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Commit 6a4ac837 authored by peastman's avatar peastman
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Parallelized CpuCustomGBForce

parent bb70341a
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Showing with 380 additions and 231 deletions
platforms/cpu/include/CpuCustomGBForce.h
View file @ 6a4ac837
......@@ -29,6 +29,7 @@
#include "CpuNeighborList.h"
#include "lepton/CompiledExpression.h"
#include "openmm/CustomGBForce.h"
#include "openmm/internal/ThreadPool.h"
#include "openmm/internal/vectorize.h"
#include <map>
#include <set>
......@@ -38,59 +39,63 @@ namespace OpenMM {
class CpuCustomGBForce {
private:
class ComputeForceTask;
class ThreadData;
bool cutoff;
bool periodic;
const CpuNeighborList* neighborList;
float periodicBoxSize[3];
float cutoffDistance;
CompiledExpressionSet expressionSet;
std::vector<Lepton::CompiledExpression> valueExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions;
const std::vector<std::set<int> > exclusions;
std::vector<std::string> valueNames;
std::vector<int> valueIndex;
std::vector<CustomGBForce::ComputationType> valueTypes;
std::vector<Lepton::CompiledExpression> energyExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions;
std::vector<std::string> paramNames;
std::vector<int> paramIndex;
std::vector<CustomGBForce::ComputationType> energyTypes;
std::vector<int> particleParamIndex;
std::vector<int> particleValueIndex;
int xindex, yindex, zindex, rindex;
ThreadPool& threads;
std::vector<ThreadData*> threadData;
std::vector<double> threadEnergy;
// Workspace vectors
std::vector<std::vector<float> > values, dEdV;
std::vector<float> dVdR1, dVdR2, dVdX, dVdY, dVdZ;
// The following variables are used to make information accessible to the individual threads.
int numberOfAtoms;
float* posq;
RealOpenMM** atomParameters;
const std::map<std::string, double>* globalParameters;
std::vector<AlignedArray<float> >* threadForce;
bool includeForce, includeEnergy;
void* atomicCounter;
/**
* This routine contains the code executed by each thread.
*/
void threadComputeForce(ThreadPool& threads, int threadIndex);
/**
* Calculate a computed value of type SingleParticle
*
* @param index the index of the value to compute
* @param data workspace for the current thread
* @param numAtoms number of atoms
* @param posq atom coordinates
* @param values the vector to store computed values into
* @param atomParameters atomParameters[atomIndex][paramterIndex]
*/
void calculateSingleParticleValue(int index, int numAtoms, float* posq, std::vector<std::vector<float> >& values,
RealOpenMM** atomParameters);
void calculateSingleParticleValue(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters);
/**
* Calculate a computed value that is based on particle pairs
*
* @param index the index of the value to compute
* @param data workspace for the current thread
* @param numAtoms number of atoms
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector to store computed values into
* @param exclusions exclusions[i] is the set of excluded indices for atom i
* @param useExclusions specifies whether to use exclusions
*/
void calculateParticlePairValue(int index, int numAtoms, float* posq, RealOpenMM** atomParameters,
std::vector<std::vector<float> >& values,
const std::vector<std::set<int> >& exclusions, bool useExclusions, const fvec4& boxSize, const fvec4& invBoxSize);
void calculateParticlePairValue(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters,
bool useExclusions, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Evaluate a single atom pair as part of calculating a computed value
......@@ -98,51 +103,43 @@ private:
* @param index the index of the value to compute
* @param atom1 the index of the first atom in the pair
* @param atom2 the index of the second atom in the pair
* @param data workspace for the current thread
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector to store computed values into
*/
void calculateOnePairValue(int index, int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
std::vector<std::vector<float> >& values, const fvec4& boxSize, const fvec4& invBoxSize);
void calculateOnePairValue(int index, int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters,
std::vector<float>& valueArray, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Calculate an energy term of type SingleParticle
*
* @param index the index of the value to compute
* @param data workspace for the current thread
* @param numAtoms number of atoms
* @param posq atom coordinates
* @param values the vector containing computed values
