OpenCL platform can use the CPU based PME

platforms/cuda/include/CudaPlatform.h

@@ -84,8 +84,8 @@ public:
     /**
      * This is the name of the parameter for selecting whether to use the CPU based PME calculation.
      */
-    static const std::string& UseCpuPme() {
-        static const std::string key = "UseCpuPme";
+    static const std::string& CudaUseCpuPme() {
+        static const std::string key = "CudaUseCpuPme";
         return key;
     }
     /**

platforms/cuda/src/CudaContext.h

@@ -457,7 +457,7 @@ public:
         return reorderListeners;
     }
     /**
-     * Add a pre-computation that should be called at the very start of force and energy evalutations.
+     * Add a pre-computation that should be called at the very start of force and energy evaluations.
      * The CudaContext assumes ownership of the object, and deletes it when the context itself is deleted.
      */
     void addPreComputation(ForcePreComputation* computation);
@@ -468,7 +468,7 @@ public:
         return preComputations;
     }
     /**
-     * Add a post-computation that should be called at the very end of force and energy evalutations.
+     * Add a post-computation that should be called at the very end of force and energy evaluations.
      * The CudaContext assumes ownership of the object, and deletes it when the context itself is deleted.
      */
     void addPostComputation(ForcePostComputation* computation);

platforms/cuda/src/CudaKernels.cpp

@@ -1337,8 +1337,7 @@ private:
 class CudaCalcNonbondedForceKernel::PmeIO : public CalcPmeReciprocalForceKernel::IO {
 public:
     PmeIO(CudaContext& cu, CUfunction addForcesKernel) : cu(cu), addForcesKernel(addForcesKernel), forceTemp(NULL) {
-        int elementSize = (cu.getUseDoublePrecision() ? sizeof(double4) : sizeof(float4));        
-        forceTemp = new CudaArray(cu, cu.getNumAtoms(), elementSize, "PmeForce");
+        forceTemp = CudaArray::create<float4>(cu, cu.getNumAtoms(), "PmeForce");
     }
     ~PmeIO() {
         if (forceTemp != NULL)
@@ -1570,6 +1569,8 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
             pmeDefines["USE_DOUBLE_PRECISION"] = "1";
         CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaKernelSources::pme, pmeDefines);
         if (cu.getPlatformData().useCpuPme) {
+            // Create the CPU PME kernel.
+            
             try {
                 cpuPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), *cu.getPlatformData().context);
                 cpuPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSizeX, gridSizeY, gridSizeZ, numParticles, alpha);
@@ -1728,7 +1729,6 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
 }
 
 double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal) {
-    double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
     if (cosSinSums != NULL && includeReciprocal) {
         void* sumsArgs[] = {&cu.getEnergyBuffer().getDevicePointer(), &cu.getPosq().getDevicePointer(), &cosSinSums->getDevicePointer(), cu.getPeriodicBoxSizePointer()};
         cu.executeKernel(ewaldSumsKernel, sumsArgs, cosSinSums->getSize());
@@ -1774,6 +1774,7 @@ double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeF
         cu.executeKernel(pmeInterpolateForceKernel, interpolateArgs, cu.getNumAtoms(), 128);
 
     }
+    double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
     if (dispersionCoefficient != 0.0 && includeDirect) {
         double4 boxSize = cu.getPeriodicBoxSize();
         energy += dispersionCoefficient/(boxSize.x*boxSize.y*boxSize.z);

