Skip to content

GitLab

Commit 2a1e9acf authored by Peter Eastman's avatar Peter Eastman
Browse files

Optimizations to updateParametersInContext() for CUDA

parent 67091abf
Hide whitespace changes
Inline Side-by-side
Showing with 181 additions and 88 deletions
platforms/cuda/include/CudaContext.h
View file @ 2a1e9acf
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009-2016 Stanford University and the Authors. *
* Portions copyright (c) 2009-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -494,6 +494,10 @@ public:
CudaNonbondedUtilities& getNonbondedUtilities() {
return *nonbonded;
}
/**
* Set the particle charges. These are packed into the fourth element of the posq array.
*/
void setCharges(const std::vector<double>& charges);
/**
* Get the thread used by this context for executing parallel computations.
*/
......@@ -577,6 +581,12 @@ public:
* and order to be revalidated.
*/
void invalidateMolecules();
/**
* Mark that the current molecule definitions from one particular force (and hence the atom order)
* may be invalid. This should be called whenever force field parameters change. It will cause the
* definitions and order to be revalidated.
*/
bool invalidateMolecules(CudaForceInfo* force);
private:
/**
* Compute a sorted list of device indices in decreasing order of desirability
......@@ -626,6 +636,7 @@ private:
CUfunction clearFourBuffersKernel;
CUfunction clearFiveBuffersKernel;
CUfunction clearSixBuffersKernel;
CUfunction setChargesKernel;
std::vector<CudaForceInfo*> forces;
std::vector<Molecule> molecules;
std::vector<MoleculeGroup> moleculeGroups;
......@@ -638,6 +649,7 @@ private:
CudaArray* energyBuffer;
CudaArray* energyParamDerivBuffer;
CudaArray* atomIndexDevice;
CudaArray* chargeBuffer;
std::vector<std::string> energyParamDerivNames;
std::map<std::string, double> energyParamDerivWorkspace;
std::vector<int> atomIndex;
......
platforms/cuda/include/CudaKernels.h
View file @ 2a1e9acf
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -292,9 +292,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force);
private:
class ForceInfo;
int numBonds;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaArray* params;
};
......@@ -332,9 +334,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomBondForce& force);
private:
class ForceInfo;
int numBonds;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaParameterSet* params;
CudaArray* globals;
......@@ -375,9 +379,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force);
private:
class ForceInfo;
int numAngles;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaArray* params;
};
......@@ -415,9 +421,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomAngleForce& force);
private:
class ForceInfo;
int numAngles;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaParameterSet* params;
CudaArray* globals;
......@@ -458,9 +466,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force);
private:
class ForceInfo;
int numTorsions;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaArray* params;
};
......@@ -498,9 +508,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const RBTorsionForce& force);
private:
class ForceInfo;
int numTorsions;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaArray* params1;
CudaArray* params2;
......@@ -539,9 +551,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private:
class ForceInfo;
int numTorsions;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
std::vector<int2> mapPositionsVec;
CudaArray* coefficients;
......@@ -582,9 +596,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force);
private:
class ForceInfo;
int numTorsions;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaParameterSet* params;
CudaArray* globals;
......@@ -647,12 +663,14 @@ private:
const char* getMaxValue() const {return "make_int2(2147483647, 2147483647)";}
const char* getSortKey() const {return "value.y";}
};
class ForceInfo;
class PmeIO;
class PmePreComputation;
class PmePostComputation;
class SyncStreamPreComputation;
class SyncStreamPostComputation;
