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Commit b441c4a7 authored by Peter Eastman's avatar Peter Eastman
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Code cleanup to CUDA platform

parent a8020adc
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Showing with 129 additions and 312 deletions
platforms/cuda/include/CudaArray.h
View file @ b441c4a7
......@@ -130,7 +130,27 @@ public:
* Copy the values in a vector to the device memory.
*/
template <class T>
void upload(const std::vector<T>& data) {
void upload(const std::vector<T>& data, bool convert = true) {
if (convert && data.size() == size && sizeof(T) != elementSize) {
if (sizeof(T) == 2*elementSize) {
// Convert values from double to single precision.
const double* d = reinterpret_cast<const double*>(&data[0]);
std::vector<float> v(elementSize*size/sizeof(float));
for (int i = 0; i < v.size(); i++)
v[i] = (float) d[i];
upload(&v[0], true);
return;
}
if (2*sizeof(T) == elementSize) {
// Convert values from single to double precision.
const float* d = reinterpret_cast<const float*>(&data[0]);
std::vector<double> v(elementSize*size/sizeof(double));
for (int i = 0; i < v.size(); i++)
v[i] = (double) d[i];
upload(&v[0], true);
return;
}
}
if (sizeof(T) != elementSize || data.size() != size)
throw OpenMMException("Error uploading array "+name+": The specified vector does not match the size of the array");
upload(&data[0], true);
......
platforms/cuda/include/CudaKernels.h
View file @ b441c4a7
......@@ -1592,10 +1592,8 @@ private:
mutable std::vector<std::vector<double4> > localPerDofValuesDouble;
std::map<std::string, double> energyParamDerivs;
std::vector<std::string> perDofEnergyParamDerivNames;
std::vector<float> localPerDofEnergyParamDerivsFloat;
std::vector<double> localPerDofEnergyParamDerivsDouble;
std::vector<float> globalValuesFloat;
std::vector<double> globalValuesDouble;
std::vector<double> localPerDofEnergyParamDerivs;
std::vector<double> localGlobalValues;
std::vector<double> initialGlobalVariables;
std::vector<std::vector<CUfunction> > kernels;
std::vector<std::vector<std::vector<void*> > > kernelArgs;
......
platforms/cuda/src/CudaContext.cpp
View file @ b441c4a7
......@@ -728,58 +728,9 @@ string CudaContext::intToString(int value) const {
}
std::string CudaContext::getErrorString(CUresult result) {
switch (result) {
case CUDA_SUCCESS: return "CUDA_SUCCESS";
case CUDA_ERROR_INVALID_VALUE: return "CUDA_ERROR_INVALID_VALUE";
case CUDA_ERROR_OUT_OF_MEMORY: return "CUDA_ERROR_OUT_OF_MEMORY";
case CUDA_ERROR_NOT_INITIALIZED: return "CUDA_ERROR_NOT_INITIALIZED";
case CUDA_ERROR_DEINITIALIZED: return "CUDA_ERROR_DEINITIALIZED";
case CUDA_ERROR_PROFILER_DISABLED: return "CUDA_ERROR_PROFILER_DISABLED";
case CUDA_ERROR_PROFILER_NOT_INITIALIZED: return "CUDA_ERROR_PROFILER_NOT_INITIALIZED";
case CUDA_ERROR_PROFILER_ALREADY_STARTED: return "CUDA_ERROR_PROFILER_ALREADY_STARTED";
case CUDA_ERROR_PROFILER_ALREADY_STOPPED: return "CUDA_ERROR_PROFILER_ALREADY_STOPPED";
case CUDA_ERROR_NO_DEVICE: return "CUDA_ERROR_NO_DEVICE";
case CUDA_ERROR_INVALID_DEVICE: return "CUDA_ERROR_INVALID_DEVICE";
case CUDA_ERROR_INVALID_IMAGE: return "CUDA_ERROR_INVALID_IMAGE";
case CUDA_ERROR_INVALID_CONTEXT: return "CUDA_ERROR_INVALID_CONTEXT";
case CUDA_ERROR_CONTEXT_ALREADY_CURRENT: return "CUDA_ERROR_CONTEXT_ALREADY_CURRENT";
case CUDA_ERROR_MAP_FAILED: return "CUDA_ERROR_MAP_FAILED";
case CUDA_ERROR_UNMAP_FAILED: return "CUDA_ERROR_UNMAP_FAILED";
case CUDA_ERROR_ARRAY_IS_MAPPED: return "CUDA_ERROR_ARRAY_IS_MAPPED";
case CUDA_ERROR_ALREADY_MAPPED: return "CUDA_ERROR_ALREADY_MAPPED";
case CUDA_ERROR_NO_BINARY_FOR_GPU: return "CUDA_ERROR_NO_BINARY_FOR_GPU";
case CUDA_ERROR_ALREADY_ACQUIRED: return "CUDA_ERROR_ALREADY_ACQUIRED";
case CUDA_ERROR_NOT_MAPPED: return "CUDA_ERROR_NOT_MAPPED";
