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Commit b8866444 authored by peastman's avatar peastman
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Finished parallelizing CPU implementation of CustomNonbondedForce

parent c053a59a
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Showing with 91 additions and 95 deletions
platforms/cpu/include/CpuCustomNonbondedForce.h
View file @ b8866444
......@@ -38,54 +38,6 @@
namespace OpenMM {
class CpuCustomNonbondedForce {
private:
class ComputeForceTask;
class ThreadData;
bool cutoff;
bool useSwitch;
bool periodic;
const CpuNeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance, switchingDistance;
ThreadPool& threads;
std::vector<ThreadData*> threadData;
std::vector<std::string> paramNames;
std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
std::vector<double> threadEnergy;
// The following variables are used to make information accessible to the individual threads.
int numberOfAtoms;
float* posq;
RealVec const* atomCoordinates;
RealOpenMM** atomParameters;
const std::map<std::string, double>* globalParameters;
std::set<int> const* exclusions;
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 custom pair ixn between two atoms
@param atom1 the index of the first atom
@param atom2 the index of the second atom
@param atomCoordinates atom coordinates
@param atomParameters atomParameters[atomIndex][parameterIndex]
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateOneIxn(int atom1, int atom2, ThreadData& data, float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
public:
/**---------------------------------------------------------------------------------------
......@@ -95,7 +47,7 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */
CpuCustomNonbondedForce(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const std::vector<std::string>& parameterNames, ThreadPool& threads);
const std::vector<std::string>& parameterNames, const std::vector<std::set<int> >& exclusions, ThreadPool& threads);
/**---------------------------------------------------------------------------------------
......@@ -103,7 +55,7 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */
~CpuCustomNonbondedForce( );
~CpuCustomNonbondedForce();
/**---------------------------------------------------------------------------------------
......@@ -114,7 +66,7 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance, const CpuNeighborList& neighbors );
void setUseCutoff(RealOpenMM distance, const CpuNeighborList& neighbors);
/**---------------------------------------------------------------------------------------
......@@ -135,7 +87,7 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */
void setUseSwitchingFunction( RealOpenMM distance );
void setUseSwitchingFunction(RealOpenMM distance);
/**---------------------------------------------------------------------------------------
......@@ -147,7 +99,7 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */
void setPeriodic( OpenMM::RealVec& boxSize );
void setPeriodic(OpenMM::RealVec& boxSize);
/**---------------------------------------------------------------------------------------
......@@ -157,8 +109,6 @@ class CpuCustomNonbondedForce {
@param posq atom coordinates in float format
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param fixedParameters non atom parameters (not currently used)
@param globalParameters the values of global parameters
@param forces force array (forces added)
......@@ -167,10 +117,52 @@ class CpuCustomNonbondedForce {
--------------------------------------------------------------------------------------- */
void calculatePairIxn(int numberOfAtoms, float* posq, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
void calculatePairIxn(int numberOfAtoms, float* posq, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** atomParameters,
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy);
private:
class ComputeForceTask;
class ThreadData;
bool cutoff;
bool useSwitch;
bool periodic;
const CpuNeighborList* neighborList;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance, switchingDistance;
ThreadPool& threads;
const std::vector<std::set<int> > exclusions;
std::vector<ThreadData*> threadData;
std::vector<std::string> paramNames;
std::vector<std::pair<int, int> > groupInteractions;
std::vector<double> threadEnergy;
// The following variables are used to make information accessible to the individual threads.
int numberOfAtoms;
float* posq;
RealVec const* atomCoordinates;
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 the interaction between two atoms.
*
* @param atom1 the index of the first atom
* @param atom2 the index of the second atom
* @param data workspace for the current thread
* @param forces force array (forces added)
* @param totalEnergy total energy
* @param boxSize the size of the periodic box
* @param boxSize the inverse size of the periodic box
*/
void calculateOneIxn(int atom1, int atom2, ThreadData& data, float* forces, double& totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Compute the displacement and squared distance between two points, optionally using
......
platforms/cpu/src/CpuCustomNonbondedForce.cpp
View file @ b8866444
......@@ -60,8 +60,8 @@ CpuCustomNonbondedForce::ThreadData::ThreadData(const Lepton::CompiledExpression
}
CpuCustomNonbondedForce::CpuCustomNonbondedForce(const Lepton::CompiledExpression& energyExpression,
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, ThreadPool& threads) :
cutoff(false), useSwitch(false), periodic(false), paramNames(parameterNames), threads(threads) {
const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, const vector<set<int> >& exclusions,ThreadPool& threads) :
cutoff(false), useSwitch(false), periodic(false), paramNames(parameterNames), exclusions(exclusions), threads(threads) {
for (int i = 0; i < threads.getNumThreads(); i++)
threadData.push_back(new ThreadData(energyExpression, forceExpression, parameterNames));
}
......@@ -78,7 +78,19 @@ void CpuCustomNonbondedForce::setUseCutoff(RealOpenMM distance, const CpuNeighbo
}
void CpuCustomNonbondedForce::setInteractionGroups(const vector<pair<set<int>, set<int> > >& groups) {
interactionGroups = groups;
for (int group = 0; group < (int) groups.size(); group++) {
const set<int>& set1 = groups[group].first;
const set<int>& set2 = groups[group].second;
for (set<int>::const_iterator atom1 = set1.begin(); atom1 != set1.end(); ++atom1) {
for (set<int>::const_iterator atom2 = set2.begin(); atom2 != set2.end(); ++atom2) {
if (*atom1 == *atom2 || exclusions[*atom1].find(*atom2) != exclusions[*atom1].end())
continue; // This is an excluded interaction.