CudaContext& cu;
ForceInfo* info;
bool hasInitializedFFT;
CudaArray* sigmaEpsilon;
CudaArray* exceptionParams;
......@@ -724,8 +742,10 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
class ForceInfo;
void initInteractionGroups(const CustomNonbondedForce& force, const std::string& interactionSource, const std::vector<std::string>& tableTypes);
CudaContext& cu;
ForceInfo* info;
CudaParameterSet* params;
CudaArray* globals;
CudaArray* interactionGroupData;
......@@ -775,10 +795,12 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
private:
class ForceInfo;
double prefactor, surfaceAreaFactor, cutoff;
bool hasCreatedKernels;
int maxTiles;
CudaContext& cu;
ForceInfo* info;
CudaArray* params;
CudaArray* bornSum;
CudaArray* bornRadii;
......@@ -825,10 +847,12 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
private:
class ForceInfo;
double cutoff;
bool hasInitializedKernels, needParameterGradient, needEnergyParamDerivs;
int maxTiles, numComputedValues;
CudaContext& cu;
ForceInfo* info;
CudaParameterSet* params;
CudaParameterSet* computedValues;
CudaParameterSet* energyDerivs;
......@@ -882,9 +906,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
private:
class ForceInfo;
int numParticles;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaParameterSet* params;
CudaArray* globals;
......@@ -926,9 +952,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force);
private:
class ForceInfo;
int numDonors, numAcceptors;
bool hasInitializedKernel;
CudaContext& cu;
ForceInfo* info;
CudaParameterSet* donorParams;
CudaParameterSet* acceptorParams;
CudaArray* globals;
......@@ -978,9 +1006,11 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force);
private:
class ForceInfo;
int numGroups, numBonds;
bool needEnergyParamDerivs;
CudaContext& cu;
ForceInfo* info;
CudaParameterSet* params;
CudaArray* globals;
CudaArray* groupParticles;
......@@ -1031,8 +1061,10 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
private:
class ForceInfo;
int numBonds;
CudaContext& cu;
ForceInfo* info;
CudaParameterSet* params;
CudaArray* globals;
std::vector<std::string> globalParamNames;
......@@ -1077,7 +1109,9 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force);
private:
class ForceInfo;
CudaContext& cu;
ForceInfo* info;
bool hasInitializedKernel;
NonbondedMethod nonbondedMethod;
int maxNeighborPairs, forceWorkgroupSize, findNeighborsWorkgroupSize;
......@@ -1139,9 +1173,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const GayBerneForce& force);
private:
class ForceInfo;
class ReorderListener;
void sortAtoms();
CudaContext& cu;
ForceInfo* info;
bool hasInitializedKernels;
int numRealParticles, numExceptions, maxNeighborBlocks;
GayBerneForce::NonbondedMethod nonbondedMethod;
......
platforms/cuda/src/CudaContext.cpp
View file @ 2a1e9acf
......@@ -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) 2009-2016 Stanford University and the Authors. *
* Portions copyright (c) 2009-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -108,7 +108,8 @@ static int executeInWindows(const string &command) {
CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const string& precision, const string& compiler,
const string& tempDir, const std::string& hostCompiler, CudaPlatform::PlatformData& platformData) : system(system), currentStream(0),
time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), contextIsValid(false), atomsWereReordered(false), hasCompilerKernel(false), isNvccAvailable(false),
pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL), chargeBuffer(NULL),
integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
// Determine what compiler to use.
this->compiler = "\""+compiler+"\"";
......@@ -291,6 +292,7 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
clearFourBuffersKernel = getKernel(utilities, "clearFourBuffers");
clearFiveBuffersKernel = getKernel(utilities, "clearFiveBuffers");
clearSixBuffersKernel = getKernel(utilities, "clearSixBuffers");
setChargesKernel = getKernel(utilities, "setCharges");
// Set defines based on the requested precision.
