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Commit 785592f4 authored by peastman's avatar peastman
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Continuing to work on CUDA implementation of CustomManyParticleForce

parent 890963b9
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Showing with 66 additions and 37 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ 785592f4
......@@ -4468,14 +4468,17 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
string arrayName = "table"+cu.intToString(i);
functionDefinitions.push_back(make_pair(name, arrayName));
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
CudaArray* array = CudaArray::create<float>(cu, f.size(), "TabulatedFunction");
tabulatedFunctions.push_back(array);
array->upload(f);
string arrayName = cu.getBondedUtilities().addArgument(array->getDevicePointer(), width == 1 ? "float" : "float"+cu.intToString(width));
functionDefinitions.push_back(make_pair(name, arrayName));
tabulatedFunctions.push_back(CudaArray::create<float>(cu, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
tableArgs << ", const float";
if (width > 1)
tableArgs << width;
tableArgs << "* __restrict__ " << arrayName;
}
// Record information about parameters.
......@@ -4486,16 +4489,19 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = (float) force.getGlobalParameterDefaultValue(i);
}
map<string, string> variables;
vector<pair<ExpressionTreeNode, string> > variables;
for (int i = 0; i < particlesPerSet; i++) {
string index = cu.intToString(i+1);
variables["x"+index] = "pos"+index+".x";
variables["y"+index] = "pos"+index+".y";
variables["z"+index] = "pos"+index+".z";
variables.push_back(makeVariable("x"+index, "pos"+index+".x"));
variables.push_back(makeVariable("y"+index, "pos"+index+".y"));
variables.push_back(makeVariable("z"+index, "pos"+index+".z"));
}
for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
const string& name = force.getPerParticleParameterName(i);
variables[name] = "params"+params->getParameterSuffix(i);
for (int j = 0; j < particlesPerSet; j++) {
string index = cu.intToString(j+1);
variables.push_back(makeVariable(name+index, "params"+params->getParameterSuffix(i, index)));
}
}
if (force.getNumGlobalParameters() > 0) {
globals = CudaArray::create<float>(cu, force.getNumGlobalParameters(), "customManyParticleGlobals");
......@@ -4503,7 +4509,7 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
const string& name = force.getGlobalParameterName(i);
string value = "globals["+cu.intToString(i)+"]";
variables[name] = value;
variables.push_back(makeVariable(name, value));
}
}
......@@ -4528,11 +4534,11 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
const vector<int>& atoms = iter->second;
string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
if (computedDeltas.count(deltaName) == 0) {
compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize);\n";
computedDeltas.insert(deltaName);
}
compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
variables[iter->first] = "r_"+deltaName;
variables.push_back(makeVariable(iter->first, "r_"+deltaName));
forceExpressions["real dEdDistance"+cu.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
}
index = 0;
......@@ -4542,15 +4548,15 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<", periodicBoxSize, invPeriodicBoxSize);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<", periodicBoxSize, invPeriodicBoxSize);\n";
computedDeltas.insert(deltaName2);
}
compute<<"real "<<angleName<<" = computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
variables[iter->first] = angleName;
variables.push_back(makeVariable(iter->first, angleName));
forceExpressions["real dEdAngle"+cu.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
}
index = 0;
......@@ -4563,22 +4569,22 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
if (computedDeltas.count(deltaName1) == 0) {
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize);\n";
computedDeltas.insert(deltaName1);
}
if (computedDeltas.count(deltaName2) == 0) {
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<");\n";
compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize);\n";
computedDeltas.insert(deltaName2);
}
if (computedDeltas.count(deltaName3) == 0) {
compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<");\n";
compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<", periodicBoxSize, invPeriodicBoxSize);\n";
computedDeltas.insert(deltaName3);
}
compute<<"real4 "<<crossName1<<" = computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
compute<<"real4 "<<crossName2<<" = computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
compute<<"real "<<dihedralName<<" = computeAngle("<<crossName1<<", "<<crossName2<<");\n";
compute<<dihedralName<<" *= (delta"<<deltaName1<<".x*"<<crossName2<<".x + delta"<<deltaName1<<".y*"<<crossName2<<".y + delta"<<deltaName1<<".z*"<<crossName2<<".z < 0 ? -1 : 1);\n";
variables[iter->first] = dihedralName;
variables.push_back(makeVariable(iter->first, dihedralName));
forceExpressions["real dEdDihedral"+cu.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
}
......@@ -4670,10 +4676,12 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
// Create other replacements that depend on the number of particles per set.
stringstream numCombinations, atomsForCombination, isValidCombination, permute, loadData;
stringstream numCombinations, atomsForCombination, isValidCombination, permute, loadData, verifyCutoff;
for (int i = 0; i < particlesPerSet; i++) {
permute<<"int atom"<<(i+1)<<" = p"<<(i+1)<<";\n";
loadData<<"real4 pos"<<(i+1)<<" = posq[atom"<<(i+1)<<"];\n";
for (int j = 0; j < (int) params->getBuffers().size(); j++)
loadData<<params->getBuffers()[j].getType()<<" params"<<(j+1)<<(i+1)<<" = global_params"<<(j+1)<<"[atom"<<(i+1)<<"];\n";
}
for (int i = 2; i < particlesPerSet; i++) {
if (i > 2)
......@@ -4688,6 +4696,14 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
atomsForCombination<<"int p"<<(i+1)<<" = p1+1+tempIndex%numNeighbors;\n";
atomsForCombination<<"tempIndex /= numNeighbors;\n";
}
if (nonbondedMethod != NoCutoff) {
int startCheckFrom = 0;
for (int i = startCheckFrom; i < particlesPerSet; i++)
verifyCutoff<<"real4 pos"<<(i+1)<<" = posq[p"<<(i+1)<<"];\n";
for (int i = startCheckFrom; i < particlesPerSet; i++)
for (int j = i+1; j < particlesPerSet; j++)
verifyCutoff<<"includeInteraction &= (delta(pos"<<(i+1)<<", pos"<<(j+1)<<", periodicBoxSize, invPeriodicBoxSize).w < CUTOFF_SQUARED);\n";
}
// Create replacements for extra arguments.