platforms/cuda/src/CudaPlatform.cpp

@@ -86,15 +86,15 @@ CudaPlatform::CudaPlatform() {
     platformProperties.push_back(CudaDeviceIndex());
     platformProperties.push_back(CudaDeviceName());
     platformProperties.push_back(CudaUseBlockingSync());
-    platformProperties.push_back(UseCpuPme());
     platformProperties.push_back(CudaPrecision());
+    platformProperties.push_back(CudaUseCpuPme());
     platformProperties.push_back(CudaCompiler());
     platformProperties.push_back(CudaTempDirectory());
     setPropertyDefaultValue(CudaDeviceIndex(), "");
     setPropertyDefaultValue(CudaDeviceName(), "");
     setPropertyDefaultValue(CudaUseBlockingSync(), "true");
     setPropertyDefaultValue(CudaPrecision(), "single");
-    setPropertyDefaultValue(UseCpuPme(), "false");
+    setPropertyDefaultValue(CudaUseCpuPme(), "false");
 #ifdef _MSC_VER
     char* bindir = getenv("CUDA_BIN_PATH");
     string nvcc = (bindir == NULL ? "nvcc.exe" : string(bindir)+"\\nvcc.exe");
@@ -143,8 +143,8 @@ void CudaPlatform::contextCreated(ContextImpl& context, const map<string, string
             getPropertyDefaultValue(CudaUseBlockingSync()) : properties.find(CudaUseBlockingSync())->second);
     string precisionPropValue = (properties.find(CudaPrecision()) == properties.end() ?
             getPropertyDefaultValue(CudaPrecision()) : properties.find(CudaPrecision())->second);
-    string cpuPmePropValue = (properties.find(UseCpuPme()) == properties.end() ?
-            getPropertyDefaultValue(UseCpuPme()) : properties.find(UseCpuPme())->second);
+    string cpuPmePropValue = (properties.find(CudaUseCpuPme()) == properties.end() ?
+            getPropertyDefaultValue(CudaUseCpuPme()) : properties.find(CudaUseCpuPme())->second);
     const string& compilerPropValue = (properties.find(CudaCompiler()) == properties.end() ?
             getPropertyDefaultValue(CudaCompiler()) : properties.find(CudaCompiler())->second);
     const string& tempPropValue = (properties.find(CudaTempDirectory()) == properties.end() ?
@@ -167,7 +167,6 @@ void CudaPlatform::contextDestroyed(ContextImpl& context) const {
 CudaPlatform::PlatformData::PlatformData(ContextImpl* context, const System& system, const string& deviceIndexProperty, const string& blockingProperty, const string& precisionProperty,
             const string& cpuPmeProperty, const string& compilerProperty, const string& tempProperty) : context(context), removeCM(false), stepCount(0), computeForceCount(0), time(0.0)  {
     bool blocking = (blockingProperty == "true");
-    useCpuPme = (cpuPmeProperty == "true");
     vector<string> devices;
     size_t searchPos = 0, nextPos;
     while ((nextPos = deviceIndexProperty.find_first_of(", ", searchPos)) != string::npos) {
@@ -195,11 +194,12 @@ CudaPlatform::PlatformData::PlatformData(ContextImpl* context, const System& sys
         CHECK_RESULT(cuDeviceGetName(name, 1000, contexts[i]->getDevice()), "Error querying device name");
         deviceName << name;
     }
+    useCpuPme = (cpuPmeProperty == "true" && !contexts[0]->getUseDoublePrecision());
     propertyValues[CudaPlatform::CudaDeviceIndex()] = deviceIndex.str();
     propertyValues[CudaPlatform::CudaDeviceName()] = deviceName.str();
     propertyValues[CudaPlatform::CudaUseBlockingSync()] = blocking ? "true" : "false";
     propertyValues[CudaPlatform::CudaPrecision()] = precisionProperty;
-    propertyValues[CudaPlatform::UseCpuPme()] = useCpuPme ? "true" : "false";
+    propertyValues[CudaPlatform::CudaUseCpuPme()] = useCpuPme ? "true" : "false";
     propertyValues[CudaPlatform::CudaCompiler()] = compilerProperty;
     propertyValues[CudaPlatform::CudaTempDirectory()] = tempProperty;
     contextEnergy.resize(contexts.size());

platforms/opencl/include/OpenCLPlatform.h

@@ -87,17 +87,25 @@ public:
         static const std::string key = "OpenCLPrecision";
         return key;
     }
+    /**
+     * This is the name of the parameter for selecting whether to use the CPU based PME calculation.
+     */
+    static const std::string& OpenCLUseCpuPme() {
+        static const std::string key = "OpenCLUseCpuPme";
+        return key;
+    }
 };
 
 class OPENMM_EXPORT_OPENCL OpenCLPlatform::PlatformData {
 public:
-    PlatformData(const System& system, const std::string& platformPropValue, const std::string& deviceIndexProperty, const std::string& precisionProperty);
+    PlatformData(const System& system, const std::string& platformPropValue, const std::string& deviceIndexProperty, const std::string& precisionProperty, const std::string& cpuPmeProperty);
     ~PlatformData();
     void initializeContexts(const System& system);
     void syncContexts();
+    ContextImpl* context;
     std::vector<OpenCLContext*> contexts;
     std::vector<double> contextEnergy;
-    bool removeCM;
+    bool removeCM, useCpuPme;
     int cmMotionFrequency;
     int stepCount, computeForceCount;
     double time;

platforms/opencl/src/OpenCLContext.cpp

@@ -334,6 +334,10 @@ OpenCLContext::~OpenCLContext() {
         delete forces[i];
     for (int i = 0; i < (int) reorderListeners.size(); i++)
         delete reorderListeners[i];
+    for (int i = 0; i < (int) preComputations.size(); i++)
+        delete preComputations[i];
+    for (int i = 0; i < (int) postComputations.size(); i++)
+        delete postComputations[i];
     if (pinnedBuffer != NULL)
         delete pinnedBuffer;
     if (posq != NULL)
@@ -1106,6 +1110,14 @@ void OpenCLContext::addReorderListener(ReorderListener* listener) {
     reorderListeners.push_back(listener);
 }
 
