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Commit dc8625a0 authored by Peter Eastman's avatar Peter Eastman
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Continuing implementation of OpenCL CustomIntegrator

parent 36f6f9e6
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Showing with 270 additions and 12 deletions
platforms/opencl/src/OpenCLKernels.cpp
View file @ dc8625a0
......@@ -3504,6 +3504,10 @@ void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co
OpenCLIntegrateCustomStepKernel::~OpenCLIntegrateCustomStepKernel() {
if (globalValues != NULL)
delete globalValues;
if (contextParameterValues != NULL)
delete contextParameterValues;
if (sumBuffer != NULL)
delete sumBuffer;
if (perDofValues != NULL)
delete perDofValues;
}
......@@ -3513,6 +3517,7 @@ 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);
perDofValues = new OpenCLParameterSet(cl, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables");
prevStepSize = -1.0;
SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
......@@ -3526,7 +3531,14 @@ string OpenCLIntegrateCustomStepKernel::createGlobalComputation(const string& va
for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
if (variable == integrator.getGlobalVariableName(i))
expressions["globals["+intToString(i)+"] = "] = expr;
for (int i = 0; i < (int) parameterNames.size(); i++)
if (variable == parameterNames[i]) {
expressions["params["+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";
......@@ -3534,6 +3546,8 @@ string OpenCLIntegrateCustomStepKernel::createGlobalComputation(const string& va
variables["energy"] = "energy";
for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
variables[integrator.getGlobalVariableName(i)] = "globals["+intToString(i)+"]";
for (int i = 0; i < (int) parameterNames.size(); i++)
variables[parameterNames[i]] = "params["+intToString(i)+"]";
vector<pair<string, string> > functions;
return OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
}
......@@ -3546,11 +3560,15 @@ string OpenCLIntegrateCustomStepKernel::createPerDofComputation(const string& va
expressions["position"+suffix+" = "] = expr;
else if (variable == "v")
expressions["velocity"+suffix+" = "] = expr;
else if (variable == "")
expressions["sum[3*index+"+intToString(component)+"] = "] = expr;
else {
for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
if (variable == integrator.getPerDofVariableName(i))
expressions["perDof"+suffix.substr(1)+perDofValues->getParameterSuffix(i)+" = "] = expr;
}
if (expressions.size() == 0)
throw OpenMMException("Unknown per-DOF variable: "+variable);
map<string, string> variables;
variables["x"] = "position"+suffix;
variables["v"] = "velocity"+suffix;
......@@ -3563,6 +3581,8 @@ string OpenCLIntegrateCustomStepKernel::createPerDofComputation(const string& va
variables[integrator.getGlobalVariableName(i)] = "globals["+intToString(i)+"]";
for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
variables[integrator.getPerDofVariableName(i)] = "perDof"+suffix.substr(1)+perDofValues->getParameterSuffix(i);
for (int i = 0; i < (int) parameterNames.size(); i++)
variables[parameterNames[i]] = "params["+intToString(i)+"]";
vector<pair<string, string> > functions;
return OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp"+intToString(component)+"_", "");
}
......@@ -3573,11 +3593,22 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
int numSteps = integrator.getNumComputations();
if (!hasInitializedKernels) {
hasInitializedKernels = true;
// Initialize various data structures.
const map<string, double>& params = context.getParameters();
contextParameterValues = new OpenCLArray<cl_float>(cl, max(1, (int) params.size()), "contextParameters", true);
for (map<string, double>::const_iterator iter = params.begin(); iter != params.end(); ++iter) {
contextParameterValues->set(parameterNames.size(), (float) iter->second);
parameterNames.push_back(iter->first);
}
contextParameterValues->upload();
kernels.resize(integrator.getNumComputations());
requiredRandoms.resize(integrator.getNumComputations());
needsForces.resize(numSteps, false);
needsEnergy.resize(numSteps, false);
invalidatesForces.resize(numSteps, false);
modifiesParameters = false;
// Build a list of all variables that affect the forces, so we can tell which
// steps invalidate them.
