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Commit 0360c770 authored by peastman's avatar peastman
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Lots of cleanup to CUDA CustomIntegrator

parent 59c809c0
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Showing with 26 additions and 123 deletions
platforms/cuda/include/CudaKernels.h
View file @ 0360c770
......@@ -1218,8 +1218,8 @@ class CudaIntegrateCustomStepKernel : public IntegrateCustomStepKernel {
public:
enum GlobalTargetType {DT, VARIABLE, PARAMETER};
CudaIntegrateCustomStepKernel(std::string name, const Platform& platform, CudaContext& cu) : IntegrateCustomStepKernel(name, platform), cu(cu),
hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), contextParameterValues(NULL), sumBuffer(NULL), potentialEnergy(NULL),
kineticEnergy(NULL), uniformRandoms(NULL), randomSeed(NULL), perDofValues(NULL) {
hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), sumBuffer(NULL), summedValue(NULL), uniformRandoms(NULL),
randomSeed(NULL), perDofValues(NULL) {
}
~CudaIntegrateCustomStepKernel();
/**
......@@ -1284,7 +1284,6 @@ public:
private:
class ReorderListener;
class GlobalTarget;
std::string createGlobalComputation(const std::string& variable, const Lepton::ParsedExpression& expr, CustomIntegrator& integrator, const std::string& energyName);
std::string createPerDofComputation(const std::string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator, const std::string& forceName, const std::string& energyName);
void prepareForComputation(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
void recordGlobalValue(double value, GlobalTarget target);
......@@ -1296,10 +1295,8 @@ private:
bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce;
mutable bool localValuesAreCurrent;
CudaArray* globalValues;
CudaArray* contextParameterValues;
CudaArray* sumBuffer;
CudaArray* potentialEnergy;
CudaArray* kineticEnergy;
CudaArray* summedValue;
CudaArray* uniformRandoms;
CudaArray* randomSeed;
std::map<int, CudaArray*> savedForces;
......@@ -1307,8 +1304,6 @@ private:
CudaParameterSet* perDofValues;
mutable std::vector<std::vector<float> > localPerDofValuesFloat;
mutable std::vector<std::vector<double> > localPerDofValuesDouble;
std::vector<float> contextValuesFloat;
std::vector<double> contextValuesDouble;
std::vector<float> globalValuesFloat;
std::vector<double> globalValuesDouble;
std::vector<double> initialGlobalVariables;
......
platforms/cuda/src/CudaKernels.cpp
View file @ 0360c770
......@@ -5672,14 +5672,10 @@ CudaIntegrateCustomStepKernel::~CudaIntegrateCustomStepKernel() {
cu.setAsCurrent();
if (globalValues != NULL)
delete globalValues;
if (contextParameterValues != NULL)
delete contextParameterValues;
if (sumBuffer != NULL)
delete sumBuffer;
if (potentialEnergy != NULL)
delete potentialEnergy;
if (kineticEnergy != NULL)
delete kineticEnergy;
if (summedValue != NULL)
delete summedValue;
if (uniformRandoms != NULL)
delete uniformRandoms;
if (randomSeed != NULL)
......@@ -5697,44 +5693,13 @@ void CudaIntegrateCustomStepKernel::initialize(const System& system, const Custo
numGlobalVariables = integrator.getNumGlobalVariables();
int elementSize = (cu.getUseDoublePrecision() || cu.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
sumBuffer = new CudaArray(cu, ((3*system.getNumParticles()+3)/4)*4, elementSize, "sumBuffer");
potentialEnergy = new CudaArray(cu, 1, cu.getEnergyBuffer().getElementSize(), "potentialEnergy");
kineticEnergy = new CudaArray(cu, 1, elementSize, "kineticEnergy");
summedValue = new CudaArray(cu, 1, elementSize, "summedValue");
