpreadChargeKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[0]);
pmeSpreadChargeKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[1]);
pmeSpreadChargeKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[2]);
pmeSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
pmeSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
pmeSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
}
cl.executeKernel(pmeSpreadChargeKernel, cl.getNumAtoms());
cl.executeKernel(pmeFinishSpreadChargeKernel, pmeGrid->getSize());
......@@ -2013,16 +2041,16 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
cl.executeKernel(pmeEvalEnergyKernel, cl.getNumAtoms());
cl.executeKernel(pmeConvolutionKernel, cl.getNumAtoms());
fft->execFFT(*pmeGrid2, *pmeGrid, false);
setPeriodicBoxSizeArg(cl, pmeInterpolateForceKernel, 3);
setPeriodicBoxArgs(cl, pmeInterpolateForceKernel, 3);
if (cl.getUseDoublePrecision()) {
pmeInterpolateForceKernel.setArg<mm_double4>(4, recipBoxVectors[0]);
pmeInterpolateForceKernel.setArg<mm_double4>(5, recipBoxVectors[1]);
pmeInterpolateForceKernel.setArg<mm_double4>(6, recipBoxVectors[2]);
pmeInterpolateForceKernel.setArg<mm_double4>(8, recipBoxVectors[0]);
pmeInterpolateForceKernel.setArg<mm_double4>(9, recipBoxVectors[1]);
pmeInterpolateForceKernel.setArg<mm_double4>(10, recipBoxVectors[2]);
}
else {
pmeInterpolateForceKernel.setArg<mm_float4>(4, recipBoxVectorsFloat[0]);
pmeInterpolateForceKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[1]);
pmeInterpolateForceKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[2]);
pmeInterpolateForceKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[0]);
pmeInterpolateForceKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[1]);
pmeInterpolateForceKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[2]);
}
if (deviceIsCpu)
cl.executeKernel(pmeInterpolateForceKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
......@@ -2222,6 +2250,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
map<string, Lepton::CustomFunction*> functions;
vector<pair<string, string> > functionDefinitions;
vector<const TabulatedFunction*> functionList;
vector<string> tableTypes;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
......@@ -2233,6 +2262,10 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
if (width == 1)
tableTypes.push_back("float");
else
tableTypes.push_back("float"+cl.intToString(width));
}
// Record information for the expressions.
......@@ -2285,7 +2318,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
}
string source = cl.replaceStrings(OpenCLKernelSources::customNonbonded, replacements);
if (force.getNumInteractionGroups() > 0)
initInteractionGroups(force, source);
initInteractionGroups(force, source, tableTypes);
else {
cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
......@@ -2311,7 +2344,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
}
}
void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbondedForce& force, const string& interactionSource) {
void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbondedForce& force, const string& interactionSource, const vector<string>& tableTypes) {
// Process groups to form tiles.
vector<vector<int> > atomLists;
......@@ -2502,6 +2535,8 @@ void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNon
stringstream args;
for (int i = 0; i < (int) buffers.size(); i++)
args<<", __global const "<<buffers[i].getType()<<"* restrict global_params"<<(i+1);
for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
args << ", __global const " << tableTypes[i]<< "* restrict table" << i;
if (globals != NULL)
args<<", __global const float* restrict globals";
replacements["PARAMETER_ARGUMENTS"] = args.str();
......@@ -2591,6 +2626,8 @@ double OpenCLCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool
index += 5;
for (int i = 0; i < (int) params->getBuffers().size(); i++)
interactionGroupKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
interactionGroupKernel.setArg<cl::Memory>(index++, tabulatedFunctions[i]->getDeviceBuffer());
if (globals != NULL)
interactionGroupKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
}
......@@ -4712,7 +4749,7 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
const vector<int>& groups = iter->second;
string deltaName = atomNames[groups[0]]+atomNames[groups[1]];
if (computedDeltas.count(deltaName) == 0) {
compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<");\n";
compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName);
}
compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
......@@ -4726,11 +4763,11 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
string deltaName2 = atomNames[groups[1]]+atomNames[groups[2]];
string angleName = "angle_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[0]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[0]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[2]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[2]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName2);
}
compute<<"real "<<angleName<<" = computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
......@@ -4747,15 +4784,15 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
