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Commit 592dc5a9 authored by Peter Eastman's avatar Peter Eastman
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Optimizations to PME reciprocal space calculation

parent c08d8a53
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Showing with 86 additions and 52 deletions
platforms/opencl/src/OpenCLFFT3D.cpp
View file @ 592dc5a9
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Portions copyright (c) 2009-2011 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 592dc5a9
......@@ -1149,8 +1149,6 @@ OpenCLCalcNonbondedForceKernel::~OpenCLCalcNonbondedForceKernel() {
delete pmeBsplineModuliZ;
if (pmeBsplineTheta != NULL)
delete pmeBsplineTheta;
if (pmeBsplineDtheta != NULL)
delete pmeBsplineDtheta;
if (pmeAtomRange != NULL)
delete pmeAtomRange;
if (pmeAtomGridIndex != NULL)
......@@ -1273,7 +1271,6 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
pmeBsplineModuliY = new OpenCLArray<cl_float>(cl, gridSizeY, "pmeBsplineModuliY");
pmeBsplineModuliZ = new OpenCLArray<cl_float>(cl, gridSizeZ, "pmeBsplineModuliZ");
pmeBsplineTheta = new OpenCLArray<mm_float4>(cl, PmeOrder*numParticles, "pmeBsplineTheta");
pmeBsplineDtheta = new OpenCLArray<mm_float4>(cl, PmeOrder*numParticles, "pmeBsplineDtheta");
pmeAtomRange = new OpenCLArray<cl_int>(cl, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
pmeAtomGridIndex = new OpenCLArray<mm_int2>(cl, numParticles, "pmeAtomGridIndex");
sort = new OpenCLSort<mm_int2>(cl, cl.getNumAtoms(), "int2", "value.y");
......@@ -1411,9 +1408,8 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
pmeInterpolateForceKernel = cl::Kernel(program, "gridInterpolateForce");
pmeUpdateBsplinesKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
pmeUpdateBsplinesKernel.setArg<cl::Buffer>(1, pmeBsplineTheta->getDeviceBuffer());
pmeUpdateBsplinesKernel.setArg<cl::Buffer>(2, pmeBsplineDtheta->getDeviceBuffer());
pmeUpdateBsplinesKernel.setArg(3, 2*OpenCLContext::ThreadBlockSize*PmeOrder*sizeof(mm_float4), NULL);
pmeUpdateBsplinesKernel.setArg<cl::Buffer>(4, pmeAtomGridIndex->getDeviceBuffer());
pmeUpdateBsplinesKernel.setArg(2, OpenCLContext::ThreadBlockSize*PmeOrder*sizeof(mm_float4), NULL);
pmeUpdateBsplinesKernel.setArg<cl::Buffer>(3, pmeAtomGridIndex->getDeviceBuffer());
pmeAtomRangeKernel.setArg<cl::Buffer>(0, pmeAtomGridIndex->getDeviceBuffer());
pmeAtomRangeKernel.setArg<cl::Buffer>(1, pmeAtomRange->getDeviceBuffer());
pmeAtomRangeKernel.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
......@@ -1429,9 +1425,8 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
pmeConvolutionKernel.setArg<cl::Buffer>(4, pmeBsplineModuliZ->getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(1, cl.getForceBuffers().getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(2, pmeBsplineTheta->getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(3, pmeBsplineDtheta->getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(4, pmeGrid->getDeviceBuffer());
pmeInterpolateForceKernel.setArg<cl::Buffer>(2, pmeGrid->getDeviceBuffer());
pmeInterpolateForceKernel.setArg(5, 2*128*PmeOrder*sizeof(mm_float4), NULL);
if (cl.getSupports64BitGlobalAtomics()) {
pmeFinishSpreadChargeKernel = cl::Kernel(program, "finishSpreadCharge");
pmeFinishSpreadChargeKernel.setArg<cl::Buffer>(0, pmeGrid->getDeviceBuffer());
......@@ -1454,8 +1449,8 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
if (pmeGrid != NULL && cl.getContextIndex() == 0) {
mm_float4 boxSize = cl.getPeriodicBoxSize();
mm_float4 invBoxSize = cl.getInvPeriodicBoxSize();
pmeUpdateBsplinesKernel.setArg<mm_float4>(5, boxSize);
pmeUpdateBsplinesKernel.setArg<mm_float4>(6, invBoxSize);
pmeUpdateBsplinesKernel.setArg<mm_float4>(4, boxSize);
pmeUpdateBsplinesKernel.setArg<mm_float4>(5, invBoxSize);
cl.executeKernel(pmeUpdateBsplinesKernel, cl.getNumAtoms());
if (deviceIsCpu) {
pmeSpreadChargeKernel.setArg<mm_float4>(5, boxSize);
......@@ -1482,9 +1477,9 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
pmeConvolutionKernel.setArg<cl_float>(6, (float) (1.0/(M_PI*boxSize.x*boxSize.y*boxSize.z)));
cl.executeKernel(pmeConvolutionKernel, cl.getNumAtoms());
fft->execFFT(*pmeGrid2, *pmeGrid, false);
pmeInterpolateForceKernel.setArg<mm_float4>(5, boxSize);
pmeInterpolateForceKernel.setArg<mm_float4>(6, invBoxSize);
cl.executeKernel(pmeInterpolateForceKernel, cl.getNumAtoms());
pmeInterpolateForceKernel.setArg<mm_float4>(3, boxSize);
pmeInterpolateForceKernel.setArg<mm_float4>(4, invBoxSize);
cl.executeKernel(pmeInterpolateForceKernel, cl.getNumAtoms(), 128);
}
double energy = ewaldSelfEnergy;
if (dispersionCoefficient != 0.0) {
......