case CUDA_ERROR_NOT_MAPPED_AS_ARRAY: return "CUDA_ERROR_NOT_MAPPED_AS_ARRAY";
case CUDA_ERROR_NOT_MAPPED_AS_POINTER: return "CUDA_ERROR_NOT_MAPPED_AS_POINTER";
case CUDA_ERROR_ECC_UNCORRECTABLE: return "CUDA_ERROR_ECC_UNCORRECTABLE";
case CUDA_ERROR_UNSUPPORTED_LIMIT: return "CUDA_ERROR_UNSUPPORTED_LIMIT";
case CUDA_ERROR_CONTEXT_ALREADY_IN_USE: return "CUDA_ERROR_CONTEXT_ALREADY_IN_USE";
case CUDA_ERROR_PEER_ACCESS_UNSUPPORTED: return "CUDA_ERROR_PEER_ACCESS_UNSUPPORTED";
case CUDA_ERROR_INVALID_SOURCE: return "CUDA_ERROR_INVALID_SOURCE";
case CUDA_ERROR_FILE_NOT_FOUND: return "CUDA_ERROR_FILE_NOT_FOUND";
case CUDA_ERROR_SHARED_OBJECT_SYMBOL_NOT_FOUND: return "CUDA_ERROR_SHARED_OBJECT_SYMBOL_NOT_FOUND";
case CUDA_ERROR_SHARED_OBJECT_INIT_FAILED: return "CUDA_ERROR_SHARED_OBJECT_INIT_FAILED";
case CUDA_ERROR_OPERATING_SYSTEM: return "CUDA_ERROR_OPERATING_SYSTEM";
case CUDA_ERROR_INVALID_HANDLE: return "CUDA_ERROR_INVALID_HANDLE";
case CUDA_ERROR_NOT_FOUND: return "CUDA_ERROR_NOT_FOUND";
case CUDA_ERROR_NOT_READY: return "CUDA_ERROR_NOT_READY";
case CUDA_ERROR_LAUNCH_FAILED: return "CUDA_ERROR_LAUNCH_FAILED";
case CUDA_ERROR_LAUNCH_OUT_OF_RESOURCES: return "CUDA_ERROR_LAUNCH_OUT_OF_RESOURCES";
case CUDA_ERROR_LAUNCH_TIMEOUT: return "CUDA_ERROR_LAUNCH_TIMEOUT";
case CUDA_ERROR_LAUNCH_INCOMPATIBLE_TEXTURING: return "CUDA_ERROR_LAUNCH_INCOMPATIBLE_TEXTURING";
case CUDA_ERROR_PEER_ACCESS_ALREADY_ENABLED: return "CUDA_ERROR_PEER_ACCESS_ALREADY_ENABLED";
case CUDA_ERROR_PEER_ACCESS_NOT_ENABLED: return "CUDA_ERROR_PEER_ACCESS_NOT_ENABLED";
case CUDA_ERROR_PRIMARY_CONTEXT_ACTIVE: return "CUDA_ERROR_PRIMARY_CONTEXT_ACTIVE";
case CUDA_ERROR_CONTEXT_IS_DESTROYED: return "CUDA_ERROR_CONTEXT_IS_DESTROYED";
case CUDA_ERROR_ASSERT: return "CUDA_ERROR_ASSERT";
case CUDA_ERROR_TOO_MANY_PEERS: return "CUDA_ERROR_TOO_MANY_PEERS";
case CUDA_ERROR_HOST_MEMORY_ALREADY_REGISTERED: return "CUDA_ERROR_HOST_MEMORY_ALREADY_REGISTERED";
case CUDA_ERROR_HOST_MEMORY_NOT_REGISTERED: return "CUDA_ERROR_HOST_MEMORY_NOT_REGISTERED";
case CUDA_ERROR_NOT_PERMITTED: return "CUDA_ERROR_NOT_PERMITTED";
case CUDA_ERROR_NOT_SUPPORTED: return "CUDA_ERROR_NOT_SUPPORTED";
case CUDA_ERROR_UNKNOWN: return "CUDA_ERROR_UNKNOWN";
}
const char* message;
if (cuGetErrorName(result, &message) == CUDA_SUCCESS)
return string(message);
return "CUDA error";
}
......@@ -886,18 +837,10 @@ double CudaContext::reduceEnergy() {
void CudaContext::setCharges(const vector<double>& charges) {
if (!chargeBuffer.isInitialized())
chargeBuffer.initialize(*this, numAtoms, useDoublePrecision ? sizeof(double) : sizeof(float), "chargeBuffer");
if (getUseDoublePrecision()) {
vector<double> c(numAtoms);
for (int i = 0; i < numAtoms; i++)
c[i] = charges[i];
chargeBuffer.upload(c);
}
else {
vector<float> c(numAtoms);
for (int i = 0; i < numAtoms; i++)
c[i] = (float) charges[i];
chargeBuffer.upload(c);
}
vector<double> c(numAtoms);
for (int i = 0; i < numAtoms; i++)
c[i] = charges[i];
chargeBuffer.upload(c, true);
void* args[] = {&chargeBuffer.getDevicePointer(), &posq.getDevicePointer(), &atomIndexDevice.getDevicePointer(), &numAtoms};
executeKernel(setChargesKernel, args, numAtoms);
}
......@@ -916,32 +859,33 @@ public:
VirtualSiteInfo(const System& system) {
for (int i = 0; i < system.getNumParticles(); i++) {
if (system.isVirtualSite(i)) {
siteTypes.push_back(&typeid(system.getVirtualSite(i)));
const VirtualSite& vsite = system.getVirtualSite(i);
siteTypes.push_back(&typeid(vsite));
vector<int> particles;
particles.push_back(i);
for (int j = 0; j < system.getVirtualSite(i).getNumParticles(); j++)
particles.push_back(system.getVirtualSite(i).getParticle(j));
for (int j = 0; j < vsite.getNumParticles(); j++)
particles.push_back(vsite.getParticle(j));
siteParticles.push_back(particles);
vector<double> weights;
