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Unverified Commit 0e396127 authored by Andy Simmonett's avatar Andy Simmonett
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Fix array resize problems in Cuda and OpenCL kernels

parent c0f7ca70
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Showing with 112 additions and 26 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ 0e396127
......@@ -7112,19 +7112,28 @@ void CudaIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, const
prevMaxPairDistance = maxPairDistance;
}
if (numAtoms !=0 && (!atomListBuffer.isInitialized() || atomListBuffer.getSize() != numAtoms)) {
if(atomListBuffer.isInitialized()) {
atomListBuffer.resize(atomList.size());
} else {
atomListBuffer.initialize<int>(cu, atomList.size(), "atomListBuffer");
}
atomListBuffer.upload(atomList);
}
if (numPairs !=0 && (!pairListBuffer.isInitialized() || pairListBuffer.getSize() != numPairs)) {
if (pairListBuffer.isInitialized()) {
pairListBuffer.resize(pairList.size());
pairTemperatureBuffer.resize(pairList.size());
} else {
pairListBuffer.initialize<int2>(cu, pairList.size(), "pairListBuffer");
pairTemperatureBuffer.initialize<float>(cu, pairList.size(), "pairTemperatureBuffer");
}
std::vector<int2> tmp;
std::vector<float> tmp2;
for(const auto &pair : pairList) {
tmp.push_back(make_int2(std::get<0>(pair), std::get<1>(pair)));
tmp2.push_back(std::get<2>(pair));
}
pairListBuffer.initialize<int2>(cu, pairList.size(), "pairListBuffer");
pairListBuffer.upload(tmp);
pairTemperatureBuffer.initialize<float>(cu, pairList.size(), "pairTemperatureBuffer");
pairTemperatureBuffer.upload(tmp2);
}
//// Call the first integration kernel.
......@@ -8447,24 +8456,42 @@ std::pair<double, double> CudaNoseHooverChainKernel::propagateChain(ContextImpl&
if (!scaleFactorBuffer.isInitialized() ||scaleFactorBuffer.getSize() == 0) {
if(useDouble){
std::vector<double2> zeros{{0,0}};
if (scaleFactorBuffer.isInitialized()) {
scaleFactorBuffer.resize(1);
} else {
scaleFactorBuffer.initialize<double2>(cu, 1, "scaleFactorBuffer");
}
scaleFactorBuffer.upload(zeros);
} else {
std::vector<float2> zeros{{0,0}};
if (scaleFactorBuffer.isInitialized()) {
scaleFactorBuffer.resize(1);
} else {
scaleFactorBuffer.initialize<float2>(cu, 1, "scaleFactorBuffer");
}
scaleFactorBuffer.upload(zeros);
}
}
std::vector<double> zeros(chainLength,0);
if (!chainForces.isInitialized() || !chainMasses.isInitialized() ){
if(useDouble){
if (chainForces.isInitialized()) {
chainMasses.resize(chainLength);
chainForces.resize(chainLength);
} else {
chainMasses.initialize<double>(cu, chainLength, "chainMasses");
chainForces.initialize<double>(cu, chainLength, "chainForces");
}
chainMasses.upload(zeros);
chainForces.upload(zeros);
} else {
if (chainForces.isInitialized()) {
chainMasses.resize(chainLength);
chainForces.resize(chainLength);
} else {
chainMasses.initialize<float>(cu, chainLength, "chainMasses");
chainForces.initialize<float>(cu, chainLength, "chainForces");
}
chainMasses.upload(zeros);
chainForces.upload(zeros);
}
......@@ -8479,11 +8506,19 @@ std::pair<double, double> CudaNoseHooverChainKernel::propagateChain(ContextImpl&
if (chainState.at(2*chainID).getSize() != chainLength) {
// We need to upload the CUDA array
if(useDouble){
if (chainState.at(2*chainID).isInitialized()) {
chainState.at(2*chainID).resize(chainLength);
} else {
chainState.at(2*chainID).initialize<double2>(cu, chainLength, "chainState" + std::to_string(2*chainID));
}
std::vector<double2> zeros(chainLength, make_double2(0, 0));
chainState.at(2*chainID).upload(zeros.data());
} else {
if (chainState.at(2*chainID).isInitialized()) {
chainState.at(2*chainID).resize(chainLength);
} else {
chainState.at(2*chainID).initialize<float2>(cu, chainLength, "chainState" + std::to_string(2*chainID));
}
std::vector<float2> zeros(chainLength, make_float2(0, 0));
chainState.at(2*chainID).upload(zeros.data());
}
......@@ -8510,11 +8545,19 @@ std::pair<double, double> CudaNoseHooverChainKernel::propagateChain(ContextImpl&
if (chainState.at(2*chainID+1).getSize() != chainLength) {
// We need to upload the CUDA array
if(useDouble){
if (chainState.at(2*chainID+1).isInitialized()) {
chainState.at(2*chainID+1).resize(chainLength);
} else {
chainState.at(2*chainID+1).initialize<double2>(cu, chainLength, "chainState" + std::to_string(2*chainID+1));
}
std::vector<double2> zeros(chainLength, make_double2(0, 0));
chainState.at(2*chainID+1).upload(zeros.data());
} else {
if (chainState.at(2*chainID+1).isInitialized()) {
chainState.at(2*chainID+1).resize(chainLength);
} else {
chainState.at(2*chainID+1).initialize<float2>(cu, chainLength, "chainState" + std::to_string(2*chainID+1));
}