+void OpenCLContext::addPreComputation(ForcePreComputation* computation) {
+    preComputations.push_back(computation);
+}
+
+void OpenCLContext::addPostComputation(ForcePostComputation* computation) {
+    postComputations.push_back(computation);
+}
+
 struct OpenCLContext::WorkThread::ThreadData {
     ThreadData(std::queue<OpenCLContext::WorkTask*>& tasks, bool& waiting,  bool& finished,
             pthread_mutex_t& queueLock, pthread_cond_t& waitForTaskCondition, pthread_cond_t& queueEmptyCondition) :

platforms/opencl/src/OpenCLContext.h

@@ -158,6 +158,8 @@ public:
     class WorkTask;
     class WorkThread;
     class ReorderListener;
+    class ForcePreComputation;
+    class ForcePostComputation;
     static const int ThreadBlockSize;
     static const int TileSize;
     OpenCLContext(const System& system, int platformIndex, int deviceIndex, const std::string& precision, OpenCLPlatform::PlatformData& platformData);
@@ -554,6 +556,28 @@ public:
     std::vector<ReorderListener*>& getReorderListeners() {
         return reorderListeners;
     }
+    /**
+     * Add a pre-computation that should be called at the very start of force and energy evaluations.
+     * The OpenCLContext assumes ownership of the object, and deletes it when the context itself is deleted.
+     */
+    void addPreComputation(ForcePreComputation* computation);
+    /**
+     * Get the list of ForcePreComputations.
+     */
+    std::vector<ForcePreComputation*>& getPreComputations() {
+        return preComputations;
+    }
+    /**
+     * Add a post-computation that should be called at the very end of force and energy evaluations.
+     * The OpenCLContext assumes ownership of the object, and deletes it when the context itself is deleted.
+     */
+    void addPostComputation(ForcePostComputation* computation);
+    /**
+     * Get the list of ForcePostComputations.
+     */
+    std::vector<ForcePostComputation*>& getPostComputations() {
+        return postComputations;
+    }
     /**
      * Mark that the current molecule definitions (and hence the atom order) may be invalid.
      * This should be called whenever force field parameters change.  It will cause the definitions
@@ -625,6 +649,8 @@ private:
     std::vector<cl::Memory*> autoclearBuffers;
     std::vector<int> autoclearBufferSizes;
     std::vector<ReorderListener*> reorderListeners;
+    std::vector<ForcePreComputation*> preComputations;
+    std::vector<ForcePostComputation*> postComputations;
     OpenCLIntegrationUtilities* integration;
     OpenCLExpressionUtilities* expression;
     OpenCLBondedUtilities* bonded;
@@ -686,7 +712,7 @@ private:
 
 /**
  * This abstract class defines a function to be executed whenever atoms get reordered.
- * Objects that need to know when reordering happens should create a reorderListener
+ * Objects that need to know when reordering happens should create a ReorderListener
  * and register it by calling addReorderListener().
  */
 class OpenCLContext::ReorderListener {
@@ -696,6 +722,38 @@ public:
     }
 };
 
+/**
+ * This abstract class defines a function to be executed at the very beginning of force and
+ * energy evaluation, before any other calculation has been done.  It is useful for operations
+ * that need to be performed at a nonstandard point in the process.  After creating a
+ * ForcePreComputation, register it by calling addForcePreComputation().
+ */
+class OpenCLContext::ForcePreComputation {
+public:
+    /**
+     * @param includeForce  true if forces should be computed
+     * @param includeEnergy true if potential energy should be computed
+     * @param groups        a set of bit flags for which force groups to include
+     */
+    virtual void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) = 0;
+};
+
+/**
+ * This abstract class defines a function to be executed at the very end of force and
+ * energy evaluation, after all other calculations have been done.  It is useful for operations
+ * that need to be performed at a nonstandard point in the process.  After creating a
+ * ForcePostComputation, register it by calling addForcePostComputation().
+ */
+class OpenCLContext::ForcePostComputation {
+public:
+    /**
+     * @param includeForce  true if forces should be computed
+     * @param includeEnergy true if potential energy should be computed
+     * @param groups        a set of bit flags for which force groups to include
+     * @return an optional contribution to add to the potential energy.     */
+    virtual double computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) = 0;
+};
+
 } // namespace OpenMM
 
 #endif /*OPENMM_OPENCLCONTEXT_H_*/

platforms/opencl/src/OpenCLKernels.cpp

@@ -104,10 +104,12 @@ void OpenCLCalcForcesAndEnergyKernel::initialize(const System& system) {
 }
 
 void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    cl.clearAutoclearBuffers();
+    for (vector<OpenCLContext::ForcePreComputation*>::iterator iter = cl.getPreComputations().begin(); iter != cl.getPreComputations().end(); ++iter)
+        (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
     OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
     bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
     cl.setComputeForceCount(cl.getComputeForceCount()+1);
-    cl.clearAutoclearBuffers();
     if (includeNonbonded)
         nb.prepareInteractions();
 }
@@ -117,8 +119,10 @@ double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context,
     if ((groups&(1<<cl.getNonbondedUtilities().getForceGroup())) != 0)
         cl.getNonbondedUtilities().computeInteractions();
     cl.reduceForces();
+    double sum = 0.0;
+    for (vector<OpenCLContext::ForcePostComputation*>::iterator iter = cl.getPostComputations().begin(); iter != cl.getPostComputations().end(); ++iter)
+        sum += (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
     cl.getIntegrationUtilities().distributeForcesFromVirtualSites();
-    double sum = 0.0f;
     if (includeEnergy) {
         OpenCLArray& energyArray = cl.getEnergyBuffer();
         if (cl.getUseDoublePrecision()) {
@@ -1323,6 +1327,58 @@ private:
     const NonbondedForce& force;
 };
 
