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Commit f7ef2dd0 authored by peastman's avatar peastman
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More bug fixes to multi-GPU

parent bd666c27
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Showing with 20 additions and 55 deletions
platforms/cuda/src/CudaNonbondedUtilities.cpp
View file @ f7ef2dd0
......@@ -264,14 +264,6 @@ void CudaNonbondedUtilities::initialize(const System& system) {
sortedBlockCenter = new CudaArray(context, numAtomBlocks+1, 4*elementSize, "sortedBlockCenter");
sortedBlockBoundingBox = new CudaArray(context, numAtomBlocks+1, 4*elementSize, "sortedBlockBoundingBox");
oldPositions = new CudaArray(context, numAtoms, 4*elementSize, "oldPositions");
if (context.getUseDoublePrecision()) {
vector<double4> oldPositionsVec(numAtoms, make_double4(1e30, 1e30, 1e30, 0));
oldPositions->upload(oldPositionsVec);
}
else {
vector<float4> oldPositionsVec(numAtoms, make_float4(1e30f, 1e30f, 1e30f, 0));
oldPositions->upload(oldPositionsVec);
}
rebuildNeighborList = CudaArray::create<int>(context, 1, "rebuildNeighborList");
blockSorter = new CudaSort(context, new BlockSortTrait(context.getUseDoublePrecision()), numAtomBlocks);
vector<unsigned int> count(1, 0);
......@@ -402,14 +394,7 @@ void CudaNonbondedUtilities::updateNeighborListSize() {
if (forceArgs.size() > 0)
forceArgs[17] = &interactingAtoms->getDevicePointer();
findInteractingBlocksArgs[7] = &interactingAtoms->getDevicePointer();
if (context.getUseDoublePrecision()) {
vector<double4> oldPositionsVec(numAtoms, make_double4(1e30, 1e30, 1e30, 0));
oldPositions->upload(oldPositionsVec);
}
else {
vector<float4> oldPositionsVec(numAtoms, make_float4(1e30f, 1e30f, 1e30f, 0));
oldPositions->upload(oldPositionsVec);
}
forceRebuildNeighborList = true;
}
void CudaNonbondedUtilities::setUsePadding(bool padding) {
......
platforms/cuda/src/CudaParallelKernels.cpp
View file @ f7ef2dd0
......@@ -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) 2011-2013 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -93,9 +93,9 @@ private:
class CudaParallelCalcForcesAndEnergyKernel::FinishComputationTask : public CudaContext::WorkTask {
public:
FinishComputationTask(ContextImpl& context, CudaContext& cu, CudaCalcForcesAndEnergyKernel& kernel,
bool includeForce, bool includeEnergy, int groups, double& energy, long long& completionTime, long long* pinnedMemory, CudaArray& contextForces, bool& valid) :
bool includeForce, bool includeEnergy, int groups, double& energy, long long& completionTime, long long* pinnedMemory, CudaArray& contextForces, bool& valid, int& numTiles) :
context(context), cu(cu), kernel(kernel), includeForce(includeForce), includeEnergy(includeEnergy), groups(groups), energy(energy),
completionTime(completionTime), pinnedMemory(pinnedMemory), contextForces(contextForces), valid(valid) {
completionTime(completionTime), pinnedMemory(pinnedMemory), contextForces(contextForces), valid(valid), numTiles(numTiles) {
}
void execute() {
// Execute the kernel, then download forces.
......@@ -120,6 +120,10 @@ public:
cu.getForce().download(&pinnedMemory[(cu.getContextIndex()-1)*numAtoms*3]);
}
}
if (cu.getNonbondedUtilities().getUsePeriodic() && numTiles > cu.getNonbondedUtilities().getInteractingTiles().getSize()) {
valid = false;
cu.getNonbondedUtilities().updateNeighborListSize();
}
}
private:
ContextImpl& context;
......@@ -132,6 +136,7 @@ private:
long long* pinnedMemory;
CudaArray& contextForces;
bool& valid;
int& numTiles;
};
CudaParallelCalcForcesAndEnergyKernel::CudaParallelCalcForcesAndEnergyKernel(string name, const Platform& platform, CudaPlatform::PlatformData& data) :
......@@ -201,16 +206,9 @@ double CudaParallelCalcForcesAndEnergyKernel::finishComputation(ContextImpl& con
for (int i = 0; i < (int) data.contexts.size(); i++) {
CudaContext& cu = *data.contexts[i];
CudaContext::WorkThread& thread = cu.getWorkThread();
thread.addTask(new FinishComputationTask(context, cu, getKernel(i), includeForce, includeEnergy, groups, data.contextEnergy[i], completionTimes[i], pinnedForceBuffer, *contextForces, valid));
thread.addTask(new FinishComputationTask(context, cu, getKernel(i), includeForce, includeEnergy, groups, data.contextEnergy[i], completionTimes[i], pinnedForceBuffer, *contextForces, valid, tileCounts[i]));
}
data.syncContexts();
if (data.contexts[0]->getNonbondedUtilities().getUsePeriodic()) {
for (int i = 0; i < (int) tileCounts.size(); i++)
if (tileCounts[i] > data.contexts[i]->getNonbondedUtilities().getInteractingTiles().getSize()) {
valid = false;
data.contexts[i]->getNonbondedUtilities().updateNeighborListSize();
}
}
double energy = 0.0;
for (int i = 0; i < (int) data.contextEnergy.size(); i++)
energy += data.contextEnergy[i];
......
