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Commit 67091abf authored by Peter Eastman's avatar Peter Eastman
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Optimizations to updateParametersInContext() for OpenCL

parent dd712841
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Showing with 200 additions and 105 deletions
platforms/opencl/include/OpenCLContext.h
View file @ 67091abf
......@@ -609,6 +609,10 @@ public:
OpenCLNonbondedUtilities& 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.
*/
......@@ -692,6 +696,12 @@ 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(OpenCLForceInfo* force);
private:
struct Molecule;
struct MoleculeGroup;
......@@ -739,6 +749,7 @@ private:
cl::Kernel clearSixBuffersKernel;
cl::Kernel reduceReal4Kernel;
cl::Kernel reduceForcesKernel;
cl::Kernel setChargesKernel;
std::vector<OpenCLForceInfo*> forces;
std::vector<Molecule> molecules;
std::vector<MoleculeGroup> moleculeGroups;
......@@ -754,6 +765,7 @@ private:
OpenCLArray* energyBuffer;
OpenCLArray* energyParamDerivBuffer;
OpenCLArray* atomIndexDevice;
OpenCLArray* chargeBuffer;
std::vector<std::string> energyParamDerivNames;
std::map<std::string, double> energyParamDerivWorkspace;
std::vector<int> atomIndex;
......
platforms/opencl/include/OpenCLKernels.h
View file @ 67091abf
......@@ -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: *
* *
......@@ -270,9 +270,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force);
private:
class ForceInfo;
int numBonds;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
OpenCLArray* params;
};
......@@ -310,9 +312,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomBondForce& force);
private:
class ForceInfo;
int numBonds;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
OpenCLParameterSet* params;
OpenCLArray* globals;
......@@ -353,9 +357,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force);
private:
class ForceInfo;
int numAngles;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
OpenCLArray* params;
};
......@@ -393,9 +399,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomAngleForce& force);
private:
class ForceInfo;
int numAngles;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
OpenCLParameterSet* params;
OpenCLArray* globals;
......@@ -436,9 +444,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force);
private:
class ForceInfo;
int numTorsions;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
OpenCLArray* params;
};
......@@ -476,9 +486,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const RBTorsionForce& force);
private:
class ForceInfo;
int numTorsions;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
OpenCLArray* params;
};
......@@ -516,9 +528,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private:
class ForceInfo;
int numTorsions;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
std::vector<mm_int2> mapPositionsVec;
OpenCLArray* coefficients;
......@@ -559,9 +573,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force);
private:
class ForceInfo;
int numTorsions;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
OpenCLParameterSet* params;
OpenCLArray* globals;
......@@ -625,12 +641,14 @@ private:
const char* getMaxValue() const {return "(int2) (INT_MAX, INT_MAX)";}
const char* getSortKey() const {return "value.y";}
};
class ForceInfo;
class PmeIO;
class PmePreComputation;
class PmePostComputation;
class SyncQueuePreComputation;
class SyncQueuePostComputation;
OpenCLContext& cl;
ForceInfo* info;
bool hasInitializedKernel;
OpenCLArray* sigmaEpsilon;
OpenCLArray* exceptionParams;
......@@ -704,8 +722,10 @@ 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);
OpenCLContext& cl;
ForceInfo* info;
OpenCLParameterSet* params;
OpenCLArray* globals;
OpenCLArray* interactionGroupData;
......@@ -756,10 +776,12 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
private:
class ForceInfo;
double prefactor, surfaceAreaFactor, cutoff;
bool hasCreatedKernels;
int maxTiles;
OpenCLContext& cl;
ForceInfo* info;
OpenCLArray* params;
OpenCLArray* bornSum;
OpenCLArray* longBornSum;
......@@ -807,10 +829,12 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
private:
class ForceInfo;
double cutoff;
