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Commit f2548616 authored by peastman's avatar peastman
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OpenCL platform can use the CPU based PME

parent 3628d973
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Showing with 290 additions and 127 deletions
platforms/cuda/include/CudaPlatform.h
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
......@@ -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
View file @ f2548616
/* -------------------------------------------------------------------------- *
* 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
View file @ f2548616
......@@ -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);
}
......
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