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Commit ec39f6ff authored by Yutong Zhao's avatar Yutong Zhao
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nonbonded.cu will now use shuffles on sm_30 or higher

parent 44665537
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Showing with 412 additions and 340 deletions
platforms/cuda/src/CudaContext.cpp
View file @ ec39f6ff
......@@ -394,7 +394,7 @@ CUmodule CudaContext::createModule(const string source, const map<string, string
// Write out the source to a temporary file.
stringstream tempFileName;
tempFileName << "openmmTempKernel" << /*rand() <<*/ this; // Include a pointer to this context as part of the filename to avoid collisions.
tempFileName << "openmmTempKernel" << this; // Include a pointer to this context as part of the filename to avoid collisions.
string inputFile = (tempDir+tempFileName.str()+".cu");
string outputFile = (tempDir+tempFileName.str()+".ptx");
string logFile = (tempDir+tempFileName.str()+".log");
......@@ -438,15 +438,15 @@ CUmodule CudaContext::createModule(const string source, const map<string, string
m<<"Error loading CUDA module: "<<getErrorString(result)<<" ("<<result<<")";
throw OpenMMException(m.str());
}
//remove(inputFile.c_str());
//remove(outputFile.c_str());
//remove(logFile.c_str());
remove(inputFile.c_str());
remove(outputFile.c_str());
remove(logFile.c_str());
return module;
}
catch (...) {
//remove(inputFile.c_str());
//remove(outputFile.c_str());
//remove(logFile.c_str());
remove(inputFile.c_str());
remove(outputFile.c_str());
remove(logFile.c_str());
throw;
}
}
......
platforms/cuda/src/CudaNonbondedUtilities.cpp
View file @ ec39f6ff
......@@ -416,6 +416,11 @@ void CudaNonbondedUtilities::setAtomBlockRange(double startFraction, double endF
}
CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source, vector<ParameterInfo>& params, vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric) {
map<string, string> defines;
if (context.getComputeCapability() >= 3.0 && !context.getUseDoublePrecision())
defines["ENABLE_SHUFFLE"] = "1";
map<string, string> replacements;
replacements["COMPUTE_INTERACTION"] = source;
const string suffixes[] = {"x", "y", "z", "w"};
......@@ -446,163 +451,145 @@ CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source,
}
replacements["PARAMETER_ARGUMENTS"] = args.str();
/*
stringstream loadLocal1;
stringstream load1;
for (int i = 0; i < (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
loadLocal1<<"localData[localAtomIndex]."<<params[i].getName()<<" = "<<params[i].getName()<<"1;\n";
}
else {
for (int j = 0; j < params[i].getNumComponents(); ++j)
loadLocal1<<"localData[localAtomIndex]."<<params[i].getName()<<"_"<<suffixes[j]<<" = "<<params[i].getName()<<"1."<<suffixes[j]<<";\n";
}
load1 << params[i].getType();
load1 << " ";
load1 << params[i].getName();
load1 << "1 = global_";
load1 << params[i].getName();
load1 << "[atom1];\n";
}
replacements["LOAD_LOCAL_PARAMETERS_FROM_1"] = loadLocal1.str();
*/
replacements["LOAD_ATOM1_PARAMETERS"] = load1.str();
bool useShuffle = (defines["ENABLE_SHUFFLE"]=="1");
// Part 1. Defines for on diagonal exclusion tiles
stringstream loadLocal1;
loadLocal1 << "tempSigmaEpsilon = sigmaEpsilon1;" << endl;
//for (int i = 0; i < (int) params.size(); i++) {
// loadLocal1<<params[i].getType()<<" temp"<<params[i].getName()<<"="<<params[i].getName()<<"1;\n";
//}