......@@ -3591,6 +3622,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
}
map<string, string> defines;
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
defines["WORK_GROUP_SIZE"] = intToString(OpenCLContext::ThreadBlockSize);
// Loop over all steps and create the kernels for them.
......@@ -3600,7 +3632,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
integrator.getComputationStep(step, type, variable, expression);
stepType.push_back(type);
invalidatesForces[step] = (type == CustomIntegrator::ConstrainPositions || affectsForce.find(variable) != affectsForce.end());
if (type == CustomIntegrator::ComputePerDof) {
if (type == CustomIntegrator::ComputePerDof || type == CustomIntegrator::ComputeSum) {
// Compute a per-DOF value.
stringstream compute;
......@@ -3614,7 +3646,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
needsForces[step] = usesVariable(expr, "f");
needsEnergy[step] = usesVariable(expr, "energy");
for (int i = 0; i < 3; i++)
compute << createPerDofComputation(variable, expr, i, integrator);
compute << createPerDofComputation(type == CustomIntegrator::ComputePerDof ? variable : "", expr, i, integrator);
if (variable == "x")
compute << "posq[index] = position;\n";
else if (variable == "v")
......@@ -3647,10 +3679,37 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
kernel.setArg<cl::Buffer>(index++, cl.getForce().getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, integration.getStepSize().getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, contextParameterValues->getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, integration.getRandom().getDeviceBuffer());
index += 2;
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
kernel.setArg<cl::Memory>(index++, perDofValues->getBuffers()[i].getMemory());
if (type == CustomIntegrator::ComputeSum) {
// Create a second kernel for this step that sums the values.
program = cl.createProgram(OpenCLKernelSources::customIntegratorSum, defines);
kernel = cl::Kernel(program, "computeSum");
kernels[step].push_back(kernel);
index = 0;
kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
bool found = false;
for (int j = 0; j < integrator.getNumGlobalVariables() && !found; j++)
if (variable == integrator.getGlobalVariableName(j)) {
kernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
kernel.setArg<cl_uint>(index++, j);
found = true;
}
for (int j = 0; j < (int) parameterNames.size() && !found; j++)
if (variable == parameterNames[j]) {
kernel.setArg<cl::Buffer>(index++, contextParameterValues->getDeviceBuffer());
kernel.setArg<cl_uint>(index++, j);
found = true;
modifiesParameters = true;
}
if (!found)
throw OpenMMException("Unknown global variable: "+variable);
}
}
else if (type == CustomIntegrator::ComputeGlobal) {
// Compute a global value.
......@@ -3668,9 +3727,13 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
int index = 0;
kernel.setArg<cl::Buffer>(index++, integration.getStepSize().getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, contextParameterValues->getDeviceBuffer());
}
}
}
// Make sure all values (variables, parameters, etc.) stored on the device are up to date.
if (!deviceValuesAreCurrent) {
perDofValues->setParameterValues(localPerDofValues);
deviceValuesAreCurrent = true;
......@@ -3682,6 +3745,16 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
integration.getStepSize().upload();
prevStepSize = stepSize;
}
bool paramsChanged = false;
for (int i = 0; i < (int) parameterNames.size(); i++) {
float value = (float) context.getParameter(parameterNames[i]);
if (value != contextParameterValues->get(i)) {
contextParameterValues->set(i, value);
paramsChanged = true;
}
}
if (paramsChanged)
contextParameterValues->upload();
// Loop over computation steps in the integrator and execute them.
......@@ -3703,27 +3776,37 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
if (j == i-1)
break;
}
recordChangedParameters(context);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy);
if (computeEnergy)
energy = e;
forcesAreValid = true;
}
if (stepType[i] == CustomIntegrator::ComputePerDof) {
kernels[i][0].setArg<cl_uint>(7, integration.prepareRandomNumbers(requiredRandoms[i][0]));
kernels[i][0].setArg<cl_float>(8, energy);
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) {
kernels[i][0].setArg<cl_float>(2, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
kernels[i][0].setArg<cl_float>(3, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
kernels[i][0].setArg<cl_float>(4, energy);
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::UpdateContextState)
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);
}
else if (stepType[i] == CustomIntegrator::UpdateContextState) {
recordChangedParameters(context);
context.updateContextState();
}
if (invalidatesForces[i])
forcesAreValid = false;
}
recordChangedParameters(context);
// Update the time and step count.
