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Commit cc279e94 authored by peastman's avatar peastman
Browse files

Fixed bugs in handling of random numbers in CustomIntegrator (see bug 1883).

parent 7ba1a10c
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Showing with 82 additions and 56 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ cc279e94
......@@ -4752,22 +4752,6 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
defines["SUM_BUFFER_SIZE"] = "0";
defines["SUM_OUTPUT_INDEX"] = "0";
// Initialize the random number generator.
uniformRandoms = CudaArray::create<float4>(cu, cu.getNumAtoms(), "uniformRandoms");
randomSeed = CudaArray::create<int4>(cu, cu.getNumThreadBlocks()*CudaContext::ThreadBlockSize, "randomSeed");
vector<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);
CUmodule randomProgram = cu.createModule(CudaKernelSources::customIntegrator, defines);
randomKernel = cu.getKernel(randomProgram, "generateRandomNumbers");
// Build a list of all variables that affect the forces, so we can tell which
// steps invalidate them.
......@@ -4880,7 +4864,13 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
}
int numGaussian = 0, numUniform = 0;
for (int j = step; j < numSteps && (j == step || merged[j]); j++) {
numGaussian += numAtoms*usesVariable(expression[j], "gaussian");
numUniform += numAtoms*usesVariable(expression[j], "uniform");
compute << "{\n";
if (numGaussian > 0)
compute << "float4 gaussian = gaussianValues[gaussianIndex];\n";
if (numUniform > 0)
compute << "float4 uniform = uniformValues[uniformIndex];\n";
for (int i = 0; i < 3; i++)
compute << createPerDofComputation(stepType[j] == CustomIntegrator::ComputePerDof ? variable[j] : "", expression[j], i, integrator, forceName[j], energyName[j]);
if (variable[j] == "x") {
......@@ -4899,9 +4889,11 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
compute << "perDofValues"<<cu.intToString(i+1)<<"[3*index+2] = perDofz"<<cu.intToString(i+1)<<";\n";
}
}
if (numGaussian > 0)
compute << "gaussianIndex += blockDim.x*gridDim.x;\n";
if (numUniform > 0)
compute << "uniformIndex += blockDim.x*gridDim.x;\n";
compute << "}\n";
numGaussian += numAtoms*usesVariable(expression[j], "gaussian");
numUniform += numAtoms*usesVariable(expression[j], "uniform");
}
map<string, string> replacements;
replacements["COMPUTE_STEP"] = compute.str();
......@@ -4931,9 +4923,9 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
args1.push_back(&globalValues->getDevicePointer());
args1.push_back(&contextParameterValues->getDevicePointer());
args1.push_back(&sumBuffer->getDevicePointer());
args1.push_back(&integration.getRandom().getDevicePointer());
args1.push_back(NULL);
args1.push_back(&uniformRandoms->getDevicePointer());
args1.push_back(NULL);
args1.push_back(NULL);
args1.push_back(&potentialEnergy->getDevicePointer());
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
args1.push_back(&perDofValues->getBuffers()[i].getMemory());
......@@ -5000,6 +4992,25 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
}
}
// Initialize the random number generator.
int maxUniformRandoms = 1;
for (int i = 0; i < (int) requiredUniform.size(); i++)
maxUniformRandoms = max(maxUniformRandoms, requiredUniform[i]);
uniformRandoms = CudaArray::create<float4>(cu, maxUniformRandoms, "uniformRandoms");
randomSeed = CudaArray::create<int4>(cu, cu.getNumThreadBlocks()*CudaContext::ThreadBlockSize, "randomSeed");
vector<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);
CUmodule randomProgram = cu.createModule(CudaKernelSources::customIntegrator, defines);
randomKernel = cu.getKernel(randomProgram, "generateRandomNumbers");
// Create the kernel for summing the potential energy.
