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Commit 9eb02774 authored by Peter Eastman's avatar Peter Eastman
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Optimizations to Ewald summation

parent cfafe7f2
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Showing with 54 additions and 74 deletions
platforms/cuda/src/kernels/cudatypes.h
View file @ 9eb02774
......@@ -337,7 +337,6 @@ struct cudaGmxSimulation {
float collisionProbability; // Collision probability for Andersen thermostat
float2* pObcData; // Pointer to fixed Born data
float2* pAttr; // Pointer to additional atom attributes (sig, eps)
float2* pEwaldEikr; // Pointer to exponents of reciprocal vectors and atom coordinates (ewald)
float2* pEwaldCosSinSum; // Pointer to the cos/sin sums (ewald)
unsigned int bonds; // Number of bonds
int4* pBondID; // Bond atom and output buffer IDs
......
platforms/cuda/src/kernels/gpu.cpp
View file @ 9eb02774
......@@ -432,8 +432,6 @@ void gpuSetEwaldParameters(gpuContext gpu)//, float alphaEwald, int kmax )
gpu->sim.alphaEwald = alpha;
gpu->sim.factorEwald = -1 / (4*alpha*alpha);
gpu->sim.kmax = 20+1;
gpu->psEwaldEikr = new CUDAStream<float2>(gpu->sim.atoms*gpu->sim.kmax*3, 1, "EwaldEikr");
gpu->sim.pEwaldEikr = gpu->psEwaldEikr->_pDevStream[0];
gpu->psEwaldCosSinSum = new CUDAStream<float2>((gpu->sim.kmax*2-1) * (gpu->sim.kmax*2-1) * (gpu->sim.kmax*2-1), 1, "EwaldCosSinSum");
gpu->sim.pEwaldCosSinSum = gpu->psEwaldCosSinSum->_pDevStream[0];
}
......@@ -1274,7 +1272,6 @@ void* gpuInit(int numAtoms)
gpu->psRbDihedralParameter2 = NULL;
gpu->psLJ14ID = NULL;
gpu->psLJ14Parameter = NULL;
gpu->psEwaldEikr = NULL;
gpu->psEwaldCosSinSum = NULL;
gpu->psShakeID = NULL;
gpu->psShakeParameter = NULL;
......@@ -1404,11 +1401,8 @@ void gpuShutDown(gpuContext gpu)
delete gpu->psxVector4;
delete gpu->psvVector4;
delete gpu->psSigEps2;
if (gpu->psEwaldEikr != NULL)
{
delete gpu->psEwaldEikr;
if (gpu->psEwaldCosSinSum != NULL)
delete gpu->psEwaldCosSinSum;
}
delete gpu->psObcData;
delete gpu->psObcChain;
delete gpu->psBornForce;
......
platforms/cuda/src/kernels/gputypes.h
View file @ 9eb02774
......@@ -86,7 +86,6 @@ struct _gpuContext {
CUDAStream<float4>* psxVector4;
CUDAStream<float4>* psvVector4;
CUDAStream<float2>* psSigEps2;
CUDAStream<float2>* psEwaldEikr;
CUDAStream<float2>* psEwaldCosSinSum;
CUDAStream<float2>* psObcData;
CUDAStream<float>* psObcChain;
......
platforms/cuda/src/kernels/kCalculateCDLJEwaldFastReciprocal.h
View file @ 9eb02774
......@@ -24,6 +24,11 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
/**
* This file contains the kernel for evaluating nonbonded forces using the
* Ewald summation method (Reciprocal space summation).
*/
/* Define multiply operations for floats */
__device__ float2 MultofFloat2(float2 a, float2 b)
......@@ -42,50 +47,9 @@ __device__ float2 ConjMultofFloat2(float2 a, float2 b)
return c;
}
#define EIR(x, y, z) cSim.pEwaldEikr[(x)+(y)*cSim.kmax+(z)*cSim.kmax*3]
__global__ void kCalculateEwaldFastEikr_kernel()
{
int kmax = cSim.kmax;
float4 apos;
unsigned int atom = threadIdx.x + blockIdx.x * blockDim.x;
while (atom < cSim.atoms)
{
apos = cSim.pPosq[atom];
//generic form of the array
// pEikr[ atomID*kmax*3 + k*3 + m]
// k = 0, explicitly
for(unsigned int m = 0; (m < 3); m++) {
EIR(atom, 0, m).x = 1;
EIR(atom, 0, m).y = 0;
}
// k = 1, explicitly
EIR(atom, 1, 0).x = cos(apos.x*cSim.recipBoxSizeX);
EIR(atom, 1, 0).y = sin(apos.x*cSim.recipBoxSizeX);
EIR(atom, 1, 1).x = cos(apos.y*cSim.recipBoxSizeY);
EIR(atom, 1, 1).y = sin(apos.y*cSim.recipBoxSizeY);
EIR(atom, 1, 2).x = cos(apos.z*cSim.recipBoxSizeZ);
EIR(atom, 1, 2).y = sin(apos.z*cSim.recipBoxSizeZ);
// k > 1, by recursion
for(unsigned int k=2; (k<kmax); k++) {
for(unsigned int m=0; (m<3); m++) {
EIR(atom, k, m) = MultofFloat2(EIR(atom, k-1, m), EIR(atom, 1, m));
}
}
atom += blockDim.x * gridDim.x;
}
}
/**
* Precompute the cosine and sine sums which appear in each force term.