......@@ -3731,6 +3814,17 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
cl.setStepCount(cl.getStepCount()+1);
}
void OpenCLIntegrateCustomStepKernel::recordChangedParameters(ContextImpl& context) {
if (!modifiesParameters)
return;
contextParameterValues->download();
for (int i = 0; i < (int) parameterNames.size(); i++) {
float value = (float) context.getParameter(parameterNames[i]);
if (value != contextParameterValues->get(i))
context.setParameter(parameterNames[i], contextParameterValues->get(i));
}
}
void OpenCLIntegrateCustomStepKernel::getGlobalVariables(ContextImpl& context, vector<double>& values) const {
globalValues->download();
values.resize(numGlobalVariables);
......
platforms/opencl/src/OpenCLKernels.h
View file @ dc8625a0
......@@ -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), perDofValues(NULL) {
hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), contextParameterValues(NULL), sumBuffer(NULL), perDofValues(NULL) {
}
~OpenCLIntegrateCustomStepKernel();
/**
......@@ -937,12 +937,15 @@ public:
private:
std::string createGlobalComputation(const std::string& variable, const Lepton::ParsedExpression& expr, CustomIntegrator& integrator);
std::string createPerDofComputation(const std::string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator);
void recordChangedParameters(ContextImpl& context);
OpenCLContext& cl;
double prevStepSize, energy;
int numGlobalVariables;
bool hasInitializedKernels, deviceValuesAreCurrent;
bool hasInitializedKernels, deviceValuesAreCurrent, modifiesParameters;
mutable bool localValuesAreCurrent;
OpenCLArray<cl_float>* globalValues;
OpenCLArray<cl_float>* contextParameterValues;
OpenCLArray<cl_float>* sumBuffer;
OpenCLParameterSet* perDofValues;
mutable std::vector<std::vector<cl_float> > localPerDofValues;
std::vector<std::vector<cl::Kernel> > kernels;
......@@ -951,6 +954,7 @@ private:
std::vector<bool> needsEnergy;
std::vector<bool> invalidatesForces;
std::vector<std::vector<int> > requiredRandoms;
std::vector<std::string> parameterNames;
};
/**
......
platforms/opencl/src/kernels/customIntegratorGlobal.cl
View file @ dc8625a0
__kernel void computeGlobal(__global float2* restrict dt, __global float* restrict globals, 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, float energy) {
COMPUTE_STEP
}
platforms/opencl/src/kernels/customIntegratorPerDof.cl
View file @ dc8625a0
__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 float4* restrict random, unsigned int randomIndex, float energy
__global const float* restrict params, __global float* restrict sum, __global const float4* restrict random,
unsigned int randomIndex, float energy
PARAMETER_ARGUMENTS) {
float stepSize = dt[0].y;
int index = get_global_id(0);
......
platforms/opencl/src/kernels/customIntegratorSum.cl 0 → 100644
View file @ dc8625a0
__kernel void computeSum(__global const float* restrict sumBuffer, __global float* result, unsigned int outputIndex) {
__local float tempBuffer[WORK_GROUP_SIZE];
const unsigned int thread = get_local_id(0);
float sum = 0.0f;
for (unsigned int index = thread; index < 3*NUM_ATOMS; index += get_local_size(0))
sum += sumBuffer[index];
tempBuffer[thread] = sum;
for (int i = 1; i < WORK_GROUP_SIZE; i *= 2) {
barrier(CLK_LOCAL_MEM_FENCE);
if (thread%(i*2) == 0 && thread+i < WORK_GROUP_SIZE)
tempBuffer[thread] += tempBuffer[thread+i];
}
if (thread == 0)
result[outputIndex] = tempBuffer[0];
}
platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp
View file @ dc8625a0
......@@ -309,6 +309,76 @@ void testMonteCarlo() {
ASSERT_USUALLY_EQUAL_TOL((double) counts[i]/numIterations, expected[i]/sum, 0.01);
}
/**
* Test the ComputeSum operation.