platforms/opencl/src/OpenCLNonbondedUtilities.cpp
View file @ f7ef2dd0
......@@ -282,14 +282,6 @@ void OpenCLNonbondedUtilities::initialize(const System& system) {
sortedBlockCenter = new OpenCLArray(context, numAtomBlocks+1, 4*elementSize, "sortedBlockCenter");
sortedBlockBoundingBox = new OpenCLArray(context, numAtomBlocks+1, 4*elementSize, "sortedBlockBoundingBox");
oldPositions = new OpenCLArray(context, numAtoms, 4*elementSize, "oldPositions");
if (context.getUseDoublePrecision()) {
vector<mm_double4> oldPositionsVec(numAtoms, mm_double4(1e30, 1e30, 1e30, 0));
oldPositions->upload(oldPositionsVec);
}
else {
vector<mm_float4> oldPositionsVec(numAtoms, mm_float4(1e30f, 1e30f, 1e30f, 0));
oldPositions->upload(oldPositionsVec);
}
rebuildNeighborList = OpenCLArray::create<int>(context, 1, "rebuildNeighborList");
blockSorter = new OpenCLSort(context, new BlockSortTrait(context.getUseDoublePrecision()), numAtomBlocks);
vector<cl_uint> count(1, 0);
......@@ -447,15 +439,7 @@ void OpenCLNonbondedUtilities::updateNeighborListSize() {
findInteractingBlocksKernel.setArg<cl::Buffer>(6, interactingTiles->getDeviceBuffer());
findInteractingBlocksKernel.setArg<cl::Buffer>(7, interactingAtoms->getDeviceBuffer());
findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
int numAtoms = context.getNumAtoms();
if (context.getUseDoublePrecision()) {
vector<mm_double4> oldPositionsVec(numAtoms, mm_double4(1e30, 1e30, 1e30, 0));
oldPositions->upload(oldPositionsVec);
}
else {
vector<mm_float4> oldPositionsVec(numAtoms, mm_float4(1e30f, 1e30f, 1e30f, 0));
oldPositions->upload(oldPositionsVec);
}
sortBoxDataKernel.setArg<cl_int>(9, true);
}
void OpenCLNonbondedUtilities::setUsePadding(bool padding) {
......
platforms/opencl/src/OpenCLParallelKernels.cpp
View file @ f7ef2dd0
......@@ -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) 2011-2013 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -79,9 +79,9 @@ private:
class OpenCLParallelCalcForcesAndEnergyKernel::FinishComputationTask : public OpenCLContext::WorkTask {
public:
FinishComputationTask(ContextImpl& context, OpenCLContext& cl, OpenCLCalcForcesAndEnergyKernel& kernel,
bool includeForce, bool includeEnergy, int groups, double& energy, long long& completionTime, void* pinnedMemory, bool& valid) :
bool includeForce, bool includeEnergy, int groups, double& energy, long long& completionTime, void* pinnedMemory, bool& valid, int& numTiles) :
context(context), cl(cl), kernel(kernel), includeForce(includeForce), includeEnergy(includeEnergy), groups(groups), energy(energy),
completionTime(completionTime), pinnedMemory(pinnedMemory), valid(valid) {
completionTime(completionTime), pinnedMemory(pinnedMemory), valid(valid), numTiles(numTiles) {
}
void execute() {
// Execute the kernel, then download forces.
......@@ -98,6 +98,10 @@ public:
cl.getQueue().finish();
}
completionTime = getTime();
if (cl.getNonbondedUtilities().getUsePeriodic() && numTiles > cl.getNonbondedUtilities().getInteractingTiles().getSize()) {
valid = false;
cl.getNonbondedUtilities().updateNeighborListSize();
}
}
private:
ContextImpl& context;
......@@ -109,6 +113,7 @@ private:
long long& completionTime;
void* pinnedMemory;
bool& valid;
int& numTiles;
};
OpenCLParallelCalcForcesAndEnergyKernel::OpenCLParallelCalcForcesAndEnergyKernel(string name, const Platform& platform, OpenCLPlatform::PlatformData& data) :
......@@ -162,16 +167,9 @@ double OpenCLParallelCalcForcesAndEnergyKernel::finishComputation(ContextImpl& c
for (int i = 0; i < (int) data.contexts.size(); i++) {
OpenCLContext& cl = *data.contexts[i];
OpenCLContext::WorkThread& thread = cl.getWorkThread();
thread.addTask(new FinishComputationTask(context, cl, getKernel(i), includeForce, includeEnergy, groups, data.contextEnergy[i], completionTimes[i], pinnedForceMemory, valid));
thread.addTask(new FinishComputationTask(context, cl, getKernel(i), includeForce, includeEnergy, groups, data.contextEnergy[i], completionTimes[i], pinnedForceMemory, valid, tileCounts[i]));
}
data.syncContexts();
if (data.contexts[0]->getNonbondedUtilities().getUsePeriodic()) {
for (int i = 0; i < (int) tileCounts.size(); i++)
if (tileCounts[i] > data.contexts[i]->getNonbondedUtilities().getInteractingTiles().getSize()) {
valid = false;
data.contexts[i]->getNonbondedUtilities().updateNeighborListSize();
}
}
double energy = 0.0;
for (int i = 0; i < (int) data.contextEnergy.size(); i++)
energy += data.contextEnergy[i];
......
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