if (*atom1 > *atom2 && set1.find(*atom2) != set1.end() && set2.find(*atom1) != set2.end())
continue; // Both atoms are in both sets, so skip duplicate interactions.
groupInteractions.push_back(make_pair(*atom1, *atom2));
}
}
}
}
void CpuCustomNonbondedForce::setUseSwitchingFunction(RealOpenMM distance) {
......@@ -98,8 +110,7 @@ void CpuCustomNonbondedForce::setPeriodic(RealVec& boxSize) {
}
void CpuCustomNonbondedForce::calculatePairIxn(int numberOfAtoms, float* posq, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, vector<set<int> >& exclusions,
void CpuCustomNonbondedForce::calculatePairIxn(int numberOfAtoms, float* posq, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
RealOpenMM* fixedParameters, const map<string, double>& globalParameters,
vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy) {
// Record the parameters for the threads.
......@@ -109,7 +120,6 @@ void CpuCustomNonbondedForce::calculatePairIxn(int numberOfAtoms, float* posq, v
this->atomCoordinates = &atomCoordinates[0];
this->atomParameters = atomParameters;
this->globalParameters = &globalParameters;
this->exclusions = &exclusions[0];
this->threadForce = &threadForce;
this->includeForce = includeForce;
this->includeEnergy = includeEnergy;
......@@ -147,29 +157,22 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
}
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
if (interactionGroups.size() > 0) {
if (threadIndex > 0)
return;
if (groupInteractions.size() > 0) {
// The user has specified interaction groups, so compute only the requested interactions.
for (int group = 0; group < (int) interactionGroups.size(); group++) {
const set<int>& set1 = interactionGroups[group].first;
const set<int>& set2 = interactionGroups[group].second;
for (set<int>::const_iterator atom1 = set1.begin(); atom1 != set1.end(); ++atom1) {
for (set<int>::const_iterator atom2 = set2.begin(); atom2 != set2.end(); ++atom2) {
if (*atom1 == *atom2 || exclusions[*atom1].find(*atom2) != exclusions[*atom1].end())
continue; // This is an excluded interaction.
if (*atom1 > *atom2 && set1.find(*atom2) != set1.end() && set2.find(*atom1) != set2.end())
continue; // Both atoms are in both sets, so skip duplicate interactions.
while (true) {
int i = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (i >= groupInteractions.size())
break;
int atom1 = groupInteractions[i].first;
int atom2 = groupInteractions[i].second;
for (int j = 0; j < (int) paramNames.size(); j++) {
ReferenceForce::setVariable(data.energyParticleParams[j*2], atomParameters[*atom1][j]);
ReferenceForce::setVariable(data.energyParticleParams[j*2+1], atomParameters[*atom2][j]);
ReferenceForce::setVariable(data.forceParticleParams[j*2], atomParameters[*atom1][j]);
ReferenceForce::setVariable(data.forceParticleParams[j*2+1], atomParameters[*atom2][j]);
}
calculateOneIxn(*atom1, *atom2, data, forces, energy, boxSize, invBoxSize);
}
ReferenceForce::setVariable(data.energyParticleParams[j*2], atomParameters[atom1][j]);
ReferenceForce::setVariable(data.energyParticleParams[j*2+1], atomParameters[atom2][j]);
ReferenceForce::setVariable(data.forceParticleParams[j*2], atomParameters[atom1][j]);
ReferenceForce::setVariable(data.forceParticleParams[j*2+1], atomParameters[atom2][j]);
}
calculateOneIxn(atom1, atom2, data, forces, energy, boxSize, invBoxSize);
}
}
else if (cutoff) {
......@@ -206,9 +209,10 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
else {
// Every particle interacts with every other one.
if (threadIndex > 0)
return;
for (int ii = 0; ii < numberOfAtoms; ii++) {
while (true) {
int ii = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
if (ii >= numberOfAtoms)
break;
for (int jj = ii+1; jj < numberOfAtoms; jj++) {
if (exclusions[jj].find(ii) == exclusions[jj].end()) {
for (int j = 0; j < (int) paramNames.size(); j++) {
......
platforms/cpu/src/CpuKernels.cpp
View file @ b8866444
......@@ -719,7 +719,7 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
interactionGroups.push_back(make_pair(set1, set2));
}
data.isPeriodic = (nonbondedMethod == CutoffPeriodic);
nonbonded = new CpuCustomNonbondedForce(energyExpression, forceExpression, parameterNames, data.threads);
nonbonded = new CpuCustomNonbondedForce(energyExpression, forceExpression, parameterNames, exclusions, data.threads);
}
double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -750,7 +750,7 @@ double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool inc
}
if (useSwitchingFunction)
nonbonded->setUseSwitchingFunction(switchingDistance);
nonbonded->calculatePairIxn(numParticles, &data.posq[0], posData, particleParamArray, exclusions, 0, globalParamValues, data.threadForce, includeForces, includeEnergy, energy);
nonbonded->calculatePairIxn(numParticles, &data.posq[0], posData, particleParamArray, 0, globalParamValues, data.threadForce, includeForces, includeEnergy, energy);
// Add in the long range correction.
......
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