Connected CPU based PME to CUDA platform

cmake_modules/FindFFTW.cmake

+# - Find FFTW
+# Find the native FFTW includes and library
+#
+#  FFTW_INCLUDES        - where to find fftw3.h
+#  FFTW_LIBRARY         - the main FFTW library.
+#  FFTW_THREADS_LIBRARY - the FFTW multithreading support library.
+#  FFTW_FOUND           - True if FFTW found.
+
+if (FFTW_INCLUDES)
+  # Already in cache, be silent
+  set (FFTW_FIND_QUIETLY TRUE)
+endif (FFTW_INCLUDES)
+
+find_path (FFTW_INCLUDES fftw3.h)
+
+find_library (FFTW_LIBRARY NAMES fftw3f)
+find_library (FFTW_THREADS_LIBRARY NAMES fftw3f_threads)
+
+# handle the QUIETLY and REQUIRED arguments and set FFTW_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (FFTW DEFAULT_MSG FFTW_LIBRARY FFTW_INCLUDES)
+find_package_handle_standard_args (FFTW_THREADS DEFAULT_MSG FFTW_THREADS_LIBRARY FFTW_INCLUDES)
+
+mark_as_advanced (FFTW_LIBRARY FFTW_THREADS_LIBRARY FFTW_INCLUDES)

platforms/cuda/sharedTarget/CMakeLists.txt

@@ -2,7 +2,8 @@
 # Include CUDA related files.
 #
 INCLUDE(FindCUDA)
-INCLUDE_DIRECTORIES(${CUDA_TOOLKIT_INCLUDE})
+INCLUDE(FindFFTW)
+INCLUDE_DIRECTORIES(${CUDA_TOOLKIT_INCLUDE} ${FFTW_INCLUDES})
 
 FILE(GLOB CUDA_KERNELS ${CUDA_SOURCE_DIR}/kernels/*.cu)
 ADD_CUSTOM_COMMAND(OUTPUT ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H}
@@ -18,7 +19,7 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
     SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
 ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB} ${CUDA_CUDA_LIBRARY} ${CUDA_cufft_LIBRARY} ${PTHREADS_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB} ${CUDA_CUDA_LIBRARY} ${CUDA_cufft_LIBRARY} ${PTHREADS_LIB} ${FFTW_LIBRARY} ${FFTW_THREADS_LIBRARY})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_CUDA_BUILDING_SHARED_LIBRARY")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

platforms/cuda/src/CudaContext.cpp

@@ -231,6 +231,10 @@ CudaContext::~CudaContext() {
         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)
         cuMemFreeHost(pinnedBuffer);
     if (posq != NULL)
@@ -1102,6 +1106,14 @@ void CudaContext::addReorderListener(ReorderListener* listener) {
     reorderListeners.push_back(listener);
 }
 
+void CudaContext::addPreComputation(ForcePreComputation* computation) {
+    preComputations.push_back(computation);
+}
+
+void CudaContext::addPostComputation(ForcePostComputation* computation) {
+    postComputations.push_back(computation);
+}
+
 struct CudaContext::WorkThread::ThreadData {
     ThreadData(std::queue<CudaContext::WorkTask*>& tasks, bool& waiting,  bool& finished,
             pthread_mutex_t& queueLock, pthread_cond_t& waitForTaskCondition, pthread_cond_t& queueEmptyCondition) :

platforms/cuda/src/CudaContext.h

@@ -70,6 +70,8 @@ public:
     class WorkTask;
     class WorkThread;
     class ReorderListener;
+    class ForcePreComputation;
+    class ForcePostComputation;
     static const int ThreadBlockSize;
     static const int TileSize;
     CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const std::string& precision,
@@ -454,6 +456,28 @@ public:
     std::vector<ReorderListener*>& getReorderListeners() {
         return reorderListeners;
     }
+    /**
+     * Add a pre-computation that should be called at the very start of force and energy evalutations.
+     * The CudaContext 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 evalutations.
+     * The CudaContext 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
@@ -519,6 +543,8 @@ private:
     std::vector<CUdeviceptr> autoclearBuffers;
     std::vector<int> autoclearBufferSizes;
     std::vector<ReorderListener*> reorderListeners;
+    std::vector<ForcePreComputation*> preComputations;
+    std::vector<ForcePostComputation*> postComputations;
     CudaIntegrationUtilities* integration;
     CudaExpressionUtilities* expression;
     CudaBondedUtilities* bonded;
@@ -580,7 +606,7 @@ 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 CudaContext::ReorderListener {
@@ -590,6 +616,38 @@ 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 CudaContext::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 CudaContext::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_CUDACONTEXT_H_*/

platforms/cuda/src/CudaKernels.cpp

@@ -84,10 +84,12 @@ void CudaCalcForcesAndEnergyKernel::initialize(const System& system) {
 
 void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
     cu.setAsCurrent();
+    cu.clearAutoclearBuffers();
+    for (vector<CudaContext::ForcePreComputation*>::iterator iter = cu.getPreComputations().begin(); iter != cu.getPreComputations().end(); ++iter)
+        (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
     CudaNonbondedUtilities& nb = cu.getNonbondedUtilities();
     bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
     cu.setComputeForceCount(cu.getComputeForceCount()+1);
-    cu.clearAutoclearBuffers();
     if (includeNonbonded)
         nb.prepareInteractions();
 }
@@ -96,8 +98,10 @@ double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bo
     cu.getBondedUtilities().computeInteractions(groups);
     if ((groups&(1<<cu.getNonbondedUtilities().getForceGroup())) != 0)
         cu.getNonbondedUtilities().computeInteractions();
-    cu.getIntegrationUtilities().distributeForcesFromVirtualSites();
     double sum = 0.0;
+    for (vector<CudaContext::ForcePostComputation*>::iterator iter = cu.getPostComputations().begin(); iter != cu.getPostComputations().end(); ++iter)
+        sum += (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
+    cu.getIntegrationUtilities().distributeForcesFromVirtualSites();
     if (includeEnergy) {
         CudaArray& energyArray = cu.getEnergyBuffer();
         if (cu.getUseDoublePrecision()) {
@@ -1330,6 +1334,59 @@ private:
     const NonbondedForce& force;
 };
 
+class CudaCalcNonbondedForceKernel::PmeIO : public CpuPme::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");
+    }
+    ~PmeIO() {
+        if (forceTemp != NULL)
+            delete forceTemp;
+    }
+    float* getPosq() {
+        cu.setAsCurrent();
+        cu.getPosq().download(posq);
+        return (float*) &posq[0];
+    }
+    void setForce(float* force) {
+        forceTemp->upload(force);
+        void* args[] = {&forceTemp->getDevicePointer(), &cu.getForce().getDevicePointer()};
+        cu.executeKernel(addForcesKernel, args, cu.getNumAtoms());
+    }
+private:
+    CudaContext& cu;
+    vector<float4> posq;
+    CudaArray* forceTemp;
+    CUfunction addForcesKernel;
+};
+
+class CudaCalcNonbondedForceKernel::PmePreComputation : public CudaContext::ForcePreComputation {
+public:
+    PmePreComputation(CudaContext& cu, CpuPme& pme, CpuPme::IO& io) : cu(cu), pme(pme), io(io) {
+    }
+    void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
+        Vec3 boxSize(cu.getPeriodicBoxSize().x, cu.getPeriodicBoxSize().y, cu.getPeriodicBoxSize().z);
+        pme.beginComputation(io, boxSize, includeEnergy);
+    }
+private:
+    CudaContext& cu;
+    CpuPme& pme;
+    CpuPme::IO& io;
+};
+
+class CudaCalcNonbondedForceKernel::PmePostComputation : public CudaContext::ForcePostComputation {
+public:
+    PmePostComputation(CpuPme& pme, CpuPme::IO& io) : pme(pme), io(io) {
+    }
+    double computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
+        return pme.finishComputation(io);
+    }
+private:
+    CpuPme& pme;
+    CpuPme::IO& io;
+};
+
 CudaCalcNonbondedForceKernel::~CudaCalcNonbondedForceKernel() {
     cu.setAsCurrent();
     if (sigmaEpsilon != NULL)
@@ -1354,6 +1411,10 @@ CudaCalcNonbondedForceKernel::~CudaCalcNonbondedForceKernel() {
         delete pmeAtomGridIndex;
     if (sort != NULL)
         delete sort;
+    if (cpuPme != NULL)
+        delete cpuPme;
+    if (pmeio != NULL)
+        delete pmeio;
     if (hasInitializedFFT) {
         cufftDestroy(fftForward);
         cufftDestroy(fftBackward);
@@ -1457,7 +1518,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
     else
         dispersionCoefficient = 0.0;
     alpha = 0;
-    if (force.getNonbondedMethod() == NonbondedForce::Ewald) {
+    if (force.getNonbondedMethod() == NonbondedForce::Ewald && cu.getContextIndex() == 0) {
         // Compute the Ewald parameters.
 
         int kmaxx, kmaxy, kmaxz;
@@ -1465,7 +1526,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         defines["EWALD_ALPHA"] = cu.doubleToString(alpha);
         defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI));
         defines["USE_EWALD"] = "1";
-        ewaldSelfEnergy = (cu.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.
 
@@ -1484,7 +1545,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         int elementSize = (cu.getUseDoublePrecision() ? sizeof(double2) : sizeof(float2));
         cosSinSums = new CudaArray(cu, (2*kmaxx-1)*(2*kmaxy-1)*(2*kmaxz-1), elementSize, "cosSinSums");
     }
-    else if (force.getNonbondedMethod() == NonbondedForce::PME) {
+    else if (force.getNonbondedMethod() == NonbondedForce::PME && cu.getContextIndex() == 0) {
         // Compute the PME parameters.
 
         int gridSizeX, gridSizeY, gridSizeZ;
@@ -1497,7 +1558,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         defines["EWALD_ALPHA"] = cu.doubleToString(alpha);
         defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI));
         defines["USE_EWALD"] = "1";
-        ewaldSelfEnergy = (cu.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
+        ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
         pmeDefines["PME_ORDER"] = cu.intToString(PmeOrder);
         pmeDefines["NUM_ATOMS"] = cu.intToString(numParticles);
         pmeDefines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
@@ -1510,6 +1571,15 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         if (cu.getUseDoublePrecision())
             pmeDefines["USE_DOUBLE_PRECISION"] = "1";
         CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaKernelSources::pme, pmeDefines);
+        bool useCpuPme = false;
+        if (useCpuPme) {
+            cpuPme = new CpuPme(gridSizeX, gridSizeY, gridSizeZ, numParticles, alpha);
+            CUfunction addForcesKernel = cu.getKernel(module, "addForces");
+            pmeio = new PmeIO(cu, addForcesKernel);
+            cu.addPreComputation(new PmePreComputation(cu, *cpuPme, *pmeio));
+            cu.addPostComputation(new PmePostComputation(*cpuPme, *pmeio));
+        }
+        else {
             pmeGridIndexKernel = cu.getKernel(module, "findAtomGridIndex");
             pmeSpreadChargeKernel = cu.getKernel(module, "gridSpreadCharge");
             pmeConvolutionKernel = cu.getKernel(module, "reciprocalConvolution");
@@ -1618,6 +1688,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
                 }
             }
         }
+    }
     else
         ewaldSelfEnergy = 0.0;
 
@@ -1654,13 +1725,14 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
 }
 
 double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal) {
-    if (cosSinSums != NULL && cu.getContextIndex() == 0 && 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());
         void* forcesArgs[] = {&cu.getForce().getDevicePointer(), &cu.getPosq().getDevicePointer(), &cosSinSums->getDevicePointer(), cu.getPeriodicBoxSizePointer()};
         cu.executeKernel(ewaldForcesKernel, forcesArgs, cu.getNumAtoms());
     }
-    if (directPmeGrid != NULL && cu.getContextIndex() == 0 && includeReciprocal) {
+    if (directPmeGrid != NULL && includeReciprocal) {
         void* gridIndexArgs[] = {&cu.getPosq().getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
         cu.executeKernel(pmeGridIndexKernel, gridIndexArgs, cu.getNumAtoms());
 
@@ -1699,7 +1771,6 @@ 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/CudaKernels.h

@@ -34,6 +34,7 @@
 #include "CudaSort.h"
 #include "openmm/kernels.h"
 #include "openmm/System.h"
+#include "CpuPme.h"
 #include <cufft.h>
 
 namespace OpenMM {
@@ -557,7 +558,7 @@ class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
 public:
     CudaCalcNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcNonbondedForceKernel(name, platform),
             cu(cu), hasInitializedFFT(false), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), directPmeGrid(NULL), reciprocalPmeGrid(NULL),
-            pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL),  pmeAtomRange(NULL), pmeAtomGridIndex(NULL), sort(NULL) {
+            pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL),  pmeAtomRange(NULL), pmeAtomGridIndex(NULL), sort(NULL), cpuPme(NULL), pmeio(NULL) {
     }
     ~CudaCalcNonbondedForceKernel();
     /**
@@ -596,6 +597,9 @@ private:
         const char* getMaxValue() const {return "make_int2(INT_MAX, INT_MAX)";}
         const char* getSortKey() const {return "value.y";}
     };
+    class PmeIO;
+    class PmePreComputation;
+    class PmePostComputation;
     CudaContext& cu;
     bool hasInitializedFFT;
     CudaArray* sigmaEpsilon;
@@ -609,6 +613,8 @@ private:
     CudaArray* pmeAtomRange;
     CudaArray* pmeAtomGridIndex;
     CudaSort* sort;
+    CpuPme* cpuPme;
+    PmeIO* pmeio;
     cufftHandle fftForward;
     cufftHandle fftBackward;
     CUfunction ewaldSumsKernel;

platforms/cuda/src/kernels/pme.cu

@@ -271,3 +271,13 @@ void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __
         forceBuffers[atom+2*PADDED_NUM_ATOMS] += static_cast<unsigned long long>((long long) (-q*force.z*GRID_SIZE_Z*invPeriodicBoxSize.z*0x100000000));
     }
 }
+
+extern "C" __global__
+void addForces(const real4* __restrict__ forces, unsigned long long* __restrict__ forceBuffers) {
+    for (int atom = blockIdx.x*blockDim.x+threadIdx.x; atom < NUM_ATOMS; atom += blockDim.x*gridDim.x) {
+        real4 f = forces[atom];
+        forceBuffers[atom] += static_cast<unsigned long long>((long long) (f.x*0x100000000));
+        forceBuffers[atom+PADDED_NUM_ATOMS] += static_cast<unsigned long long>((long long) (f.y*0x100000000));
+        forceBuffers[atom+2*PADDED_NUM_ATOMS] += static_cast<unsigned long long>((long long) (f.z*0x100000000));
+    }
+}
\ No newline at end of file