......@@ -407,6 +409,8 @@ CudaContext::~CudaContext() {
delete energyParamDerivBuffer;
if (atomIndexDevice != NULL)
delete atomIndexDevice;
if (chargeBuffer != NULL)
delete chargeBuffer;
if (integration != NULL)
delete integration;
if (expression != NULL)
......@@ -860,6 +864,25 @@ void CudaContext::clearAutoclearBuffers() {
}
}
void CudaContext::setCharges(const vector<double>& charges) {
if (chargeBuffer == NULL)
chargeBuffer = new CudaArray(*this, numAtoms, useDoublePrecision ? sizeof(double) : sizeof(float), "chargeBuffer");
if (getUseDoublePrecision()) {
double* c = (double*) getPinnedBuffer();
for (int i = 0; i < charges.size(); i++)
c[i] = charges[i];
chargeBuffer->upload(c);
}
else {
float* c = (float*) getPinnedBuffer();
for (int i = 0; i < charges.size(); i++)
c[i] = (float) charges[i];
chargeBuffer->upload(c);
}
void* args[] = {&chargeBuffer->getDevicePointer(), &posq->getDevicePointer(), &atomIndexDevice->getDevicePointer(), &numAtoms};
executeKernel(setChargesKernel, args, numAtoms);
}
/**
* This class ensures that atom reordering doesn't break virtual sites.
*/
......@@ -1058,9 +1081,19 @@ void CudaContext::findMoleculeGroups() {
}
void CudaContext::invalidateMolecules() {
for (int i = 0; i < forces.size(); i++)
if (invalidateMolecules(forces[i]))
return;
}
bool CudaContext::invalidateMolecules(CudaForceInfo* force) {
if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff())
return;
return false;
bool valid = true;
int forceIndex = -1;
for (int i = 0; i < forces.size(); i++)
if (forces[i] == force)
forceIndex = i;
for (int group = 0; valid && group < (int) moleculeGroups.size(); group++) {
MoleculeGroup& mol = moleculeGroups[group];
vector<int>& instances = mol.instances;
......@@ -1075,22 +1108,21 @@ void CudaContext::invalidateMolecules() {
Molecule& m2 = molecules[instances[j]];
int offset2 = offsets[j];
for (int i = 0; i < (int) atoms.size() && valid; i++) {
for (int k = 0; k < (int) forces.size(); k++)
if (!forces[k]->areParticlesIdentical(atoms[i]+offset1, atoms[i]+offset2))
valid = false;
if (!force->areParticlesIdentical(atoms[i]+offset1, atoms[i]+offset2))
valid = false;
}
// See if the force groups are identical.
for (int i = 0; i < (int) forces.size() && valid; i++) {
for (int k = 0; k < (int) m1.groups[i].size() && valid; k++)
if (!forces[i]->areGroupsIdentical(m1.groups[i][k], m2.groups[i][k]))
if (valid && forceIndex > -1) {
for (int k = 0; k < (int) m1.groups[forceIndex].size() && valid; k++)
if (!force->areGroupsIdentical(m1.groups[forceIndex][k], m2.groups[forceIndex][k]))
valid = false;
}
}
}
if (valid)
return;
return false;
// The list of which molecules are identical is no longer valid. We need to restore the
// atoms to their original order, rebuild the list of identical molecules, and sort them
......@@ -1158,6 +1190,7 @@ void CudaContext::invalidateMolecules() {
for (int i = 0; i < (int) reorderListeners.size(); i++)
reorderListeners[i]->execute();
reorderAtoms();
return true;
}
void CudaContext::reorderAtoms() {
......
platforms/cuda/src/CudaKernels.cpp
View file @ 2a1e9acf
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -502,9 +502,9 @@ void CudaVirtualSitesKernel::computePositions(ContextImpl& context) {
cu.getIntegrationUtilities().computeVirtualSites();
}
class CudaHarmonicBondForceInfo : public CudaForceInfo {
class CudaCalcHarmonicBondForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaHarmonicBondForceInfo(const HarmonicBondForce& force) : force(force) {
ForceInfo(const HarmonicBondForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -556,7 +556,8 @@ void CudaCalcHarmonicBondForceKernel::initialize(const System& system, const Har
replacements["COMPUTE_FORCE"] = CudaKernelSources::harmonicBondForce;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaKernelSources::bondForce, replacements), force.getForceGroup());
cu.addForce(new CudaHarmonicBondForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
}
double CudaCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -589,9 +590,9 @@ void CudaCalcHarmonicBondForceKernel::copyParametersToContext(ContextImpl& conte
cu.invalidateMolecules();
}
class CudaCustomBondForceInfo : public CudaForceInfo {
class CudaCalcCustomBondForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomBondForceInfo(const CustomBondForce& force) : force(force) {
ForceInfo(const CustomBondForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -645,7 +646,8 @@ void CudaCalcCustomBondForceKernel::initialize(const System& system, const Custo
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
cu.addForce(new CudaCustomBondForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
// Record information for the expressions.