bool hasInitializedKernels, needParameterGradient, needEnergyParamDerivs;
int maxTiles, numComputedValues;
OpenCLContext& cl;
ForceInfo* info;
OpenCLParameterSet* params;
OpenCLParameterSet* computedValues;
OpenCLParameterSet* energyDerivs;
......@@ -864,9 +888,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
private:
class ForceInfo;
int numParticles;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
const System& system;
OpenCLParameterSet* params;
OpenCLArray* globals;
......@@ -908,9 +934,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force);
private:
class ForceInfo;
int numDonors, numAcceptors;
bool hasInitializedKernel;
OpenCLContext& cl;
ForceInfo* info;
OpenCLParameterSet* donorParams;
OpenCLParameterSet* acceptorParams;
OpenCLArray* globals;
......@@ -961,9 +989,11 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force);
private:
class ForceInfo;
int numGroups, numBonds;
bool needEnergyParamDerivs;
OpenCLContext& cl;
ForceInfo* info;
OpenCLParameterSet* params;
OpenCLArray* globals;
OpenCLArray* groupParticles;
......@@ -1013,8 +1043,10 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
private:
class ForceInfo;
int numBonds;
OpenCLContext& cl;
ForceInfo* info;
OpenCLParameterSet* params;
OpenCLArray* globals;
std::vector<std::string> globalParamNames;
......@@ -1059,7 +1091,9 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force);
private:
class ForceInfo;
OpenCLContext& cl;
ForceInfo* info;
bool hasInitializedKernel;
NonbondedMethod nonbondedMethod;
int maxNeighborPairs, forceWorkgroupSize, findNeighborsWorkgroupSize;
......@@ -1119,9 +1153,11 @@ public:
*/
void copyParametersToContext(ContextImpl& context, const GayBerneForce& force);
private:
class ForceInfo;
class ReorderListener;
void sortAtoms();
OpenCLContext& cl;
ForceInfo* info;
bool hasInitializedKernels;
int numRealParticles, maxNeighborBlocks;
GayBerneForce::NonbondedMethod nonbondedMethod;
......
platforms/opencl/src/OpenCLContext.cpp
View file @ 67091abf
......@@ -69,8 +69,8 @@ static void CL_CALLBACK errorCallback(const char* errinfo, const void* private_i
OpenCLContext::OpenCLContext(const System& system, int platformIndex, int deviceIndex, const string& precision, OpenCLPlatform::PlatformData& platformData) :
system(system), time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), atomsWereReordered(false), posq(NULL),
posqCorrection(NULL), velm(NULL), forceBuffers(NULL), longForceBuffer(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL), integration(NULL),
expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
posqCorrection(NULL), velm(NULL), forceBuffers(NULL), longForceBuffer(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL),
chargeBuffer(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
if (precision == "single") {
useDoublePrecision = false;
useMixedPrecision = false;
......@@ -309,6 +309,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
reduceReal4Kernel = cl::Kernel(utilities, "reduceReal4Buffer");
if (supports64BitGlobalAtomics)
reduceForcesKernel = cl::Kernel(utilities, "reduceForces");
setChargesKernel = cl::Kernel(utilities, "setCharges");
// Decide whether native_sqrt(), native_rsqrt(), and native_recip() are sufficiently accurate to use.
......@@ -439,6 +440,8 @@ OpenCLContext::~OpenCLContext() {
delete energyParamDerivBuffer;
if (atomIndexDevice != NULL)
delete atomIndexDevice;
if (chargeBuffer != NULL)
delete chargeBuffer;
if (integration != NULL)
delete integration;
if (expression != NULL)
......@@ -747,6 +750,28 @@ void OpenCLContext::reduceBuffer(OpenCLArray& array, int numBuffers) {
executeKernel(reduceReal4Kernel, bufferSize, 128);
}
void OpenCLContext::setCharges(const vector<double>& charges) {
if (chargeBuffer == NULL)
chargeBuffer = new OpenCLArray(*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);
}
setChargesKernel.setArg<cl::Buffer>(0, chargeBuffer->getDeviceBuffer());
setChargesKernel.setArg<cl::Buffer>(1, posq->getDeviceBuffer());
setChargesKernel.setArg<cl::Buffer>(2, atomIndexDevice->getDeviceBuffer());
setChargesKernel.setArg<cl_int>(3, numAtoms);
executeKernel(setChargesKernel, numAtoms);
}
/**
* This class ensures that atom reordering doesn't break virtual sites.