std::vector<float2> zeros(chainLength, make_float2(0, 0));
chainState.at(2*chainID+1).upload(zeros.data());
}
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 0e396127
......@@ -7426,19 +7426,28 @@ void OpenCLIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, cons
prevMaxPairDistance = maxPairDistance;
}
if (numAtoms !=0 && (!atomListBuffer.isInitialized() || atomListBuffer.getSize() != numAtoms)) {
if (atomListBuffer.isInitialized()) {
atomListBuffer.resize(atomList.size());
} else {
atomListBuffer.initialize<cl_int>(cl, atomList.size(), "atomListBuffer");
}
atomListBuffer.upload(atomList);
}
if (numPairs !=0 && (!pairListBuffer.isInitialized() || pairListBuffer.getSize() != numPairs)) {
if (pairListBuffer.isInitialized()) {
pairListBuffer.resize(pairList.size());
pairTemperatureBuffer.resize(pairList.size());
} else {
pairListBuffer.initialize<mm_int2>(cl, pairList.size(), "pairListBuffer");
pairTemperatureBuffer.initialize<cl_float>(cl, pairList.size(), "pairTemperatureBuffer");
}
std::vector<mm_int2> tmp;
std::vector<float> tmp2;
for(const auto &pair : pairList) {
tmp.push_back(mm_int2(std::get<0>(pair), std::get<1>(pair)));
tmp2.push_back(std::get<2>(pair));
}
pairListBuffer.initialize<mm_int2>(cl, pairList.size(), "pairListBuffer");
pairListBuffer.upload(tmp);
pairTemperatureBuffer.initialize<cl_float>(cl, pairList.size(), "pairTemperatureBuffer");
pairTemperatureBuffer.upload(tmp2);
}
......@@ -8873,25 +8882,43 @@ std::pair<double, double> OpenCLNoseHooverChainKernel::propagateChain(ContextImp
if (!scaleFactorBuffer.isInitialized() ||scaleFactorBuffer.getSize() == 0) {
if(useDouble){
std::vector<mm_double2> zeros{{0,0}};
if (scaleFactorBuffer.isInitialized()) {
scaleFactorBuffer.resize(1);
} else {
scaleFactorBuffer.initialize<mm_double2>(cl, 1, "scaleFactorBuffer");
}
scaleFactorBuffer.upload(zeros);
} else {
std::vector<mm_float2> zeros{{0,0}};
if (scaleFactorBuffer.isInitialized()) {
scaleFactorBuffer.resize(1);
} else {
scaleFactorBuffer.initialize<mm_float2>(cl, 1, "scaleFactorBuffer");
}
scaleFactorBuffer.upload(zeros);
}
}
if (!chainForces.isInitialized() || !chainMasses.isInitialized() ){
if(useDouble){
std::vector<cl_double> zeros(chainLength,0);
if (chainForces.isInitialized()) {
chainMasses.resize(chainLength);
chainForces.resize(chainLength);
} else {
chainMasses.initialize<cl_double>(cl, chainLength, "chainMasses");
chainForces.initialize<cl_double>(cl, chainLength, "chainForces");
}
chainMasses.upload(zeros);
chainForces.upload(zeros);
} else {
std::vector<cl_float> zeros(chainLength,0);
if (chainForces.isInitialized()) {
chainMasses.resize(chainLength);
chainForces.resize(chainLength);
} else {
chainMasses.initialize<cl_float>(cl, chainLength, "chainMasses");
chainForces.initialize<cl_float>(cl, chainLength, "chainForces");
}
chainMasses.upload(zeros);
chainForces.upload(zeros);
}
......@@ -8906,11 +8933,19 @@ std::pair<double, double> OpenCLNoseHooverChainKernel::propagateChain(ContextImp
if (chainState.at(2*chainID).getSize() != chainLength) {
// We need to upload the OpenCL array
if(useDouble){
if (chainState.at(2*chainID).isInitialized()) {
chainState.at(2*chainID).resize(chainLength);
} else {
chainState.at(2*chainID).initialize<mm_double2>(cl, chainLength, "chainState" + std::to_string(2*chainID));
}
std::vector<mm_double2> zeros(chainLength, mm_double2(0.0, 0.0));
chainState.at(2*chainID).upload(zeros.data());
} else {
if (chainState.at(2*chainID).isInitialized()) {
chainState.at(2*chainID).resize(chainLength);
} else {
chainState.at(2*chainID).initialize<mm_float2>(cl, chainLength, "chainState" + std::to_string(2*chainID));
}
std::vector<mm_float2> zeros(chainLength, mm_float2(0.0f, 0.0f));
chainState.at(2*chainID).upload(zeros.data());
}
......@@ -8941,11 +8976,19 @@ std::pair<double, double> OpenCLNoseHooverChainKernel::propagateChain(ContextImp
if (chainState.at(2*chainID+1).getSize() != chainLength) {
// We need to upload the OpenCL array
if(useDouble){
if (chainState.at(2*chainID+1).isInitialized()) {
chainState.at(2*chainID+1).resize(chainLength);
} else {
chainState.at(2*chainID+1).initialize<mm_double2>(cl, chainLength, "chainState" + std::to_string(2*chainID+1));
}
std::vector<mm_double2> zeros(chainLength, mm_double2(0.0, 0.0));
chainState.at(2*chainID+1).upload(zeros.data());
} else {
if (chainState.at(2*chainID+1).isInitialized()) {
chainState.at(2*chainID+1).resize(chainLength);
} else {
chainState.at(2*chainID+1).initialize<mm_float2>(cl, chainLength, "chainState" + std::to_string(2*chainID+1));
}
std::vector<mm_float2> zeros(chainLength, mm_float2(0.0f, 0.0f));
chainState.at(2*chainID+1).upload(zeros.data());
}
......
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