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Commit 0d5f265c authored by Peter Eastman's avatar Peter Eastman
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Optimizations to CustomIntegrator: sum energy on the device, merge kernels when possible

parent b45e0d8e
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Showing with 77 additions and 41 deletions
platforms/opencl/src/OpenCLKernels.cpp
View file @ 0d5f265c
......@@ -3507,6 +3507,8 @@ OpenCLIntegrateCustomStepKernel::~OpenCLIntegrateCustomStepKernel() {
delete contextParameterValues;
if (sumBuffer != NULL)
delete sumBuffer;
if (energy != NULL)
delete energy;
if (perDofValues != NULL)
delete perDofValues;
}
......@@ -3516,7 +3518,8 @@ void OpenCLIntegrateCustomStepKernel::initialize(const System& system, const Cus
cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
numGlobalVariables = integrator.getNumGlobalVariables();
globalValues = new OpenCLArray<cl_float>(cl, max(1, numGlobalVariables), "globalVariables", true);
sumBuffer = new OpenCLArray<cl_float>(cl, 3*system.getNumParticles(), "sumBuffer", true);
sumBuffer = new OpenCLArray<cl_float>(cl, 3*system.getNumParticles(), "sumBuffer");
energy = new OpenCLArray<cl_float>(cl, 1, "energy");
perDofValues = new OpenCLParameterSet(cl, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables");
prevStepSize = -1.0;
SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
......@@ -3542,7 +3545,7 @@ string OpenCLIntegrateCustomStepKernel::createGlobalComputation(const string& va
variables["dt"] = "dt[0].y";
variables["uniform"] = "uniform";
variables["gaussian"] = "gaussian";
variables["energy"] = "energy";
variables["energy"] = "energy[0]";
for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
variables[integrator.getGlobalVariableName(i)] = "globals["+intToString(i)+"]";
for (int i = 0; i < (int) parameterNames.size(); i++)
......@@ -3575,7 +3578,7 @@ string OpenCLIntegrateCustomStepKernel::createPerDofComputation(const string& va
variables["gaussian"] = "gaussian"+suffix;
variables["m"] = "mass";
variables["dt"] = "stepSize";
variables["energy"] = "energy";
variables["energy"] = "energy[0]";
for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
variables[integrator.getGlobalVariableName(i)] = "globals["+intToString(i)+"]";
for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
......@@ -3608,6 +3611,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
needsForces.resize(numSteps, false);
needsEnergy.resize(numSteps, false);
invalidatesForces.resize(numSteps, false);
merged.resize(numSteps, false);
modifiesParameters = false;
// Build a list of all variables that affect the forces, so we can tell which
......@@ -3632,8 +3636,12 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
for (int step = 0; step < numSteps; step++) {
string expr;
integrator.getComputationStep(step, stepType[step], variable[step], expr);
if (expr.size() > 0)
if (expr.size() > 0) {
expression[step] = Lepton::Parser::parse(expr).optimize();
needsForces[step] = usesVariable(expression[step], "f");
needsEnergy[step] = usesVariable(expression[step], "energy");
}
invalidatesForces[step] = (stepType[step] == CustomIntegrator::ConstrainPositions || affectsForce.find(variable[step]) != affectsForce.end());
}
// Determine how each step will represent the position (as just a value, or a value plus a delta).
......@@ -3656,11 +3664,22 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
storedAsDelta = false;
}
// Identify steps that can be merged into a single kernel.
for (int step = 1; step < numSteps; step++) {
if ((needsForces[step] || needsEnergy[step]) && invalidatesForces[step-1])
continue;
if (stepType[step-1] == CustomIntegrator::ComputeGlobal && stepType[step] == CustomIntegrator::ComputeGlobal)
merged[step] = true;
if (stepType[step-1] == CustomIntegrator::ComputePerDof && stepType[step] == CustomIntegrator::ComputePerDof &&
storePosAsDelta[step-1] == storePosAsDelta[step] && loadPosAsDelta[step-1] == loadPosAsDelta[step])
merged[step] = true;
}
// Loop over all steps and create the kernels for them.
for (int step = 0; step < numSteps; step++) {
invalidatesForces[step] = (stepType[step] == CustomIntegrator::ConstrainPositions || affectsForce.find(variable[step]) != affectsForce.end());
if (stepType[step] == CustomIntegrator::ComputePerDof || stepType[step] == CustomIntegrator::ComputeSum) {
if ((stepType[step] == CustomIntegrator::ComputePerDof || stepType[step] == CustomIntegrator::ComputeSum) && !merged[step]) {
// Compute a per-DOF value.
