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Commit ef627240 authored by peastman's avatar peastman
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Very minor optimizations

parent c744444a
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Showing with 60 additions and 44 deletions
platforms/cuda/include/CudaBondedUtilities.h
View file @ ef627240
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011-2012 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -130,7 +130,7 @@ private:
std::vector<std::vector<CudaArray*> > atomIndices;
std::vector<std::string> prefixCode;
std::vector<void*> kernelArgs;
int numForceBuffers, maxBonds;
int numForceBuffers, maxBonds, allGroups;
bool hasInitializedKernels, hasInteractions;
};
......
platforms/cuda/include/CudaKernels.h
View file @ ef627240
......@@ -1294,7 +1294,7 @@ private:
double prevStepSize, energy;
float energyFloat;
int numGlobalVariables;
bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce;
bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce, hasAnyConstraints;
mutable bool localValuesAreCurrent;
CudaArray* globalValues;
CudaArray* sumBuffer;
......
platforms/cuda/src/CudaBondedUtilities.cpp
View file @ ef627240
......@@ -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) 2011-2012 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,7 +34,7 @@
using namespace OpenMM;
using namespace std;
CudaBondedUtilities::CudaBondedUtilities(CudaContext& context) : context(context), numForceBuffers(0), maxBonds(0), hasInitializedKernels(false) {
CudaBondedUtilities::CudaBondedUtilities(CudaContext& context) : context(context), numForceBuffers(0), maxBonds(0), allGroups(0), hasInitializedKernels(false) {
}
CudaBondedUtilities::~CudaBondedUtilities() {
......@@ -48,6 +48,7 @@ void CudaBondedUtilities::addInteraction(const vector<vector<int> >& atoms, cons
forceAtoms.push_back(atoms);
forceSource.push_back(source);
forceGroup.push_back(group);
allGroups |= 1<<group;
}
}
......@@ -152,6 +153,8 @@ string CudaBondedUtilities::createForceSource(int forceIndex, int numBonds, int
}
void CudaBondedUtilities::computeInteractions(int groups) {
if ((groups&allGroups) == 0)
return;
if (!hasInitializedKernels) {
hasInitializedKernels = true;
kernelArgs.push_back(&context.getForce().getDevicePointer());
......
platforms/cuda/src/CudaKernels.cpp
View file @ ef627240
......@@ -5877,22 +5877,25 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
// Determine how each step will represent the position (as just a value, or a value plus a delta).
hasAnyConstraints = (context.getSystem().getNumConstraints() > 0);
vector<bool> storePosAsDelta(numSteps, false);
vector<bool> loadPosAsDelta(numSteps, false);
bool beforeConstrain = false;
for (int step = numSteps-1; step >= 0; step--) {
if (stepType[step] == CustomIntegrator::ConstrainPositions)
beforeConstrain = true;
else if (stepType[step] == CustomIntegrator::ComputePerDof && variable[step] == "x" && beforeConstrain)
storePosAsDelta[step] = true;
}
bool storedAsDelta = false;
for (int step = 0; step < numSteps; step++) {
loadPosAsDelta[step] = storedAsDelta;
if (storePosAsDelta[step] == true)
storedAsDelta = true;
if (stepType[step] == CustomIntegrator::ConstrainPositions)
storedAsDelta = false;
if (hasAnyConstraints) {
bool beforeConstrain = false;
for (int step = numSteps-1; step >= 0; step--) {
if (stepType[step] == CustomIntegrator::ConstrainPositions)
beforeConstrain = true;
else if (stepType[step] == CustomIntegrator::ComputePerDof && variable[step] == "x" && beforeConstrain)
storePosAsDelta[step] = true;
}
bool storedAsDelta = false;
for (int step = 0; step < numSteps; step++) {
loadPosAsDelta[step] = storedAsDelta;
if (storePosAsDelta[step] == true)
storedAsDelta = true;
if (stepType[step] == CustomIntegrator::ConstrainPositions)
storedAsDelta = false;
}
}
// Identify steps that can be merged into a single kernel.
......@@ -6214,9 +6217,11 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
context.updateContextState();
}
else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
cu.getIntegrationUtilities().applyConstraints(integrator.getConstraintTolerance());
kernelArgs[step][0][1] = &posCorrection;
cu.executeKernel(kernels[step][0], &kernelArgs[step][0][0], numAtoms);
if (hasAnyConstraints) {
cu.getIntegrationUtilities().applyConstraints(integrator.getConstraintTolerance());
kernelArgs[step][0][1] = &posCorrection;
cu.executeKernel(kernels[step][0], &kernelArgs[step][0][0], numAtoms);
}
cu.getIntegrationUtilities().computeVirtualSites();
}
else if (stepType[step] == CustomIntegrator::ConstrainVelocities) {
......