+class OpenCLCalcNonbondedForceKernel::PmeIO : public CalcPmeReciprocalForceKernel::IO {
+public:
+    PmeIO(OpenCLContext& cl, cl::Kernel addForcesKernel) : cl(cl), addForcesKernel(addForcesKernel), forceTemp(NULL) {
+        forceTemp = OpenCLArray::create<mm_float4>(cl, cl.getNumAtoms(), "PmeForce");
+        addForcesKernel.setArg<cl::Buffer>(0, forceTemp->getDeviceBuffer());
+    }
+    ~PmeIO() {
+        if (forceTemp != NULL)
+            delete forceTemp;
+    }
+    float* getPosq() {
+        cl.getPosq().download(posq);
+        return (float*) &posq[0];
+    }
+    void setForce(float* force) {
+        forceTemp->upload(force);
+        addForcesKernel.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
+        cl.executeKernel(addForcesKernel, cl.getNumAtoms());
+    }
+private:
+    OpenCLContext& cl;
+    vector<mm_float4> posq;
+    OpenCLArray* forceTemp;
+    cl::Kernel addForcesKernel;
+};
+
+class OpenCLCalcNonbondedForceKernel::PmePreComputation : public OpenCLContext::ForcePreComputation {
+public:
+    PmePreComputation(OpenCLContext& cl, Kernel& pme, CalcPmeReciprocalForceKernel::IO& io) : cl(cl), pme(pme), io(io) {
+    }
+    void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
+        Vec3 boxSize(cl.getPeriodicBoxSize().x, cl.getPeriodicBoxSize().y, cl.getPeriodicBoxSize().z);
+        pme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, boxSize, includeEnergy);
+    }
+private:
+    OpenCLContext& cl;
+    Kernel pme;
+    CalcPmeReciprocalForceKernel::IO& io;
+};
+
+class OpenCLCalcNonbondedForceKernel::PmePostComputation : public OpenCLContext::ForcePostComputation {
+public:
+    PmePostComputation(Kernel& pme, CalcPmeReciprocalForceKernel::IO& io) : pme(pme), io(io) {
+    }
+    double computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
+        return pme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
+    }
+private:
+    Kernel pme;
+    CalcPmeReciprocalForceKernel::IO& io;
+};
+
 OpenCLCalcNonbondedForceKernel::~OpenCLCalcNonbondedForceKernel() {
     if (sigmaEpsilon != NULL)
         delete sigmaEpsilon;
@@ -1350,6 +1406,8 @@ OpenCLCalcNonbondedForceKernel::~OpenCLCalcNonbondedForceKernel() {
         delete sort;
     if (fft != NULL)
         delete fft;
+    if (pmeio != NULL)
+        delete pmeio;
 }
 
 void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {
@@ -1430,7 +1488,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
     else
         dispersionCoefficient = 0.0;
     alpha = 0;
-    if (force.getNonbondedMethod() == NonbondedForce::Ewald) {
+    if (force.getNonbondedMethod() == NonbondedForce::Ewald && cl.getContextIndex() == 0) {
         // Compute the Ewald parameters.
 
         int kmaxx, kmaxy, kmaxz;
@@ -1438,7 +1496,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         defines["EWALD_ALPHA"] = cl.doubleToString(alpha);
         defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
         defines["USE_EWALD"] = "1";
-        ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
+        ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
 
         // Create the reciprocal space kernels.
 
@@ -1454,7 +1512,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         int elementSize = (cl.getUseDoublePrecision() ? sizeof(mm_double2) : sizeof(mm_float2));
         cosSinSums = new OpenCLArray(cl, (2*kmaxx-1)*(2*kmaxy-1)*(2*kmaxz-1), elementSize, "cosSinSums");
     }
-    else if (force.getNonbondedMethod() == NonbondedForce::PME) {
+    else if (force.getNonbondedMethod() == NonbondedForce::PME && cl.getContextIndex() == 0) {
         // Compute the PME parameters.
 