platforms/opencl/src/OpenCLKernels.h
View file @ 592dc5a9
......@@ -475,8 +475,8 @@ private:
class OpenCLCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
OpenCLCalcNonbondedForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcNonbondedForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), sigmaEpsilon(NULL), exceptionParams(NULL), exceptionIndices(NULL), cosSinSums(NULL), pmeGrid(NULL), pmeGrid2(NULL),
pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeBsplineTheta(NULL), pmeBsplineDtheta(NULL), pmeAtomRange(NULL),
hasInitializedKernel(false), cl(cl), sigmaEpsilon(NULL), exceptionParams(NULL), exceptionIndices(NULL), cosSinSums(NULL), pmeGrid(NULL),
pmeGrid2(NULL), pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeBsplineTheta(NULL), pmeAtomRange(NULL),
pmeAtomGridIndex(NULL), sort(NULL), fft(NULL) {
}
~OpenCLCalcNonbondedForceKernel();
......@@ -509,7 +509,6 @@ private:
OpenCLArray<cl_float>* pmeBsplineModuliY;
OpenCLArray<cl_float>* pmeBsplineModuliZ;
OpenCLArray<mm_float4>* pmeBsplineTheta;
OpenCLArray<mm_float4>* pmeBsplineDtheta;
OpenCLArray<cl_int>* pmeAtomRange;
OpenCLArray<mm_int2>* pmeAtomGridIndex;
OpenCLSort<mm_int2>* sort;
......
platforms/opencl/src/kernels/pme.cl
View file @ 592dc5a9
__kernel void updateBsplines(__global float4* posq, __global float4* pmeBsplineTheta, __global float4* pmeBsplineDTheta, __local float4* bsplinesCache, __global int2* pmeAtomGridIndex, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
__kernel void updateBsplines(__global float4* posq, __global float4* pmeBsplineTheta, __local float4* bsplinesCache, __global int2* pmeAtomGridIndex, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
const float4 scale = 1.0f/(PME_ORDER-1);
for (int i = get_global_id(0); i < NUM_ATOMS; i += get_global_size(0)) {
__local float4* data = &bsplinesCache[get_local_id(0)*PME_ORDER];
__local float4* ddata = &bsplinesCache[get_local_id(0)*PME_ORDER + get_local_size(0)*PME_ORDER];
for (int j = 0; j < PME_ORDER; j++) {
data[j] = 0.0f;
ddata[j] = 0.0f;
}
float4 pos = posq[i];
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
......@@ -29,9 +24,6 @@ __kernel void updateBsplines(__global float4* posq, __global float4* pmeBsplineT
data[j-k-1] = div*((dr+(float4) k) *data[j-k-2] + (-dr+(float4) (j-k))*data[j-k-1]);
data[0] = div*(- dr+1.0f)*data[0];
}
ddata[0] = -data[0];
for (int j = 1; j < PME_ORDER; j++)
ddata[j] = data[j-1]-data[j];
data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
for (int j = 1; j < (PME_ORDER-1); j++)
data[PME_ORDER-j-1] = scale*((dr+(float4) j)*data[PME_ORDER-j-2] + (-dr+(float4) (PME_ORDER-j))*data[PME_ORDER-j-1]);
......@@ -39,7 +31,6 @@ __kernel void updateBsplines(__global float4* posq, __global float4* pmeBsplineT
for (int j = 0; j < PME_ORDER; j++) {
data[j].w = pos.w; // Storing the charge here improves cache coherency in the charge spreading kernel
pmeBsplineTheta[i+j*NUM_ATOMS] = data[j];
pmeBsplineDTheta[i+j*NUM_ATOMS] = ddata[j];
}
}
}
......@@ -81,26 +72,52 @@ __kernel void findAtomRangeForGrid(__global int2* pmeAtomGridIndex, __global int
#ifdef SUPPORTS_64_BIT_ATOMICS
#pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable
#define BUFFER_SIZE (PME_ORDER*PME_ORDER*PME_ORDER)
__kernel __attribute__((reqd_work_group_size(BUFFER_SIZE, 1, 1)))
__kernel void gridSpreadCharge(__global float4* posq, __global int2* pmeAtomGridIndex, __global int* pmeAtomRange, __global long* pmeGrid, __global float4* pmeBsplineTheta, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
int ix = get_local_id(0)/(PME_ORDER*PME_ORDER);
int remainder = get_local_id(0)-ix*PME_ORDER*PME_ORDER;
int iy = remainder/PME_ORDER;
int iz = remainder-iy*PME_ORDER;
__local float4 theta[PME_ORDER];
__local float charge[BUFFER_SIZE];
__local int basex[BUFFER_SIZE];
__local int basey[BUFFER_SIZE];
__local int basez[BUFFER_SIZE];
if (ix < PME_ORDER) {
for (int atomIndex = get_group_id(0); atomIndex < NUM_ATOMS; atomIndex += get_num_groups(0)) {
float4 pos = posq[atomIndex];
float atomCharge = pos.w;
float add = atomCharge*pmeBsplineTheta[atomIndex+ix*NUM_ATOMS].x*pmeBsplineTheta[atomIndex+iy*NUM_ATOMS].y*pmeBsplineTheta[atomIndex+iz*NUM_ATOMS].z;
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
int x = (int) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X)+ix;
int y = (int) ((pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y)+iy;
int z = (int) ((pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z)+iz;
x -= (x >= GRID_SIZE_X ? GRID_SIZE_X : 0);
y -= (y >= GRID_SIZE_Y ? GRID_SIZE_Y : 0);
z -= (z >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
atom_add(&pmeGrid[x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z+z], (long) (add*0xFFFFFFFF));
for (int baseIndex = get_group_id(0)*BUFFER_SIZE; baseIndex < NUM_ATOMS; baseIndex += get_num_groups(0)*BUFFER_SIZE) {
// Load the next block of atoms into the buffers.
if (get_local_id(0) < BUFFER_SIZE) {
int atomIndex = baseIndex+get_local_id(0);
if (atomIndex < NUM_ATOMS) {
float4 pos = posq[atomIndex];
charge[get_local_id(0)] = pos.w;
pos.x -= floor(pos.x*invPeriodicBoxSize.x)*periodicBoxSize.x;
pos.y -= floor(pos.y*invPeriodicBoxSize.y)*periodicBoxSize.y;
pos.z -= floor(pos.z*invPeriodicBoxSize.z)*periodicBoxSize.z;
basex[get_local_id(0)] = (int) ((pos.x*invPeriodicBoxSize.x)*GRID_SIZE_X);
basey[get_local_id(0)] = (int) ((pos.y*invPeriodicBoxSize.y)*GRID_SIZE_Y);
basez[get_local_id(0)] = (int) ((pos.z*invPeriodicBoxSize.z)*GRID_SIZE_Z);
}
}
barrier(CLK_LOCAL_MEM_FENCE);
int lastIndex = min(BUFFER_SIZE, NUM_ATOMS-baseIndex);
for (int index = 0; index < lastIndex; index++) {
int atomIndex = index+baseIndex;
if (get_local_id(0) < PME_ORDER)
theta[get_local_id(0)] = pmeBsplineTheta[atomIndex+get_local_id(0)*NUM_ATOMS];
barrier(CLK_LOCAL_MEM_FENCE);
float add = charge[index]*theta[ix].x*theta[iy].y*theta[iz].z;
int x = basex[index]+ix;
int y = basey[index]+iy;
int z = basez[index]+iz;
x -= (x >= GRID_SIZE_X ? GRID_SIZE_X : 0);
y -= (y >= GRID_SIZE_Y ? GRID_SIZE_Y : 0);
z -= (z >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
atom_add(&pmeGrid[x*GRID_SIZE_Y*GRID_SIZE_Z+y*GRID_SIZE_Z+z], (long) (add*0xFFFFFFFF));
}
}
}
}
......@@ -203,7 +220,11 @@ __kernel void reciprocalConvolution(__global float2* pmeGrid, __global float* en
