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Unverified Commit ed9df876 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Fixed errors when running on multiple GPUs (#3340)

parent 768963ae
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Showing with 93 additions and 47 deletions
platforms/common/src/kernels/nonbondedParameters.cc
View file @ ed9df876
......@@ -76,7 +76,7 @@ KERNEL void computeExclusionParameters(GLOBAL real4* RESTRICT posq, GLOBAL real*
#else
real chargeProd = charge[atoms.x]*charge[atoms.y];
#endif
#ifdef INCLUDE_LJPME
#ifdef INCLUDE_LJPME_EXCEPTIONS
float2 sigEps1 = sigmaEpsilon[atoms.x];
float2 sigEps2 = sigmaEpsilon[atoms.y];
float sigma = sigEps1.x*sigEps2.x;
......
platforms/cuda/src/CudaKernels.cpp
View file @ ed9df876
......@@ -672,6 +672,8 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
paramsDefines["HAS_OFFSETS"] = "1";
if (usePosqCharges)
paramsDefines["USE_POSQ_CHARGES"] = "1";
if (doLJPME)
paramsDefines["INCLUDE_LJPME_EXCEPTIONS"] = "1";
if (nonbondedMethod == Ewald) {
// Compute the Ewald parameters.
......@@ -723,8 +725,16 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI));
defines["USE_EWALD"] = "1";
defines["DO_LJPME"] = doLJPME ? "1" : "0";
if (doLJPME)
if (doLJPME) {
defines["EWALD_DISPERSION_ALPHA"] = cu.doubleToString(dispersionAlpha);
double invRCut6 = pow(force.getCutoffDistance(), -6);
double dalphaR = dispersionAlpha * force.getCutoffDistance();
double dar2 = dalphaR*dalphaR;
double dar4 = dar2*dar2;
double multShift6 = -invRCut6*(1.0 - exp(-dar2) * (1.0 + dar2 + 0.5*dar4));
defines["INVCUT6"] = cu.doubleToString(invRCut6);
defines["MULTSHIFT6"] = cu.doubleToString(multShift6);
}
if (cu.getContextIndex() == 0) {
paramsDefines["INCLUDE_EWALD"] = "1";
paramsDefines["EWALD_SELF_ENERGY_SCALE"] = cu.doubleToString(ONE_4PI_EPS0*alpha/sqrt(M_PI));
......@@ -790,13 +800,6 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
pmeDefines["CHARGE_FROM_SIGEPS"] = "1";
if (cu.getUseDoublePrecision() || cu.getPlatformData().deterministicForces)
pmeDefines["USE_FIXED_POINT_CHARGE_SPREADING"] = "1";
double invRCut6 = pow(force.getCutoffDistance(), -6);
double dalphaR = dispersionAlpha * force.getCutoffDistance();
double dar2 = dalphaR*dalphaR;
double dar4 = dar2*dar2;
double multShift6 = -invRCut6*(1.0 - exp(-dar2) * (1.0 + dar2 + 0.5*dar4));
defines["INVCUT6"] = cu.doubleToString(invRCut6);
defines["MULTSHIFT6"] = cu.doubleToString(multShift6);
module = cu.createModule(CudaKernelSources::vectorOps+CommonKernelSources::pme, pmeDefines);
pmeDispersionFinishSpreadChargeKernel = cu.getKernel(module, "finishSpreadCharge");
pmeDispersionGridIndexKernel = cu.getKernel(module, "findAtomGridIndex");
......@@ -1055,7 +1058,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
// Initialize parameter offsets.