*/
......@@ -945,9 +970,19 @@ void OpenCLContext::findMoleculeGroups() {
}
void OpenCLContext::invalidateMolecules() {
for (int i = 0; i < forces.size(); i++)
if (invalidateMolecules(forces[i]))
return;
}
bool OpenCLContext::invalidateMolecules(OpenCLForceInfo* 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;
......@@ -962,22 +997,21 @@ void OpenCLContext::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
......@@ -1045,6 +1079,7 @@ void OpenCLContext::invalidateMolecules() {
for (int i = 0; i < (int) reorderListeners.size(); i++)
reorderListeners[i]->execute();
reorderAtoms();
return true;
}
void OpenCLContext::reorderAtoms() {
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 67091abf
......@@ -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: *
* *
......@@ -529,9 +529,9 @@ void OpenCLVirtualSitesKernel::computePositions(ContextImpl& context) {
cl.getIntegrationUtilities().computeVirtualSites();
}
class OpenCLHarmonicBondForceInfo : public OpenCLForceInfo {
class OpenCLCalcHarmonicBondForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLHarmonicBondForceInfo(const HarmonicBondForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const HarmonicBondForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -581,7 +581,8 @@ void OpenCLCalcHarmonicBondForceKernel::initialize(const System& system, const H
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicBondForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLHarmonicBondForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
}
double OpenCLCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -610,12 +611,12 @@ void OpenCLCalcHarmonicBondForceKernel::copyParametersToContext(ContextImpl& con
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCustomBondForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomBondForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomBondForceInfo(const CustomBondForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const CustomBondForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -667,7 +668,8 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomBondForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
// Record information for the expressions.
......@@ -761,12 +763,12 @@ void OpenCLCalcCustomBondForceKernel::copyParametersToContext(ContextImpl& conte
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLHarmonicAngleForceInfo : public OpenCLForceInfo {
class OpenCLCalcHarmonicAngleForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLHarmonicAngleForceInfo(const HarmonicAngleForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const HarmonicAngleForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
......@@ -818,7 +820,8 @@ void OpenCLCalcHarmonicAngleForceKernel::initialize(const System& system, const
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicAngleForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLHarmonicAngleForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
}
double OpenCLCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -847,12 +850,12 @@ void OpenCLCalcHarmonicAngleForceKernel::copyParametersToContext(ContextImpl& co
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCustomAngleForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomAngleForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomAngleForceInfo(const CustomAngleForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const CustomAngleForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
......@@ -905,7 +908,8 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomAngleForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
// Record information for the expressions.
......@@ -999,12 +1003,12 @@ void OpenCLCalcCustomAngleForceKernel::copyParametersToContext(ContextImpl& cont
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLPeriodicTorsionForceInfo : public OpenCLForceInfo {
class OpenCLCalcPeriodicTorsionForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLPeriodicTorsionForceInfo(const PeriodicTorsionForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const PeriodicTorsionForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
......@@ -1057,7 +1061,8 @@ void OpenCLCalcPeriodicTorsionForceKernel::initialize(const System& system, cons
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::periodicTorsionForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float4");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLPeriodicTorsionForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
}
double OpenCLCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1086,12 +1091,12 @@ void OpenCLCalcPeriodicTorsionForceKernel::copyParametersToContext(ContextImpl&
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLRBTorsionForceInfo : public OpenCLForceInfo {
class OpenCLCalcRBTorsionForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLRBTorsionForceInfo(const RBTorsionForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const RBTorsionForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
......@@ -1144,7 +1149,8 @@ void OpenCLCalcRBTorsionForceKernel::initialize(const System& system, const RBTo
replacements["COMPUTE_FORCE"] = OpenCLKernelSources::rbTorsionForce;
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float8");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLRBTorsionForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
}
double OpenCLCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1173,12 +1179,12 @@ void OpenCLCalcRBTorsionForceKernel::copyParametersToContext(ContextImpl& contex
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCMAPTorsionForceInfo : public OpenCLForceInfo {
class OpenCLCalcCMAPTorsionForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCMAPTorsionForceInfo(const CMAPTorsionForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const CMAPTorsionForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
......@@ -1257,7 +1263,8 @@ void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CM
replacements["MAP_POS"] = cl.getBondedUtilities().addArgument(mapPositions->getDeviceBuffer(), "int2");
replacements["MAPS"] = cl.getBondedUtilities().addArgument(torsionMaps->getDeviceBuffer(), "int");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::cmapTorsionForce, replacements), force.getForceGroup());
cl.addForce(new OpenCLCMAPTorsionForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
}
double OpenCLCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1307,9 +1314,9 @@ void OpenCLCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& cont
torsionMaps->upload(torsionMapsVec);
}
class OpenCLCustomTorsionForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomTorsionForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomTorsionForceInfo(const CustomTorsionForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const CustomTorsionForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumTorsions();
......@@ -1363,7 +1370,8 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomTorsionForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
// Record information for the expressions.