string dihedralName = "dihedral_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]]+atomNames[groups[3]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[1]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName2);
}
if (computedDeltas.count(deltaName3) == 0) {
compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[3]]<<");\n";
compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[3]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName3);
}
compute<<"real4 "<<crossName1<<" = computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
......@@ -4876,6 +4913,7 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
index++; // Energy buffer hasn't been created yet
groupForcesKernel.setArg<cl::Buffer>(index++, centerPositions->getDeviceBuffer());
groupForcesKernel.setArg<cl::Buffer>(index++, bondGroups->getDeviceBuffer());
index += 5; // Periodic box information
for (int i = 0; i < tabulatedFunctions.size(); i++)
groupForcesKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
if (globals != NULL)
......@@ -4906,6 +4944,7 @@ double OpenCLCalcCustomCentroidBondForceKernel::execute(ContextImpl& context, bo
}
cl.executeKernel(computeCentersKernel, OpenCLContext::TileSize*numGroups);
groupForcesKernel.setArg<cl::Buffer>(1, cl.getEnergyBuffer().getDeviceBuffer());
setPeriodicBoxArgs(cl, groupForcesKernel, 4);
cl.executeKernel(groupForcesKernel, numBonds);
applyForcesKernel.setArg<cl::Buffer>(4, cl.getLongForceBuffer().getDeviceBuffer());
cl.executeKernel(applyForcesKernel, OpenCLContext::TileSize*numGroups);
......@@ -5061,7 +5100,7 @@ void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, c
const vector<int>& atoms = iter->second;
string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
if (computedDeltas.count(deltaName) == 0) {
compute<<"real4 delta"<<deltaName<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName);
}
compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
......@@ -5075,11 +5114,11 @@ void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, c
string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName2);
}
compute<<"real "<<angleName<<" = ccb_computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
......@@ -5096,15 +5135,15 @@ void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, c
string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName2);
}
if (computedDeltas.count(deltaName3) == 0) {
compute<<"real4 delta"<<deltaName3<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<");\n";
compute<<"real4 delta"<<deltaName3<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
computedDeltas.insert(deltaName3);
}
compute<<"real4 "<<crossName1<<" = ccb_computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
......@@ -6513,9 +6552,9 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
for (int step = 0; step < numSteps; step++) {
string expr;
integrator.getComputationStep(step, stepType[step], variable[step], expr);
if (stepType[step] == CustomIntegrator::BeginWhileBlock)
if (stepType[step] == CustomIntegrator::WhileBlockStart)
blockEnd[blockEnd[step]] = step; // Record where to branch back to.
if (stepType[step] == CustomIntegrator::ComputeGlobal || stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock)
if (stepType[step] == CustomIntegrator::ComputeGlobal || stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
for (int i = 0; i < (int) expression[step].size(); i++)
globalExpressions[step].push_back(expression[step][i].createCompiledExpression());
}
......@@ -6961,15 +7000,15 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
else if (stepType[step] == CustomIntegrator::ConstrainVelocities) {
cl.getIntegrationUtilities().applyVelocityConstraints(integrator.getConstraintTolerance());
}
else if (stepType[step] == CustomIntegrator::BeginIfBlock) {
else if (stepType[step] == CustomIntegrator::IfBlockStart) {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
}
else if (stepType[step] == CustomIntegrator::BeginWhileBlock) {
else if (stepType[step] == CustomIntegrator::WhileBlockStart) {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
}
else if (stepType[step] == CustomIntegrator::EndBlock) {
else if (stepType[step] == CustomIntegrator::BlockEnd) {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
}
......
platforms/opencl/src/OpenCLNonbondedUtilities.cpp
View file @ 73183c61
......@@ -57,7 +57,7 @@ private:
OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : context(context), useCutoff(false), usePeriodic(false), anyExclusions(false), usePadding(true),
numForceBuffers(0), exclusionIndices(NULL), exclusionRowIndices(NULL), exclusionTiles(NULL), exclusions(NULL), interactingTiles(NULL), interactingAtoms(NULL),
interactionCount(NULL), blockCenter(NULL), blockBoundingBox(NULL), sortedBlocks(NULL), sortedBlockCenter(NULL), sortedBlockBoundingBox(NULL),
oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0) {
oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), pinnedCountBuffer(NULL), pinnedCountMemory(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0) {
// Decide how many thread blocks and force buffers to use.