//cout << loadLocal1.str() << endl;
if(useShuffle) {
// not needed if using shuffles as we can directly fetch from
// LOAD_ATOM1_PARAMETERS
} else {
for (int i = 0; i < (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
loadLocal1<<"localData[threadIdx.x]."<<params[i].getName()<<" = "<<params[i].getName()<<"1;\n";
}
else {
for (int j = 0; j < params[i].getNumComponents(); ++j)
loadLocal1<<"localData[threadIdx.x]."<<params[i].getName()<<"_"<<suffixes[j]<<" = "<<params[i].getName()<<"1."<<suffixes[j]<<";\n";
}
}
}
replacements["LOAD_LOCAL_PARAMETERS_FROM_1"] = loadLocal1.str();
/*
stringstream loadLocal2;
for (int i = 0; i < (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
loadLocal2<<"localData[localAtomIndex]."<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
}
else {
loadLocal2<<params[i].getType()<<" temp_"<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
for (int j = 0; j < params[i].getNumComponents(); ++j)
loadLocal2<<"localData[localAtomIndex]."<<params[i].getName()<<"_"<<suffixes[j]<<" = temp_"<<params[i].getName()<<"."<<suffixes[j]<<";\n";
stringstream broadcastWarpData;
if(useShuffle) {
broadcastWarpData << "posq2.x = real_shfl(shflPosq.x, j);\n";
broadcastWarpData << "posq2.y = real_shfl(shflPosq.y, j);\n";
broadcastWarpData << "posq2.z = real_shfl(shflPosq.z, j);\n";
broadcastWarpData << "posq2.w = real_shfl(shflPosq.w, j);\n";
for(int i=0; i< (int) params.size();i++) {
broadcastWarpData << params[i].getType() << " shfl" << params[i].getName() << ";\n";
for(int j=0; j < params[i].getNumComponents(); j++) {
string name;
if (params[i].getNumComponents() == 1) {
broadcastWarpData << "shfl" << params[i].getName() << "=real_shfl(" << params[i].getName() <<"1,j);\n";
} else {
broadcastWarpData << "shfl" << params[i].getName()+"."+suffixes[j] << "=real_shfl(" << params[i].getName()+"1."+suffixes[j] <<",j);\n";
}
}
}
} else {
// not used if not shuffling
}
replacements["LOAD_LOCAL_PARAMETERS_FROM_GLOBAL"] = loadLocal2.str();
*/
replacements["BROADCAST_WARP_DATA"] = broadcastWarpData.str();
// Part 2. Defines for off-diagonal exclusions, and neighborlist tiles.
stringstream declareLocal2;
for(int i=0; i< (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
// loadLocal2<<params[i].getType()<<" "<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
} else {
declareLocal2<<params[i].getType()<<" temp"<<params[i].getName()<<";\n";
if(useShuffle) {
for(int i=0; i< (int) params.size(); i++) {
declareLocal2<<params[i].getType()<<" shfl"<<params[i].getName()<<";\n";
//if (params[i].getNumComponents() == 1) {
//declareLocal2<<params[i].getType()<<" "<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
//} else {
// declareLocal2<<params[i].getType()<<" temp"<<params[i].getName()<<";\n";
//}
}
} else {
// not used if using shared memory
}
replacements["DECLARE_LOCAL_PARAMETERS"] = declareLocal2.str();
stringstream loadLocal2;
for(int i=0; i< (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
// loadLocal2<<params[i].getType()<<" "<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
} else {
loadLocal2<<"temp"<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
if(useShuffle) {
for(int i=0; i< (int) params.size(); i++) {
loadLocal2<<"shfl"<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
}
}
/*
for (int i = 0; i < (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
loadLocal2<<params[i].getType()<<" "<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
}
else {
loadLocal2<<params[i].getType()<<" temp_"<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
for (int j = 0; j < params[i].getNumComponents(); ++j)
loadLocal2<<params[i].getType()<<" "<<params[i].getName()<<"_"<<suffixes[j]<<" = temp_"<<params[i].getName()<<"."<<suffixes[j]<<";\n";
} else {
for (int i = 0; i < (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
loadLocal2<<"localData[threadIdx.x]."<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
}
else {
loadLocal2<<params[i].getType()<<" temp_"<<params[i].getName()<<" = global_"<<params[i].getName()<<"[j];\n";
for (int j = 0; j < params[i].getNumComponents(); ++j)
loadLocal2<<"localData[threadIdx.x]."<<params[i].getName()<<"_"<<suffixes[j]<<" = temp_"<<params[i].getName()<<"."<<suffixes[j]<<";\n";
}
}
}
*/
replacements["LOAD_LOCAL_PARAMETERS_FROM_GLOBAL"] = loadLocal2.str();
stringstream load1;
for (int i = 0; i < (int) params.size(); i++) {
load1 << params[i].getType();
load1 << " ";
load1 << params[i].getName();
load1 << "1 = global_";
load1 << params[i].getName();
load1 << "[atom1];\n";
}
replacements["LOAD_ATOM1_PARAMETERS"] = load1.str();
/*
stringstream load2j;
for (int i = 0; i < (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
load2j<<params[i].getType()<<" "<<params[i].getName()<<"2 = localData[atom2]."<<params[i].getName()<<";\n";
}
else {
load2j<<params[i].getType()<<" "<<params[i].getName()<<"2 = make_"<<params[i].getType()<<"(";
for (int j = 0; j < params[i].getNumComponents(); ++j) {
if (j > 0)
load2j<<", ";
load2j<<"localData[atom2]."<<params[i].getName()<<"_"<<suffixes[j];
if(useShuffle) {
for(int i = 0; i < (int) params.size(); i++)
load2j<<params[i].getType()<<" "<<params[i].getName()<<"2 = shfl"<<params[i].getName()<<";\n";
} else {
for (int i = 0; i < (int) params.size(); i++) {
if (params[i].getNumComponents() == 1) {
load2j<<params[i].getType()<<" "<<params[i].getName()<<"2 = localData[atom2]."<<params[i].getName()<<";\n";
}
load2j<<");\n";
}
}
replacements["LOAD_ATOM2_PARAMETERS"] = load2j.str();
*/
stringstream load2j;
for (int i = 0; i < (int) params.size(); i++) {
/*
if (params[i].getNumComponents() == 1) {
load2j<<params[i].getType()<<" "<<params[i].getName()<<"2 = "<<params[i].getName()<<";\n";
}
else {
load2j<<params[i].getType()<<" "<<params[i].getName()<<"2 = make_"<<params[i].getType()<<"(";
for (int j = 0; j < params[i].getNumComponents(); ++j) {
if (j > 0)
load2j<<", ";
load2j<<params[i].getName()<<"_"<<suffixes[j];
else {
load2j<<params[i].getType()<<" "<<params[i].getName()<<"2 = make_"<<params[i].getType()<<"(";
for (int j = 0; j < params[i].getNumComponents(); ++j) {
if (j > 0)
load2j<<", ";
load2j<<"localData[atom2]."<<params[i].getName()<<"_"<<suffixes[j];
}
load2j<<");\n";
}
load2j<<");\n";
}*/
load2j<<params[i].getType()<<" "<<params[i].getName()<<"2 = temp"<<params[i].getName()<<";\n";
}
}
replacements["LOAD_ATOM2_PARAMETERS"] = load2j.str();
stringstream broadcastWarpData;
broadcastWarpData << "posq2.x = __shfl(tempPosq.x, j);\n";
broadcastWarpData << "posq2.y = __shfl(tempPosq.y, j);\n";
broadcastWarpData << "posq2.z = __shfl(tempPosq.z, j);\n";
broadcastWarpData << "posq2.w = __shfl(tempPosq.w, j);\n";
for(int i=0; i< (int) params.size();i++) {
broadcastWarpData << params[i].getType() << " temp" << params[i].getName() << ";\n";
for(int j=0; j < params[i].getNumComponents(); j++) {
