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Commit 052aea3e authored by Peter Eastman's avatar Peter Eastman
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Implemented per-DOF uniform random numbers for OpenCL. Also fixed some bugs... 

Implemented per-DOF uniform random numbers for OpenCL.  Also fixed some bugs in getting and setting per-DOF variables.
parent 0d5f265c
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Showing with 246 additions and 22 deletions
openmmapi/src/CustomIntegrator.cpp
View file @ 052aea3e
......@@ -55,8 +55,11 @@ void CustomIntegrator::initialize(ContextImpl& contextRef) {
kernel = context->getPlatform().createKernel(IntegrateCustomStepKernel::Name(), contextRef);
dynamic_cast<IntegrateCustomStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
dynamic_cast<IntegrateCustomStepKernel&>(kernel.getImpl()).setGlobalVariables(contextRef, globalValues);
for (int i = 0; i < (int) perDofValues.size(); i++)
for (int i = 0; i < (int) perDofValues.size(); i++) {
if (perDofValues[i].size() == 1)
perDofValues[i].resize(context->getSystem().getNumParticles(), perDofValues[i][0]);
dynamic_cast<IntegrateCustomStepKernel&>(kernel.getImpl()).setPerDofVariable(contextRef, i, perDofValues[i]);
}
}
void CustomIntegrator::stateChanged(State::DataType changed) {
......@@ -146,6 +149,8 @@ void CustomIntegrator::getPerDofVariable(int index, vector<Vec3>& values) const
void CustomIntegrator::setPerDofVariable(int index, const vector<Vec3>& values) {
if (index < 0 || index >= perDofNames.size())
throw OpenMMException("Index out of range");
if (values.size() != context->getSystem().getNumParticles())
throw OpenMMException("setPerDofVariable() called with wrong number of values");
if (owner == NULL)
perDofValues[index] = values;
else
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 052aea3e
......@@ -3509,6 +3509,10 @@ OpenCLIntegrateCustomStepKernel::~OpenCLIntegrateCustomStepKernel() {
delete sumBuffer;
if (energy != NULL)
delete energy;
if (uniformRandoms != NULL)
delete uniformRandoms;
if (randomSeed != NULL)
delete randomSeed;
if (perDofValues != NULL)
delete perDofValues;
}
......@@ -3576,6 +3580,7 @@ string OpenCLIntegrateCustomStepKernel::createPerDofComputation(const string& va
variables["v"] = "velocity"+suffix;
variables["f"] = "f"+suffix;
variables["gaussian"] = "gaussian"+suffix;
variables["uniform"] = "uniform"+suffix;
variables["m"] = "mass";
variables["dt"] = "stepSize";
variables["energy"] = "energy[0]";
......@@ -3607,12 +3612,34 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
}
contextParameterValues->upload();
kernels.resize(integrator.getNumComputations());
requiredRandoms.resize(integrator.getNumComputations());
requiredGaussian.resize(integrator.getNumComputations(), 0);
requiredUniform.resize(integrator.getNumComputations(), 0);
needsForces.resize(numSteps, false);
needsEnergy.resize(numSteps, false);
invalidatesForces.resize(numSteps, false);
merged.resize(numSteps, false);
modifiesParameters = false;
map<string, string> defines;
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
defines["WORK_GROUP_SIZE"] = intToString(OpenCLContext::ThreadBlockSize);
// Initialize the random number generator.
uniformRandoms = new OpenCLArray<mm_float4>(cl, cl.getNumAtoms(), "uniformRandoms");
randomSeed = new OpenCLArray<mm_int4>(cl, cl.getNumThreadBlocks()*OpenCLContext::ThreadBlockSize, "randomSeed");
vector<mm_int4> seed(randomSeed->getSize());
unsigned int r = integrator.getRandomNumberSeed()+1;
for (int i = 0; i < randomSeed->getSize(); i++) {
seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
seed[i].z = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
seed[i].w = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
}
randomSeed->upload(seed);
cl::Program randomProgram = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
randomKernel = cl::Kernel(randomProgram, "generateRandomNumbers");
randomKernel.setArg<cl::Buffer>(0, uniformRandoms->getDeviceBuffer());
randomKernel.setArg<cl::Buffer>(1, randomSeed->getDeviceBuffer());
// Build a list of all variables that affect the forces, so we can tell which
// steps invalidate them.
