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"openmmapi/src/PythonForceImpl.cpp" did not exist on "0307a0db5654a9092975a8392531ec7d3ed9aca0"
Commit 859bfd6c authored by peastman's avatar peastman
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Use lambdas for thread pool tasks

parent 2c559596
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Showing with 51 additions and 118 deletions
CMakeLists.txt
View file @ 859bfd6c
......@@ -117,6 +117,7 @@ ELSE( CMAKE_SIZEOF_VOID_P EQUAL 8 )
SET( LIB64 )
ENDIF( CMAKE_SIZEOF_VOID_P EQUAL 8 )
SET (CMAKE_CXX_STANDARD 11)
IF (APPLE AND (NOT PNACL))
# Build 64 bit binaries compatible with OS X 10.7
......
openmmapi/include/openmm/internal/ThreadPool.h
View file @ 859bfd6c
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,6 +34,7 @@
#define NOMINMAX
#include "windowsExport.h"
#include <functional>
#include <pthread.h>
#include <vector>
......@@ -69,6 +70,10 @@ public:
* Execute a Task in parallel on the worker threads.
*/
void execute(Task& task);
/**
* Execute a function in parallel on the worker threads.
*/
void execute(std::function<void (ThreadPool&, int)> task);
/**
* This is called by the worker threads to block until all threads have reached the same point
* and the master thread instructs them to continue by calling resumeThreads().
......@@ -90,6 +95,8 @@ private:
std::vector<ThreadData*> threadData;
pthread_cond_t startCondition, endCondition;
pthread_mutex_t lock;
Task* currentTask;
std::function<void (ThreadPool& pool, int)> currentFunction;
};
/**
......
openmmapi/src/ThreadPool.cpp
View file @ 859bfd6c
......@@ -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) 2013-2014 Stanford University and the Authors. *
* Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -40,10 +40,17 @@ class ThreadPool::ThreadData {
public:
ThreadData(ThreadPool& owner, int index) : owner(owner), index(index), isDeleted(false) {
}
void executeTask() {
if (owner.currentTask != NULL)
owner.currentTask->execute(owner, index);
else
owner.currentFunction(owner, index);
}
ThreadPool& owner;
int index;
bool isDeleted;
Task* currentTask;
function<void (ThreadPool& pool, int)> currentFunction;
};
static void* threadBody(void* args) {
......@@ -54,13 +61,13 @@ static void* threadBody(void* args) {
data.owner.syncThreads();
if (data.isDeleted)
break;
data.currentTask->execute(data.owner, data.index);
data.executeTask();
}
delete &data;
return 0;
}
ThreadPool::ThreadPool(int numThreads) {
ThreadPool::ThreadPool(int numThreads) : currentTask(NULL) {
if (numThreads <= 0)
numThreads = getNumProcessors();
this->numThreads = numThreads;
......@@ -99,8 +106,13 @@ int ThreadPool::getNumThreads() const {
}
void ThreadPool::execute(Task& task) {
for (int i = 0; i < (int) threadData.size(); i++)
threadData[i]->currentTask = &task;
currentTask = &task;
resumeThreads();
}
void ThreadPool::execute(function<void (ThreadPool&, int)> task) {
currentTask = NULL;
currentFunction = task;
resumeThreads();
}
......
platforms/cpu/include/CpuBondForce.h
View file @ 859bfd6c
......@@ -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) 2014 Stanford University and the Authors. *
* Portions copyright (c) 2014-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -46,7 +46,6 @@ namespace OpenMM {
*/
class OPENMM_EXPORT_CPU CpuBondForce {
public:
class ComputeForceTask;
CpuBondForce();
/**
* Analyze the set of bonds and decide which to compute with each thread.
......
platforms/cpu/include/CpuCustomGBForce.h
View file @ 859bfd6c
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,7 +39,6 @@ namespace OpenMM {
class CpuCustomGBForce {
private:
class ComputeForceTask;
class ThreadData;
bool cutoff;
......
platforms/cpu/include/CpuCustomManyParticleForce.h
View file @ 859bfd6c
/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -48,7 +48,6 @@ private:
class DistanceTermInfo;
class AngleTermInfo;
class DihedralTermInfo;
class ComputeForceTask;
class ThreadData;
int numParticles, numParticlesPerSet, numPerParticleParameters, numTypes;
bool useCutoff, usePeriodic, triclinic, centralParticleMode;
......
platforms/cpu/include/CpuCustomNonbondedForce.h
View file @ 859bfd6c
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -122,7 +122,6 @@ class CpuCustomNonbondedForce {
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs);
private:
class ComputeForceTask;
class ThreadData;
bool cutoff;
......
platforms/cpu/include/CpuGBSAOBCForce.h
View file @ 859bfd6c
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -36,7 +36,6 @@ namespace OpenMM {
class CpuGBSAOBCForce {
public:
class ComputeTask;
CpuGBSAOBCForce();
/**
......
platforms/cpu/include/CpuGayBerneForce.h
View file @ 859bfd6c
......@@ -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) 2016 Stanford University and the Authors. *
* Portions copyright (c) 2016-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,7 +45,6 @@ namespace OpenMM {
class CpuGayBerneForce {
public:
struct Matrix;
class ComputeTask;
/**
* Constructor.
