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Commit 7b3a8266 authored by Peter Eastman's avatar Peter Eastman
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Reduced bank conflicts in nonbonded kernel

parent cd6cb66a
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Showing with 50 additions and 22 deletions
platforms/opencl/src/OpenCLNonbondedUtilities.cpp
View file @ 7b3a8266
......@@ -282,7 +282,7 @@ void OpenCLNonbondedUtilities::computeInteractions() {
cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& source, const vector<ParameterInfo>& params, const vector<ParameterInfo>& arguments, bool useExclusions) const {
map<string, string> replacements;
replacements["COMPUTE_INTERACTION"] = source;
int localDataSize = 2*sizeof(cl_float4);
int localDataSize = 7*sizeof(cl_float);
stringstream localData;
for (int i = 0; i < (int) params.size(); i++) {
localData << params[i].getType() << " " << params[i].getName() << ";\n";
......
platforms/opencl/src/kernels/nonbonded_default.cl
View file @ 7b3a8266
#define TILE_SIZE 32
typedef struct {
float4 posq;
float4 force;
float x, y, z;
float q;
float fx, fy, fz;
ATOM_PARAMETER_DATA
} AtomData;
......@@ -42,7 +43,10 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
if (x == y) {
// This tile is on the diagonal.
localData[get_local_id(0)].posq = posq1;
localData[get_local_id(0)].x = posq1.x;
localData[get_local_id(0)].y = posq1.y;
localData[get_local_id(0)].z = posq1.z;
localData[get_local_id(0)].q = posq1.w;
LOAD_LOCAL_PARAMETERS_FROM_1
barrier(CLK_LOCAL_MEM_FENCE);
unsigned int xi = x/TILE_SIZE;
......@@ -55,7 +59,7 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
bool isExcluded = !(excl & 0x1);
#endif
int atom2 = baseLocalAtom+j;
float4 posq2 = localData[atom2].posq;
float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
......@@ -95,10 +99,16 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
if (lasty != y && get_local_id(0) < TILE_SIZE) {
unsigned int j = y + tgx;
localData[get_local_id(0)].posq = posq[j];
float4 tempPosq = posq[j];
localData[get_local_id(0)].x = tempPosq.x;
localData[get_local_id(0)].y = tempPosq.y;
localData[get_local_id(0)].z = tempPosq.z;
localData[get_local_id(0)].q = tempPosq.w;
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
}
localData[get_local_id(0)].force = 0.0f;
localData[get_local_id(0)].fx = 0.0f;
localData[get_local_id(0)].fy = 0.0f;
localData[get_local_id(0)].fz = 0.0f;
barrier(CLK_LOCAL_MEM_FENCE);
// Compute the full set of interactions in this tile.
......@@ -117,7 +127,7 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
bool isExcluded = !(excl & 0x1);
#endif
int atom2 = baseLocalAtom+tj;
float4 posq2 = localData[atom2].posq;
float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
......@@ -135,7 +145,9 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
localData[baseLocalAtom+tj+forceBufferOffset].force.xyz += delta.xyz;
localData[baseLocalAtom+tj+forceBufferOffset].fx += delta.x;
localData[baseLocalAtom+tj+forceBufferOffset].fy += delta.y;
localData[baseLocalAtom+tj+forceBufferOffset].fz += delta.z;
barrier(CLK_LOCAL_MEM_FENCE);
excl >>= 1;
tj = (tj+1)%(TILE_SIZE/2);
......@@ -155,7 +167,8 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
unsigned int offset2 = y + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
#endif
forceBuffers[offset1].xyz = forceBuffers[offset1].xyz+force.xyz+tempBuffer[get_local_id(0)+TILE_SIZE].xyz;
forceBuffers[offset2].xyz = forceBuffers[offset2].xyz+localData[get_local_id(0)].force.xyz+localData[get_local_id(0)+TILE_SIZE].force.xyz;
float4 sum = (float4) (localData[get_local_id(0)].fx+localData[get_local_id(0)+TILE_SIZE].fx, localData[get_local_id(0)].fy+localData[get_local_id(0)+TILE_SIZE].fy, localData[get_local_id(0)].fz+localData[get_local_id(0)+TILE_SIZE].fz, 0.0f);
forceBuffers[offset2].xyz = forceBuffers[offset2].xyz+sum.xyz;
}
lasty = y;
}
......