vector<vector<float4> > particleOffsetVec(force.getNumParticles());
vector<vector<float4> > exceptionOffsetVec(force.getNumExceptions());
vector<vector<float4> > exceptionOffsetVec(numExceptions);
for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
string param;
int particle;
......@@ -1076,6 +1079,9 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
int exception;
double charge, sigma, epsilon;
force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
int index = exceptionIndex[exception];
if (index < startIndex || index >= endIndex)
continue;
auto paramPos = find(paramNames.begin(), paramNames.end(), param);
int paramIndex;
if (paramPos == paramNames.end()) {
......@@ -1084,13 +1090,11 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
}
else
paramIndex = paramPos-paramNames.begin();
exceptionOffsetVec[exceptionIndex[exception]].push_back(make_float4(charge, sigma, epsilon, paramIndex));
exceptionOffsetVec[index-startIndex].push_back(make_float4(charge, sigma, epsilon, paramIndex));
}
paramValues.resize(paramNames.size(), 0.0);
particleParamOffsets.initialize<float4>(cu, max(force.getNumParticleParameterOffsets(), 1), "particleParamOffsets");
exceptionParamOffsets.initialize<float4>(cu, max(force.getNumExceptionParameterOffsets(), 1), "exceptionParamOffsets");
particleOffsetIndices.initialize<int>(cu, cu.getPaddedNumAtoms()+1, "particleOffsetIndices");
exceptionOffsetIndices.initialize<int>(cu, force.getNumExceptions()+1, "exceptionOffsetIndices");
vector<int> particleOffsetIndicesVec, exceptionOffsetIndicesVec;
vector<float4> p, e;
for (int i = 0; i < particleOffsetVec.size(); i++) {
......@@ -1110,7 +1114,9 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
particleParamOffsets.upload(p);
particleOffsetIndices.upload(particleOffsetIndicesVec);
}
if (force.getNumExceptionParameterOffsets() > 0) {
exceptionParamOffsets.initialize<float4>(cu, max((int) e.size(), 1), "exceptionParamOffsets");
exceptionOffsetIndices.initialize<int>(cu, exceptionOffsetIndicesVec.size(), "exceptionOffsetIndices");
if (e.size() > 0) {
exceptionParamOffsets.upload(e);
exceptionOffsetIndices.upload(exceptionOffsetIndicesVec);
}
......@@ -1380,20 +1386,28 @@ void CudaCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context,
throw OpenMMException("updateParametersInContext: The nonbonded force kernel does not include Lennard-Jones interactions, because all epsilons were originally 0");
}
}
set<int> exceptionsWithOffsets;
for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
string param;
int exception;
double charge, sigma, epsilon;
force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
exceptionsWithOffsets.insert(exception);
}
vector<int> exceptions;
for (int i = 0; i < force.getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if (exceptionAtoms.size() > exceptions.size() && make_pair(particle1, particle2) == exceptionAtoms[exceptions.size()])
if (chargeProd != 0.0 || epsilon != 0.0 || exceptionsWithOffsets.find(i) != exceptionsWithOffsets.end())
exceptions.push_back(i);
else if (chargeProd != 0.0 || epsilon != 0.0)
throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
}
int numContexts = cu.getPlatformData().contexts.size();
int startIndex = cu.getContextIndex()*exceptions.size()/numContexts;
int endIndex = (cu.getContextIndex()+1)*exceptions.size()/numContexts;
int numExceptions = endIndex-startIndex;
if (numExceptions != exceptionAtoms.size())
throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
// Record the per-particle parameters.
......@@ -1409,11 +1423,13 @@ void CudaCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context,
// Record the exceptions.
if (numExceptions > 0) {
vector<vector<int> > atoms(numExceptions, vector<int>(2));
vector<float4> baseExceptionParamsVec(numExceptions);
for (int i = 0; i < numExceptions; i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
force.getExceptionParameters(exceptions[startIndex+i], atoms[i][0], atoms[i][1], chargeProd, sigma, epsilon);
force.getExceptionParameters(exceptions[startIndex+i], particle1, particle2, chargeProd, sigma, epsilon);
if (make_pair(particle1, particle2) != exceptionAtoms[i])
throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
baseExceptionParamsVec[i] = make_float4(chargeProd, sigma, epsilon, 0);
}
baseExceptionParams.upload(baseExceptionParamsVec);
......
platforms/cuda/tests/CudaTests.h
View file @ ed9df876
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2015-2016 Stanford University and the Authors. *
* Portions copyright (c) 2015-2021 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -40,4 +40,6 @@ OpenMM::CudaPlatform platform;
void initializeTests(int argc, char* argv[]) {
if (argc > 1)
platform.setPropertyDefaultValue("Precision", std::string(argv[1]));
if (argc > 2)
platform.setPropertyDefaultValue("DeviceIndex", std::string(argv[2]));
}
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ ed9df876
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Portions copyright (c) 2008-2021 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -50,12 +50,18 @@ void testParallelComputation(NonbondedForce::NonbondedMethod method) {
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(5*genrand_real2(sfmt), 5*genrand_real2(sfmt), 5*genrand_real2(sfmt));
force->addGlobalParameter("scale", 0.5);
for (int i = 0; i < numParticles; ++i)
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
if (delta.dot(delta) < 0.1) {
force->addException(i, j, 0, 1, 0);
}
else if (delta.dot(delta) < 0.2) {
int index = force->addException(i, j, 0.5, 1, 1.0);
force->addExceptionParameterOffset("scale", index, 0.5, 0.4, 0.3);
}
}
// Create two contexts, one with a single device and one with two devices.