......@@ -4696,7 +4712,7 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
extraArgs<<", const float* __restrict__ globals";
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
CudaNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
extraArgs<<", const "<<buffer.getType()<<"* __restrict__ global_params";
extraArgs<<", const "<<buffer.getType()<<"* __restrict__ global_params"<<(i+1);
}
// Create the kernels.
......@@ -4706,13 +4722,19 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
replacements["NUM_CANDIDATE_COMBINATIONS"] = numCombinations.str();
replacements["FIND_ATOMS_FOR_COMBINATION_INDEX"] = atomsForCombination.str();
replacements["IS_VALID_COMBINATION"] = isValidCombination.str();
replacements["VERIFY_CUTOFF"] = verifyCutoff.str();
replacements["PERMUTE_ATOMS"] = permute.str();
replacements["LOAD_PARTICLE_DATA"] = loadData.str();
replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
map<string, string> defines;
if (nonbondedMethod != NoCutoff)
defines["USE_CUTOFF"] = "1";
if (nonbondedMethod == CutoffPeriodic)
defines["USE_PERIODIC"] = "1";
defines["NUM_ATOMS"] = cu.intToString(cu.getNumAtoms());
defines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
defines["M_PI"] = cu.doubleToString(M_PI);
defines["CUTOFF_SQUARED"] = cu.doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
std::cout << cu.replaceStrings(CudaKernelSources::vectorOps+CudaKernelSources::customManyParticle, replacements)<< std::endl;
CUmodule module = cu.createModule(cu.replaceStrings(CudaKernelSources::vectorOps+CudaKernelSources::customManyParticle, replacements), defines);
forceKernel = cu.getKernel(module, "computeInteraction");
......@@ -4725,10 +4747,8 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
forceArgs.push_back(&cu.getForce().getDevicePointer());
forceArgs.push_back(&cu.getEnergyBuffer().getDevicePointer());
forceArgs.push_back(&cu.getPosq().getDevicePointer());
if (nonbondedMethod != NoCutoff) {
forceArgs.push_back(cu.getPeriodicBoxSizePointer());
forceArgs.push_back(cu.getInvPeriodicBoxSizePointer());
}
if (globals != NULL)
forceArgs.push_back(&globals->getDevicePointer());
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
......
platforms/cuda/src/kernels/customManyParticle.cu
View file @ 785592f4
......@@ -15,10 +15,16 @@ inline __device__ real3 trim(real4 v) {
}
/**
* Compute the difference between two vectors, setting the fourth component to the squared magnitude.
* Compute the difference between two vectors, taking periodic boundary conditions into account
* and setting the fourth component to the squared magnitude.
*/
inline __device__ real4 delta(real4 vec1, real4 vec2) {
real4 result = make_real4(vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
inline __device__ real4 delta(real4 vec1, real4 vec2, real4 periodicBoxSize, real4 invPeriodicBoxSize) {
real4 result = make_real4(vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0.0f);
#ifdef USE_PERIODIC
result.x -= floor(result.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
result.y -= floor(result.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
result.z -= floor(result.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
#endif
result.w = result.x*result.x + result.y*result.y + result.z*result.z;
return result;
}
......@@ -56,10 +62,8 @@ inline __device__ real4 computeCross(real4 vec1, real4 vec2) {
* Compute the interaction.
*/
extern "C" __global__ void computeInteraction(
unsigned long long* __restrict__ forceBuffers, real* __restrict__ energyBuffer, const real4* __restrict__ posq
#ifdef USE_CUTOFF
, real4 periodicBoxSize, real4 invPeriodicBoxSize
#endif
unsigned long long* __restrict__ forceBuffers, real* __restrict__ energyBuffer, const real4* __restrict__ posq,
real4 periodicBoxSize, real4 invPeriodicBoxSize
PARAMETER_ARGUMENTS) {
real energy = 0.0f;
......@@ -71,6 +75,11 @@ extern "C" __global__ void computeInteraction(
for (int index = threadIdx.x; index < numCombinations; index += blockDim.x) {
FIND_ATOMS_FOR_COMBINATION_INDEX;
bool includeInteraction = IS_VALID_COMBINATION;
#ifdef USE_CUTOFF
if (includeInteraction) {
VERIFY_CUTOFF;
}
#endif
if (includeInteraction) {
PERMUTE_ATOMS;
LOAD_PARTICLE_DATA;
......
platforms/cuda/tests/TestCudaCustomManyParticleForce.cpp
View file @ 785592f4
......@@ -466,12 +466,12 @@ int main(int argc, char* argv[]) {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testNoCutoff();
// testCutoff();
// testPeriodic();
testCutoff();
testPeriodic();
// testExclusions();
// testAllTerms();
// testParameters();
// testTabulatedFunctions();
testParameters();
testTabulatedFunctions();
// testTypeFilters();
}
catch(const exception& e) {
......
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