platforms/opencl/src/kernels/nonbonded_nvidia.cl
View file @ 7b3a8266
#define TILE_SIZE 32
typedef struct {
float4 posq;
float4 force;
float x, y, z;
float q;
float fx, fy, fz;
ATOM_PARAMETER_DATA
} AtomData;
......@@ -43,7 +44,10 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
if (x == y) {
// This tile is on the diagonal.
localData[get_local_id(0)].posq = posq1;
localData[get_local_id(0)].x = posq1.x;
localData[get_local_id(0)].y = posq1.y;
localData[get_local_id(0)].z = posq1.z;
localData[get_local_id(0)].q = posq1.w;
LOAD_LOCAL_PARAMETERS_FROM_1
unsigned int xi = x/TILE_SIZE;
unsigned int tile = xi+xi*PADDED_NUM_ATOMS/TILE_SIZE-xi*(xi+1)/2;
......@@ -55,7 +59,7 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
bool isExcluded = !(excl & 0x1);
#endif
int atom2 = tbx+j;
float4 posq2 = localData[atom2].posq;
float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
......@@ -89,10 +93,16 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
if (lasty != y) {
unsigned int j = y + tgx;
localData[get_local_id(0)].posq = posq[j];
float4 tempPosq = posq[j];
localData[get_local_id(0)].x = tempPosq.x;
localData[get_local_id(0)].y = tempPosq.y;
localData[get_local_id(0)].z = tempPosq.z;
localData[get_local_id(0)].q = tempPosq.w;
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
}
localData[get_local_id(0)].force = 0.0f;
localData[get_local_id(0)].fx = 0.0f;
localData[get_local_id(0)].fy = 0.0f;
localData[get_local_id(0)].fz = 0.0f;
#ifdef USE_CUTOFF
unsigned int flags = interactionFlags[pos];
if (!hasExclusions && flags != 0xFFFFFFFF && flags == 0) {
......@@ -106,7 +116,7 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
if ((flags&(1<<j)) != 0) {
bool isExcluded = false;
int atom2 = tbx+j;
float4 posq2 = localData[atom2].posq;
float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
......@@ -136,8 +146,11 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
tempBuffer[get_local_id(0)].xyz += tempBuffer[get_local_id(0)+4].xyz;
if (tgx % 16 == 0)
tempBuffer[get_local_id(0)].xyz += tempBuffer[get_local_id(0)+8].xyz;
if (tgx == 0)
localData[tbx+j].force.xyz += tempBuffer[get_local_id(0)].xyz + tempBuffer[get_local_id(0)+16].xyz;
if (tgx == 0) {
localData[tbx+j].fx += tempBuffer[get_local_id(0)].x + tempBuffer[get_local_id(0)+16].x;
localData[tbx+j].fy += tempBuffer[get_local_id(0)].y + tempBuffer[get_local_id(0)+16].y;
localData[tbx+j].fz += tempBuffer[get_local_id(0)].z + tempBuffer[get_local_id(0)+16].z;
}
}
}
}
......@@ -160,7 +173,7 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
bool isExcluded = !(excl & 0x1);
#endif
int atom2 = tbx+tj;
float4 posq2 = localData[atom2].posq;
float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*INV_PERIODIC_BOX_SIZE_X+0.5f)*PERIODIC_BOX_SIZE_X;
......@@ -178,7 +191,9 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
localData[tbx+tj].force.xyz += delta.xyz;
localData[tbx+tj].fx += delta.x;
localData[tbx+tj].fy += delta.y;
localData[tbx+tj].fz += delta.z;
excl >>= 1;
tj = (tj + 1) & (TILE_SIZE - 1);
}
......@@ -193,7 +208,7 @@ __kernel void computeNonbonded(__global float4* forceBuffers, __global float* en
unsigned int offset2 = y + tgx + warp*PADDED_NUM_ATOMS;
#endif
forceBuffers[offset1].xyz += force.xyz;
forceBuffers[offset2].xyz += localData[get_local_id(0)].force.xyz;
forceBuffers[offset2] += (float4) (localData[get_local_id(0)].fx, localData[get_local_id(0)].fy, localData[get_local_id(0)].fz, 0.0f);
lasty = y;
}
pos++;
......
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