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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
This diff is collapsed.
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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