deviceIsCpu = (context.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
......@@ -90,6 +90,8 @@ OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : con
numForceBuffers = numForceThreadBlocks*forceThreadBlockSize/OpenCLContext::TileSize;
}
}
pinnedCountBuffer = new cl::Buffer(context.getContext(), CL_MEM_ALLOC_HOST_PTR, sizeof(int));
pinnedCountMemory = (int*) context.getQueue().enqueueMapBuffer(*pinnedCountBuffer, CL_TRUE, CL_MAP_READ, 0, sizeof(int));
}
OpenCLNonbondedUtilities::~OpenCLNonbondedUtilities() {
......@@ -123,6 +125,8 @@ OpenCLNonbondedUtilities::~OpenCLNonbondedUtilities() {
delete rebuildNeighborList;
if (blockSorter != NULL)
delete blockSorter;
if (pinnedCountBuffer != NULL)
delete pinnedCountBuffer;
}
void OpenCLNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const vector<vector<int> >& exclusionList, const string& kernel, int forceGroup) {
......@@ -357,8 +361,6 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
if (lastCutoff != kernels.cutoffDistance)
forceRebuildNeighborList = true;
bool rebuild = false;
do {
setPeriodicBoxArgs(context, kernels.findBlockBoundsKernel, 1);
context.executeKernel(kernels.findBlockBoundsKernel, context.getNumAtoms());
blockSorter->sort(*sortedBlocks);
......@@ -367,10 +369,8 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
setPeriodicBoxArgs(context, kernels.findInteractingBlocksKernel, 0);
context.executeKernel(kernels.findInteractingBlocksKernel, context.getNumAtoms(), interactingBlocksThreadBlockSize);
forceRebuildNeighborList = false;
if (context.getComputeForceCount() == 1)
rebuild = updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
} while (rebuild);
lastCutoff = kernels.cutoffDistance;
context.getQueue().enqueueReadBuffer(interactionCount->getDeviceBuffer(), CL_FALSE, 0, sizeof(int), pinnedCountMemory, NULL, &downloadCountEvent);
}
void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) {
......@@ -385,20 +385,22 @@ void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool include
setPeriodicBoxArgs(context, kernel, 9);
context.executeKernel(kernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
}
if (useCutoff && numTiles > 0) {
downloadCountEvent.wait();
updateNeighborListSize();
}
}
bool OpenCLNonbondedUtilities::updateNeighborListSize() {
if (!useCutoff)
return false;
unsigned int* pinnedInteractionCount = (unsigned int*) context.getPinnedBuffer();
interactionCount->download(pinnedInteractionCount);
if (pinnedInteractionCount[0] <= (unsigned int) interactingTiles->getSize())
if (pinnedCountMemory[0] <= (unsigned int) interactingTiles->getSize())
return false;
// The most recent timestep had too many interactions to fit in the arrays. Make the arrays bigger to prevent
// this from happening in the future.
int maxTiles = (int) (1.2*pinnedInteractionCount[0]);
int maxTiles = (int) (1.2*pinnedCountMemory[0]);
int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
if (maxTiles > totalTiles)
maxTiles = totalTiles;
......@@ -430,6 +432,7 @@ bool OpenCLNonbondedUtilities::updateNeighborListSize() {
kernels.findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
}
forceRebuildNeighborList = true;
context.setForcesValid(false);
return true;
}
......
platforms/opencl/src/OpenCLPlatform.cpp
View file @ 73183c61
......@@ -56,6 +56,11 @@ extern "C" OPENMM_EXPORT_OPENCL void registerPlatforms() {
#endif
OpenCLPlatform::OpenCLPlatform() {
deprecatedPropertyReplacements["OpenCLDeviceIndex"] = OpenCLDeviceIndex();
deprecatedPropertyReplacements["OpenCLDeviceName"] = OpenCLDeviceName();
deprecatedPropertyReplacements["OpenCLPrecision"] = OpenCLPrecision();
deprecatedPropertyReplacements["OpenCLUseCpuPme"] = OpenCLUseCpuPme();
deprecatedPropertyReplacements["OpenCLDisablePmeStream"] = OpenCLDisablePmeStream();
OpenCLKernelFactory* factory = new OpenCLKernelFactory();
registerKernelFactory(CalcForcesAndEnergyKernel::Name(), factory);
registerKernelFactory(UpdateStateDataKernel::Name(), factory);
......@@ -139,7 +144,10 @@ bool OpenCLPlatform::isPlatformSupported() {
const string& OpenCLPlatform::getPropertyValue(const Context& context, const string& property) const {
const ContextImpl& impl = getContextImpl(context);
const PlatformData* data = reinterpret_cast<const PlatformData*>(impl.getPlatformData());
map<string, string>::const_iterator value = data->propertyValues.find(property);
string propertyName = property;
if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
propertyName = deprecatedPropertyReplacements.find(property)->second;
map<string, string>::const_iterator value = data->propertyValues.find(propertyName);
if (value != data->propertyValues.end())
return value->second;
return Platform::getPropertyValue(context, property);
......
platforms/opencl/src/kernels/angleForce.cl
View file @ 73183c61
real4 v0 = pos2-pos1;
real4 v1 = pos2-pos3;
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(v0)
APPLY_PERIODIC_TO_DELTA(v1)
#endif
real4 cp = cross(v0, v1);
real rp = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
rp = max(SQRT(rp), (real) 1.0e-06f);
......