string name;
if (params[i].getNumComponents() == 1) {
broadcastWarpData << "temp" << params[i].getName() << "=__shfl(" << params[i].getName() <<"1,j);\n";
stringstream shuffleWarpData;
if(useShuffle) {
shuffleWarpData << "shflPosq.x = real_shfl(shflPosq.x, tgx+1);\n";
shuffleWarpData << "shflPosq.y = real_shfl(shflPosq.y, tgx+1);\n";
shuffleWarpData << "shflPosq.z = real_shfl(shflPosq.z, tgx+1);\n";
shuffleWarpData << "shflPosq.w = real_shfl(shflPosq.w, tgx+1);\n";
shuffleWarpData << "shflForce.x = real_shfl(shflForce.x, tgx+1);\n";
shuffleWarpData << "shflForce.y = real_shfl(shflForce.y, tgx+1);\n";
shuffleWarpData << "shflForce.z = real_shfl(shflForce.z, tgx+1);\n";
for(int i=0; i < (int) params.size(); i++) {
if(params[i].getNumComponents() == 1) {
shuffleWarpData<<"shfl"<<params[i].getName()<<"=real_shfl(shfl"<<params[i].getName()<<", tgx+1);\n";
} else {
broadcastWarpData << "temp" << params[i].getName()+"."+suffixes[j] << "=__shfl(" << params[i].getName()+"1."+suffixes[j] <<",j);\n";
for(int j=0;j<params[i].getNumComponents();j++) {
// looks something like
// shflsigmaEpsilon.x = real_shfl(shflsigmaEpsilon.x,tgx+1);
shuffleWarpData<<"shfl"<<params[i].getName()
<<"."<<suffixes[j]<<"=real_shfl(shfl"
<<params[i].getName()<<"."<<suffixes[j]
<<", tgx+1);\n";
}
}
}
} else {
// not used otherwise
}
replacements["BROADCAST_WARP_DATA"] = broadcastWarpData.str();
stringstream shuffleWarpData;
shuffleWarpData << "tempPosq.x = __shfl(tempPosq.x, tgx+1);\n";
shuffleWarpData << "tempPosq.y = __shfl(tempPosq.y, tgx+1);\n";
shuffleWarpData << "tempPosq.z = __shfl(tempPosq.z, tgx+1);\n";
shuffleWarpData << "tempPosq.w = __shfl(tempPosq.w, tgx+1);\n";
shuffleWarpData << "tempForces.x = __shfl(tempForces.x, tgx+1);\n";
shuffleWarpData << "tempForces.y = __shfl(tempForces.y, tgx+1);\n";
shuffleWarpData << "tempForces.z = __shfl(tempForces.z, tgx+1);\n";
shuffleWarpData << "tempsigmaEpsilon.x = __shfl(tempsigmaEpsilon.x, tgx+1);\n";
shuffleWarpData << "tempsigmaEpsilon.y = __shfl(tempsigmaEpsilon.y, tgx+1);\n";
/*
for(int i=0; i< (int) params.size(); i++) {
shuffleWarpData << params[i].getName() << "=__shfl(" << params[i].getName() << ", tgx+1);\n";
}
*/
replacements["SHUFFLE_WARP_DATA"] = shuffleWarpData.str();
map<string, string> defines;
if (useCutoff)
defines["USE_CUTOFF"] = "1";
if (usePeriodic)
......
platforms/cuda/src/kernels/nonbonded.cu
View file @ ec39f6ff
This diff is collapsed.
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ ec39f6ff
......@@ -872,21 +872,21 @@ int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
//testCoulomb();
//testLJ();
//testExclusionsAnd14();
//testCutoff();
//testCutoff14();
//testPeriodic();
testCoulomb();
testLJ();
testExclusionsAnd14();
testCutoff();
testCutoff14();
testPeriodic();
testLargeSystem();
//testBlockInteractions(false);
//testBlockInteractions(true);
//testDispersionCorrection();
//testChangingParameters();
//testParallelComputation(false);
//testParallelComputation(true);
//testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
//testSwitchingFunction(NonbondedForce::PME);
testDispersionCorrection();
testChangingParameters();
testParallelComputation(false);
testParallelComputation(true);
testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
testSwitchingFunction(NonbondedForce::PME);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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