*/
__global__ void kCalculateEwaldFastCosSinSums_kernel()
{
......@@ -94,27 +58,42 @@ __global__ void kCalculateEwaldFastCosSinSums_kernel()
unsigned int index = threadIdx.x + blockIdx.x * blockDim.x;
while (index < totalK)
{
// Find the wave vector (kx, ky, kz) this index corresponds to.
int rx = index/(ksize*ksize);
int remainder = index - rx*ksize*ksize;
int ry = remainder/ksize;
int rz = remainder - ry*ksize - cSim.kmax + 1;
ry += -cSim.kmax + 1;
float kx = rx*cSim.recipBoxSizeX;
float ky = ry*cSim.recipBoxSizeY;
float kz = rz*cSim.recipBoxSizeZ;
// Compute the sum for this wave vector.
float2 sum = make_float2(0.0f, 0.0f);
for (int atom = 0; atom < cSim.atoms; atom++)
{
float2 tab_xy = (ry >= 0 ? MultofFloat2(EIR(atom, rx, 0), EIR(atom, ry, 1)) :
ConjMultofFloat2(EIR(atom, rx, 0), EIR(atom, -ry, 1)));
float charge = cSim.pPosq[atom].w;
float2 structureFactor = (rz >= 0 ? MultofFloat2(tab_xy, EIR(atom, rz, 2)) :
ConjMultofFloat2(tab_xy, EIR(atom, -rz, 2)));
sum.x += charge*structureFactor.x;
sum.y += charge*structureFactor.y;
float4 apos = cSim.pPosq[atom];
float phase = apos.x*kx;
float2 structureFactor = make_float2(cos(phase), sin(phase));
phase = apos.y*ky;
structureFactor = MultofFloat2(structureFactor, make_float2(cos(phase), sin(phase)));
phase = apos.z*kz;
structureFactor = MultofFloat2(structureFactor, make_float2(cos(phase), sin(phase)));
sum.x += apos.w*structureFactor.x;
sum.y += apos.w*structureFactor.y;
}
cSim.pEwaldCosSinSum[index] = sum;
index += blockDim.x * gridDim.x;
}
}
/**
* Compute the reciprocal space part of the Ewald force, using the precomputed sums from the
* previous routine.
*/
__global__ void kCalculateEwaldFastForces_kernel()
{
......@@ -122,8 +101,6 @@ __global__ void kCalculateEwaldFastForces_kernel()
const float epsilon = 1.0;
float recipCoeff = cSim.epsfac*(4*PI/cSim.cellVolume/epsilon);
int lowry = 0;
int lowrz = 1;
const int numRx = cSim.kmax;
const int numRy = cSim.kmax;
const int numRz = cSim.kmax;
......@@ -133,22 +110,32 @@ __global__ void kCalculateEwaldFastForces_kernel()
while (atom < cSim.atoms)
{
float4 force = cSim.pForce4[atom];
float charge = cSim.pPosq[atom].w;
float4 apos = cSim.pPosq[atom];
// Loop over all wave vectors.
int lowry = 0;
int lowrz = 1;
for (int rx = 0; rx < numRx; rx++) {
float kx = rx * cSim.recipBoxSizeX;
for (int ry = lowry; ry < numRy; ry++) {
float ky = ry * cSim.recipBoxSizeY;
float2 tab_xy = (ry >= 0 ? MultofFloat2(EIR(atom, rx, 0), EIR(atom, ry, 1)) :
ConjMultofFloat2(EIR(atom, rx, 0), EIR(atom, -ry, 1)));
float phase = apos.x*kx;
float2 tab_xy = make_float2(cos(phase), sin(phase));
phase = apos.y*ky;
tab_xy = MultofFloat2(tab_xy, make_float2(cos(phase), sin(phase)));
for (int rz = lowrz; rz < numRz; rz++) {
float kz = rz * cSim.recipBoxSizeZ;
// Compute the force contribution of this wave vector.
int index = rx*(numRy*2-1)*(numRz*2-1) + (ry+numRy-1)*(numRz*2-1) + (rz+numRz-1);
float k2 = kx*kx + ky*ky + kz*kz;
float ak = exp(k2*cSim.factorEwald) / k2;
float2 structureFactor = (rz >= 0 ? MultofFloat2(tab_xy, EIR(atom, rz, 2)) :
ConjMultofFloat2(tab_xy, EIR(atom, -rz, 2)));
phase = apos.z*kz;
float2 structureFactor = MultofFloat2(tab_xy, make_float2(cos(phase), sin(phase)));
float2 cosSinSum = cSim.pEwaldCosSinSum[index];
float dEdR = ak * charge * (cosSinSum.x*structureFactor.y - cosSinSum.y*structureFactor.x);
float dEdR = ak * apos.w * (cosSinSum.x*structureFactor.y - cosSinSum.y*structureFactor.x);
force.x += 2 * recipCoeff * dEdR * kx;
force.y += 2 * recipCoeff * dEdR * ky;
force.z += 2 * recipCoeff * dEdR * kz;
......@@ -157,6 +144,9 @@ __global__ void kCalculateEwaldFastForces_kernel()
lowry = 1 - numRy;
}
}
// Record the force on the atom.
cSim.pForce4[atom] = force;
atom += blockDim.x * gridDim.x;
}
......
platforms/cuda/src/kernels/kCalculateCDLJForces.cu
View file @ 9eb02774
......@@ -212,10 +212,8 @@ void kCalculateCDLJForces(gpuContext gpu)
}
else
{
// O(N3/2) Ewald summation
kCalculateEwaldFastEikr_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kCalculateEwaldFastEikr");
kCalculateEwaldFastCosSinSums_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>();
// Fast Ewald summation
kCalculateEwaldFastCosSinSums_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block>>>();
LAUNCHERROR("kCalculateEwaldFastCosSinSums");
kCalculateEwaldFastForces_kernel<<<gpu->sim.blocks, gpu->sim.update_threads_per_block>>>();
LAUNCHERROR("kCalculateEwaldFastForces");
......
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