......@@ -743,9 +745,9 @@ void CudaCalcCustomBondForceKernel::copyParametersToContext(ContextImpl& context
cu.invalidateMolecules();
}
class CudaHarmonicAngleForceInfo : public CudaForceInfo {
class CudaCalcHarmonicAngleForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaHarmonicAngleForceInfo(const HarmonicAngleForce& force) : force(force) {
ForceInfo(const HarmonicAngleForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
......@@ -799,7 +801,8 @@ void CudaCalcHarmonicAngleForceKernel::initialize(const System& system, const Ha
replacements["COMPUTE_FORCE"] = CudaKernelSources::harmonicAngleForce;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaKernelSources::angleForce, replacements), force.getForceGroup());
cu.addForce(new CudaHarmonicAngleForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
}
double CudaCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -832,9 +835,9 @@ void CudaCalcHarmonicAngleForceKernel::copyParametersToContext(ContextImpl& cont
cu.invalidateMolecules();
}
class CudaCustomAngleForceInfo : public CudaForceInfo {
class CudaCalcCustomAngleForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomAngleForceInfo(const CustomAngleForce& force) : force(force) {
ForceInfo(const CustomAngleForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
......@@ -889,7 +892,8 @@ void CudaCalcCustomAngleForceKernel::initialize(const System& system, const Cust
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
cu.addForce(new CudaCustomAngleForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
// Record information for the expressions.
......@@ -987,9 +991,9 @@ void CudaCalcCustomAngleForceKernel::copyParametersToContext(ContextImpl& contex
cu.invalidateMolecules();
}
class CudaPeriodicTorsionForceInfo : public CudaForceInfo {
class CudaCalcPeriodicTorsionForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaPeriodicTorsionForceInfo(const PeriodicTorsionForce& force) : force(force) {
ForceInfo(const PeriodicTorsionForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
......@@ -1044,7 +1048,8 @@ void CudaCalcPeriodicTorsionForceKernel::initialize(const System& system, const
replacements["COMPUTE_FORCE"] = CudaKernelSources::periodicTorsionForce;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float4");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaKernelSources::torsionForce, replacements), force.getForceGroup());
cu.addForce(new CudaPeriodicTorsionForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
}
double CudaCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1077,9 +1082,9 @@ void CudaCalcPeriodicTorsionForceKernel::copyParametersToContext(ContextImpl& co
cu.invalidateMolecules();
}
class CudaRBTorsionForceInfo : public CudaForceInfo {
class CudaCalcRBTorsionForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaRBTorsionForceInfo(const RBTorsionForce& force) : force(force) {
ForceInfo(const RBTorsionForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
......@@ -1141,7 +1146,8 @@ void CudaCalcRBTorsionForceKernel::initialize(const System& system, const RBTors
replacements["PARAMS1"] = cu.getBondedUtilities().addArgument(params1->getDevicePointer(), "float4");
replacements["PARAMS2"] = cu.getBondedUtilities().addArgument(params2->getDevicePointer(), "float2");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaKernelSources::torsionForce, replacements), force.getForceGroup());
cu.addForce(new CudaRBTorsionForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
}
double CudaCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1177,9 +1183,9 @@ void CudaCalcRBTorsionForceKernel::copyParametersToContext(ContextImpl& context,
cu.invalidateMolecules();
}
class CudaCMAPTorsionForceInfo : public CudaForceInfo {
class CudaCalcCMAPTorsionForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCMAPTorsionForceInfo(const CMAPTorsionForce& force) : force(force) {
ForceInfo(const CMAPTorsionForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
......@@ -1259,7 +1265,8 @@ void CudaCalcCMAPTorsionForceKernel::initialize(const System& system, const CMAP
replacements["MAP_POS"] = cu.getBondedUtilities().addArgument(mapPositions->getDevicePointer(), "int2");
replacements["MAPS"] = cu.getBondedUtilities().addArgument(torsionMaps->getDevicePointer(), "int");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaKernelSources::cmapTorsionForce, replacements), force.getForceGroup());
cu.addForce(new CudaCMAPTorsionForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
}
double CudaCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1309,9 +1316,9 @@ void CudaCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& contex
torsionMaps->upload(torsionMapsVec);
}
class CudaCustomTorsionForceInfo : public CudaForceInfo {
class CudaCalcCustomTorsionForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomTorsionForceInfo(const CustomTorsionForce& force) : force(force) {
ForceInfo(const CustomTorsionForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
......@@ -1366,7 +1373,8 @@ void CudaCalcCustomTorsionForceKernel::initialize(const System& system, const Cu
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
cu.addForce(new CudaCustomTorsionForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
// Record information for the expressions.