perDofValues = new CudaParameterSet(cu, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables", false, cu.getUseDoublePrecision() || cu.getUseMixedPrecision());
cu.addReorderListener(new ReorderListener(cu, *perDofValues, localPerDofValuesFloat, localPerDofValuesDouble, deviceValuesAreCurrent));
prevStepSize = -1.0;
SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
}
string CudaIntegrateCustomStepKernel::createGlobalComputation(const string& variable, const Lepton::ParsedExpression& expr, CustomIntegrator& integrator, const string& energyName) {
map<string, Lepton::ParsedExpression> expressions;
if (variable == "dt")
expressions["dt[0].y = "] = expr;
else {
for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
if (variable == integrator.getGlobalVariableName(i))
expressions["globals["+cu.intToString(i)+"] = "] = expr;
for (int i = 0; i < (int) parameterNames.size(); i++)
if (variable == parameterNames[i]) {
expressions["params["+cu.intToString(i)+"] = "] = expr;
modifiesParameters = true;
}
}
if (expressions.size() == 0)
throw OpenMMException("Unknown global variable: "+variable);
map<string, string> variables;
variables["dt"] = "dt[0].y";
variables["uniform"] = "uniform";
variables["gaussian"] = "gaussian";
variables[energyName] = "energy";
for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
variables[integrator.getGlobalVariableName(i)] = "globals["+cu.intToString(i)+"]";
for (int i = 0; i < (int) parameterNames.size(); i++)
variables[parameterNames[i]] = "params["+cu.intToString(i)+"]";
vector<const TabulatedFunction*> functions;
vector<pair<string, string> > functionNames;
return cu.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
}
string CudaIntegrateCustomStepKernel::createPerDofComputation(const string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator, const string& forceName, const string& energyName) {
const string suffixes[] = {".x", ".y", ".z"};
string suffix = suffixes[component];
......@@ -5785,24 +5750,8 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
// Initialize various data structures.
const map<string, double>& params = context.getParameters();
if (useDouble) {
contextParameterValues = CudaArray::create<double>(cu, max(1, (int) params.size()), "contextParameters");
contextValuesDouble.resize(contextParameterValues->getSize());
for (map<string, double>::const_iterator iter = params.begin(); iter != params.end(); ++iter) {
contextValuesDouble[parameterNames.size()] = iter->second;
for (map<string, double>::const_iterator iter = params.begin(); iter != params.end(); ++iter)
parameterNames.push_back(iter->first);
}
contextParameterValues->upload(contextValuesDouble);
}
else {
contextParameterValues = CudaArray::create<float>(cu, max(1, (int) params.size()), "contextParameters");
contextValuesFloat.resize(contextParameterValues->getSize());
for (map<string, double>::const_iterator iter = params.begin(); iter != params.end(); ++iter) {
contextValuesFloat[parameterNames.size()] = (float) iter->second;
parameterNames.push_back(iter->first);
}
contextParameterValues->upload(contextValuesFloat);
}
kernels.resize(integrator.getNumComputations());
kernelArgs.resize(integrator.getNumComputations());
requiredGaussian.resize(integrator.getNumComputations(), 0);
......@@ -5906,8 +5855,10 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
if (variable[step] == integrator.getGlobalVariableName(i))
stepTarget[step].type = VARIABLE;
for (int i = 0; i < (int) parameterNames.size(); i++)
if (variable[step] == parameterNames[i])
if (variable[step] == parameterNames[i]) {
stepTarget[step].type = PARAMETER;
modifiesParameters = true;
}
stepTarget[step].variableIndex = expressionSet.getVariableIndex(variable[step]);