         int gridSizeX, gridSizeY, gridSizeZ;
@@ -1465,7 +1523,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         defines["EWALD_ALPHA"] = cl.doubleToString(alpha);
         defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
         defines["USE_EWALD"] = "1";
-        ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
+        ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
         pmeDefines["PME_ORDER"] = cl.intToString(PmeOrder);
         pmeDefines["NUM_ATOMS"] = cl.intToString(numParticles);
         pmeDefines["RECIP_EXP_FACTOR"] = cl.doubleToString(M_PI*M_PI/(alpha*alpha));
@@ -1476,92 +1534,109 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
         if (deviceIsCpu)
             pmeDefines["DEVICE_IS_CPU"] = "1";
-
-        // Create required data structures.
-
-        int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
-        pmeGrid = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid");
-        cl.addAutoclearBuffer(*pmeGrid);
-        pmeGrid2 = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid2");
-        pmeBsplineModuliX = new OpenCLArray(cl, gridSizeX, elementSize, "pmeBsplineModuliX");
-        pmeBsplineModuliY = new OpenCLArray(cl, gridSizeY, elementSize, "pmeBsplineModuliY");
-        pmeBsplineModuliZ = new OpenCLArray(cl, gridSizeZ, elementSize, "pmeBsplineModuliZ");
-        pmeBsplineTheta = new OpenCLArray(cl, PmeOrder*numParticles, 4*elementSize, "pmeBsplineTheta");
-        pmeAtomRange = OpenCLArray::create<cl_int>(cl, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
-        pmeAtomGridIndex = OpenCLArray::create<mm_int2>(cl, numParticles, "pmeAtomGridIndex");
-        sort = new OpenCLSort(cl, new SortTrait(), cl.getNumAtoms());
-        fft = new OpenCLFFT3D(cl, gridSizeX, gridSizeY, gridSizeZ);
-
-        // Initialize the b-spline moduli.
-
-        int maxSize = max(max(gridSizeX, gridSizeY), gridSizeZ);
-        vector<double> data(PmeOrder);
-        vector<double> ddata(PmeOrder);
-        vector<double> bsplines_data(maxSize);
-        data[PmeOrder-1] = 0.0;
-        data[1] = 0.0;
-        data[0] = 1.0;
-        for (int i = 3; i < PmeOrder; i++) {
-            double div = 1.0/(i-1.0);
-            data[i-1] = 0.0;
-            for (int j = 1; j < (i-1); j++)
-                data[i-j-1] = div*(j*data[i-j-2]+(i-j)*data[i-j-1]);
-            data[0] = div*data[0];
-        }
-
-        // Differentiate.
-
-        ddata[0] = -data[0];
-        for (int i = 1; i < PmeOrder; i++)
-            ddata[i] = data[i-1]-data[i];
-        double div = 1.0/(PmeOrder-1);
-        data[PmeOrder-1] = 0.0;
-        for (int i = 1; i < (PmeOrder-1); i++)
-            data[PmeOrder-i-1] = div*(i*data[PmeOrder-i-2]+(PmeOrder-i)*data[PmeOrder-i-1]);
-        data[0] = div*data[0];
-        for (int i = 0; i < maxSize; i++)
-            bsplines_data[i] = 0.0;
-        for (int i = 1; i <= PmeOrder; i++)
-            bsplines_data[i] = data[i-1];
-
-        // Evaluate the actual bspline moduli for X/Y/Z.
-
-        for(int dim = 0; dim < 3; dim++) {
-            int ndata = (dim == 0 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
-            vector<cl_double> moduli(ndata);
-            for (int i = 0; i < ndata; i++) {
-                double sc = 0.0;
-                double ss = 0.0;
-                for (int j = 0; j < ndata; j++) {
-                    double arg = (2.0*M_PI*i*j)/ndata;
-                    sc += bsplines_data[j]*cos(arg);
-                    ss += bsplines_data[j]*sin(arg);
-                }
-                moduli[i] = (float) (sc*sc+ss*ss);
+        if (cl.getPlatformData().useCpuPme) {
+            // Create the CPU PME kernel.
+            
+            try {
+                cpuPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), *cl.getPlatformData().context);
+                cpuPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSizeX, gridSizeY, gridSizeZ, numParticles, alpha);
+                cl::Program program = cl.createProgram(OpenCLKernelSources::pme, pmeDefines);
+                cl::Kernel addForcesKernel = cl::Kernel(program, "addForces");
+                pmeio = new PmeIO(cl, addForcesKernel);
+                cl.addPreComputation(new PmePreComputation(cl, cpuPme, *pmeio));
+                cl.addPostComputation(new PmePostComputation(cpuPme, *pmeio));
             }
-            for (int i = 0; i < ndata; i++)
-            {
-                if (moduli[i] < 1.0e-7)
-                    moduli[i] = (moduli[i-1]+moduli[i+1])*0.5f;
+            catch (OpenMMException& ex) {
+                // The CPU PME plugin isn't available.
             }
-            if (cl.getUseDoublePrecision()) {
-                if (dim == 0)
-                    pmeBsplineModuliX->upload(moduli);
-                else if (dim == 1)
-                    pmeBsplineModuliY->upload(moduli);
-                else
-                    pmeBsplineModuliZ->upload(moduli);
+        }
+        if (pmeio == NULL) {
+            // Create required data structures.
+
+            int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
+            pmeGrid = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid");
+            cl.addAutoclearBuffer(*pmeGrid);