......
platforms/cpu/include/CpuKernels.h
View file @ 859bfd6c
......@@ -54,8 +54,6 @@ namespace OpenMM {
*/
class CpuCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
public:
class InitForceTask;
class SumForceTask;
CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context);
/**
* Initialize the kernel.
......
platforms/cpu/include/CpuLangevinDynamics.h
View file @ 859bfd6c
/* Portions copyright (c) 2013-2016 Stanford University and Simbios.
/* Portions copyright (c) 2013-2017 Stanford University and Simbios.
* Authors: Peter Eastman
* Contributors:
*
......@@ -35,9 +35,6 @@ namespace OpenMM {
class CpuLangevinDynamics : public ReferenceStochasticDynamics {
public:
class Update1Task;
class Update2Task;
class Update3Task;
/**
* Constructor.
*
......
platforms/cpu/include/CpuNeighborList.h
View file @ 859bfd6c
......@@ -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) 2013-2016 Stanford University and the Authors. *
* Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,7 +45,6 @@ namespace OpenMM {
class OPENMM_EXPORT_CPU CpuNeighborList {
public:
class ThreadTask;
class Voxels;
CpuNeighborList(int blockSize);
void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
......
platforms/cpu/include/CpuNonbondedForce.h
View file @ 859bfd6c
/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,7 +39,6 @@ namespace OpenMM {
class CpuNonbondedForce {
public:
class ComputeDirectTask;
/**---------------------------------------------------------------------------------------
......
platforms/cpu/include/CpuSETTLE.h
View file @ 859bfd6c
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,8 +45,6 @@ namespace OpenMM {
*/
class OPENMM_EXPORT_CPU CpuSETTLE : public ReferenceConstraintAlgorithm {
public:
class ApplyToPositionsTask;
class ApplyToVelocitiesTask;
CpuSETTLE(const System& system, const ReferenceSETTLEAlgorithm& settle, ThreadPool& threads);
~CpuSETTLE();
......
platforms/cpu/src/CpuBondForce.cpp
View file @ 859bfd6c
......@@ -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) 2014-2016 Stanford University and the Authors. *
* Portions copyright (c) 2014-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -35,25 +35,6 @@
using namespace OpenMM;
using namespace std;
class CpuBondForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuBondForce& owner, vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces,
vector<RealOpenMM>& threadEnergy, RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) : owner(owner), atomCoordinates(atomCoordinates),
parameters(parameters), forces(forces), threadEnergy(threadEnergy), totalEnergy(totalEnergy), referenceBondIxn(referenceBondIxn) {
}
void execute(ThreadPool& threads, int threadIndex) {
RealOpenMM* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
owner.threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
}
CpuBondForce& owner;
vector<RealVec>& atomCoordinates;
RealOpenMM** parameters;
vector<RealVec>& forces;
vector<RealOpenMM>& threadEnergy;
RealOpenMM* totalEnergy;
ReferenceBondIxn& referenceBondIxn;
};
CpuBondForce::CpuBondForce() {
}
......@@ -188,8 +169,10 @@ void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM**
// Have the worker threads compute their forces.
vector<RealOpenMM> threadEnergy(threads->getNumThreads(), 0);
ComputeForceTask task(*this, atomCoordinates, parameters, forces, threadEnergy, totalEnergy, referenceBondIxn);
threads->execute(task);
threads->execute([&] (ThreadPool& threads, int threadIndex) {
RealOpenMM* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
});
threads->waitForThreads();
// Compute any "extra" bonds.
......
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ 859bfd6c
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -33,16 +33,6 @@
using namespace OpenMM;
using namespace std;
class CpuCustomGBForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuCustomGBForce& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeForce(threads, threadIndex);
}
CpuCustomGBForce& owner;
};
CpuCustomGBForce::ThreadData::ThreadData(int numAtoms, int numThreads, int threadIndex,
const vector<Lepton::CompiledExpression>& valueExpressions,
const vector<vector<Lepton::CompiledExpression> >& valueDerivExpressions,
......@@ -206,7 +196,7 @@ void CpuCustomGBForce::calculateIxn(int numberOfAtoms, float* posq, RealOpenMM**
// Calculate the first computed value.