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param forces forces on atoms are added to this
* @param totalEnergy the energy contribution is added to this
* @param dEdV the derivative of energy with respect to computed values is stored in this
*/
void calculateSingleParticleEnergyTerm(int index, int numAtoms, float* posq, const std::vector<std::vector<float> >& values,
RealOpenMM** atomParameters, float* forces,
double* totalEnergy, std::vector<std::vector<float> >& dEdV);
void calculateSingleParticleEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters, float* forces, double& totalEnergy);
/**
* Calculate an energy term that is based on particle pairs
*
* @param index the index of the term to compute
* @param data workspace for the current thread
* @param numAtoms number of atoms
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values
* @param exclusions exclusions[i] is the set of excluded indices for atom i
* @param useExclusions specifies whether to use exclusions
* @param forces forces on atoms are added to this
* @param totalEnergy the energy contribution is added to this
* @param dEdV the derivative of energy with respect to computed values is stored in this
*/
void calculateParticlePairEnergyTerm(int index, int numAtoms, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<float> >& values,
const std::vector<std::set<int> >& exclusions, bool useExclusions,
float* forces, double* totalEnergy, std::vector<std::vector<float> >& dEdV,
const fvec4& boxSize, const fvec4& invBoxSize);
void calculateParticlePairEnergyTerm(int index, ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters,
bool useExclusions, float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Evaluate a single atom pair as part of calculating an energy term
......@@ -150,54 +147,43 @@ private:
* @param index the index of the term to compute
* @param atom1 the index of the first atom in the pair
* @param atom2 the index of the second atom in the pair
* @param data workspace for the current thread
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values
* @param forces forces on atoms are added to this
* @param totalEnergy the energy contribution is added to this
* @param dEdV the derivative of energy with respect to computed values is stored in this
*/
void calculateOnePairEnergyTerm(int index, int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<float> >& values,
float* forces, double* totalEnergy, std::vector<std::vector<float> >& dEdV,
const fvec4& boxSize, const fvec4& invBoxSize);
void calculateOnePairEnergyTerm(int index, int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters,
float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Apply the chain rule to compute forces on atoms
*
* @param data workspace for the current thread
* @param numAtoms number of atoms
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values
* @param exclusions exclusions[i] is the set of excluded indices for atom i
* @param forces forces on atoms are added to this
* @param dEdV the derivative of energy with respect to computed values is stored in this
*/
void calculateChainRuleForces(int numAtoms, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<float> >& values,
const std::vector<std::set<int> >& exclusions,
float* forces, std::vector<std::vector<float> >& dEdV,
const fvec4& boxSize, const fvec4& invBoxSize);
void calculateChainRuleForces(ThreadData& data, int numAtoms, float* posq, RealOpenMM** atomParameters,
float* forces, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Evaluate a single atom pair as part of applying the chain rule
*
* @param atom1 the index of the first atom in the pair
* @param atom2 the index of the second atom in the pair
* @param data workspace for the current thread
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param values the vector containing computed values
* @param forces forces on atoms are added to this
* @param dEdV the derivative of energy with respect to computed values is stored in this
* @param isExcluded specifies whether this is an excluded pair
*/
void calculateOnePairChainRule(int atom1, int atom2, float* posq, RealOpenMM** atomParameters,
const std::vector<std::vector<float> >& values,
float* forces, std::vector<std::vector<float> >& dEdV,
bool isExcluded, const fvec4& boxSize, const fvec4& invBoxSize);
void calculateOnePairChainRule(int atom1, int atom2, ThreadData& data, float* posq, RealOpenMM** atomParameters,
float* forces, bool isExcluded, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Compute the displacement and squared distance between two points, optionally using
......@@ -211,7 +197,8 @@ public:
* Construct a new CpuCustomGBForce.