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
if (dynamic_cast<const TwoParticleAverageSite*>(&vsite) != NULL) {
// A two particle average.
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(system.getVirtualSite(i));
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(vsite);
weights.push_back(site.getWeight(0));
weights.push_back(site.getWeight(1));
}
else if (dynamic_cast<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
else if (dynamic_cast<const ThreeParticleAverageSite*>(&vsite) != NULL) {
// A three particle average.
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(system.getVirtualSite(i));
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(vsite);
weights.push_back(site.getWeight(0));
weights.push_back(site.getWeight(1));
weights.push_back(site.getWeight(2));
}
else if (dynamic_cast<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
else if (dynamic_cast<const OutOfPlaneSite*>(&vsite) != NULL) {
// An out of plane site.
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(system.getVirtualSite(i));
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(vsite);
weights.push_back(site.getWeight12());
weights.push_back(site.getWeight13());
weights.push_back(site.getWeightCross());
......
platforms/cuda/src/CudaIntegrationUtilities.cpp
View file @ b441c4a7
......@@ -376,58 +376,31 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
vector<int> atomConstraintsVec(ccmaAtomConstraints.getSize());
vector<int> numAtomConstraintsVec(ccmaNumAtomConstraints.getSize());
vector<int> constraintMatrixColumnVec(ccmaConstraintMatrixColumn.getSize());
if (context.getUseDoublePrecision() || context.getUseMixedPrecision()) {
ccmaDistance.initialize<double4>(context, numCCMA, "CcmaDistance");
ccmaDelta1.initialize<double>(context, numCCMA, "CcmaDelta1");
ccmaDelta2.initialize<double>(context, numCCMA, "CcmaDelta2");
ccmaReducedMass.initialize<double>(context, numCCMA, "CcmaReducedMass");
ccmaConstraintMatrixValue.initialize<double>(context, numCCMA*maxRowElements, "ConstraintMatrixValue");
vector<double4> distanceVec(ccmaDistance.getSize());
vector<double> reducedMassVec(ccmaReducedMass.getSize());
vector<double> constraintMatrixValueVec(ccmaConstraintMatrixValue.getSize());
for (int i = 0; i < numCCMA; i++) {
int index = constraintOrder[i];
int c = ccmaConstraints[index];
atomsVec[i].x = atom1[c];
atomsVec[i].y = atom2[c];
distanceVec[i].w = distance[c];
reducedMassVec[i] = (0.5/(1.0/system.getParticleMass(atom1[c])+1.0/system.getParticleMass(atom2[c])));
for (unsigned int j = 0; j < matrix[index].size(); j++) {
constraintMatrixColumnVec[i+j*numCCMA] = matrix[index][j].first;
constraintMatrixValueVec[i+j*numCCMA] = matrix[index][j].second;
}
constraintMatrixColumnVec[i+matrix[index].size()*numCCMA] = numCCMA;
}
ccmaDistance.upload(distanceVec);
ccmaReducedMass.upload(reducedMassVec);
ccmaConstraintMatrixValue.upload(constraintMatrixValueVec);
}
else {
ccmaDistance.initialize<float4>(context, numCCMA, "CcmaDistance");
ccmaDelta1.initialize<float>(context, numCCMA, "CcmaDelta1");
ccmaDelta2.initialize<float>(context, numCCMA, "CcmaDelta2");
ccmaReducedMass.initialize<float>(context, numCCMA, "CcmaReducedMass");
ccmaConstraintMatrixValue.initialize<float>(context, numCCMA*maxRowElements, "ConstraintMatrixValue");
vector<float4> distanceVec(ccmaDistance.getSize());
vector<float> reducedMassVec(ccmaReducedMass.getSize());
vector<float> constraintMatrixValueVec(ccmaConstraintMatrixValue.getSize());
for (int i = 0; i < numCCMA; i++) {
int index = constraintOrder[i];
int c = ccmaConstraints[index];
atomsVec[i].x = atom1[c];
atomsVec[i].y = atom2[c];
distanceVec[i].w = (float) distance[c];
reducedMassVec[i] = (float) (0.5/(1.0/system.getParticleMass(atom1[c])+1.0/system.getParticleMass(atom2[c])));
for (unsigned int j = 0; j < matrix[index].size(); j++) {