......@@ -3624,9 +3651,6 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
for (map<string, double>::const_iterator param = params.begin(); param != params.end(); ++param)
affectsForce.insert(param->first);
}
map<string, string> defines;
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
defines["WORK_GROUP_SIZE"] = intToString(OpenCLContext::ThreadBlockSize);
// Record information about all the computation steps.
......@@ -3672,7 +3696,8 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
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])
storePosAsDelta[step-1] == storePosAsDelta[step] && loadPosAsDelta[step-1] == loadPosAsDelta[step] &&
!usesVariable(expression[step], "uniform"))
merged[step] = true;
}
......@@ -3690,7 +3715,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
compute << buffer.getType()<<" perDofz"<<intToString(i+1)<<" = perDofValues"<<intToString(i+1)<<"[3*index+2];\n";
}
string convert = (cl.getSupportsDoublePrecision() ? "convert_float4(" : "(");
int randoms = 0;
int numGaussian = 0, numUniform = 0;
for (int j = step; j < numSteps && (j == step || merged[j]); j++) {
compute << "{\n";
for (int i = 0; i < 3; i++)
......@@ -3714,7 +3739,8 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
compute << "perDofValues"<<intToString(i+1)<<"[3*index+2] = perDofz"<<intToString(i+1)<<";\n";
}
compute << "}\n";
randoms += numAtoms*usesVariable(expression[j], "gaussian");
numGaussian += numAtoms*usesVariable(expression[j], "gaussian");
numUniform += numAtoms*usesVariable(expression[j], "uniform");
}
map<string, string> replacements;
replacements["COMPUTE_STEP"] = compute.str();
......@@ -3732,9 +3758,8 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customIntegratorPerDof, replacements), defines);
cl::Kernel kernel = cl::Kernel(program, "computePerDof");
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(randoms);
requiredGaussian[step] = numGaussian;
requiredUniform[step] = numUniform;
int index = 0;
kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
......@@ -3746,6 +3771,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
kernel.setArg<cl::Buffer>(index++, integration.getRandom().getDeviceBuffer());
index++;
kernel.setArg<cl::Buffer>(index++, uniformRandoms->getDeviceBuffer());
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());
......@@ -3867,7 +3893,9 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
forcesAreValid = true;
}
if (stepType[i] == CustomIntegrator::ComputePerDof && !merged[i]) {
kernels[i][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredRandoms[i][0]));
kernels[i][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredGaussian[i]));
if (requiredUniform[i] > 0)
cl.executeKernel(randomKernel, numAtoms);
cl.executeKernel(kernels[i][0], numAtoms);
}
else if (stepType[i] == CustomIntegrator::ComputeGlobal && !merged[i]) {
......@@ -3876,7 +3904,9 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
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_uint>(9, integration.prepareRandomNumbers(requiredGaussian[i]));
if (requiredUniform[i] > 0)
cl.executeKernel(randomKernel, numAtoms);
cl.executeKernel(kernels[i][0], numAtoms);
cl.executeKernel(kernels[i][1], OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
}
......@@ -3934,7 +3964,7 @@ void OpenCLIntegrateCustomStepKernel::getPerDofVariable(ContextImpl& context, in
values.resize(perDofValues->getNumObjects()/3);
for (int i = 0; i < (int) values.size(); i++)
for (int j = 0; j < 3; j++)
values[i][j] = localPerDofValues[variable][3*i+j];
values[i][j] = localPerDofValues[3*i+j][variable];
}
void OpenCLIntegrateCustomStepKernel::setPerDofVariable(ContextImpl& context, int variable, const vector<Vec3>& values) {
......@@ -3944,7 +3974,7 @@ void OpenCLIntegrateCustomStepKernel::setPerDofVariable(ContextImpl& context, in
}
for (int i = 0; i < (int) values.size(); i++)
for (int j = 0; j < 3; j++)
localPerDofValues[variable][3*i+j] = (float) values[i][j];
localPerDofValues[3*i+j][variable] = (float) values[i][j];
deviceValuesAreCurrent = false;
}
......