*/
CpuCustomGBForce(int numAtoms, const std::vector<Lepton::CompiledExpression>& valueExpressions,
CpuCustomGBForce(int numAtoms, const std::vector<std::set<int> >& exclusions,
const std::vector<Lepton::CompiledExpression>& valueExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> >& valueDerivExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> >& valueGradientExpressions,
const std::vector<std::string>& valueNames,
......@@ -220,7 +207,7 @@ public:
const std::vector<std::vector<Lepton::CompiledExpression> >& energyDerivExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> >& energyGradientExpressions,
const std::vector<CustomGBForce::ComputationType>& energyTypes,
const std::vector<std::string>& parameterNames);
const std::vector<std::string>& parameterNames, ThreadPool& threads);
~CpuCustomGBForce();
......@@ -249,14 +236,42 @@ public:
* @param numberOfAtoms number of atoms
* @param posq atom coordinates
* @param atomParameters atomParameters[atomIndex][paramterIndex]
* @param exclusions exclusions[i] is the set of excluded indices for atom i
* @param globalParameters the values of global parameters
* @param forces force array (forces added)
* @param totalEnergy total energy
*/
void calculateIxn(int numberOfAtoms, float* posq, RealOpenMM** atomParameters, const std::vector<std::set<int> >& exclusions,
std::map<std::string, double>& globalParameters, float* forces, double* totalEnergy);
void calculateIxn(int numberOfAtoms, float* posq, RealOpenMM** atomParameters,
std::map<std::string, double>& globalParameters, std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy);
};
class CpuCustomGBForce::ThreadData {
public:
ThreadData(int numAtoms, int numThreads, int threadIndex,
const std::vector<Lepton::CompiledExpression>& valueExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> >& valueDerivExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> >& valueGradientExpressions,
const std::vector<std::string>& valueNames,
const std::vector<Lepton::CompiledExpression>& energyExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> >& energyDerivExpressions,
const std::vector<std::vector<Lepton::CompiledExpression> >& energyGradientExpressions,
const std::vector<std::string>& parameterNames);
CompiledExpressionSet expressionSet;
std::vector<Lepton::CompiledExpression> valueExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > valueGradientExpressions;
std::vector<int> valueIndex;
std::vector<Lepton::CompiledExpression> energyExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyDerivExpressions;
std::vector<std::vector<Lepton::CompiledExpression> > energyGradientExpressions;
std::vector<int> paramIndex;
std::vector<int> particleParamIndex;
std::vector<int> particleValueIndex;
int xindex, yindex, zindex, rindex;
int firstAtom, lastAtom;
// Workspace vectors
std::vector<float> value0, dVdR1, dVdR2, dVdX, dVdY, dVdZ;
std::vector<std::vector<float> > dEdV;
};
} // namespace OpenMM
......
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ 6a4ac837
This diff is collapsed.
platforms/cpu/src/CpuKernels.cpp
View file @ 6a4ac837
......@@ -957,8 +957,8 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
for (map<string, Lepton::CustomFunction*>::iterator iter = functions.begin(); iter != functions.end(); iter++)
delete iter->second;
ixn = new CpuCustomGBForce(numParticles, valueExpressions, valueDerivExpressions, valueGradientExpressions, valueNames, valueTypes, energyExpressions,
energyDerivExpressions, energyGradientExpressions, energyTypes, particleParameterNames);
ixn = new CpuCustomGBForce(numParticles, exclusions, valueExpressions, valueDerivExpressions, valueGradientExpressions, valueNames, valueTypes, energyExpressions,
energyDerivExpressions, energyGradientExpressions, energyTypes, particleParameterNames, data.threads);
data.isPeriodic = (force.getNonbondedMethod() == CustomGBForce::CutoffPeriodic);
}
......@@ -977,7 +977,7 @@ double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFor
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ixn->calculateIxn(numParticles, &data.posq[0], particleParamArray, exclusions, globalParameters, &data.threadForce[0][0], includeEnergy ? &energy : NULL);
ixn->calculateIxn(numParticles, &data.posq[0], particleParamArray, globalParameters, data.threadForce, includeForces, includeEnergy, energy);
return energy;
}
......
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