stringstream compute;
......@@ -3670,28 +3689,32 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
compute << buffer.getType()<<" perDofy"<<intToString(i+1)<<" = perDofValues"<<intToString(i+1)<<"[3*index+1];\n";
compute << buffer.getType()<<" perDofz"<<intToString(i+1)<<" = perDofValues"<<intToString(i+1)<<"[3*index+2];\n";
}
needsForces[step] = usesVariable(expression[step], "f");
needsEnergy[step] = usesVariable(expression[step], "energy");
for (int i = 0; i < 3; i++)
compute << createPerDofComputation(stepType[step] == CustomIntegrator::ComputePerDof ? variable[step] : "", expression[step], i, integrator);
string convert = (cl.getSupportsDoublePrecision() ? "convert_float4(" : "(");
if (variable[step] == "x") {
if (storePosAsDelta[step]) {
if (cl.getSupportsDoublePrecision())
compute << "posDelta[index] = convert_float4(position-convert_double4(posq[index]));\n";
int randoms = 0;
for (int j = step; j < numSteps && (j == step || merged[j]); j++) {
compute << "{\n";
for (int i = 0; i < 3; i++)
compute << createPerDofComputation(stepType[j] == CustomIntegrator::ComputePerDof ? variable[j] : "", expression[j], i, integrator);
if (variable[j] == "x") {
if (storePosAsDelta[j]) {
if (cl.getSupportsDoublePrecision())
compute << "posDelta[index] = convert_float4(position-convert_double4(posq[index]));\n";
else
compute << "posDelta[index] = position-posq[index];\n";
}
else
compute << "posDelta[index] = position-posq[index];\n";
compute << "posq[index] = " << convert << "position);\n";
}
else
compute << "posq[index] = " << convert << "position);\n";
}
else if (variable[step] == "v")
compute << "velm[index] = " << convert << "velocity);\n";
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
compute << "perDofValues"<<intToString(i+1)<<"[3*index] = perDofx"<<intToString(i+1)<<";\n";
compute << "perDofValues"<<intToString(i+1)<<"[3*index+1] = perDofy"<<intToString(i+1)<<";\n";
compute << "perDofValues"<<intToString(i+1)<<"[3*index+2] = perDofz"<<intToString(i+1)<<";\n";
else if (variable[j] == "v")
compute << "velm[index] = " << convert << "velocity);\n";
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
compute << "perDofValues"<<intToString(i+1)<<"[3*index] = perDofx"<<intToString(i+1)<<";\n";
compute << "perDofValues"<<intToString(i+1)<<"[3*index+1] = perDofy"<<intToString(i+1)<<";\n";
compute << "perDofValues"<<intToString(i+1)<<"[3*index+2] = perDofz"<<intToString(i+1)<<";\n";
}
compute << "}\n";
randoms += numAtoms*usesVariable(expression[j], "gaussian");
}
map<string, string> replacements;
replacements["COMPUTE_STEP"] = compute.str();
......@@ -3711,7 +3734,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
kernels[step].push_back(kernel);
if (usesVariable(expression[step], "uniform"))
throw OpenMMException("OpenCL platform does not currently support per-DOF uniform random numbers");
requiredRandoms[step].push_back(numAtoms*usesVariable(expression[step], "gaussian"));
requiredRandoms[step].push_back(randoms);
int index = 0;
kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
......@@ -3722,7 +3745,8 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
kernel.setArg<cl::Buffer>(index++, contextParameterValues->getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, integration.getRandom().getDeviceBuffer());
index += 2;
index++;
kernel.setArg<cl::Buffer>(index++, energy->getDeviceBuffer());
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
kernel.setArg<cl::Memory>(index++, perDofValues->getBuffers()[i].getMemory());
if (stepType[step] == CustomIntegrator::ComputeSum) {
......@@ -3751,12 +3775,12 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
throw OpenMMException("Unknown global variable: "+variable[step]);
}
}
else if (stepType[step] == CustomIntegrator::ComputeGlobal) {
else if (stepType[step] == CustomIntegrator::ComputeGlobal && !merged[step]) {
// Compute a global value.
stringstream compute;
needsEnergy[step] = usesVariable(expression[step], "energy");
compute << createGlobalComputation(variable[step], expression[step], integrator);
for (int i = step; i < numSteps && (i == step || merged[i]); i++)
compute << "{\n" << createGlobalComputation(variable[i], expression[i], integrator) << "}\n";
map<string, string> replacements;
replacements["COMPUTE_STEP"] = compute.str();
stringstream args;
......@@ -3767,6 +3791,8 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
kernel.setArg<cl::Buffer>(index++, integration.getStepSize().getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, contextParameterValues->getDeviceBuffer());
index += 2;
kernel.setArg<cl::Buffer>(index++, energy->getDeviceBuffer());
}
else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
// Apply position constraints.