......@@ -179,6 +185,7 @@ void runPlatformTests() {
testParallelComputation(NonbondedForce::NoCutoff);
testParallelComputation(NonbondedForce::Ewald);
testParallelComputation(NonbondedForce::PME);
testParallelComputation(NonbondedForce::LJPME);
testReordering();
testDeterministicForces();
if (canRunHugeTest())
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ ed9df876
......@@ -677,6 +677,8 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
paramsDefines["HAS_OFFSETS"] = "1";
if (usePosqCharges)
paramsDefines["USE_POSQ_CHARGES"] = "1";
if (doLJPME)
paramsDefines["INCLUDE_LJPME_EXCEPTIONS"] = "1";
if (nonbondedMethod == Ewald) {
// Compute the Ewald parameters.
......@@ -727,8 +729,16 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
defines["USE_EWALD"] = "1";
defines["DO_LJPME"] = doLJPME ? "1" : "0";
if (doLJPME)
if (doLJPME) {
defines["EWALD_DISPERSION_ALPHA"] = cl.doubleToString(dispersionAlpha);
double invRCut6 = pow(force.getCutoffDistance(), -6);
double dalphaR = dispersionAlpha * force.getCutoffDistance();
double dar2 = dalphaR*dalphaR;
double dar4 = dar2*dar2;
double multShift6 = -invRCut6*(1.0 - exp(-dar2) * (1.0 + dar2 + 0.5*dar4));
defines["INVCUT6"] = cl.doubleToString(invRCut6);
defines["MULTSHIFT6"] = cl.doubleToString(multShift6);
}
if (cl.getContextIndex() == 0) {
paramsDefines["INCLUDE_EWALD"] = "1";
paramsDefines["EWALD_SELF_ENERGY_SCALE"] = cl.doubleToString(ONE_4PI_EPS0*alpha/sqrt(M_PI));
......@@ -772,15 +782,6 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
if (pmeio == NULL) {
// Create required data structures.
if (doLJPME) {
double invRCut6 = pow(force.getCutoffDistance(), -6);
double dalphaR = dispersionAlpha * force.getCutoffDistance();
double dar2 = dalphaR*dalphaR;
double dar4 = dar2*dar2;
double multShift6 = -invRCut6*(1.0 - exp(-dar2) * (1.0 + dar2 + 0.5*dar4));
defines["INVCUT6"] = cl.doubleToString(invRCut6);
defines["MULTSHIFT6"] = cl.doubleToString(multShift6);
}
int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
int roundedZSize = PmeOrder*(int) ceil(gridSizeZ/(double) PmeOrder);
int gridElements = gridSizeX*gridSizeY*roundedZSize;
......@@ -1001,7 +1002,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
// Initialize parameter offsets.
vector<vector<mm_float4> > particleOffsetVec(force.getNumParticles());
vector<vector<mm_float4> > exceptionOffsetVec(force.getNumExceptions());
vector<vector<mm_float4> > exceptionOffsetVec(numExceptions);
for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
string param;
int particle;
......@@ -1022,6 +1023,9 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
int exception;
double charge, sigma, epsilon;
force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
int index = exceptionIndex[exception];
if (index < startIndex || index >= endIndex)
continue;
auto paramPos = find(paramNames.begin(), paramNames.end(), param);
int paramIndex;
if (paramPos == paramNames.end()) {
......@@ -1030,13 +1034,11 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
}
else
paramIndex = paramPos-paramNames.begin();
exceptionOffsetVec[exceptionIndex[exception]].push_back(mm_float4(charge, sigma, epsilon, paramIndex));
exceptionOffsetVec[index-startIndex].push_back(mm_float4(charge, sigma, epsilon, paramIndex));
}
paramValues.resize(paramNames.size(), 0.0);
particleParamOffsets.initialize<mm_float4>(cl, max(force.getNumParticleParameterOffsets(), 1), "particleParamOffsets");
exceptionParamOffsets.initialize<mm_float4>(cl, max(force.getNumExceptionParameterOffsets(), 1), "exceptionParamOffsets");
particleOffsetIndices.initialize<cl_int>(cl, cl.getPaddedNumAtoms()+1, "particleOffsetIndices");
exceptionOffsetIndices.initialize<cl_int>(cl, force.getNumExceptions()+1, "exceptionOffsetIndices");
vector<cl_int> particleOffsetIndicesVec, exceptionOffsetIndicesVec;
vector<mm_float4> p, e;
for (int i = 0; i < particleOffsetVec.size(); i++) {
......@@ -1056,7 +1058,9 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