constraintMatrixColumnVec[i+j*numCCMA] = matrix[index][j].first;
constraintMatrixValueVec[i+j*numCCMA] = (float) matrix[index][j].second;
}
constraintMatrixColumnVec[i+matrix[index].size()*numCCMA] = numCCMA;
int elementSize = (context.getUseDoublePrecision() || context.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
ccmaDistance.initialize(context, numCCMA, 4*elementSize, "CcmaDistance");
ccmaDelta1.initialize(context, numCCMA, elementSize, "CcmaDelta1");
ccmaDelta2.initialize(context, numCCMA, elementSize, "CcmaDelta2");
ccmaReducedMass.initialize(context, numCCMA, elementSize, "CcmaReducedMass");
ccmaConstraintMatrixValue.initialize(context, numCCMA*maxRowElements, elementSize, "ConstraintMatrixValue");
vector<double4> distanceVec(ccmaDistance.getSize());
vector<double> reducedMassVec(ccmaReducedMass.getSize());
vector<double> constraintMatrixValueVec(ccmaConstraintMatrixValue.getSize());
for (int i = 0; i < numCCMA; i++) {
int index = constraintOrder[i];
int c = ccmaConstraints[index];
atomsVec[i].x = atom1[c];
atomsVec[i].y = atom2[c];
distanceVec[i].w = distance[c];
reducedMassVec[i] = (0.5/(1.0/system.getParticleMass(atom1[c])+1.0/system.getParticleMass(atom2[c])));
for (unsigned int j = 0; j < matrix[index].size(); j++) {
constraintMatrixColumnVec[i+j*numCCMA] = matrix[index][j].first;
constraintMatrixValueVec[i+j*numCCMA] = matrix[index][j].second;
}
ccmaDistance.upload(distanceVec);
ccmaReducedMass.upload(reducedMassVec);
ccmaConstraintMatrixValue.upload(constraintMatrixValueVec);
constraintMatrixColumnVec[i+matrix[index].size()*numCCMA] = numCCMA;
}
ccmaDistance.upload(distanceVec, true);
ccmaReducedMass.upload(reducedMassVec, true);
ccmaConstraintMatrixValue.upload(constraintMatrixValueVec, true);
for (unsigned int i = 0; i < atomConstraints.size(); i++) {
numAtomConstraintsVec[i] = atomConstraints[i].size();
for (unsigned int j = 0; j < atomConstraints[i].size(); j++) {
......@@ -521,57 +494,21 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
vsiteLocalCoordsAtoms.upload(vsiteLocalCoordsAtomVec);
vsiteLocalCoordsStartIndex.upload(vsiteLocalCoordsStartVec);
}
if (context.getUseDoublePrecision()) {
vsite2AvgWeights.initialize<double2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgWeights.initialize<double4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneWeights.initialize<double4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
vsiteLocalCoordsWeights.initialize<double>(context, max(1, (int) vsiteLocalCoordsWeightVec.size()), "vsiteLocalCoordsWeights");
vsiteLocalCoordsPos.initialize<double4>(context, max(1, (int) vsiteLocalCoordsPosVec.size()), "vsiteLocalCoordsPos");
if (num2Avg > 0)
vsite2AvgWeights.upload(vsite2AvgWeightVec);
if (num3Avg > 0)
vsite3AvgWeights.upload(vsite3AvgWeightVec);
if (numOutOfPlane > 0)
vsiteOutOfPlaneWeights.upload(vsiteOutOfPlaneWeightVec);
if (numLocalCoords > 0) {
vsiteLocalCoordsWeights.upload(vsiteLocalCoordsWeightVec);
vsiteLocalCoordsPos.upload(vsiteLocalCoordsPosVec);
}
}
else {
vsite2AvgWeights.initialize<float2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgWeights.initialize<float4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneWeights.initialize<float4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
vsiteLocalCoordsWeights.initialize<float>(context, max(1, (int) vsiteLocalCoordsWeightVec.size()), "vsiteLocalCoordsWeights");
vsiteLocalCoordsPos.initialize<float4>(context, max(1, (int) vsiteLocalCoordsPosVec.size()), "vsiteLocalCoordsPos");
if (num2Avg > 0) {
vector<float2> floatWeights(num2Avg);
for (int i = 0; i < num2Avg; i++)
floatWeights[i] = make_float2((float) vsite2AvgWeightVec[i].x, (float) vsite2AvgWeightVec[i].y);
vsite2AvgWeights.upload(floatWeights);
}
if (num3Avg > 0) {
vector<float4> floatWeights(num3Avg);