+            pmeGrid2 = new OpenCLArray(cl, gridSizeX*gridSizeY*gridSizeZ, 2*elementSize, "pmeGrid2");
+            pmeBsplineModuliX = new OpenCLArray(cl, gridSizeX, elementSize, "pmeBsplineModuliX");
+            pmeBsplineModuliY = new OpenCLArray(cl, gridSizeY, elementSize, "pmeBsplineModuliY");
+            pmeBsplineModuliZ = new OpenCLArray(cl, gridSizeZ, elementSize, "pmeBsplineModuliZ");
+            pmeBsplineTheta = new OpenCLArray(cl, PmeOrder*numParticles, 4*elementSize, "pmeBsplineTheta");
+            pmeAtomRange = OpenCLArray::create<cl_int>(cl, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
+            pmeAtomGridIndex = OpenCLArray::create<mm_int2>(cl, numParticles, "pmeAtomGridIndex");
+            sort = new OpenCLSort(cl, new SortTrait(), cl.getNumAtoms());
+            fft = new OpenCLFFT3D(cl, gridSizeX, gridSizeY, gridSizeZ);
+
+            // Initialize the b-spline moduli.
+
+            int maxSize = max(max(gridSizeX, gridSizeY), gridSizeZ);
+            vector<double> data(PmeOrder);
+            vector<double> ddata(PmeOrder);
+            vector<double> bsplines_data(maxSize);
+            data[PmeOrder-1] = 0.0;
+            data[1] = 0.0;
+            data[0] = 1.0;
+            for (int i = 3; i < PmeOrder; i++) {
+                double div = 1.0/(i-1.0);
+                data[i-1] = 0.0;
+                for (int j = 1; j < (i-1); j++)
+                    data[i-j-1] = div*(j*data[i-j-2]+(i-j)*data[i-j-1]);
+                data[0] = div*data[0];
             }
-            else {
-                vector<float> modulif(ndata);
+
+            // Differentiate.
+
+            ddata[0] = -data[0];
+            for (int i = 1; i < PmeOrder; i++)
+                ddata[i] = data[i-1]-data[i];
+            double div = 1.0/(PmeOrder-1);
+            data[PmeOrder-1] = 0.0;
+            for (int i = 1; i < (PmeOrder-1); i++)
+                data[PmeOrder-i-1] = div*(i*data[PmeOrder-i-2]+(PmeOrder-i)*data[PmeOrder-i-1]);
+            data[0] = div*data[0];
+            for (int i = 0; i < maxSize; i++)
+                bsplines_data[i] = 0.0;
+            for (int i = 1; i <= PmeOrder; i++)
+                bsplines_data[i] = data[i-1];
+
+            // Evaluate the actual bspline moduli for X/Y/Z.
+
+            for(int dim = 0; dim < 3; dim++) {
+                int ndata = (dim == 0 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
+                vector<cl_double> moduli(ndata);
+                for (int i = 0; i < ndata; i++) {
+                    double sc = 0.0;
+                    double ss = 0.0;
+                    for (int j = 0; j < ndata; j++) {
+                        double arg = (2.0*M_PI*i*j)/ndata;
+                        sc += bsplines_data[j]*cos(arg);
+                        ss += bsplines_data[j]*sin(arg);
+                    }
+                    moduli[i] = (float) (sc*sc+ss*ss);
+                }
                 for (int i = 0; i < ndata; i++)
-                    modulif[i] = (float) moduli[i];
-                if (dim == 0)
-                    pmeBsplineModuliX->upload(modulif);
-                else if (dim == 1)
-                    pmeBsplineModuliY->upload(modulif);
-                else
-                    pmeBsplineModuliZ->upload(modulif);
+                {
+                    if (moduli[i] < 1.0e-7)
+                        moduli[i] = (moduli[i-1]+moduli[i+1])*0.5f;
+                }
+                if (cl.getUseDoublePrecision()) {
+                    if (dim == 0)
+                        pmeBsplineModuliX->upload(moduli);
+                    else if (dim == 1)
+                        pmeBsplineModuliY->upload(moduli);
+                    else
+                        pmeBsplineModuliZ->upload(moduli);
+                }
+                else {
+                    vector<float> modulif(ndata);
+                    for (int i = 0; i < ndata; i++)
+                        modulif[i] = (float) moduli[i];
+                    if (dim == 0)
+                        pmeBsplineModuliX->upload(modulif);
+                    else if (dim == 1)
+                        pmeBsplineModuliY->upload(modulif);
+                    else
+                        pmeBsplineModuliZ->upload(modulif);
+                }
             }
         }
     }
@@ -1650,7 +1725,7 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
             }
        }
     }
-    if (cosSinSums != NULL && cl.getContextIndex() == 0 && includeReciprocal) {
+    if (cosSinSums != NULL && includeReciprocal) {
         mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
         mm_double4 recipBoxSize = mm_double4(2*M_PI/boxSize.x, 2*M_PI/boxSize.y, 2*M_PI/boxSize.z, 0.0);
         double recipCoefficient = ONE_4PI_EPS0*4*M_PI/(boxSize.x*boxSize.y*boxSize.z);
@@ -1669,7 +1744,7 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
         cl.executeKernel(ewaldSumsKernel, cosSinSums->getSize());
         cl.executeKernel(ewaldForcesKernel, cl.getNumAtoms());
     }
-    if (pmeGrid != NULL && cl.getContextIndex() == 0 && includeReciprocal) {
+    if (pmeGrid != NULL && includeReciprocal) {
         setPeriodicBoxSizeArg(cl, pmeUpdateBsplinesKernel, 4);
         setInvPeriodicBoxSizeArg(cl, pmeUpdateBsplinesKernel, 5);
         cl.executeKernel(pmeUpdateBsplinesKernel, cl.getNumAtoms());