......@@ -1457,12 +1465,12 @@ void OpenCLCalcCustomTorsionForceKernel::copyParametersToContext(ContextImpl& co
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLNonbondedForceInfo : public OpenCLForceInfo {
class OpenCLCalcNonbondedForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLNonbondedForceInfo(int requiredBuffers, const NonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
ForceInfo(int requiredBuffers, const NonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
double charge1, charge2, sigma1, sigma2, epsilon1, epsilon2;
......@@ -1910,7 +1918,8 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
replacements["PARAMS"] = cl.getBondedUtilities().addArgument(exceptionParams->getDeviceBuffer(), "float4");
cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::nonbondedExceptions, replacements), force.getForceGroup());
}
cl.addForce(new OpenCLNonbondedForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
info = new ForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force);
cl.addForce(info);
}
double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal) {
......@@ -2149,25 +2158,17 @@ void OpenCLCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& contex
// Record the per-particle parameters.
OpenCLArray& posq = cl.getPosq();
posq.download(cl.getPinnedBuffer());
mm_float4* posqf = (mm_float4*) cl.getPinnedBuffer();
mm_double4* posqd = (mm_double4*) cl.getPinnedBuffer();
vector<double> chargeVector(cl.getNumAtoms());
vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms(), mm_float2(0,0));
double sumSquaredCharges = 0.0;
const vector<cl_int>& order = cl.getAtomIndex();
for (int i = 0; i < force.getNumParticles(); i++) {
int index = order[i];
double charge, sigma, epsilon;
force.getParticleParameters(index, charge, sigma, epsilon);
if (cl.getUseDoublePrecision())
posqd[i].w = charge;
else
posqf[i].w = (float) charge;
sigmaEpsilonVector[index] = mm_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
force.getParticleParameters(i, charge, sigma, epsilon);
chargeVector[i] = charge;
sigmaEpsilonVector[i] = mm_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
sumSquaredCharges += charge*charge;
}
posq.upload(cl.getPinnedBuffer());
cl.setCharges(chargeVector);
sigmaEpsilon->upload(sigmaEpsilonVector);
// Record the exceptions.
......@@ -2189,7 +2190,7 @@ void OpenCLCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& contex
ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
if (force.getUseDispersionCorrection() && cl.getContextIndex() == 0 && (nonbondedMethod == CutoffPeriodic || nonbondedMethod == Ewald || nonbondedMethod == PME))
dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
void OpenCLCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
......@@ -2205,9 +2206,9 @@ void OpenCLCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, in
}
}
class OpenCLCustomNonbondedForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomNonbondedForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomNonbondedForceInfo(int requiredBuffers, const CustomNonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
ForceInfo(int requiredBuffers, const CustomNonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
if (force.getNumInteractionGroups() > 0) {
groupsForParticle.resize(force.getNumParticles());
for (int i = 0; i < force.getNumInteractionGroups(); i++) {
......@@ -2384,7 +2385,8 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(cl_float), globals->getDeviceBuffer()));
}
}
cl.addForce(new OpenCLCustomNonbondedForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
info = new ForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force);
cl.addForce(info);
// Record information for the long range correction.
......@@ -2723,12 +2725,12 @@ void OpenCLCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl&
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLGBSAOBCForceInfo : public OpenCLForceInfo {
class OpenCLCalcGBSAOBCForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLGBSAOBCForceInfo(int requiredBuffers, const GBSAOBCForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
ForceInfo(int requiredBuffers, const GBSAOBCForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
double charge1, charge2, radius1, radius2, scale1, scale2;
......@@ -2806,7 +2808,8 @@ void OpenCLCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOB
nb.addInteraction(useCutoff, usePeriodic, false, cutoff, vector<vector<int> >(), source, force.getForceGroup());
nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("obcParams", "float", 2, sizeof(cl_float2), params->getDeviceBuffer()));;
nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("bornForce", "real", 1, elementSize, bornForce->getDeviceBuffer()));;
cl.addForce(new OpenCLGBSAOBCForceInfo(nb.getNumForceBuffers(), force));
info = new ForceInfo(nb.getNumForceBuffers(), force);
cl.addForce(info);
}
double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -2938,33 +2941,27 @@ void OpenCLCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context,
// Record the per-particle parameters.
OpenCLArray& posq = cl.getPosq();
mm_float4* posqf = (mm_float4*) cl.getPinnedBuffer();
mm_double4* posqd = (mm_double4*) cl.getPinnedBuffer();
posq.download(cl.getPinnedBuffer());
vector<double> chargeVector(cl.getNumAtoms());
vector<mm_float2> paramsVector(cl.getPaddedNumAtoms(), mm_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] = mm_float2((float) radius, (float) (scalingFactor*radius));
if (cl.getUseDoublePrecision())
posqd[i].w = charge;
else
posqf[i].w = (float) charge;
}
posq.upload(cl.getPinnedBuffer());
cl.setCharges(chargeVector);
params->upload(paramsVector);
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCustomGBForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomGBForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomGBForceInfo(int requiredBuffers, const CustomGBForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
ForceInfo(int requiredBuffers, const CustomGBForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
vector<double> params1;
......@@ -3812,7 +3809,8 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
for (int i = 0; i < (int) arguments.size(); i++)
cl.getNonbondedUtilities().addArgument(arguments[i]);
}
cl.addForce(new OpenCLCustomGBForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
info = new ForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force);
cl.addForce(info);
if (useLong)
cl.addAutoclearBuffer(*longEnergyDerivs);
else {
......@@ -4073,12 +4071,12 @@ void OpenCLCalcCustomGBForceKernel::copyParametersToContext(ContextImpl& context
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCustomExternalForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomExternalForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomExternalForceInfo(const CustomExternalForce& force, int numParticles) : OpenCLForceInfo(0), force(force), indices(numParticles, -1) {
ForceInfo(const CustomExternalForce& force, int numParticles) : OpenCLForceInfo(0), force(force), indices(numParticles, -1) {
vector<double> params;
for (int i = 0; i < force.getNumParticles(); i++) {
int particle;
......@@ -4133,7 +4131,8 @@ void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomExternalForceInfo(force, system.getNumParticles()));
info = new ForceInfo(force, system.getNumParticles());
cl.addForce(info);
// Record information for the expressions.
......@@ -4228,12 +4227,12 @@ void OpenCLCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl& c
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCustomHbondForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomHbondForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomHbondForceInfo(int requiredBuffers, const CustomHbondForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
ForceInfo(int requiredBuffers, const CustomHbondForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
return true;
......@@ -4406,7 +4405,8 @@ void OpenCLCalcCustomHbondForceKernel::initialize(const System& system, const Cu
maxBuffers = max(maxBuffers, donorBufferCounter[i]);
for (int i = 0; i < (int) acceptorBufferCounter.size(); i++)
maxBuffers = max(maxBuffers, acceptorBufferCounter[i]);
cl.addForce(new OpenCLCustomHbondForceInfo(maxBuffers, force));
info = new ForceInfo(maxBuffers, force);
cl.addForce(info);
// Record exclusions.
......@@ -4767,12 +4767,12 @@ void OpenCLCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& cont
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCustomCentroidBondForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomCentroidBondForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomCentroidBondForceInfo(const CustomCentroidBondForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const CustomCentroidBondForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -4840,7 +4840,8 @@ void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, c
return;
if (!cl.getSupports64BitGlobalAtomics())
throw OpenMMException("CustomCentroidBondForce requires a device that supports 64 bit atomic operations");
cl.addForce(new OpenCLCustomCentroidBondForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
// Record the groups.
......@@ -5229,12 +5230,12 @@ void OpenCLCalcCustomCentroidBondForceKernel::copyParametersToContext(ContextImp
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCustomCompoundBondForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomCompoundBondForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomCompoundBondForceInfo(const CustomCompoundBondForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const CustomCompoundBondForce& force) : OpenCLForceInfo(0), force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -5285,7 +5286,8 @@ void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, c
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomCompoundBondForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
// Record the tabulated functions.
......@@ -5543,12 +5545,12 @@ void OpenCLCalcCustomCompoundBondForceKernel::copyParametersToContext(ContextImp
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLCustomManyParticleForceInfo : public OpenCLForceInfo {
class OpenCLCalcCustomManyParticleForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomManyParticleForceInfo(const CustomManyParticleForce& force) : OpenCLForceInfo(0), force(force) {
ForceInfo(const CustomManyParticleForce& force) : OpenCLForceInfo(0), force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
vector<double> params1, params2;
......@@ -5635,7 +5637,8 @@ void OpenCLCalcCustomManyParticleForceKernel::initialize(const System& system, c
paramVector[i][j] = (float) parameters[j];
}
params->setParameterValues(paramVector);
cl.addForce(new OpenCLCustomManyParticleForceInfo(force));
info = new ForceInfo(force);
cl.addForce(info);
// Record the tabulated functions.
......@@ -6209,12 +6212,12 @@ void OpenCLCalcCustomManyParticleForceKernel::copyParametersToContext(ContextImp
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
cl.invalidateMolecules(info);
}
class OpenCLGayBerneForceInfo : public OpenCLForceInfo {
class OpenCLCalcGayBerneForceKernel::ForceInfo : public OpenCLForceInfo {
public:
OpenCLGayBerneForceInfo(int requiredBuffers, const GayBerneForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
ForceInfo(int requiredBuffers, const GayBerneForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
}
bool areParticlesIdentical(int particle1, int particle2) {
int xparticle1, yparticle1;
......@@ -6426,7 +6429,8 @@ void OpenCLCalcGayBerneForceKernel::initialize(const System& system, const GayBe
neighborsKernel = cl::Kernel(program, "findNeighbors");
forceKernel = cl::Kernel(program, "computeForce");
torqueKernel = cl::Kernel(program, "applyTorques");
cl.addForce(new OpenCLGayBerneForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
info = new ForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force);
cl.addForce(info);
cl.addReorderListener(new ReorderListener(*this));
}
......@@ -6577,7 +6581,7 @@ void OpenCLCalcGayBerneForceKernel::copyParametersToContext(ContextImpl& context
}
exceptionParams->upload(exceptionParamsVec);
}
cl.invalidateMolecules();
cl.invalidateMolecules(info);
sortAtoms();
}
......
platforms/opencl/src/kernels/utilities.cl
View file @ 67091abf
......@@ -107,3 +107,11 @@ __kernel void determineNativeAccuracy(__global float8* restrict values, int numV
values[i] = (float8) (v, native_sqrt(v), native_rsqrt(v), native_recip(v), native_exp(v), native_log(v), 0.0f, 0.0f);
}
}
/**
* Record the atomic charges into the posq array.
*/
__kernel void setCharges(__global real* restrict charges, __global real4* restrict posq, __global int* restrict atomOrder, int numAtoms) {
for (int i = get_global_id(0); i < numAtoms; i += get_global_size(0))
posq[i].w = charges[atomOrder[i]];
}
\ No newline at end of file
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