for (int i = 0; i < num3Avg; i++)
floatWeights[i] = make_float4((float) vsite3AvgWeightVec[i].x, (float) vsite3AvgWeightVec[i].y, (float) vsite3AvgWeightVec[i].z, 0.0f);
vsite3AvgWeights.upload(floatWeights);
}
if (numOutOfPlane > 0) {
vector<float4> floatWeights(numOutOfPlane);
for (int i = 0; i < numOutOfPlane; i++)
floatWeights[i] = make_float4((float) vsiteOutOfPlaneWeightVec[i].x, (float) vsiteOutOfPlaneWeightVec[i].y, (float) vsiteOutOfPlaneWeightVec[i].z, 0.0f);
vsiteOutOfPlaneWeights.upload(floatWeights);
}
if (numLocalCoords > 0) {
vector<float> floatWeights(vsiteLocalCoordsWeightVec.size());
for (int i = 0; i < (int) vsiteLocalCoordsWeightVec.size(); i++)
floatWeights[i] = (float) vsiteLocalCoordsWeightVec[i];
vsiteLocalCoordsWeights.upload(floatWeights);
vector<float4> floatPos(vsiteLocalCoordsPosVec.size());
for (int i = 0; i < (int) vsiteLocalCoordsPosVec.size(); i++)
floatPos[i] = make_float4((float) vsiteLocalCoordsPosVec[i].x, (float) vsiteLocalCoordsPosVec[i].y, (float) vsiteLocalCoordsPosVec[i].z, 0.0f);
vsiteLocalCoordsPos.upload(floatPos);
}
int elementSize = (context.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
vsite2AvgWeights.initialize(context, max(1, num2Avg), 2*elementSize, "vsite2AvgWeights");
vsite3AvgWeights.initialize(context, max(1, num3Avg), 4*elementSize, "vsite3AvgWeights");
vsiteOutOfPlaneWeights.initialize(context, max(1, numOutOfPlane), 4*elementSize, "vsiteOutOfPlaneWeights");
vsiteLocalCoordsWeights.initialize(context, max(1, (int) vsiteLocalCoordsWeightVec.size()), elementSize, "vsiteLocalCoordsWeights");
vsiteLocalCoordsPos.initialize(context, max(1, (int) vsiteLocalCoordsPosVec.size()), 4*elementSize, "vsiteLocalCoordsPos");
if (num2Avg > 0)
vsite2AvgWeights.upload(vsite2AvgWeightVec, true);
if (num3Avg > 0)
vsite3AvgWeights.upload(vsite3AvgWeightVec, true);
if (numOutOfPlane > 0)
vsiteOutOfPlaneWeights.upload(vsiteOutOfPlaneWeightVec, true);
if (numLocalCoords > 0) {
vsiteLocalCoordsWeights.upload(vsiteLocalCoordsWeightVec, true);
vsiteLocalCoordsPos.upload(vsiteLocalCoordsPosVec, true);
}
// Create the kernels used by this class.
......
platforms/cuda/src/CudaKernels.cpp
View file @ b441c4a7
......@@ -1905,25 +1905,12 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
for (int i = 0; i < ndata; i++)
if (moduli[i] < 1.0e-7)
moduli[i] = (moduli[i-1]+moduli[i+1])*0.5;
if (cu.getUseDoublePrecision()) {
if (dim == 0)
xmoduli->upload(moduli);
else if (dim == 1)
ymoduli->upload(moduli);
else
zmoduli->upload(moduli);
}
else {
vector<float> modulif(ndata);
for (int i = 0; i < ndata; i++)
modulif[i] = (float) moduli[i];
if (dim == 0)
xmoduli->upload(modulif);
else if (dim == 1)
ymoduli->upload(modulif);
else
zmoduli->upload(modulif);
}
if (dim == 0)
xmoduli->upload(moduli, true);
else if (dim == 1)
ymoduli->upload(moduli, true);
else
zmoduli->upload(moduli, true);
}
}
}
......@@ -1941,14 +1928,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
replacements["CHARGE2"] = "posq2.w";
}
else {
if (cu.getUseDoublePrecision())
charges.upload(chargeVec);
else {
vector<float> c(charges.getSize());
for (int i = 0; i < c.size(); i++)
c[i] = (float) chargeVec[i];
charges.upload(c);
}
charges.upload(chargeVec, true);
replacements["CHARGE1"] = prefix+"charge1";
replacements["CHARGE2"] = prefix+"charge2";
}
......@@ -2214,16 +2194,8 @@ void CudaCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context,
sigmaEpsilonVector[i] = make_float2(0,0);
if (usePosqCharges)
cu.setCharges(chargeVector);
else {
if (cu.getUseDoublePrecision())
charges.upload(chargeVector);
else {
vector<float> c(charges.getSize());
for (int i = 0; i < c.size(); i++)
c[i] = (float) chargeVector[i];
charges.upload(c);
}
}
else
charges.upload(chargeVector, true);
sigmaEpsilon.upload(sigmaEpsilonVector);
// Record the exceptions.