}
}
......@@ -6026,7 +5977,6 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
args1.push_back(&cu.getForce().getDevicePointer());
args1.push_back(&integration.getStepSize().getDevicePointer());
args1.push_back(&globalValues->getDevicePointer());
args1.push_back(&contextParameterValues->getDevicePointer());
args1.push_back(&sumBuffer->getDevicePointer());
args1.push_back(NULL);
args1.push_back(NULL);
......@@ -6043,20 +5993,7 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
vector<void*> args2;
args2.push_back(&sumBuffer->getDevicePointer());
bool found = false;
for (int j = 0; j < integrator.getNumGlobalVariables() && !found; j++)
if (variable[step] == integrator.getGlobalVariableName(j)) {
args2.push_back(&kineticEnergy->getDevicePointer());
found = true;
}
for (int j = 0; j < (int) parameterNames.size() && !found; j++)
if (variable[step] == parameterNames[j]) {
args2.push_back(&kineticEnergy->getDevicePointer());
found = true;
modifiesParameters = true;
}
if (!found)
throw OpenMMException("Unknown global variable: "+variable[step]);
args2.push_back(&summedValue->getDevicePointer());
defines["SUM_BUFFER_SIZE"] = cu.intToString(3*numAtoms);
module = cu.createModule(CudaKernelSources::customIntegrator, defines);
kernel = cu.getKernel(module, useDouble ? "computeDoubleSum" : "computeFloatSum");
......@@ -6064,29 +6001,6 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
kernelArgs[step].push_back(args2);
}
}
else if (stepType[step] == CustomIntegrator::ComputeGlobal && !merged[step]) {
// Compute a global value.
stringstream compute;
for (int i = step; i < numSteps && (i == step || merged[i]); i++)
compute << "{\n" << createGlobalComputation(variable[i], expression[i][0], integrator, energyName[i]) << "}\n";
map<string, string> replacements;
replacements["COMPUTE_STEP"] = compute.str();
CUmodule module = cu.createModule(cu.replaceStrings(CudaKernelSources::customIntegratorGlobal, replacements), defines);
CUfunction kernel = cu.getKernel(module, "computeGlobal");
kernels[step].push_back(kernel);
vector<void*> args;
args.push_back(&integration.getStepSize().getDevicePointer());
args.push_back(&globalValues->getDevicePointer());
args.push_back(&contextParameterValues->getDevicePointer());
args.push_back(NULL);
args.push_back(NULL);
if (cu.getUseDoublePrecision())
args.push_back(&energy);
else
args.push_back(&energyFloat);
kernelArgs[step].push_back(args);
}
else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
// Apply position constraints.
......@@ -6157,7 +6071,6 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
kineticEnergyArgs.push_back(&cu.getForce().getDevicePointer());
kineticEnergyArgs.push_back(&integration.getStepSize().getDevicePointer());
kineticEnergyArgs.push_back(&globalValues->getDevicePointer());
kineticEnergyArgs.push_back(&contextParameterValues->getDevicePointer());
kineticEnergyArgs.push_back(&sumBuffer->getDevicePointer());
kineticEnergyArgs.push_back(NULL);
kineticEnergyArgs.push_back(NULL);
......@@ -6255,9 +6168,9 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
if (stepType[i] == CustomIntegrator::ComputePerDof && !merged[i]) {
int randomIndex = integration.prepareRandomNumbers(requiredGaussian[i]);
kernelArgs[i][0][1] = &posCorrection;
kernelArgs[i][0][9] = &integration.getRandom().getDevicePointer();
kernelArgs[i][0][10] = &randomIndex;
kernelArgs[i][0][11] = &uniformRandoms->getDevicePointer();
kernelArgs[i][0][8] = &integration.getRandom().getDevicePointer();
kernelArgs[i][0][9] = &randomIndex;
kernelArgs[i][0][10] = &uniformRandoms->getDevicePointer();
if (requiredUniform[i] > 0)