platforms/opencl/src/OpenCLKernels.h
View file @ 052aea3e
......@@ -883,7 +883,8 @@ 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), energy(NULL), perDofValues(NULL) {
hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), contextParameterValues(NULL), sumBuffer(NULL), energy(NULL),
uniformRandoms(NULL), randomSeed(NULL), perDofValues(NULL) {
}
~OpenCLIntegrateCustomStepKernel();
/**
......@@ -947,16 +948,19 @@ private:
OpenCLArray<cl_float>* contextParameterValues;
OpenCLArray<cl_float>* sumBuffer;
OpenCLArray<cl_float>* energy;
OpenCLArray<mm_float4>* uniformRandoms;
OpenCLArray<mm_int4>* randomSeed;
OpenCLParameterSet* perDofValues;
mutable std::vector<std::vector<cl_float> > localPerDofValues;
std::vector<std::vector<cl::Kernel> > kernels;
cl::Kernel sumEnergyKernel;
cl::Kernel sumEnergyKernel, randomKernel;
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<int> requiredGaussian;
std::vector<int> requiredUniform;
std::vector<std::string> parameterNames;
};
......
platforms/opencl/src/kernels/customIntegrator.cl
View file @ 052aea3e
......@@ -22,3 +22,47 @@ __kernel void applyPositionDeltas(__global float4* restrict posq, __global float
posDelta[index] = (float4) 0.0f;
}
}
__kernel void generateRandomNumbers(__global float4* restrict random, __global uint4* restrict seed) {
uint4 state = seed[get_global_id(0)];
unsigned int carry = 0;
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
// Generate three uniform random numbers.
state.x = state.x * 69069 + 1;
state.y ^= state.y << 13;
state.y ^= state.y >> 17;
state.y ^= state.y << 5;
unsigned int k = (state.z >> 2) + (state.w >> 3) + (carry >> 2);
unsigned int m = state.w + state.w + state.z + carry;
state.z = state.w;
state.w = m;
carry = k >> 30;
float x1 = (float)max(state.x + state.y + state.w, 0x00000001u) / (float)0xffffffff;
state.x = state.x * 69069 + 1;
state.y ^= state.y << 13;
state.y ^= state.y >> 17;
state.y ^= state.y << 5;
k = (state.z >> 2) + (state.w >> 3) + (carry >> 2);
m = state.w + state.w + state.z + carry;
state.z = state.w;
state.w = m;
carry = k >> 30;
float x2 = (float)max(state.x + state.y + state.w, 0x00000001u) / (float)0xffffffff;
state.x = state.x * 69069 + 1;
state.y ^= state.y << 13;
state.y ^= state.y >> 17;
state.y ^= state.y << 5;
k = (state.z >> 2) + (state.w >> 3) + (carry >> 2);
m = state.w + state.w + state.z + carry;
state.z = state.w;
state.w = m;
carry = k >> 30;
float x3 = (float)max(state.x + state.y + state.w, 0x00000001u) / (float)0xffffffff;
// Record the values.
random[index] = (float4) (x1, x2, x3, 0.0f);
}
seed[get_global_id(0)] = state;
}
platforms/opencl/src/kernels/customIntegratorPerDof.cl
View file @ 052aea3e
......@@ -4,8 +4,8 @@
__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, __global const float* restrict energy
__global const float* restrict params, __global float* restrict sum, __global const float4* restrict gaussianValues,
unsigned int randomIndex, __global const float4* restrict uniformValues, __global const float* restrict energy
PARAMETER_ARGUMENTS) {
float stepSize = dt[0].y;
int index = get_global_id(0);
......@@ -30,7 +30,8 @@ __kernel void computePerDof(__global float4* restrict posq, __global float4* res
float4 f = force[index];
float mass = 1.0f/velocity.w;
#endif
float4 gaussian = random[randomIndex];
float4 gaussian = gaussianValues[randomIndex];
float4 uniform = uniformValues[index];
COMPUTE_STEP
randomIndex += get_global_size(0);
index += get_global_size(0);
......
platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp
View file @ 052aea3e
......@@ -398,6 +398,75 @@ void testParameter() {
}
}
/**
* Test random number distributions.