......@@ -2889,14 +2861,7 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
chargeVec[i] = charge;
paramsVector[i] = make_float2((float) radius, (float) (scalingFactor*radius));
}
if (cu.getUseDoublePrecision())
charges.upload(chargeVec);
else {
vector<float> c(charges.getSize());
for (int i = 0; i < c.size(); i++)
c[i] = (float) chargeVec[i];
charges.upload(c);
}
charges.upload(chargeVec, true);
params.upload(paramsVector);
prefactor = -ONE_4PI_EPS0*((1.0/force.getSoluteDielectric())-(1.0/force.getSolventDielectric()));
surfaceAreaFactor = -6.0*4*M_PI*force.getSurfaceAreaEnergy();
......@@ -3044,14 +3009,7 @@ void CudaCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, c
}
for (int i = numParticles; i < cu.getPaddedNumAtoms(); i++)
paramsVector[i] = make_float2(1, 1);
if (cu.getUseDoublePrecision())
charges.upload(chargeVector);
else {
vector<float> c(charges.getSize());
for (int i = 0; i < c.size(); i++)
c[i] = (float) chargeVector[i];
charges.upload(c);
}
charges.upload(chargeVector, true);
params.upload(paramsVector);
// Mark that the current reordering may be invalid.
......@@ -4781,8 +4739,7 @@ void CudaCalcCustomCentroidBondForceKernel::initialize(const System& system, con
numGroups = force.getNumGroups();
vector<int> groupParticleVec;
vector<float> groupWeightVecFloat;
vector<double> groupWeightVecDouble;
vector<double> groupWeightVec;
vector<int> groupOffsetVec;
groupOffsetVec.push_back(0);
for (int i = 0; i < numGroups; i++) {
......@@ -4794,27 +4751,19 @@ void CudaCalcCustomCentroidBondForceKernel::initialize(const System& system, con
}
vector<vector<double> > normalizedWeights;
CustomCentroidBondForceImpl::computeNormalizedWeights(force, system, normalizedWeights);
if (cu.getUseDoublePrecision()) {
for (int i = 0; i < numGroups; i++)
groupWeightVecDouble.insert(groupWeightVecDouble.end(), normalizedWeights[i].begin(), normalizedWeights[i].end());
}
else {
for (int i = 0; i < numGroups; i++)
for (int j = 0; j < normalizedWeights[i].size(); j++)
groupWeightVecFloat.push_back((float) normalizedWeights[i][j]);
}
for (int i = 0; i < numGroups; i++)
groupWeightVec.insert(groupWeightVec.end(), normalizedWeights[i].begin(), normalizedWeights[i].end());
groupParticles.initialize<int>(cu, groupParticleVec.size(), "groupParticles");
groupParticles.upload(groupParticleVec);
if (cu.getUseDoublePrecision()) {
groupWeights.initialize<double>(cu, groupParticleVec.size(), "groupWeights");
groupWeights.upload(groupWeightVecDouble);
centerPositions.initialize<double4>(cu, numGroups, "centerPositions");
}
else {
groupWeights.initialize<float>(cu, groupParticleVec.size(), "groupWeights");
groupWeights.upload(groupWeightVecFloat);
centerPositions.initialize<float4>(cu, numGroups, "centerPositions");
}
groupWeights.upload(groupWeightVec, true);
groupOffsets.initialize<int>(cu, groupOffsetVec.size(), "groupOffsets");
groupOffsets.upload(groupOffsetVec);
groupForces.initialize<long long>(cu, numGroups*3, "groupForces");
......@@ -6736,18 +6685,10 @@ void CudaCalcRMSDForceKernel::recordParameters(const RMSDForce& force) {
// Upload them to the device.
particles.upload(particleVec);
if (cu.getUseDoublePrecision()) {
vector<double4> pos;
for (Vec3 p : centeredPositions)
pos.push_back(make_double4(p[0], p[1], p[2], 0));
referencePos.upload(pos);
}
else {
vector<float4> pos;
for (Vec3 p : centeredPositions)
pos.push_back(make_float4(p[0], p[1], p[2], 0));
referencePos.upload(pos);
}
vector<double4> pos;
for (Vec3 p : centeredPositions)
pos.push_back(make_double4(p[0], p[1], p[2], 0));
referencePos.upload(pos, true);
// Record the sum of the norms of the reference positions.