cu.executeKernel(randomKernel, &randomArgs[0], numAtoms);
cu.executeKernel(kernels[i][0], &kernelArgs[i][0][0], numAtoms);
......@@ -6271,9 +6184,9 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
else if (stepType[i] == CustomIntegrator::ComputeSum) {
int randomIndex = integration.prepareRandomNumbers(requiredGaussian[i]);
kernelArgs[i][0][1] = &posCorrection;
kernelArgs[i][0][9] = &integration.getRandom().getDevicePointer();
kernelArgs[i][0][10] = &randomIndex;
kernelArgs[i][0][11] = &uniformRandoms->getDevicePointer();
kernelArgs[i][0][8] = &integration.getRandom().getDevicePointer();
kernelArgs[i][0][9] = &randomIndex;
kernelArgs[i][0][10] = &uniformRandoms->getDevicePointer();
if (requiredUniform[i] > 0)
cu.executeKernel(randomKernel, &randomArgs[0], numAtoms);
cu.clearBuffer(*sumBuffer);
......@@ -6281,12 +6194,12 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
cu.executeKernel(kernels[i][1], &kernelArgs[i][1][0], CudaContext::ThreadBlockSize, CudaContext::ThreadBlockSize);
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
double value;
kineticEnergy->download(&value);
summedValue->download(&value);
globalValuesDouble[stepTarget[i].variableIndex] = value;
}
else {
float value;
kineticEnergy->download(&value);
summedValue->download(&value);
globalValuesDouble[stepTarget[i].variableIndex] = value;
}
}
......@@ -6335,20 +6248,20 @@ double CudaIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context,
CUdeviceptr posCorrection = (cu.getUseMixedPrecision() ? cu.getPosqCorrection().getDevicePointer() : 0);
int randomIndex = 0;
kineticEnergyArgs[1] = &posCorrection;
kineticEnergyArgs[9] = &cu.getIntegrationUtilities().getRandom().getDevicePointer();
kineticEnergyArgs[10] = &randomIndex;
kineticEnergyArgs[8] = &cu.getIntegrationUtilities().getRandom().getDevicePointer();
kineticEnergyArgs[9] = &randomIndex;
cu.clearBuffer(*sumBuffer);
cu.executeKernel(kineticEnergyKernel, &kineticEnergyArgs[0], cu.getNumAtoms());
void* args[] = {&sumBuffer->getDevicePointer(), &kineticEnergy->getDevicePointer()};
void* args[] = {&sumBuffer->getDevicePointer(), &summedValue->getDevicePointer()};
cu.executeKernel(sumKineticEnergyKernel, args, CudaContext::ThreadBlockSize, CudaContext::ThreadBlockSize);
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
double ke;
kineticEnergy->download(&ke);
summedValue->download(&ke);
return ke;
}
else {
float ke;
kineticEnergy->download(&ke);
summedValue->download(&ke);
return ke;
}
}
......
platforms/cuda/src/kernels/customIntegratorGlobal.cu deleted 100644 → 0
View file @ 59c809c0
extern "C" __global__ void computeGlobal(mixed2* __restrict__ dt, mixed* __restrict__ globals, mixed* __restrict__ params,
float uniform, float gaussian, const real energy) {
COMPUTE_STEP
}
platforms/cuda/src/kernels/customIntegratorPerDof.cu
View file @ 0360c770
......@@ -33,8 +33,7 @@ inline __device__ mixed4 convertFromDouble4(double4 a) {
extern "C" __global__ void computePerDof(real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ posDelta,
mixed4* __restrict__ velm, const long long* __restrict__ force, const mixed2* __restrict__ dt, const mixed* __restrict__ globals,
const mixed* __restrict__ params, mixed* __restrict__ sum, const float4* __restrict__ gaussianValues,
unsigned int gaussianBaseIndex, const float4* __restrict__ uniformValues, const real energy
mixed* __restrict__ sum, const float4* __restrict__ gaussianValues, unsigned int gaussianBaseIndex, const float4* __restrict__ uniformValues, const real energy
PARAMETER_ARGUMENTS) {
mixed stepSize = dt[0].y;
int index = blockIdx.x*blockDim.x+threadIdx.x;
......
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