......@@ -1464,9 +1472,9 @@ void CudaCalcCustomTorsionForceKernel::copyParametersToContext(ContextImpl& cont
cu.invalidateMolecules();
}
class CudaNonbondedForceInfo : public CudaForceInfo {
class CudaCalcNonbondedForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaNonbondedForceInfo(const NonbondedForce& force) : force(force) {
ForceInfo(const NonbondedForce& force) : force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
double charge1, charge2, sigma1, sigma2, epsilon1, epsilon2;
......@@ -1946,7 +1954,8 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(exceptionParams->getDevicePointer(), "float4");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaKernelSources::nonbondedExceptions, replacements), force.getForceGroup());
}
cu.addForce(new CudaNonbondedForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
}
double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal) {
......@@ -2087,25 +2096,18 @@ void CudaCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context,
// Record the per-particle parameters.
CudaArray& posq = cu.getPosq();
posq.download(cu.getPinnedBuffer());
float4* posqf = (float4*) cu.getPinnedBuffer();
double4* posqd = (double4*) cu.getPinnedBuffer();
vector<double> chargeVector(cu.getNumAtoms());
vector<float2> sigmaEpsilonVector(cu.getPaddedNumAtoms(), make_float2(0, 0));
double sumSquaredCharges = 0.0;
const vector<int>& order = cu.getAtomIndex();
for (int i = 0; i < force.getNumParticles(); i++) {
int index = order[i];
double charge, sigma, epsilon;
force.getParticleParameters(index, charge, sigma, epsilon);
if (cu.getUseDoublePrecision())
posqd[i].w = charge;
else
posqf[i].w = (float) charge;
sigmaEpsilonVector[index] = make_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
force.getParticleParameters(i, charge, sigma, epsilon);
chargeVector[i] = charge;
sigmaEpsilonVector[i] = make_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
sumSquaredCharges += charge*charge;
}
posq.upload(cu.getPinnedBuffer());
cu.setCharges(chargeVector);
sigmaEpsilon->upload(sigmaEpsilonVector);
// Record the exceptions.
......@@ -2143,9 +2145,9 @@ void CudaCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int&
}
}
class CudaCustomNonbondedForceInfo : public CudaForceInfo {
class CudaCalcCustomNonbondedForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomNonbondedForceInfo(const CustomNonbondedForce& force) : force(force) {
ForceInfo(const CustomNonbondedForce& force) : force(force) {
if (force.getNumInteractionGroups() > 0) {
groupsForParticle.resize(force.getNumParticles());
for (int i = 0; i < force.getNumInteractionGroups(); i++) {
......@@ -2324,7 +2326,8 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
cu.getNonbondedUtilities().addArgument(CudaNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(float), globals->getDevicePointer()));
}
}
cu.addForce(new CudaCustomNonbondedForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
// Record information for the long range correction.