......@@ -3779,6 +3805,15 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
kernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
}
}
// Create the kernel for summing energy.
cl::Program program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
sumEnergyKernel = cl::Kernel(program, "computeSum");
int index = 0;
sumEnergyKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
sumEnergyKernel.setArg<cl::Buffer>(index++, energy->getDeviceBuffer());
sumEnergyKernel.setArg<cl_float>(index++, 0);
}
// Make sure all values (variables, parameters, etc.) stored on the device are up to date.
......@@ -3826,25 +3861,22 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
break;
}
recordChangedParameters(context);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy);
context.calcForcesAndEnergy(computeForce, false);
if (computeEnergy)
energy = e;
cl.executeKernel(sumEnergyKernel, OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
forcesAreValid = true;
}
if (stepType[i] == CustomIntegrator::ComputePerDof) {
if (stepType[i] == CustomIntegrator::ComputePerDof && !merged[i]) {
kernels[i][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredRandoms[i][0]));
kernels[i][0].setArg<cl_float>(10, energy);
cl.executeKernel(kernels[i][0], numAtoms);
}
else if (stepType[i] == CustomIntegrator::ComputeGlobal) {
else if (stepType[i] == CustomIntegrator::ComputeGlobal && !merged[i]) {
kernels[i][0].setArg<cl_float>(3, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
kernels[i][0].setArg<cl_float>(4, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
kernels[i][0].setArg<cl_float>(5, energy);
cl.executeKernel(kernels[i][0], 1);
}
else if (stepType[i] == CustomIntegrator::ComputeSum) {
kernels[i][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredRandoms[i][0]));
kernels[i][0].setArg<cl_float>(10, energy);
cl.executeKernel(kernels[i][0], numAtoms);
cl.executeKernel(kernels[i][1], OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
}
......
platforms/opencl/src/OpenCLKernels.h
View file @ 0d5f265c
......@@ -883,7 +883,7 @@ private:
class OpenCLIntegrateCustomStepKernel : public IntegrateCustomStepKernel {
public:
OpenCLIntegrateCustomStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateCustomStepKernel(name, platform), cl(cl),
hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), contextParameterValues(NULL), sumBuffer(NULL), perDofValues(NULL) {
hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), contextParameterValues(NULL), sumBuffer(NULL), energy(NULL), perDofValues(NULL) {
}
~OpenCLIntegrateCustomStepKernel();
/**
......@@ -939,20 +939,23 @@ private:
std::string createPerDofComputation(const std::string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator);
void recordChangedParameters(ContextImpl& context);
OpenCLContext& cl;
double prevStepSize, energy;
double prevStepSize;
int numGlobalVariables;
bool hasInitializedKernels, deviceValuesAreCurrent, modifiesParameters;
mutable bool localValuesAreCurrent;
OpenCLArray<cl_float>* globalValues;
OpenCLArray<cl_float>* contextParameterValues;
OpenCLArray<cl_float>* sumBuffer;
OpenCLArray<cl_float>* energy;
OpenCLParameterSet* perDofValues;
mutable std::vector<std::vector<cl_float> > localPerDofValues;
std::vector<std::vector<cl::Kernel> > kernels;
cl::Kernel sumEnergyKernel;
std::vector<CustomIntegrator::ComputationType> stepType;
std::vector<bool> needsForces;
std::vector<bool> needsEnergy;
std::vector<bool> invalidatesForces;
std::vector<bool> merged;
std::vector<std::vector<int> > requiredRandoms;
std::vector<std::string> parameterNames;
};
......
platforms/opencl/src/kernels/customIntegratorGlobal.cl
View file @ 0d5f265c
__kernel void computeGlobal(__global float2* restrict dt, __global float* restrict globals, __global float* restrict params, float uniform, float gaussian, float energy) {
__kernel void computeGlobal(__global float2* restrict dt, __global float* restrict globals, __global float* restrict params,
float uniform, float gaussian, __global const float* restrict energy) {
COMPUTE_STEP
}
platforms/opencl/src/kernels/customIntegratorPerDof.cl
View file @ 0d5f265c
......@@ -5,7 +5,7 @@
__kernel void computePerDof(__global float4* restrict posq, __global float4* restrict posDelta, __global float4* restrict velm,
__global const float4* restrict force, __global const float2* restrict dt, __global const float* restrict globals,
__global const float* restrict params, __global float* restrict sum, __global const float4* restrict random,
unsigned int randomIndex, float energy
unsigned int randomIndex, __global const float* restrict energy
PARAMETER_ARGUMENTS) {
float stepSize = dt[0].y;
int index = get_global_id(0);
......
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