defines["SUM_OUTPUT_INDEX"] = "0";
......@@ -5042,7 +5053,7 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
kineticEnergyArgs.push_back(&globalValues->getDevicePointer());
kineticEnergyArgs.push_back(&contextParameterValues->getDevicePointer());
kineticEnergyArgs.push_back(&sumBuffer->getDevicePointer());
kineticEnergyArgs.push_back(&integration.getRandom().getDevicePointer());
kineticEnergyArgs.push_back(NULL);
kineticEnergyArgs.push_back(NULL);
kineticEnergyArgs.push_back(&uniformRandoms->getDevicePointer());
kineticEnergyArgs.push_back(&potentialEnergy->getDevicePointer());
......@@ -5161,7 +5172,9 @@ 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();
if (requiredUniform[i] > 0)
cu.executeKernel(randomKernel, &randomArgs[0], numAtoms);
cu.executeKernel(kernels[i][0], &kernelArgs[i][0][0], numAtoms);
......@@ -5176,7 +5189,9 @@ 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();
if (requiredUniform[i] > 0)
cu.executeKernel(randomKernel, &randomArgs[0], numAtoms);
cu.clearBuffer(*sumBuffer);
......@@ -5227,6 +5242,7 @@ 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;
cu.clearBuffer(*sumBuffer);
cu.executeKernel(kineticEnergyKernel, &kineticEnergyArgs[0], cu.getNumAtoms());
......
platforms/cuda/src/kernels/customIntegratorPerDof.cu
View file @ cc279e94
......@@ -34,11 +34,12 @@ 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 randomIndex, const float4* __restrict__ uniformValues, const real* __restrict__ energy
unsigned int gaussianIndex, const float4* __restrict__ uniformValues, const real* __restrict__ energy
PARAMETER_ARGUMENTS) {
mixed stepSize = dt[0].y;
int index = blockIdx.x*blockDim.x+threadIdx.x;
randomIndex += index;
gaussianIndex += index;
int uniformIndex = index;
const double forceScale = 1.0/0xFFFFFFFF;
while (index < NUM_ATOMS) {
#ifdef LOAD_POS_AS_DELTA
......@@ -50,11 +51,8 @@ extern "C" __global__ void computePerDof(real4* __restrict__ posq, real4* __rest
double4 f = make_double4(forceScale*force[index], forceScale*force[index+PADDED_NUM_ATOMS], forceScale*force[index+PADDED_NUM_ATOMS*2], 0.0);
double mass = 1.0/velocity.w;
if (velocity.w != 0.0) {
float4 gaussian = gaussianValues[randomIndex];
float4 uniform = uniformValues[index];
COMPUTE_STEP
}
randomIndex += blockDim.x*gridDim.x;
index += blockDim.x*gridDim.x;
}
}
platforms/opencl/src/OpenCLKernels.cpp
View file @ cc279e94
......@@ -4980,24 +4980,6 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
defines["WORK_GROUP_SIZE"] = cl.intToString(OpenCLContext::ThreadBlockSize);
// Initialize the random number generator.
uniformRandoms = OpenCLArray::create<mm_float4>(cl, cl.getNumAtoms(), "uniformRandoms");
randomSeed = OpenCLArray::create<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.
......@@ -5110,7 +5092,13 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
}
int numGaussian = 0, numUniform = 0;
for (int j = step; j < numSteps && (j == step || merged[j]); j++) {
numGaussian += numAtoms*usesVariable(expression[j], "gaussian");
numUniform += numAtoms*usesVariable(expression[j], "uniform");
compute << "{\n";
if (numGaussian > 0)
compute << "float4 gaussian = gaussianValues[gaussianIndex];\n";
if (numUniform > 0)
compute << "float4 uniform = uniformValues[uniformIndex];\n";
for (int i = 0; i < 3; i++)
compute << createPerDofComputation(stepType[j] == CustomIntegrator::ComputePerDof ? variable[j] : "", expression[j], i, integrator, forceName[j], energyName[j]);
if (variable[j] == "x") {
......@@ -5133,9 +5121,11 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
compute << "perDofValues"<<cl.intToString(i+1)<<"[3*index+2] = perDofz"<<cl.intToString(i+1)<<";\n";
}
}
if (numGaussian > 0)
compute << "gaussianIndex += get_global_size(0);\n";
if (numUniform > 0)
compute << "uniformIndex += get_global_size(0);\n";
compute << "}\n";
numGaussian += numAtoms*usesVariable(expression[j], "gaussian");
numUniform += numAtoms*usesVariable(expression[j], "uniform");
}
map<string, string> replacements;
replacements["COMPUTE_STEP"] = compute.str();
......@@ -5165,9 +5155,7 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
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++;
kernel.setArg<cl::Buffer>(index++, uniformRandoms->getDeviceBuffer());
index += 3;
kernel.setArg<cl::Buffer>(index++, potentialEnergy->getDeviceBuffer());
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
kernel.setArg<cl::Memory>(index++, perDofValues->getBuffers()[i].getMemory());
......@@ -5229,6 +5217,27 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
}
}
// Initialize the random number generator.