particleParamOffsets.upload(p);
particleOffsetIndices.upload(particleOffsetIndicesVec);
}
if (force.getNumExceptionParameterOffsets() > 0) {
exceptionParamOffsets.initialize<mm_float4>(cl, max((int) e.size(), 1), "exceptionParamOffsets");
exceptionOffsetIndices.initialize<cl_int>(cl, exceptionOffsetIndicesVec.size(), "exceptionOffsetIndices");
if (e.size() > 0) {
exceptionParamOffsets.upload(e);
exceptionOffsetIndices.upload(exceptionOffsetIndicesVec);
}
......@@ -1534,20 +1538,28 @@ void OpenCLCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& contex
throw OpenMMException("updateParametersInContext: The nonbonded force kernel does not include Lennard-Jones interactions, because all epsilons were originally 0");
}
}
set<int> exceptionsWithOffsets;
for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
string param;
int exception;
double charge, sigma, epsilon;
force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
exceptionsWithOffsets.insert(exception);
}
vector<int> exceptions;
for (int i = 0; i < force.getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if (exceptionAtoms.size() > exceptions.size() && make_pair(particle1, particle2) == exceptionAtoms[exceptions.size()])
if (chargeProd != 0.0 || epsilon != 0.0 || exceptionsWithOffsets.find(i) != exceptionsWithOffsets.end())
exceptions.push_back(i);
else if (chargeProd != 0.0 || epsilon != 0.0)
throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
}
int numContexts = cl.getPlatformData().contexts.size();
int startIndex = cl.getContextIndex()*exceptions.size()/numContexts;
int endIndex = (cl.getContextIndex()+1)*exceptions.size()/numContexts;
int numExceptions = endIndex-startIndex;
if (numExceptions != exceptionAtoms.size())
throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
// Record the per-particle parameters.
......@@ -1562,11 +1574,13 @@ void OpenCLCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& contex
// Record the exceptions.
if (numExceptions > 0) {
vector<vector<int> > atoms(numExceptions, vector<int>(2));
vector<mm_float4> baseExceptionParamsVec(numExceptions);
for (int i = 0; i < numExceptions; i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
force.getExceptionParameters(exceptions[startIndex+i], atoms[i][0], atoms[i][1], chargeProd, sigma, epsilon);
force.getExceptionParameters(exceptions[startIndex+i], particle1, particle2, chargeProd, sigma, epsilon);
if (make_pair(particle1, particle2) != exceptionAtoms[i])
throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
baseExceptionParamsVec[i] = mm_float4(chargeProd, sigma, epsilon, 0);
}
baseExceptionParams.upload(baseExceptionParamsVec);
......
platforms/opencl/tests/TestOpenCLNonbondedForce.cpp
View file @ ed9df876
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Portions copyright (c) 2008-2021 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -53,12 +53,18 @@ void testParallelComputation(NonbondedForce::NonbondedMethod method) {
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(5*genrand_real2(sfmt), 5*genrand_real2(sfmt), 5*genrand_real2(sfmt));
force->addGlobalParameter("scale", 0.5);
for (int i = 0; i < numParticles; ++i)
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
if (delta.dot(delta) < 0.1) {
force->addException(i, j, 0, 1, 0);
}
else if (delta.dot(delta) < 0.2) {
int index = force->addException(i, j, 0.5, 1, 1.0);
force->addExceptionParameterOffset("scale", index, 0.5, 0.4, 0.3);
}
}
// Create two contexts, one with a single device and one with two devices.
......@@ -154,6 +160,7 @@ void runPlatformTests() {
testParallelComputation(NonbondedForce::NoCutoff);
testParallelComputation(NonbondedForce::Ewald);
testParallelComputation(NonbondedForce::PME);
testParallelComputation(NonbondedForce::LJPME);
testReordering();
if (canRunHugeTest()) {
double tol = (platform.getPropertyDefaultValue("Precision") == "single" ? 1e-4 : 1e-5);
......
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