ComputeForceTask task(*this);
auto task = [&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex); };
gmx_atomic_set(&counter, 0);
threads.execute(task);
threads.waitForThreads();
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ 859bfd6c
/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -37,16 +37,6 @@
using namespace OpenMM;
using namespace std;
class CpuCustomManyParticleForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuCustomManyParticleForce& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeForce(threads, threadIndex);
}
CpuCustomManyParticleForce& owner;
};
CpuCustomManyParticleForce::CpuCustomManyParticleForce(const CustomManyParticleForce& force, ThreadPool& threads) :
threads(threads), useCutoff(false), usePeriodic(false), neighborList(NULL) {
numParticles = force.getNumParticles();
......@@ -141,8 +131,7 @@ void CpuCustomManyParticleForce::calculateIxn(AlignedArray<float>& posq, RealOpe
// Signal the threads to start running and wait for them to finish.
ComputeForceTask task(*this);
threads.execute(task);
threads.execute([&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex); });
threads.waitForThreads();
// Combine the energies from all the threads.
......
platforms/cpu/src/CpuCustomNonbondedForce.cpp
View file @ 859bfd6c
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -33,16 +33,6 @@
using namespace OpenMM;
using namespace std;
class CpuCustomNonbondedForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuCustomNonbondedForce& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeForce(threads, threadIndex);
}
CpuCustomNonbondedForce& owner;
};
CpuCustomNonbondedForce::ThreadData::ThreadData(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
const vector<string>& parameterNames, const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions) :
energyExpression(energyExpression), forceExpression(forceExpression), energyParamDerivExpressions(energyParamDerivExpressions) {
......@@ -150,8 +140,7 @@ void CpuCustomNonbondedForce::calculatePairIxn(int numberOfAtoms, float* posq, v
// Signal the threads to start running and wait for them to finish.
ComputeForceTask task(*this);
threads.execute(task);
threads.execute([&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex); });
threads.waitForThreads();
// Combine the energies from all the threads.
......
platforms/cpu/src/CpuGBSAOBCForce.cpp
View file @ 859bfd6c
/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -36,16 +36,6 @@ const int CpuGBSAOBCForce::NUM_TABLE_POINTS = 4096;
const float CpuGBSAOBCForce::TABLE_MIN = 0.25f;
const float CpuGBSAOBCForce::TABLE_MAX = 1.5f;
class CpuGBSAOBCForce::ComputeTask : public ThreadPool::Task {
public:
ComputeTask(CpuGBSAOBCForce& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeForce(threads, threadIndex);
}
CpuGBSAOBCForce& owner;
};
CpuGBSAOBCForce::CpuGBSAOBCForce() : cutoff(false), periodic(false) {
logDX = (TABLE_MAX-TABLE_MIN)/NUM_TABLE_POINTS;
logDXInv = 1.0f/logDX;
......@@ -110,9 +100,8 @@ void CpuGBSAOBCForce::computeForce(const AlignedArray<float>& posq, vector<Align
// Signal the threads to start running and wait for them to finish.
ComputeTask task(*this);
gmx_atomic_set(&counter, 0);
threads.execute(task);
threads.execute([&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex); });
threads.waitForThreads(); // Compute Born radii
gmx_atomic_set(&counter, 0);
threads.resumeThreads();
......
platforms/cpu/src/CpuGayBerneForce.cpp
View file @ 859bfd6c
......@@ -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) 2016 Stanford University and the Authors. *
* Portions copyright (c) 2016-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -44,17 +44,6 @@
using namespace OpenMM;
using namespace std;
class CpuGayBerneForce::ComputeTask : public ThreadPool::Task {
public:
ComputeTask(CpuGayBerneForce& owner, CpuNeighborList* neighborList) : owner(owner), neighborList(neighborList) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeForce(threads, threadIndex, neighborList);
}
CpuGayBerneForce& owner;
CpuNeighborList* neighborList;
};
CpuGayBerneForce::CpuGayBerneForce(const GayBerneForce& force) {
// Record the force parameters.
......@@ -137,8 +126,7 @@ RealOpenMM CpuGayBerneForce::calculateForce(const vector<RealVec>& positions, st
// Signal the threads to compute the pairwise interactions.
ComputeTask task(*this, data.neighborList);
threads.execute(task);
threads.execute([&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex, data.neighborList); });
threads.waitForThreads();
// Signal the threads to compute exceptions.
......
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