platforms/opencl/src/kernels/bondForce.cl
View file @ 73183c61
real4 delta = pos2-pos1;
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(delta)
#endif
real r = SQRT(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
COMPUTE_FORCE
dEdR = (r > 0.0f) ? (dEdR / r) : 0.0f;
......
platforms/opencl/src/kernels/cmapTorsionForce.cl
View file @ 73183c61
......@@ -5,6 +5,11 @@ const real PI = 3.14159265358979323846f;
real4 v0a = (real4) (pos1.xyz-pos2.xyz, 0.0f);
real4 v1a = (real4) (pos3.xyz-pos2.xyz, 0.0f);
real4 v2a = (real4) (pos3.xyz-pos4.xyz, 0.0f);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(v0a)
APPLY_PERIODIC_TO_DELTA(v1a)
APPLY_PERIODIC_TO_DELTA(v2a)
#endif
real4 cp0a = cross(v0a, v1a);
real4 cp1a = cross(v1a, v2a);
real cosangle = dot(normalize(cp0a), normalize(cp1a));
......@@ -28,6 +33,11 @@ angleA = fmod(angleA+2.0f*PI, 2.0f*PI);
real4 v0b = (real4) (pos5.xyz-pos6.xyz, 0.0f);
real4 v1b = (real4) (pos7.xyz-pos6.xyz, 0.0f);
real4 v2b = (real4) (pos7.xyz-pos8.xyz, 0.0f);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(v0b)
APPLY_PERIODIC_TO_DELTA(v1b)
APPLY_PERIODIC_TO_DELTA(v2b)
#endif
real4 cp0b = cross(v0b, v1b);
real4 cp1b = cross(v1b, v2b);
cosangle = dot(normalize(cp0b), normalize(cp1b));
......
platforms/opencl/src/kernels/customCentroidBond.cl
View file @ 73183c61
......@@ -70,8 +70,11 @@ __kernel void computeGroupCenters(__global const real4* restrict posq, __global
/**
* Compute the difference between two vectors, setting the fourth component to the squared magnitude.
*/
real4 delta(real4 vec1, real4 vec2) {
real4 delta(real4 vec1, real4 vec2, bool periodic, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ) {
real4 result = (real4) (vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
if (periodic)
APPLY_PERIODIC_TO_DELTA(result);
result.w = result.x*result.x + result.y*result.y + result.z*result.z;
return result;
}
......@@ -110,7 +113,7 @@ real4 computeCross(real4 vec1, real4 vec2) {
* Compute the forces on groups based on the bonds.
*/
__kernel void computeGroupForces(__global long* restrict groupForce, __global mixed* restrict energyBuffer, __global const real4* restrict centerPositions,
__global const int* restrict bondGroups
__global const int* restrict bondGroups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ
EXTRA_ARGS) {
mixed energy = 0;
for (int index = get_global_id(0); index < NUM_BONDS; index += get_global_size(0)) {
......
platforms/opencl/src/kernels/customCompoundBond.cl
View file @ 73183c61
/**
* Compute the difference between two vectors, setting the fourth component to the squared magnitude.
*/
real4 ccb_delta(real4 vec1, real4 vec2) {
real4 ccb_delta(real4 vec1, real4 vec2, bool periodic, real4 periodicBoxSize, real4 invPeriodicBoxSize,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ) {
real4 result = (real4) (vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
if (periodic)
APPLY_PERIODIC_TO_DELTA(result);
result.w = result.x*result.x + result.y*result.y + result.z*result.z;
return result;
}
......
platforms/opencl/src/kernels/customGBEnergyN2.cl
View file @ 73183c61
......@@ -181,6 +181,8 @@ __kernel void computeN2Energy(
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -204,16 +206,12 @@ __kernel void computeN2Energy(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -239,7 +237,7 @@ __kernel void computeN2Energy(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
View file @ 73183c61
......@@ -201,6 +201,8 @@ __kernel void computeN2Energy(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else
......@@ -220,16 +222,12 @@ __kernel void computeN2Energy(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -248,7 +246,7 @@ __kernel void computeN2Energy(
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/customGBValueN2.cl
View file @ 73183c61
......@@ -157,6 +157,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -178,16 +180,12 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -213,7 +211,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/customGBValueN2_cpu.cl
View file @ 73183c61
......@@ -170,6 +170,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else
......@@ -188,16 +190,12 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -216,7 +214,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/gbsaObc.cl
View file @ 73183c61
......@@ -169,6 +169,8 @@ __kernel void computeBornSum(
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -190,16 +192,12 @@ __kernel void computeBornSum(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -225,7 +223,7 @@ __kernel void computeBornSum(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......@@ -556,6 +554,8 @@ __kernel void computeGBSAForce1(
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -577,16 +577,12 @@ __kernel void computeGBSAForce1(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -612,7 +608,7 @@ __kernel void computeGBSAForce1(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
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