......@@ -2660,9 +2663,9 @@ void CudaCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& co
cu.invalidateMolecules();
}
class CudaGBSAOBCForceInfo : public CudaForceInfo {
class CudaCalcGBSAOBCForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaGBSAOBCForceInfo(const GBSAOBCForce& force) : force(force) {
ForceInfo(const GBSAOBCForce& force) : force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
double charge1, charge2, radius1, radius2, scale1, scale2;
......@@ -2733,7 +2736,8 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
nb.addInteraction(useCutoff, usePeriodic, false, cutoff, vector<vector<int> >(), source, force.getForceGroup());
nb.addParameter(CudaNonbondedUtilities::ParameterInfo("obcParams", "float", 2, sizeof(float2), params->getDevicePointer()));
nb.addParameter(CudaNonbondedUtilities::ParameterInfo("bornForce", "long long", 1, sizeof(long long), bornForce->getDevicePointer()));
cu.addForce(new CudaGBSAOBCForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
}
double CudaCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -2846,23 +2850,17 @@ void CudaCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, c
// Record the per-particle parameters.
CudaArray& posq = cu.getPosq();
float4* posqf = (float4*) cu.getPinnedBuffer();
double4* posqd = (double4*) cu.getPinnedBuffer();
posq.download(cu.getPinnedBuffer());
vector<double> chargeVector(cu.getNumAtoms());
vector<float2> paramsVector(cu.getPaddedNumAtoms(), make_float2(1, 1));
const double dielectricOffset = 0.009;
for (int i = 0; i < numParticles; i++) {
double charge, radius, scalingFactor;
force.getParticleParameters(i, charge, radius, scalingFactor);
chargeVector[i] = charge;
radius -= dielectricOffset;
paramsVector[i] = make_float2((float) radius, (float) (scalingFactor*radius));
if (cu.getUseDoublePrecision())
posqd[i].w = charge;
else
posqf[i].w = (float) charge;
}
posq.upload(cu.getPinnedBuffer());
cu.setCharges(chargeVector);
params->upload(paramsVector);
// Mark that the current reordering may be invalid.
......@@ -2870,9 +2868,9 @@ void CudaCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, c
cu.invalidateMolecules();
}
class CudaCustomGBForceInfo : public CudaForceInfo {
class CudaCalcCustomGBForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomGBForceInfo(const CustomGBForce& force) : force(force) {
ForceInfo(const CustomGBForce& force) : force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
vector<double> params1;
......@@ -3660,7 +3658,8 @@ void CudaCalcCustomGBForceKernel::initialize(const System& system, const CustomG
for (int i = 0; i < (int) arguments.size(); i++)
cu.getNonbondedUtilities().addArgument(arguments[i]);
}
cu.addForce(new CudaCustomGBForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
cu.addAutoclearBuffer(*longEnergyDerivs);
}
......@@ -3876,9 +3875,9 @@ void CudaCalcCustomGBForceKernel::copyParametersToContext(ContextImpl& context,
cu.invalidateMolecules();
}
class CudaCustomExternalForceInfo : public CudaForceInfo {
class CudaCalcCustomExternalForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomExternalForceInfo(const CustomExternalForce& force, int numParticles) : force(force), indices(numParticles, -1) {
ForceInfo(const CustomExternalForce& force, int numParticles) : force(force), indices(numParticles, -1) {
vector<double> params;
for (int i = 0; i < force.getNumParticles(); i++) {
int particle;
......@@ -3935,7 +3934,8 @@ void CudaCalcCustomExternalForceKernel::initialize(const System& system, const C
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
cu.addForce(new CudaCustomExternalForceInfo(force, system.getNumParticles()));
info = new ForceInfo(force, system.getNumParticles());
cu.addForce(info);
// Record information for the expressions.