......@@ -6930,20 +6871,11 @@ void CudaIntegrateLangevinStepKernel::execute(ContextImpl& context, const Langev
double vscale = exp(-stepSize*friction);
double fscale = (friction == 0 ? stepSize : (1-vscale)/friction);
double noisescale = sqrt(kT*(1-vscale*vscale));
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
vector<double> p(params.getSize());
p[0] = vscale;
p[1] = fscale;
p[2] = noisescale;
params.upload(p);
}
else {
vector<float> p(params.getSize());
p[0] = (float) vscale;
p[1] = (float) fscale;
p[2] = (float) noisescale;
params.upload(p);
}
vector<double> p(params.getSize());
p[0] = vscale;
p[1] = fscale;
p[2] = noisescale;
params.upload(p, true);
prevTemp = temperature;
prevFriction = friction;
prevStepSize = stepSize;
......@@ -7442,22 +7374,20 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
// Allocate space for storing global values, both on the host and the device.
globalValuesFloat.resize(expressionSet.getNumVariables());
globalValuesDouble.resize(expressionSet.getNumVariables());
localGlobalValues.resize(expressionSet.getNumVariables());
int elementSize = (cu.getUseDoublePrecision() || cu.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
globalValues.initialize(cu, expressionSet.getNumVariables(), elementSize, "globalValues");
for (int i = 0; i < integrator.getNumGlobalVariables(); i++) {
globalValuesDouble[globalVariableIndex[i]] = initialGlobalVariables[i];
localGlobalValues[globalVariableIndex[i]] = initialGlobalVariables[i];
expressionSet.setVariable(globalVariableIndex[i], initialGlobalVariables[i]);
}
for (int i = 0; i < (int) parameterVariableIndex.size(); i++) {
double value = context.getParameter(parameterNames[i]);
globalValuesDouble[parameterVariableIndex[i]] = value;
localGlobalValues[parameterVariableIndex[i]] = value;
expressionSet.setVariable(parameterVariableIndex[i], value);
}
int numContextParams = context.getParameters().size();
localPerDofEnergyParamDerivsFloat.resize(numContextParams);
localPerDofEnergyParamDerivsDouble.resize(numContextParams);
localPerDofEnergyParamDerivs.resize(numContextParams);
perDofEnergyParamDerivs.initialize(cu, max(1, numContextParams), elementSize, "perDofEnergyParamDerivs");
// Record information about the targets of steps that will be stored in global variables.
......@@ -7732,8 +7662,8 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
recordGlobalValue(stepSize, GlobalTarget(DT, dtVariableIndex), integrator);
for (int i = 0; i < (int) parameterNames.size(); i++) {
double value = context.getParameter(parameterNames[i]);
if (value != globalValuesDouble[parameterVariableIndex[i]]) {
globalValuesDouble[parameterVariableIndex[i]] = value;
if (value != localGlobalValues[parameterVariableIndex[i]]) {
localGlobalValues[parameterVariableIndex[i]] = value;
deviceGlobalsAreCurrent = false;
}
}
......@@ -7830,16 +7760,9 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
if (needsEnergyParamDerivs) {
context.getEnergyParameterDerivatives(energyParamDerivs);
if (perDofEnergyParamDerivNames.size() > 0) {
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
for (int i = 0; i < perDofEnergyParamDerivNames.size(); i++)
localPerDofEnergyParamDerivsDouble[i] = energyParamDerivs[perDofEnergyParamDerivNames[i]];
perDofEnergyParamDerivs.upload(localPerDofEnergyParamDerivsDouble);
}
else {
for (int i = 0; i < perDofEnergyParamDerivNames.size(); i++)
localPerDofEnergyParamDerivsFloat[i] = (float) energyParamDerivs[perDofEnergyParamDerivNames[i]];
perDofEnergyParamDerivs.upload(localPerDofEnergyParamDerivsFloat);
}
for (int i = 0; i < perDofEnergyParamDerivNames.size(); i++)
localPerDofEnergyParamDerivs[i] = energyParamDerivs[perDofEnergyParamDerivNames[i]];
perDofEnergyParamDerivs.upload(localPerDofEnergyParamDerivs, true);
}
}
}
......@@ -7852,13 +7775,7 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
if (needsGlobals[step] && !deviceGlobalsAreCurrent) {
// Upload the global values to the device.