platforms/opencl/src/OpenCLKernels.h

@@ -557,7 +557,7 @@ public:
     OpenCLCalcNonbondedForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, const System& system) : CalcNonbondedForceKernel(name, platform),
             hasInitializedKernel(false), cl(cl), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), pmeGrid(NULL),
             pmeGrid2(NULL), pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeBsplineTheta(NULL),
-            pmeAtomRange(NULL), pmeAtomGridIndex(NULL), sort(NULL), fft(NULL) {
+            pmeAtomRange(NULL), pmeAtomGridIndex(NULL), sort(NULL), fft(NULL), pmeio(NULL) {
     }
     ~OpenCLCalcNonbondedForceKernel();
     /**
@@ -596,6 +596,9 @@ private:
         const char* getMaxValue() const {return "(int2) (INT_MAX, INT_MAX)";}
         const char* getSortKey() const {return "value.y";}
     };
+    class PmeIO;
+    class PmePreComputation;
+    class PmePostComputation;
     OpenCLContext& cl;
     bool hasInitializedKernel;
     OpenCLArray* sigmaEpsilon;
@@ -611,6 +614,8 @@ private:
     OpenCLArray* pmeAtomGridIndex;
     OpenCLSort* sort;
     OpenCLFFT3D* fft;
+    Kernel cpuPme;
+    PmeIO* pmeio;
     cl::Kernel ewaldSumsKernel;
     cl::Kernel ewaldForcesKernel;
     cl::Kernel pmeGridIndexKernel;

platforms/opencl/src/OpenCLPlatform.cpp

@@ -31,6 +31,7 @@
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/Context.h"
 #include "openmm/System.h"
+#include <algorithm>
 #include <sstream>
 
 using namespace OpenMM;
@@ -78,11 +79,13 @@ OpenCLPlatform::OpenCLPlatform() {
     platformProperties.push_back(OpenCLPlatformIndex());
     platformProperties.push_back(OpenCLPlatformName());
     platformProperties.push_back(OpenCLPrecision());
+    platformProperties.push_back(OpenCLUseCpuPme());
     setPropertyDefaultValue(OpenCLDeviceIndex(), "");
     setPropertyDefaultValue(OpenCLDeviceName(), "");
     setPropertyDefaultValue(OpenCLPlatformIndex(), "");
     setPropertyDefaultValue(OpenCLPlatformName(), "");
     setPropertyDefaultValue(OpenCLPrecision(), "single");
+    setPropertyDefaultValue(OpenCLUseCpuPme(), "false");
 }
 
 double OpenCLPlatform::getSpeed() const {
@@ -112,7 +115,15 @@ void OpenCLPlatform::contextCreated(ContextImpl& context, const map<string, stri
             getPropertyDefaultValue(OpenCLDeviceIndex()) : properties.find(OpenCLDeviceIndex())->second);
     string precisionPropValue = (properties.find(OpenCLPrecision()) == properties.end() ?
             getPropertyDefaultValue(OpenCLPrecision()) : properties.find(OpenCLPrecision())->second);
-    context.setPlatformData(new PlatformData(context.getSystem(), platformPropValue, devicePropValue, precisionPropValue));
+    string cpuPmePropValue = (properties.find(OpenCLUseCpuPme()) == properties.end() ?
+            getPropertyDefaultValue(OpenCLUseCpuPme()) : properties.find(OpenCLUseCpuPme())->second);
+    transform(precisionPropValue.begin(), precisionPropValue.end(), precisionPropValue.begin(), ::tolower);
+    transform(cpuPmePropValue.begin(), cpuPmePropValue.end(), cpuPmePropValue.begin(), ::tolower);
+    vector<string> pmeKernelName;
+    pmeKernelName.push_back(CalcPmeReciprocalForceKernel::Name());
+    if (!supportsKernels(pmeKernelName))
+        cpuPmePropValue = "false";
+    context.setPlatformData(new PlatformData(context.getSystem(), platformPropValue, devicePropValue, precisionPropValue, cpuPmePropValue));
 }
 
 void OpenCLPlatform::contextDestroyed(ContextImpl& context) const {
@@ -121,7 +132,7 @@ void OpenCLPlatform::contextDestroyed(ContextImpl& context) const {
 }
 
 OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& platformPropValue, const string& deviceIndexProperty,
-        const string& precisionProperty) : removeCM(false), stepCount(0), computeForceCount(0), time(0.0)  {
+        const string& precisionProperty, const string& cpuPmeProperty) : removeCM(false), stepCount(0), computeForceCount(0), time(0.0)  {
     int platformIndex = 0;
     if (platformPropValue.length() > 0)
         stringstream(platformPropValue) >> platformIndex;
@@ -150,6 +161,7 @@ OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& p
         deviceIndex << contexts[i]->getDeviceIndex();
         deviceName << contexts[i]->getDevice().getInfo<CL_DEVICE_NAME>();
     }
+    useCpuPme = (cpuPmeProperty == "true" && !contexts[0]->getUseDoublePrecision());
     propertyValues[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex.str();
     propertyValues[OpenCLPlatform::OpenCLDeviceName()] = deviceName.str();
     propertyValues[OpenCLPlatform::OpenCLPlatformIndex()] = contexts[0]->intToString(platformIndex);
@@ -157,6 +169,7 @@ OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& p
     cl::Platform::get(&platforms);
     propertyValues[OpenCLPlatform::OpenCLPlatformName()] = platforms[platformIndex].getInfo<CL_PLATFORM_NAME>();
     propertyValues[OpenCLPlatform::OpenCLPrecision()] = precisionProperty;
+    propertyValues[OpenCLPlatform::OpenCLUseCpuPme()] = useCpuPme ? "true" : "false";
     contextEnergy.resize(contexts.size());
 }
 

platforms/opencl/src/kernels/pme.cl

@@ -391,3 +391,8 @@ __kernel void gridInterpolateForce(__global const real4* restrict posq, __global
         forceBuffers[atom] = totalForce;
     }
 }
+
+__kernel void addForces(__global const real4* restrict forces, __global real4* restrict forceBuffers) {
+    for (int atom = get_global_id(0); atom < NUM_ATOMS; atom += get_global_size(0))
+        forceBuffers[atom] += forces[atom];
+}

platforms/opencl/tests/TestOpenCLFFT.cpp

@@ -54,7 +54,7 @@ template <class Real2>
 void testTransform() {
     System system;
     system.addParticle(0.0);
-    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"));
+    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false");
     OpenCLContext& context = *platformData.contexts[0];
     context.initialize();
     OpenMM_SFMT::SFMT sfmt;

platforms/opencl/tests/TestOpenCLRandom.cpp

@@ -54,7 +54,7 @@ void testGaussian() {
     System system;
     for (int i = 0; i < numAtoms; i++)
         system.addParticle(1.0);
-    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"));
+    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false");
     OpenCLContext& context = *platformData.contexts[0];
     context.initialize();
     context.getIntegrationUtilities().initRandomNumberGenerator(0);

platforms/opencl/tests/TestOpenCLSort.cpp

@@ -64,7 +64,7 @@ void verifySorting(vector<float> array) {
 
     System system;
     system.addParticle(0.0);
-    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"));
+    OpenCLPlatform::PlatformData platformData(system, "", "", platform.getPropertyDefaultValue("OpenCLPrecision"), "false");
     OpenCLContext& context = *platformData.contexts[0];
     context.initialize();
     OpenCLArray data(context, array.size(), sizeof(float), "sortData");

plugins/cpupme/src/CpuPmeKernelFactory.cpp

 /* -------------------------------------------------------------------------- *
- *                              OpenMMAmoeba                                  *
+ *                              OpenMMCpuPme                                  *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

plugins/cpupme/src/CpuPmeKernels.cpp

@@ -514,11 +514,6 @@ CpuCalcPmeReciprocalForceKernel::~CpuCalcPmeReciprocalForceKernel() {
     }
 }
 
-#include <sys/time.h>
-double diff(struct timeval t1, struct timeval t2) {
-    return t2.tv_usec-t1.tv_usec+1e6*(t2.tv_sec-t1.tv_sec);
-}
-
 void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
     if (index == -1) {
         // This is the main thread that coordinates all the other ones.
@@ -531,26 +526,17 @@ void CpuCalcPmeReciprocalForceKernel::runThread(int index) {
             if (isDeleted)
                 break;
             posq = io->getPosq();
-            struct timeval t1, t2, t3, t4, t5, t6, t7;
-            gettimeofday(&t1, NULL);
             advanceThreads(); // Signal threads to perform charge spreading.
             advanceThreads(); // Signal threads to sum the charge grids.
-            gettimeofday(&t2, NULL);
             fftwf_execute_dft_r2c(forwardFFT, realGrid, complexGrid);
-            gettimeofday(&t3, NULL);
             if (lastBoxSize != periodicBoxSize)
                 advanceThreads(); // Signal threads to compute the reciprocal scale factors.
             if (includeEnergy)
                 advanceThreads(); // Signal threads to compute energy.
-            gettimeofday(&t4, NULL);
             advanceThreads(); // Signal threads to perform reciprocal convolution.
-            gettimeofday(&t5, NULL);
             fftwf_execute_dft_c2r(backwardFFT, complexGrid, realGrid);
-            gettimeofday(&t6, NULL);
             advanceThreads(); // Signal threads to interpolate forces.
             isFinished = true;
-            gettimeofday(&t7, NULL);
-            printf("time %g %g %g %g %g %g\n", diff(t1, t2), diff(t2, t3), diff(t3, t4), diff(t4, t5), diff(t5, t6), diff(t6, t7));
             lastBoxSize = periodicBoxSize;
             pthread_cond_signal(&mainThreadEndCondition);
         }