......@@ -4034,9 +4034,9 @@ void CudaCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl& con
cu.invalidateMolecules();
}
class CudaCustomHbondForceInfo : public CudaForceInfo {
class CudaCalcCustomHbondForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomHbondForceInfo(const CustomHbondForce& force) : force(force) {
ForceInfo(const CustomHbondForce& force) : force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
return true;
......@@ -4183,7 +4183,8 @@ void CudaCalcCustomHbondForceKernel::initialize(const System& system, const Cust
}
acceptors->upload(acceptorVector);
acceptorParams->setParameterValues(acceptorParamVector);
cu.addForce(new CudaCustomHbondForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
// Record exclusions.
......@@ -4551,9 +4552,9 @@ void CudaCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& contex
cu.invalidateMolecules();
}
class CudaCustomCentroidBondForceInfo : public CudaForceInfo {
class CudaCalcCustomCentroidBondForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomCentroidBondForceInfo(const CustomCentroidBondForce& force) : force(force) {
ForceInfo(const CustomCentroidBondForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -4621,7 +4622,8 @@ void CudaCalcCustomCentroidBondForceKernel::initialize(const System& system, con
numBonds = force.getNumBonds();
if (numBonds == 0)
return;
cu.addForce(new CudaCustomCentroidBondForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
// Record the groups.
......@@ -5009,9 +5011,9 @@ void CudaCalcCustomCentroidBondForceKernel::copyParametersToContext(ContextImpl&
cu.invalidateMolecules();
}
class CudaCustomCompoundBondForceInfo : public CudaForceInfo {
class CudaCalcCustomCompoundBondForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomCompoundBondForceInfo(const CustomCompoundBondForce& force) : force(force) {
ForceInfo(const CustomCompoundBondForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -5064,7 +5066,8 @@ void CudaCalcCustomCompoundBondForceKernel::initialize(const System& system, con
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
cu.addForce(new CudaCustomCompoundBondForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
// Record the tabulated functions.
......@@ -5325,9 +5328,9 @@ void CudaCalcCustomCompoundBondForceKernel::copyParametersToContext(ContextImpl&
cu.invalidateMolecules();
}
class CudaCustomManyParticleForceInfo : public CudaForceInfo {
class CudaCalcCustomManyParticleForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaCustomManyParticleForceInfo(const CustomManyParticleForce& force) : force(force) {
ForceInfo(const CustomManyParticleForce& force) : force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
vector<double> params1, params2;
......@@ -5412,7 +5415,8 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
cu.addForce(new CudaCustomManyParticleForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
// Record the tabulated functions.
......@@ -5992,9 +5996,9 @@ void CudaCalcCustomManyParticleForceKernel::copyParametersToContext(ContextImpl&
cu.invalidateMolecules();
}
class CudaGayBerneForceInfo : public CudaForceInfo {
class CudaCalcGayBerneForceKernel::ForceInfo : public CudaForceInfo {
public:
CudaGayBerneForceInfo(const GayBerneForce& force) : force(force) {
ForceInfo(const GayBerneForce& force) : force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
int xparticle1, yparticle1;
......@@ -6205,7 +6209,8 @@ void CudaCalcGayBerneForceKernel::initialize(const System& system, const GayBern
neighborsKernel = cu.getKernel(module, "findNeighbors");
forceKernel = cu.getKernel(module, "computeForce");
torqueKernel = cu.getKernel(module, "applyTorques");
cu.addForce(new CudaGayBerneForceInfo(force));
info = new ForceInfo(force);
cu.addForce(info);
cu.addReorderListener(new ReorderListener(*this));
}
......
platforms/cuda/src/kernels/utilities.cu
View file @ 2a1e9acf
......@@ -73,4 +73,11 @@ __global__ void clearSixBuffers(int* __restrict__ buffer1, int size1, int* __res
clearSingleBuffer(buffer6, size6);
}
/**
* Record the atomic charges into the posq array.
*/
__global__ void setCharges(real* __restrict__ charges, real4* __restrict__ posq, int* __restrict__ atomOrder, int numAtoms) {
for (int i = blockDim.x*blockIdx.x+threadIdx.x; i < numAtoms; i += blockDim.x*gridDim.x)
posq[i].w = charges[atomOrder[i]];
}
}
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment