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Commit 2a1e9acf authored by Peter Eastman's avatar Peter Eastman
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Optimizations to updateParametersInContext() for CUDA

parent 67091abf
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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() {
if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff())
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 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))
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
This diff is collapsed.
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
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