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision())
globalValues.upload(globalValuesDouble);
else {
for (int j = 0; j < (int) globalValuesDouble.size(); j++)
globalValuesFloat[j] = (float) globalValuesDouble[j];
globalValues.upload(globalValuesFloat);
}
globalValues.upload(localGlobalValues, true);
}
bool stepInvalidatesForces = invalidatesForces[step];
if (stepType[step] == CustomIntegrator::ComputePerDof && !merged[step]) {
......@@ -8005,17 +7922,17 @@ double CudaIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context,
void CudaIntegrateCustomStepKernel::recordGlobalValue(double value, GlobalTarget target, CustomIntegrator& integrator) {
switch (target.type) {
case DT:
if (value != globalValuesDouble[dtVariableIndex])
if (value != localGlobalValues[dtVariableIndex])
deviceGlobalsAreCurrent = false;
expressionSet.setVariable(dtVariableIndex, value);
globalValuesDouble[dtVariableIndex] = value;
localGlobalValues[dtVariableIndex] = value;
cu.getIntegrationUtilities().setNextStepSize(value);
integrator.setStepSize(value);
break;
case VARIABLE:
case PARAMETER:
expressionSet.setVariable(target.variableIndex, value);
globalValuesDouble[target.variableIndex] = value;
localGlobalValues[target.variableIndex] = value;
deviceGlobalsAreCurrent = false;
break;
}
......@@ -8026,8 +7943,8 @@ void CudaIntegrateCustomStepKernel::recordChangedParameters(ContextImpl& context
return;
for (int i = 0; i < (int) parameterNames.size(); i++) {
double value = context.getParameter(parameterNames[i]);
if (value != globalValuesDouble[parameterVariableIndex[i]])
context.setParameter(parameterNames[i], globalValuesDouble[parameterVariableIndex[i]]);
if (value != localGlobalValues[parameterVariableIndex[i]])
context.setParameter(parameterNames[i], localGlobalValues[parameterVariableIndex[i]]);
}
}
......@@ -8040,7 +7957,7 @@ void CudaIntegrateCustomStepKernel::getGlobalVariables(ContextImpl& context, vec
}
values.resize(numGlobalVariables);
for (int i = 0; i < numGlobalVariables; i++)
values[i] = globalValuesDouble[globalVariableIndex[i]];
values[i] = localGlobalValues[globalVariableIndex[i]];
}
void CudaIntegrateCustomStepKernel::setGlobalVariables(ContextImpl& context, const vector<double>& values) {
......@@ -8053,7 +7970,7 @@ void CudaIntegrateCustomStepKernel::setGlobalVariables(ContextImpl& context, con
return;
}
for (int i = 0; i < numGlobalVariables; i++) {
globalValuesDouble[globalVariableIndex[i]] = values[i];
localGlobalValues[globalVariableIndex[i]] = values[i];
expressionSet.setVariable(globalVariableIndex[i], values[i]);
}
deviceGlobalsAreCurrent = false;
......
platforms/opencl/src/OpenCLContext.cpp
View file @ b441c4a7
......@@ -794,32 +794,33 @@ public:
VirtualSiteInfo(const System& system) : OpenCLForceInfo(0) {
for (int i = 0; i < system.getNumParticles(); i++) {
if (system.isVirtualSite(i)) {
siteTypes.push_back(&typeid(system.getVirtualSite(i)));
const VirtualSite& vsite = system.getVirtualSite(i);
siteTypes.push_back(&typeid(vsite));
vector<int> particles;
particles.push_back(i);
for (int j = 0; j < system.getVirtualSite(i).getNumParticles(); j++)
particles.push_back(system.getVirtualSite(i).getParticle(j));
for (int j = 0; j < vsite.getNumParticles(); j++)
particles.push_back(vsite.getParticle(j));
siteParticles.push_back(particles);
vector<double> weights;
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
if (dynamic_cast<const TwoParticleAverageSite*>(&vsite) != NULL) {
// A two particle average.
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(system.getVirtualSite(i));
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(vsite);
weights.push_back(site.getWeight(0));
weights.push_back(site.getWeight(1));
}
else if (dynamic_cast<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
else if (dynamic_cast<const ThreeParticleAverageSite*>(&vsite) != NULL) {
// A three particle average.
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(system.getVirtualSite(i));
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(vsite);
weights.push_back(site.getWeight(0));
weights.push_back(site.getWeight(1));
weights.push_back(site.getWeight(2));
}
else if (dynamic_cast<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
else if (dynamic_cast<const OutOfPlaneSite*>(&vsite) != NULL) {
// An out of plane site.
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(system.getVirtualSite(i));
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(vsite);
weights.push_back(site.getWeight12());
weights.push_back(site.getWeight13());
weights.push_back(site.getWeightCross());
......
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