Parallelized the initialization of positions and forces in the CPU platform

platforms/cpu/include/CpuKernels.h

@@ -50,6 +50,7 @@ namespace OpenMM {
  */
 class CpuCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
 public:
+    class InitForceTask;
     class SumForceTask;
     CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context);
     /**

platforms/cpu/src/CpuKernels.cpp

@@ -132,21 +132,11 @@ public:
     CpuPlatform::PlatformData& data;
 };
 
-CpuCalcForcesAndEnergyKernel::CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context) :
-        CalcForcesAndEnergyKernel(name, platform), data(data) {
-    // Create a Reference platform version of this kernel.
-    
-    ReferenceKernelFactory referenceFactory;
-    referenceKernel = Kernel(referenceFactory.createKernelImpl(name, platform, context));
-}
-
-void CpuCalcForcesAndEnergyKernel::initialize(const System& system) {
-    referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().initialize(system);
-}
-
-void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
-    referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().beginComputation(context, includeForce, includeEnergy, groups);
-    
+class CpuCalcForcesAndEnergyKernel::InitForceTask : public ThreadPool::Task {
+public:
+    InitForceTask(int numParticles, ContextImpl& context, CpuPlatform::PlatformData& data) : numParticles(numParticles), context(context), data(data) {
+    }
+    void execute(ThreadPool& threads, int threadIndex) {
         // Convert the positions to single precision and apply periodic boundary conditions
 
         AlignedArray<float>& posq = data.posq;
@@ -154,15 +144,18 @@ void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool i
         RealVec boxSize = extractBoxSize(context);
         double invBoxSize[3] = {1/boxSize[0], 1/boxSize[1], 1/boxSize[2]};
         int numParticles = context.getSystem().getNumParticles();
+        int numThreads = threads.getNumThreads();
+        int start = threadIndex*numParticles/numThreads;
+        int end = (threadIndex+1)*numParticles/numThreads;
         if (data.isPeriodic)
-        for (int i = 0; i < numParticles; i++)
+            for (int i = start; i < end; i++)
                 for (int j = 0; j < 3; j++) {
                     RealOpenMM x = posData[i][j];
                     double base = floor(x*invBoxSize[j])*boxSize[j];
                     posq[4*i+j] = (float) (x-base);
                 }
         else
-        for (int i = 0; i < numParticles; i++) {
+            for (int i = start; i < end; i++) {
                 posq[4*i] = (float) posData[i][0];
                 posq[4*i+1] = (float) posData[i][1];
                 posq[4*i+2] = (float) posData[i][2];
@@ -171,9 +164,34 @@ void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool i
         // Clear the forces.
 
         fvec4 zero(0.0f);
-    for (int i = 0; i < (int) data.threadForce.size(); i++)
         for (int j = 0; j < numParticles; j++)
-            zero.store(&data.threadForce[i][j*4]);
+            zero.store(&data.threadForce[threadIndex][j*4]);
+    }
+    int numParticles;
+    ContextImpl& context;
+    CpuPlatform::PlatformData& data;
+};
+
+CpuCalcForcesAndEnergyKernel::CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context) :
+        CalcForcesAndEnergyKernel(name, platform), data(data) {
+    // Create a Reference platform version of this kernel.
+    
+    ReferenceKernelFactory referenceFactory;
+    referenceKernel = Kernel(referenceFactory.createKernelImpl(name, platform, context));
+}
+
+void CpuCalcForcesAndEnergyKernel::initialize(const System& system) {
+    referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().initialize(system);
+}
+
+void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
+    referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().beginComputation(context, includeForce, includeEnergy, groups);
+    
+    // Convert positions to single precision and clear the forces.
+    
+    InitForceTask task(context.getSystem().getNumParticles(), context, data);
+    data.threads.execute(task);
+    data.threads.waitForThreads();
 }
 
 double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {