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Commit 932a61b6 authored by peastman's avatar peastman
Browse files

Connected CPU based PME to CUDA platform

parent 56c071cc
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Showing with 299 additions and 116 deletions
cmake_modules/FindFFTW.cmake 0 → 100644
View file @ 932a61b6
# - 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
View file @ 932a61b6
...@@ -2,7 +2,8 @@ ...@@ -2,7 +2,8 @@
# Include CUDA related files. # Include CUDA related files.
# #
INCLUDE(FindCUDA) 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) FILE(GLOB CUDA_KERNELS ${CUDA_SOURCE_DIR}/kernels/*.cu)
ADD_CUSTOM_COMMAND(OUTPUT ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H} ADD_CUSTOM_COMMAND(OUTPUT ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H}
...@@ -18,7 +19,7 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug) ...@@ -18,7 +19,7 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug) ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME}) SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug) ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
TARGET_LINK_LIBRARIES(${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") SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_CUDA_BUILDING_SHARED_LIBRARY")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET}) INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
platforms/cuda/src/CudaContext.cpp
View file @ 932a61b6
...@@ -231,6 +231,10 @@ CudaContext::~CudaContext() { ...@@ -231,6 +231,10 @@ CudaContext::~CudaContext() {
delete forces[i]; delete forces[i];
for (int i = 0; i < (int) reorderListeners.size(); i++) for (int i = 0; i < (int) reorderListeners.size(); i++)
delete reorderListeners[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) if (pinnedBuffer != NULL)
cuMemFreeHost(pinnedBuffer); cuMemFreeHost(pinnedBuffer);
if (posq != NULL) if (posq != NULL)
...@@ -1102,6 +1106,14 @@ void CudaContext::addReorderListener(ReorderListener* listener) { ...@@ -1102,6 +1106,14 @@ void CudaContext::addReorderListener(ReorderListener* listener) {
reorderListeners.push_back(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 { struct CudaContext::WorkThread::ThreadData {
ThreadData(std::queue<CudaContext::WorkTask*>& tasks, bool& waiting, bool& finished, ThreadData(std::queue<CudaContext::WorkTask*>& tasks, bool& waiting, bool& finished,
pthread_mutex_t& queueLock, pthread_cond_t& waitForTaskCondition, pthread_cond_t& queueEmptyCondition) : pthread_mutex_t& queueLock, pthread_cond_t& waitForTaskCondition, pthread_cond_t& queueEmptyCondition) :
......
platforms/cuda/src/CudaContext.h
View file @ 932a61b6
...@@ -70,6 +70,8 @@ public: ...@@ -70,6 +70,8 @@ public:
class WorkTask; class WorkTask;
class WorkThread; class WorkThread;
class ReorderListener; class ReorderListener;
class ForcePreComputation;
class ForcePostComputation;
static const int ThreadBlockSize; static const int ThreadBlockSize;
static const int TileSize; static const int TileSize;
CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const std::string& precision, CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const std::string& precision,
...@@ -454,6 +456,28 @@ public: ...@@ -454,6 +456,28 @@ public:
std::vector<ReorderListener*>& getReorderListeners() { std::vector<ReorderListener*>& getReorderListeners() {
return reorderListeners; 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. * 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 * This should be called whenever force field parameters change. It will cause the definitions
...@@ -519,6 +543,8 @@ private: ...@@ -519,6 +543,8 @@ private:
std::vector<CUdeviceptr> autoclearBuffers; std::vector<CUdeviceptr> autoclearBuffers;
std::vector<int> autoclearBufferSizes; std::vector<int> autoclearBufferSizes;
std::vector<ReorderListener*> reorderListeners; std::vector<ReorderListener*> reorderListeners;
std::vector<ForcePreComputation*> preComputations;
std::vector<ForcePostComputation*> postComputations;
CudaIntegrationUtilities* integration; CudaIntegrationUtilities* integration;
CudaExpressionUtilities* expression; CudaExpressionUtilities* expression;
CudaBondedUtilities* bonded; CudaBondedUtilities* bonded;
...@@ -580,7 +606,7 @@ private: ...@@ -580,7 +606,7 @@ private:
/** /**
* This abstract class defines a function to be executed whenever atoms get reordered. * 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(). * and register it by calling addReorderListener().
*/ */
class CudaContext::ReorderListener { class CudaContext::ReorderListener {
...@@ -590,6 +616,38 @@ public: ...@@ -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 } // namespace OpenMM
#endif /*OPENMM_CUDACONTEXT_H_*/ #endif /*OPENMM_CUDACONTEXT_H_*/
platforms/cuda/src/CudaKernels.cpp
View file @ 932a61b6
...@@ -84,10 +84,12 @@ void CudaCalcForcesAndEnergyKernel::initialize(const System& system) { ...@@ -84,10 +84,12 @@ void CudaCalcForcesAndEnergyKernel::initialize(const System& system) {
void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) { void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
cu.setAsCurrent(); 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(); CudaNonbondedUtilities& nb = cu.getNonbondedUtilities();
bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0); bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
cu.setComputeForceCount(cu.getComputeForceCount()+1); cu.setComputeForceCount(cu.getComputeForceCount()+1);
cu.clearAutoclearBuffers();
if (includeNonbonded) if (includeNonbonded)
nb.prepareInteractions(); nb.prepareInteractions();
} }
...@@ -96,8 +98,10 @@ double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bo ...@@ -96,8 +98,10 @@ double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bo
cu.getBondedUtilities().computeInteractions(groups); cu.getBondedUtilities().computeInteractions(groups);
if ((groups&(1<<cu.getNonbondedUtilities().getForceGroup())) != 0) if ((groups&(1<<cu.getNonbondedUtilities().getForceGroup())) != 0)
cu.getNonbondedUtilities().computeInteractions(); cu.getNonbondedUtilities().computeInteractions();
cu.getIntegrationUtilities().distributeForcesFromVirtualSites();
double sum = 0.0; 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) { if (includeEnergy) {
CudaArray& energyArray = cu.getEnergyBuffer(); CudaArray& energyArray = cu.getEnergyBuffer();
if (cu.getUseDoublePrecision()) { if (cu.getUseDoublePrecision()) {
...@@ -1330,6 +1334,59 @@ private: ...@@ -1330,6 +1334,59 @@ private:
const NonbondedForce& force; 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() { CudaCalcNonbondedForceKernel::~CudaCalcNonbondedForceKernel() {
cu.setAsCurrent(); cu.setAsCurrent();
if (sigmaEpsilon != NULL) if (sigmaEpsilon != NULL)
...@@ -1354,6 +1411,10 @@ CudaCalcNonbondedForceKernel::~CudaCalcNonbondedForceKernel() { ...@@ -1354,6 +1411,10 @@ CudaCalcNonbondedForceKernel::~CudaCalcNonbondedForceKernel() {
delete pmeAtomGridIndex; delete pmeAtomGridIndex;
if (sort != NULL) if (sort != NULL)
delete sort; delete sort;
if (cpuPme != NULL)
delete cpuPme;
if (pmeio != NULL)
delete pmeio;
if (hasInitializedFFT) { if (hasInitializedFFT) {
cufftDestroy(fftForward); cufftDestroy(fftForward);
cufftDestroy(fftBackward); cufftDestroy(fftBackward);
...@@ -1457,7 +1518,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon ...@@ -1457,7 +1518,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
else else
dispersionCoefficient = 0.0; dispersionCoefficient = 0.0;
alpha = 0; alpha = 0;
if (force.getNonbondedMethod() == NonbondedForce::Ewald) { if (force.getNonbondedMethod() == NonbondedForce::Ewald && cu.getContextIndex() == 0) {
// Compute the Ewald parameters. // Compute the Ewald parameters.
int kmaxx, kmaxy, kmaxz; int kmaxx, kmaxy, kmaxz;
...@@ -1465,7 +1526,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon ...@@ -1465,7 +1526,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
defines["EWALD_ALPHA"] = cu.doubleToString(alpha); defines["EWALD_ALPHA"] = cu.doubleToString(alpha);
defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI)); defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI));
defines["USE_EWALD"] = "1"; 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. // Create the reciprocal space kernels.
...@@ -1484,7 +1545,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon ...@@ -1484,7 +1545,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
int elementSize = (cu.getUseDoublePrecision() ? sizeof(double2) : sizeof(float2)); int elementSize = (cu.getUseDoublePrecision() ? sizeof(double2) : sizeof(float2));
cosSinSums = new CudaArray(cu, (2*kmaxx-1)*(2*kmaxy-1)*(2*kmaxz-1), elementSize, "cosSinSums"); 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. // Compute the PME parameters.
int gridSizeX, gridSizeY, gridSizeZ; int gridSizeX, gridSizeY, gridSizeZ;
...@@ -1497,7 +1558,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon ...@@ -1497,7 +1558,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
defines["EWALD_ALPHA"] = cu.doubleToString(alpha); defines["EWALD_ALPHA"] = cu.doubleToString(alpha);
defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI)); defines["TWO_OVER_SQRT_PI"] = cu.doubleToString(2.0/sqrt(M_PI));
defines["USE_EWALD"] = "1"; 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["PME_ORDER"] = cu.intToString(PmeOrder);
pmeDefines["NUM_ATOMS"] = cu.intToString(numParticles); pmeDefines["NUM_ATOMS"] = cu.intToString(numParticles);
pmeDefines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms()); pmeDefines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
...@@ -1510,111 +1571,121 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon ...@@ -1510,111 +1571,121 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
if (cu.getUseDoublePrecision()) if (cu.getUseDoublePrecision())
pmeDefines["USE_DOUBLE_PRECISION"] = "1"; pmeDefines["USE_DOUBLE_PRECISION"] = "1";
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaKernelSources::pme, pmeDefines); CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaKernelSources::pme, pmeDefines);
pmeGridIndexKernel = cu.getKernel(module, "findAtomGridIndex"); bool useCpuPme = false;
pmeSpreadChargeKernel = cu.getKernel(module, "gridSpreadCharge"); if (useCpuPme) {
pmeConvolutionKernel = cu.getKernel(module, "reciprocalConvolution"); cpuPme = new CpuPme(gridSizeX, gridSizeY, gridSizeZ, numParticles, alpha);
pmeInterpolateForceKernel = cu.getKernel(module, "gridInterpolateForce"); CUfunction addForcesKernel = cu.getKernel(module, "addForces");
pmeEvalEnergyKernel = cu.getKernel(module, "gridEvaluateEnergy"); pmeio = new PmeIO(cu, addForcesKernel);
pmeFinishSpreadChargeKernel = cu.getKernel(module, "finishSpreadCharge"); cu.addPreComputation(new PmePreComputation(cu, *cpuPme, *pmeio));
cuFuncSetCacheConfig(pmeSpreadChargeKernel, CU_FUNC_CACHE_PREFER_L1); cu.addPostComputation(new PmePostComputation(*cpuPme, *pmeio));
cuFuncSetCacheConfig(pmeInterpolateForceKernel, CU_FUNC_CACHE_PREFER_L1); }
else {
// Create required data structures. pmeGridIndexKernel = cu.getKernel(module, "findAtomGridIndex");
pmeSpreadChargeKernel = cu.getKernel(module, "gridSpreadCharge");
int elementSize = (cu.getUseDoublePrecision() ? sizeof(double) : sizeof(float)); pmeConvolutionKernel = cu.getKernel(module, "reciprocalConvolution");
pmeInterpolateForceKernel = cu.getKernel(module, "gridInterpolateForce");
directPmeGrid = new CudaArray(cu, gridSizeX*gridSizeY*gridSizeZ, cu.getComputeCapability() >= 2.0 ? elementSize : sizeof(long long), "originalPmeGrid"); pmeEvalEnergyKernel = cu.getKernel(module, "gridEvaluateEnergy");
reciprocalPmeGrid = new CudaArray(cu, gridSizeX*gridSizeY*(gridSizeZ/2+1), 2*elementSize, "reciprocalPmeGrid"); pmeFinishSpreadChargeKernel = cu.getKernel(module, "finishSpreadCharge");
cuFuncSetCacheConfig(pmeSpreadChargeKernel, CU_FUNC_CACHE_PREFER_L1);
cu.addAutoclearBuffer(*directPmeGrid); cuFuncSetCacheConfig(pmeInterpolateForceKernel, CU_FUNC_CACHE_PREFER_L1);
pmeBsplineModuliX = new CudaArray(cu, gridSizeX, elementSize, "pmeBsplineModuliX"); // Create required data structures.
pmeBsplineModuliY = new CudaArray(cu, gridSizeY, elementSize, "pmeBsplineModuliY");
pmeBsplineModuliZ = new CudaArray(cu, gridSizeZ, elementSize, "pmeBsplineModuliZ"); int elementSize = (cu.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
pmeAtomRange = CudaArray::create<int>(cu, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
pmeAtomGridIndex = CudaArray::create<int2>(cu, numParticles, "pmeAtomGridIndex"); directPmeGrid = new CudaArray(cu, gridSizeX*gridSizeY*gridSizeZ, cu.getComputeCapability() >= 2.0 ? elementSize : sizeof(long long), "originalPmeGrid");
sort = new CudaSort(cu, new SortTrait(), cu.getNumAtoms()); reciprocalPmeGrid = new CudaArray(cu, gridSizeX*gridSizeY*(gridSizeZ/2+1), 2*elementSize, "reciprocalPmeGrid");
cufftResult result = cufftPlan3d(&fftForward, gridSizeX, gridSizeY, gridSizeZ, cu.getUseDoublePrecision() ? CUFFT_D2Z : CUFFT_R2C); cu.addAutoclearBuffer(*directPmeGrid);
if (result != CUFFT_SUCCESS)
throw OpenMMException("Error initializing FFT: "+cu.intToString(result)); pmeBsplineModuliX = new CudaArray(cu, gridSizeX, elementSize, "pmeBsplineModuliX");
result = cufftPlan3d(&fftBackward, gridSizeX, gridSizeY, gridSizeZ, cu.getUseDoublePrecision() ? CUFFT_Z2D : CUFFT_C2R); pmeBsplineModuliY = new CudaArray(cu, gridSizeY, elementSize, "pmeBsplineModuliY");
if (result != CUFFT_SUCCESS) pmeBsplineModuliZ = new CudaArray(cu, gridSizeZ, elementSize, "pmeBsplineModuliZ");
throw OpenMMException("Error initializing FFT: "+cu.intToString(result)); pmeAtomRange = CudaArray::create<int>(cu, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
pmeAtomGridIndex = CudaArray::create<int2>(cu, numParticles, "pmeAtomGridIndex");
cufftSetCompatibilityMode(fftForward, CUFFT_COMPATIBILITY_NATIVE); sort = new CudaSort(cu, new SortTrait(), cu.getNumAtoms());
cufftSetCompatibilityMode(fftBackward, CUFFT_COMPATIBILITY_NATIVE);
cufftResult result = cufftPlan3d(&fftForward, gridSizeX, gridSizeY, gridSizeZ, cu.getUseDoublePrecision() ? CUFFT_D2Z : CUFFT_R2C);
if (result != CUFFT_SUCCESS)
throw OpenMMException("Error initializing FFT: "+cu.intToString(result));
result = cufftPlan3d(&fftBackward, gridSizeX, gridSizeY, gridSizeZ, cu.getUseDoublePrecision() ? CUFFT_Z2D : CUFFT_C2R);
if (result != CUFFT_SUCCESS)
throw OpenMMException("Error initializing FFT: "+cu.intToString(result));
cufftSetCompatibilityMode(fftForward, CUFFT_COMPATIBILITY_NATIVE);
cufftSetCompatibilityMode(fftBackward, CUFFT_COMPATIBILITY_NATIVE);
hasInitializedFFT = true;
// 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];
}
hasInitializedFFT = true; // Differentiate.
// Initialize the b-spline moduli. ddata[0] = -data[0];
for (int i = 1; i < PmeOrder; i++)
int maxSize = max(max(gridSizeX, gridSizeY), gridSizeZ); ddata[i] = data[i-1]-data[i];
vector<double> data(PmeOrder); double div = 1.0/(PmeOrder-1);
vector<double> ddata(PmeOrder); data[PmeOrder-1] = 0.0;
vector<double> bsplines_data(maxSize); for (int i = 1; i < (PmeOrder-1); i++)
data[PmeOrder-1] = 0.0; data[PmeOrder-i-1] = div*(i*data[PmeOrder-i-2]+(PmeOrder-i)*data[PmeOrder-i-1]);
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]; data[0] = div*data[0];
} for (int i = 0; i < maxSize; i++)
bsplines_data[i] = 0.0;
// Differentiate. for (int i = 1; i <= PmeOrder; i++)
bsplines_data[i] = data[i-1];
ddata[0] = -data[0];
for (int i = 1; i < PmeOrder; i++) // Evaluate the actual bspline moduli for X/Y/Z.
ddata[i] = data[i-1]-data[i];
double div = 1.0/(PmeOrder-1); for(int dim = 0; dim < 3; dim++) {
data[PmeOrder-1] = 0.0; int ndata = (dim == 0 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
for (int i = 1; i < (PmeOrder-1); i++) vector<double> moduli(ndata);
data[PmeOrder-i-1] = div*(i*data[PmeOrder-i-2]+(PmeOrder-i)*data[PmeOrder-i-1]); for (int i = 0; i < ndata; i++) {
data[0] = div*data[0]; double sc = 0.0;
for (int i = 0; i < maxSize; i++) double ss = 0.0;
bsplines_data[i] = 0.0; for (int j = 0; j < ndata; j++) {
for (int i = 1; i <= PmeOrder; i++) double arg = (2.0*M_PI*i*j)/ndata;
bsplines_data[i] = data[i-1]; sc += bsplines_data[j]*cos(arg);
ss += bsplines_data[j]*sin(arg);
// Evaluate the actual bspline moduli for X/Y/Z. }
moduli[i] = sc*sc+ss*ss;
for(int dim = 0; dim < 3; dim++) {
int ndata = (dim == 0 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
vector<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] = sc*sc+ss*ss;
}
for (int i = 0; i < ndata; i++)
if (moduli[i] < 1.0e-7)
moduli[i] = (moduli[i-1]+moduli[i+1])*0.5;
if (cu.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++) for (int i = 0; i < ndata; i++)
modulif[i] = (float) moduli[i]; if (moduli[i] < 1.0e-7)
if (dim == 0) moduli[i] = (moduli[i-1]+moduli[i+1])*0.5;
pmeBsplineModuliX->upload(modulif); if (cu.getUseDoublePrecision()) {
else if (dim == 1) if (dim == 0)
pmeBsplineModuliY->upload(modulif); pmeBsplineModuliX->upload(moduli);
else else if (dim == 1)
pmeBsplineModuliZ->upload(modulif); 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);
}
} }
} }
} }
...@@ -1654,13 +1725,14 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon ...@@ -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) { 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()}; void* sumsArgs[] = {&cu.getEnergyBuffer().getDevicePointer(), &cu.getPosq().getDevicePointer(), &cosSinSums->getDevicePointer(), cu.getPeriodicBoxSizePointer()};
cu.executeKernel(ewaldSumsKernel, sumsArgs, cosSinSums->getSize()); cu.executeKernel(ewaldSumsKernel, sumsArgs, cosSinSums->getSize());
void* forcesArgs[] = {&cu.getForce().getDevicePointer(), &cu.getPosq().getDevicePointer(), &cosSinSums->getDevicePointer(), cu.getPeriodicBoxSizePointer()}; void* forcesArgs[] = {&cu.getForce().getDevicePointer(), &cu.getPosq().getDevicePointer(), &cosSinSums->getDevicePointer(), cu.getPeriodicBoxSizePointer()};
cu.executeKernel(ewaldForcesKernel, forcesArgs, cu.getNumAtoms()); 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()}; void* gridIndexArgs[] = {&cu.getPosq().getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxSizePointer(), cu.getInvPeriodicBoxSizePointer()};
cu.executeKernel(pmeGridIndexKernel, gridIndexArgs, cu.getNumAtoms()); cu.executeKernel(pmeGridIndexKernel, gridIndexArgs, cu.getNumAtoms());
...@@ -1699,7 +1771,6 @@ double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeF ...@@ -1699,7 +1771,6 @@ double CudaCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeF
cu.executeKernel(pmeInterpolateForceKernel, interpolateArgs, cu.getNumAtoms(), 128); cu.executeKernel(pmeInterpolateForceKernel, interpolateArgs, cu.getNumAtoms(), 128);
} }
double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
if (dispersionCoefficient != 0.0 && includeDirect) { if (dispersionCoefficient != 0.0 && includeDirect) {
double4 boxSize = cu.getPeriodicBoxSize(); double4 boxSize = cu.getPeriodicBoxSize();
energy += dispersionCoefficient/(boxSize.x*boxSize.y*boxSize.z); energy += dispersionCoefficient/(boxSize.x*boxSize.y*boxSize.z);
......
platforms/cuda/src/CudaKernels.h
View file @ 932a61b6
...@@ -34,6 +34,7 @@ ...@@ -34,6 +34,7 @@
#include "CudaSort.h" #include "CudaSort.h"
#include "openmm/kernels.h" #include "openmm/kernels.h"
#include "openmm/System.h" #include "openmm/System.h"
#include "CpuPme.h"
#include <cufft.h> #include <cufft.h>
namespace OpenMM { namespace OpenMM {
...@@ -557,7 +558,7 @@ class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel { ...@@ -557,7 +558,7 @@ class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public: public:
CudaCalcNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcNonbondedForceKernel(name, platform), 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), 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(); ~CudaCalcNonbondedForceKernel();
/** /**
...@@ -596,6 +597,9 @@ private: ...@@ -596,6 +597,9 @@ private:
const char* getMaxValue() const {return "make_int2(INT_MAX, INT_MAX)";} const char* getMaxValue() const {return "make_int2(INT_MAX, INT_MAX)";}
const char* getSortKey() const {return "value.y";} const char* getSortKey() const {return "value.y";}
}; };
class PmeIO;
class PmePreComputation;
class PmePostComputation;
CudaContext& cu; CudaContext& cu;
bool hasInitializedFFT; bool hasInitializedFFT;
CudaArray* sigmaEpsilon; CudaArray* sigmaEpsilon;
...@@ -609,6 +613,8 @@ private: ...@@ -609,6 +613,8 @@ private:
CudaArray* pmeAtomRange; CudaArray* pmeAtomRange;
CudaArray* pmeAtomGridIndex; CudaArray* pmeAtomGridIndex;
CudaSort* sort; CudaSort* sort;
CpuPme* cpuPme;
PmeIO* pmeio;
cufftHandle fftForward; cufftHandle fftForward;
cufftHandle fftBackward; cufftHandle fftBackward;
CUfunction ewaldSumsKernel; CUfunction ewaldSumsKernel;
......
platforms/cuda/src/kernels/pme.cu
View file @ 932a61b6
...@@ -266,8 +266,18 @@ void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __ ...@@ -266,8 +266,18 @@ void gridInterpolateForce(const real4* __restrict__ posq, unsigned long long* __
} }
} }
real q = pos.w*EPSILON_FACTOR; real q = pos.w*EPSILON_FACTOR;
forceBuffers[atom] += static_cast<unsigned long long>((long long) (-q*force.x*GRID_SIZE_X*invPeriodicBoxSize.x*0x100000000)); forceBuffers[atom] += static_cast<unsigned long long>((long long) (-q*force.x*GRID_SIZE_X*invPeriodicBoxSize.x*0x100000000));
forceBuffers[atom+PADDED_NUM_ATOMS] += static_cast<unsigned long long>((long long) (-q*force.y*GRID_SIZE_Y*invPeriodicBoxSize.y*0x100000000)); forceBuffers[atom+PADDED_NUM_ATOMS] += static_cast<unsigned long long>((long long) (-q*force.y*GRID_SIZE_Y*invPeriodicBoxSize.y*0x100000000));
forceBuffers[atom+2*PADDED_NUM_ATOMS] += static_cast<unsigned long long>((long long) (-q*force.z*GRID_SIZE_Z*invPeriodicBoxSize.z*0x100000000)); 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
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