energyBuffer[get_global_id(0)] += 0.5f*energy;
}
__kernel void gridInterpolateForce(__global float4* posq, __global float4* forceBuffers, __global float4* pmeBsplineTheta, __global float4* pmeBsplineDTheta, __global float2* pmeGrid, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
__kernel __attribute__((reqd_work_group_size(128, 1, 1)))
__kernel void gridInterpolateForce(__global float4* posq, __global float4* forceBuffers, __global float2* pmeGrid, float4 periodicBoxSize, float4 invPeriodicBoxSize, __local float4* bsplinesCache) {
const float4 scale = 1.0f/(PME_ORDER-1);
__local float4* data = &bsplinesCache[get_local_id(0)*PME_ORDER];
__local float4* ddata = &bsplinesCache[get_local_id(0)*PME_ORDER + get_local_size(0)*PME_ORDER];
for (int atom = get_global_id(0); atom < NUM_ATOMS; atom += get_global_size(0)) {
float4 force = 0.0f;
float4 pos = posq[atom];
......@@ -216,26 +237,45 @@ __kernel void gridInterpolateForce(__global float4* posq, __global float4* force
int4 gridIndex = (int4) (((int) t.x) % GRID_SIZE_X,
((int) t.y) % GRID_SIZE_Y,
((int) t.z) % GRID_SIZE_Z, 0);
// Since we need the full set of thetas, it's faster to compute them here than load them
// from global memory.
float4 dr = (float4) (t.x-(int) t.x, t.y-(int) t.y, t.z-(int) t.z, 0.0f);
data[PME_ORDER-1] = 0.0f;
data[1] = dr;
data[0] = 1.0f-dr;
for (int j = 3; j < PME_ORDER; j++) {
float div = 1.0f/(j-1.0f);
data[j-1] = div*dr*data[j-2];
for (int k = 1; k < (j-1); k++)
data[j-k-1] = div*((dr+(float4) k) *data[j-k-2] + (-dr+(float4) (j-k))*data[j-k-1]);
data[0] = div*(- dr+1.0f)*data[0];
}
ddata[0] = -data[0];
for (int j = 1; j < PME_ORDER; j++)
ddata[j] = data[j-1]-data[j];
data[PME_ORDER-1] = scale*dr*data[PME_ORDER-2];
for (int j = 1; j < (PME_ORDER-1); j++)
data[PME_ORDER-j-1] = scale*((dr+(float4) j)*data[PME_ORDER-j-2] + (-dr+(float4) (PME_ORDER-j))*data[PME_ORDER-j-1]);
data[0] = scale*(-dr+1.0f)*data[0];
// Compute the force on this atom.
for (int ix = 0; ix < PME_ORDER; ix++) {
int xindex = gridIndex.x+ix;
xindex -= (xindex >= GRID_SIZE_X ? GRID_SIZE_X : 0);
float tx = pmeBsplineTheta[atom+ix*NUM_ATOMS].x;
float dtx = pmeBsplineDTheta[atom+ix*NUM_ATOMS].x;
for (int iy = 0; iy < PME_ORDER; iy++) {
int yindex = gridIndex.y+iy;
yindex -= (yindex >= GRID_SIZE_Y ? GRID_SIZE_Y : 0);
float ty = pmeBsplineTheta[atom+iy*NUM_ATOMS].y;
float dty = pmeBsplineDTheta[atom+iy*NUM_ATOMS].y;
for (int iz = 0; iz < PME_ORDER; iz++) {
int zindex = gridIndex.z+iz;
zindex -= (zindex >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
float tz = pmeBsplineTheta[atom+iz*NUM_ATOMS].z;
float dtz = pmeBsplineDTheta[atom+iz*NUM_ATOMS].z;
int index = xindex*GRID_SIZE_Y*GRID_SIZE_Z + yindex*GRID_SIZE_Z + zindex;
float gridvalue = pmeGrid[index].x;
force.x += dtx*ty*tz*gridvalue;
force.y += tx*dty*tz*gridvalue;
force.z += tx*ty*dtz*gridvalue;
force.x += ddata[ix].x*data[iy].y*data[iz].z*gridvalue;
force.y += data[ix].x*ddata[iy].y*data[iz].z*gridvalue;
force.z += data[ix].x*data[iy].y*ddata[iz].z*gridvalue;
}
}
}
......
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