*/
void testSum() {
const int numParticles = 200;
const double boxSize = 10;
OpenCLPlatform platform;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nb = new NonbondedForce();
system.addForce(nb);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.5);
nb->addParticle(i%2 == 0 ? 1 : -1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
close = true;
}
}
}
CustomIntegrator integrator(0.01);
integrator.addGlobalVariable("ke", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputeSum("ke", "m*v*v/2");
Context context(system, integrator, platform);
context.setPositions(positions);
// See if the sum is being computed correctly.
State state = context.getState(State::Energy);
const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 100; ++i) {
state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state.getKineticEnergy(), integrator.getGlobalVariable(0), 1e-5);
integrator.step(1);
}
}
/**
* Test an integrator that both uses and modifies a context parameter.
*/
void testParameter() {
OpenCLPlatform platform;
System system;
system.addParticle(1.0);
AndersenThermostat* thermostat = new AndersenThermostat(0.1, 0.1);
system.addForce(thermostat);
CustomIntegrator integrator(0.1);
integrator.addGlobalVariable("temp", 0);
integrator.addComputeGlobal("temp", "AndersenTemperature");
integrator.addComputeGlobal("AndersenTemperature", "temp*2");
Context context(system, integrator, platform);
// See if the parameter is being used correctly.
for (int i = 0; i < 10; i++) {
integrator.step(1);
ASSERT_EQUAL_TOL(context.getParameter("AndersenTemperature"), 0.1*(1<<(i+1)), 1e-5);
}
}
int main() {
try {
testSingleBond();
......@@ -316,6 +386,8 @@ int main() {
// testVelocityConstraints();
testWithThermostat();
testMonteCarlo();
testSum();
testParameter();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/tests/TestReferenceCustomIntegrator.cpp
View file @ dc8625a0
......@@ -309,6 +309,76 @@ void testMonteCarlo() {
ASSERT_USUALLY_EQUAL_TOL((double) counts[i]/numIterations, expected[i]/sum, 0.01);
}
/**
* Test the ComputeSum operation.
*/
void testSum() {
const int numParticles = 200;
const double boxSize = 10;
ReferencePlatform platform;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
NonbondedForce* nb = new NonbondedForce();
system.addForce(nb);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.5);
nb->addParticle(i%2 == 0 ? 1 : -1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
close = true;
}
}
}
CustomIntegrator integrator(0.01);
integrator.addGlobalVariable("ke", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.addComputeSum("ke", "m*v*v/2");
Context context(system, integrator, platform);
context.setPositions(positions);
// See if the sum is being computed correctly.
State state = context.getState(State::Energy);
const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 100; ++i) {
state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state.getKineticEnergy(), integrator.getGlobalVariable(0), 1e-5);
integrator.step(1);
}
}
/**
* Test an integrator that both uses and modifies a context parameter.
*/
void testParameter() {
ReferencePlatform platform;
System system;
system.addParticle(1.0);
AndersenThermostat* thermostat = new AndersenThermostat(0.1, 0.1);
system.addForce(thermostat);
CustomIntegrator integrator(0.1);
integrator.addGlobalVariable("temp", 0);
integrator.addComputeGlobal("temp", "AndersenTemperature");
integrator.addComputeGlobal("AndersenTemperature", "temp*2");
Context context(system, integrator, platform);
// See if the parameter is being used correctly.
for (int i = 0; i < 10; i++) {
integrator.step(1);
ASSERT_EQUAL_TOL(context.getParameter("AndersenTemperature"), 0.1*(1<<(i+1)), 1e-10);
}
}
int main() {
try {
testSingleBond();
......@@ -316,6 +386,8 @@ int main() {
testVelocityConstraints();
testWithThermostat();
testMonteCarlo();
testSum();
testParameter();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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