platforms/opencl/include/OpenCLBondedUtilities.h
View file @ ef627240
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -137,7 +137,7 @@ private:
std::vector<OpenCLArray*> atomIndices;
std::vector<OpenCLArray*> bufferIndices;
std::vector<std::string> prefixCode;
int numForceBuffers, maxBonds;
int numForceBuffers, maxBonds, allGroups;
bool hasInitializedKernels;
};
......
platforms/opencl/include/OpenCLKernels.h
View file @ ef627240
......@@ -1283,7 +1283,7 @@ private:
double prevStepSize, energy;
float energyFloat;
int numGlobalVariables;
bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce;
bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce, hasAnyConstraints;
mutable bool localValuesAreCurrent;
OpenCLArray* globalValues;
OpenCLArray* sumBuffer;
......
platforms/opencl/src/OpenCLBondedUtilities.cpp
View file @ ef627240
......@@ -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) 2011-2012 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -33,7 +33,7 @@
using namespace OpenMM;
using namespace std;
OpenCLBondedUtilities::OpenCLBondedUtilities(OpenCLContext& context) : context(context), numForceBuffers(0), maxBonds(0), hasInitializedKernels(false) {
OpenCLBondedUtilities::OpenCLBondedUtilities(OpenCLContext& context) : context(context), numForceBuffers(0), maxBonds(0), allGroups(0), hasInitializedKernels(false) {
}
OpenCLBondedUtilities::~OpenCLBondedUtilities() {
......@@ -48,6 +48,7 @@ void OpenCLBondedUtilities::addInteraction(const vector<vector<int> >& atoms, co
forceAtoms.push_back(atoms);
forceSource.push_back(source);
forceGroup.push_back(group);
allGroups |= 1<<group;
int width = 1;
while (width < (int) atoms[0].size())
width *= 2;
......@@ -73,7 +74,7 @@ void OpenCLBondedUtilities::initialize(const System& system) {
if (numForces == 0)
return;
// Build the lists of atom indicse and buffer indices.
// Build the lists of atom indices and buffer indices.
vector<vector<cl_uint> > bufferVec(numForces);
vector<vector<int> > bufferCounter(numForces, vector<int>(system.getNumParticles(), 0));
......@@ -253,6 +254,8 @@ string OpenCLBondedUtilities::createForceSource(int forceIndex, int numBonds, in
}
void OpenCLBondedUtilities::computeInteractions(int groups) {
if ((groups&allGroups) == 0)
return;
if (!hasInitializedKernels) {
hasInitializedKernels = true;
for (int i = 0; i < (int) forceSets.size(); i++) {
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ ef627240
......@@ -6141,22 +6141,25 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
// Determine how each step will represent the position (as just a value, or a value plus a delta).
hasAnyConstraints = (context.getSystem().getNumConstraints() > 0);
vector<bool> storePosAsDelta(numSteps, false);
vector<bool> loadPosAsDelta(numSteps, false);
bool beforeConstrain = false;
for (int step = numSteps-1; step >= 0; step--) {
if (stepType[step] == CustomIntegrator::ConstrainPositions)
beforeConstrain = true;
else if (stepType[step] == CustomIntegrator::ComputePerDof && variable[step] == "x" && beforeConstrain)
storePosAsDelta[step] = true;
}
bool storedAsDelta = false;
for (int step = 0; step < numSteps; step++) {
loadPosAsDelta[step] = storedAsDelta;
if (storePosAsDelta[step] == true)
storedAsDelta = true;
if (stepType[step] == CustomIntegrator::ConstrainPositions)
storedAsDelta = false;
if (hasAnyConstraints) {
bool beforeConstrain = false;
for (int step = numSteps-1; step >= 0; step--) {
if (stepType[step] == CustomIntegrator::ConstrainPositions)
beforeConstrain = true;
else if (stepType[step] == CustomIntegrator::ComputePerDof && variable[step] == "x" && beforeConstrain)
storePosAsDelta[step] = true;
}
bool storedAsDelta = false;
for (int step = 0; step < numSteps; step++) {
loadPosAsDelta[step] = storedAsDelta;
if (storePosAsDelta[step] == true)
storedAsDelta = true;
if (stepType[step] == CustomIntegrator::ConstrainPositions)
storedAsDelta = false;
}
}
// Identify steps that can be merged into a single kernel.
......@@ -6478,8 +6481,10 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
context.updateContextState();
}
else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
cl.getIntegrationUtilities().applyConstraints(integrator.getConstraintTolerance());
cl.executeKernel(kernels[step][0], numAtoms);
if (hasAnyConstraints) {
cl.getIntegrationUtilities().applyConstraints(integrator.getConstraintTolerance());
cl.executeKernel(kernels[step][0], numAtoms);
}
cl.getIntegrationUtilities().computeVirtualSites();
}
else if (stepType[step] == CustomIntegrator::ConstrainVelocities) {
......
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