Use lambdas for thread pool tasks

CMakeLists.txt

@@ -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

@@ -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

@@ -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

@@ -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

 
-/* 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

 
-/* 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

 
-/* 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

 
-/* 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

@@ -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

@@ -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

 
-/* 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

@@ -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

 
-/* 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

@@ -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

@@ -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

 
-/* 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

 
-/* 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

 
-/* 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

-/* 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

@@ -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.