*/
void testRandomDistributions() {
const int numParticles = 100;
const int numBins = 20;
const int numSteps = 100;
OpenCLPlatform platform;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
integrator.addPerDofVariable("a", 0);
integrator.addPerDofVariable("b", 0);
integrator.addComputePerDof("a", "uniform");
integrator.addComputePerDof("b", "gaussian");
Context context(system, integrator, platform);
// See if the random numbers are distributed correctly.
vector<int> bins(numBins);
double mean = 0.0;
double var = 0.0;
double skew = 0.0;
double kurtosis = 0.0;
vector<Vec3> values;
for (int i = 0; i < numSteps; i++) {
integrator.step(1);
integrator.getPerDofVariable(0, values);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
double v = values[i][j];
ASSERT(v >= 0 && v < 1);
bins[(int) (v*numBins)]++;
}
integrator.getPerDofVariable(1, values);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
double v = values[i][j];
mean += v;
var += v*v;
skew += v*v*v;
kurtosis += v*v*v*v;
}
}
// Check the distribution of uniform randoms.
int numValues = numParticles*numSteps*3;
double expected = numValues/(double) numBins;
double tol = 4*sqrt(expected);
for (int i = 0; i < numBins; i++)
ASSERT(bins[i] >= expected-tol && bins[i] <= expected+tol);
// Check the distribution of gaussian randoms.
mean /= numValues;
var /= numValues;
skew /= numValues;
kurtosis /= numValues;
double c2 = var-mean*mean;
double c3 = skew-3*var*mean+2*mean*mean*mean;
double c4 = kurtosis-4*skew*mean-3*var*var+12*var*mean*mean-6*mean*mean*mean*mean;
ASSERT_EQUAL_TOL(0.0, mean, 3.0/sqrt((double) numValues));
ASSERT_EQUAL_TOL(1.0, c2, 3.0/pow(numValues, 1.0/3.0));
ASSERT_EQUAL_TOL(0.0, c3, 3.0/pow(numValues, 1.0/4.0));
ASSERT_EQUAL_TOL(0.0, c4, 3.0/pow(numValues, 1.0/4.0));
}
int main() {
try {
testSingleBond();
......@@ -407,6 +476,7 @@ int main() {
testMonteCarlo();
testSum();
testParameter();
testRandomDistributions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/tests/TestReferenceCustomIntegrator.cpp
View file @ 052aea3e
......@@ -384,6 +384,75 @@ void testParameter() {
}
}
/**
* Test random number distributions.
*/
void testRandomDistributions() {
const int numParticles = 100;
const int numBins = 20;
const int numSteps = 100;
ReferencePlatform platform;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
integrator.addPerDofVariable("a", 0);
integrator.addPerDofVariable("b", 0);
integrator.addComputePerDof("a", "uniform");
integrator.addComputePerDof("b", "gaussian");
Context context(system, integrator, platform);
// See if the random numbers are distributed correctly.
vector<int> bins(numBins);
double mean = 0.0;
double var = 0.0;
double skew = 0.0;
double kurtosis = 0.0;
vector<Vec3> values;
for (int i = 0; i < numSteps; i++) {
integrator.step(1);
integrator.getPerDofVariable(0, values);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
double v = values[i][j];
ASSERT(v >= 0 && v < 1);
bins[(int) (v*numBins)]++;
}
integrator.getPerDofVariable(1, values);
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
double v = values[i][j];
mean += v;
var += v*v;
skew += v*v*v;
kurtosis += v*v*v*v;
}
}
// Check the distribution of uniform randoms.
int numValues = numParticles*numSteps*3;
double expected = numValues/(double) numBins;
double tol = 4*sqrt(expected);
for (int i = 0; i < numBins; i++)
ASSERT(bins[i] >= expected-tol && bins[i] <= expected+tol);
// Check the distribution of gaussian randoms.
mean /= numValues;
var /= numValues;
skew /= numValues;
kurtosis /= numValues;
double c2 = var-mean*mean;
double c3 = skew-3*var*mean+2*mean*mean*mean;
double c4 = kurtosis-4*skew*mean-3*var*var+12*var*mean*mean-6*mean*mean*mean*mean;
ASSERT_EQUAL_TOL(0.0, mean, 3.0/sqrt((double) numValues));
ASSERT_EQUAL_TOL(1.0, c2, 3.0/pow(numValues, 1.0/3.0));
ASSERT_EQUAL_TOL(0.0, c3, 3.0/pow(numValues, 1.0/4.0));
ASSERT_EQUAL_TOL(0.0, c4, 3.0/pow(numValues, 1.0/4.0));
}
int main() {
try {
testSingleBond();
......@@ -393,6 +462,7 @@ int main() {
testMonteCarlo();
testSum();
testParameter();
testRandomDistributions();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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