int maxUniformRandoms = 1;
for (int i = 0; i < (int) requiredUniform.size(); i++)
maxUniformRandoms = max(maxUniformRandoms, requiredUniform[i]);
uniformRandoms = OpenCLArray::create<mm_float4>(cl, maxUniformRandoms, "uniformRandoms");
randomSeed = OpenCLArray::create<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());
// Create the kernel for summing the potential energy.
cl::Program program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
......@@ -5274,8 +5283,7 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
kineticEnergyKernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
kineticEnergyKernel.setArg<cl::Buffer>(index++, contextParameterValues->getDeviceBuffer());
kineticEnergyKernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
kineticEnergyKernel.setArg<cl::Buffer>(index++, integration.getRandom().getDeviceBuffer());
kineticEnergyKernel.setArg<cl_uint>(index++, 0);
index += 2;
kineticEnergyKernel.setArg<cl::Buffer>(index++, uniformRandoms->getDeviceBuffer());
kineticEnergyKernel.setArg<cl::Buffer>(index++, potentialEnergy->getDeviceBuffer());
for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
......@@ -5392,6 +5400,8 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
}
if (stepType[i] == CustomIntegrator::ComputePerDof && !merged[i]) {
kernels[i][0].setArg<cl_uint>(10, integration.prepareRandomNumbers(requiredGaussian[i]));
kernels[i][0].setArg<cl::Buffer>(9, integration.getRandom().getDeviceBuffer());
kernels[i][0].setArg<cl::Buffer>(11, uniformRandoms->getDeviceBuffer());
if (requiredUniform[i] > 0)
cl.executeKernel(randomKernel, numAtoms);
cl.executeKernel(kernels[i][0], numAtoms);
......@@ -5403,6 +5413,8 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
}
else if (stepType[i] == CustomIntegrator::ComputeSum) {
kernels[i][0].setArg<cl_uint>(10, integration.prepareRandomNumbers(requiredGaussian[i]));
kernels[i][0].setArg<cl::Buffer>(9, integration.getRandom().getDeviceBuffer());
kernels[i][0].setArg<cl::Buffer>(11, uniformRandoms->getDeviceBuffer());
if (requiredUniform[i] > 0)
cl.executeKernel(randomKernel, numAtoms);
cl.clearBuffer(*sumBuffer);
......@@ -5454,6 +5466,8 @@ double OpenCLIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& contex
forcesAreValid = true;
}
cl.clearBuffer(*sumBuffer);
kineticEnergyKernel.setArg<cl::Buffer>(9, cl.getIntegrationUtilities().getRandom().getDeviceBuffer());
kineticEnergyKernel.setArg<cl_uint>(10, 0);
cl.executeKernel(kineticEnergyKernel, cl.getNumAtoms());
cl.executeKernel(sumKineticEnergyKernel, OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
......
platforms/opencl/src/kernels/customIntegratorPerDof.cl
View file @ cc279e94
......@@ -26,11 +26,12 @@ void storePos(__global real4* restrict posq, __global real4* restrict posqCorrec
__kernel void computePerDof(__global real4* restrict posq, __global real4* restrict posqCorrection, __global mixed4* restrict posDelta,
__global mixed4* restrict velm, __global const real4* restrict force, __global const mixed2* restrict dt, __global const mixed* restrict globals,
__global const mixed* restrict params, __global mixed* restrict sum, __global const float4* restrict gaussianValues,
unsigned int randomIndex, __global const float4* restrict uniformValues, __global const real* restrict energy
unsigned int gaussianIndex, __global const float4* restrict uniformValues, __global const real* restrict energy
PARAMETER_ARGUMENTS) {
mixed stepSize = dt[0].y;
int index = get_global_id(0);
randomIndex += index;
gaussianIndex += index;
int uniformIndex = index;
while (index < NUM_ATOMS) {
#ifdef LOAD_POS_AS_DELTA
mixed4 position = loadPos(posq, posqCorrection, index)+posDelta[index];
......@@ -41,11 +42,8 @@ __kernel void computePerDof(__global real4* restrict posq, __global real4* restr
real4 f = force[index];
mixed mass = 1/velocity.w;
if (velocity.w != 0.0) {
float4 gaussian = gaussianValues[randomIndex];
float4 uniform = uniformValues[index];
COMPUTE_STEP
}
randomIndex += get_global_size(0);
index += get_global_size(0);
}
}
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