Skip to content

GitLab

"platforms/vscode:/vscode.git/clone" did not exist on "d9941f475d4a2d64e7a5c8573ee143b1d9694ce4"
Commit a8fe9cea authored by Peter Eastman's avatar Peter Eastman
Browse files

Continuing changes to reduce memory use for large systems

parent b0d2357c
Hide whitespace changes
Inline Side-by-side
Showing with 155 additions and 88 deletions
platforms/opencl/src/OpenCLContext.h
View file @ a8fe9cea
......@@ -84,6 +84,13 @@ struct mm_float16 {
s8(s8), s9(s9), s10(s10), s11(s11), s12(s12), s13(s13), s14(s14), s15(15) {
}
};
struct mm_ushort2 {
cl_ushort x, y;
mm_ushort2() {
}
mm_ushort2(cl_ushort x, cl_ushort y) : x(x), y(y) {
}
};
struct mm_int2 {
cl_int x, y;
mm_int2() {
......
platforms/opencl/src/OpenCLNonbondedUtilities.cpp
View file @ a8fe9cea
......@@ -200,7 +200,7 @@ void OpenCLNonbondedUtilities::initialize(const System& system) {
// Create data structures for the neighbor list.
if (useCutoff) {
interactingTiles = new OpenCLArray<cl_uint>(context, numTiles, "interactingTiles");
interactingTiles = new OpenCLArray<mm_ushort2>(context, numTiles, "interactingTiles");
interactionFlags = new OpenCLArray<cl_uint>(context, numTiles, "interactionFlags");
interactionCount = new OpenCLArray<cl_uint>(context, 1, "interactionCount");
blockCenter = new OpenCLArray<mm_float4>(context, numAtomBlocks, "blockCenter");
......@@ -230,6 +230,7 @@ void OpenCLNonbondedUtilities::initialize(const System& system) {
findInteractingBlocksKernel.setArg<cl::Buffer>(4, blockBoundingBox->getDeviceBuffer());
findInteractingBlocksKernel.setArg<cl::Buffer>(5, interactionCount->getDeviceBuffer());
findInteractingBlocksKernel.setArg<cl::Buffer>(6, interactingTiles->getDeviceBuffer());
findInteractingBlocksKernel.setArg<cl::Buffer>(7, context.getPosq().getDeviceBuffer());
findInteractionsWithinBlocksKernel = cl::Kernel(interactingBlocksProgram, "findInteractionsWithinBlocks");
findInteractionsWithinBlocksKernel.setArg<cl_float>(0, (cl_float) (cutoff*cutoff));
findInteractionsWithinBlocksKernel.setArg<cl::Buffer>(3, context.getPosq().getDeviceBuffer());
......
platforms/opencl/src/OpenCLNonbondedUtilities.h
View file @ a8fe9cea
......@@ -148,7 +148,7 @@ public:
/**
* Get the array containing tiles with interactions.
*/
OpenCLArray<cl_uint>& getInteractingTiles() {
OpenCLArray<mm_ushort2>& getInteractingTiles() {
return *interactingTiles;
}
/**
......@@ -197,7 +197,7 @@ private:
OpenCLArray<cl_uint>* exclusions;
OpenCLArray<cl_uint>* exclusionIndices;
OpenCLArray<cl_uint>* exclusionRowIndices;
OpenCLArray<cl_uint>* interactingTiles;
OpenCLArray<mm_ushort2>* interactingTiles;
OpenCLArray<cl_uint>* interactionFlags;
OpenCLArray<cl_uint>* interactionCount;
OpenCLArray<mm_float4>* blockCenter;
......
platforms/opencl/src/kernels/customGBEnergyN2_default.cl
View file @ a8fe9cea
......@@ -11,7 +11,7 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
__global float4* posq, __local float4* local_posq, __global unsigned int* exclusions, __global unsigned int* exclusionIndices,
__global unsigned int* exclusionRowIndices, __local float4* tempForceBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
#else
unsigned int numTiles
#endif
......@@ -30,9 +30,9 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -207,8 +207,8 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
STORE_DERIVATIVES_1
STORE_DERIVATIVES_2
}
lasty = y;
}
lasty = y;
pos++;
}
energyBuffer[get_global_id(0)] += energy;
......
platforms/opencl/src/kernels/customGBEnergyN2_nvidia.cl
View file @ a8fe9cea
......@@ -11,7 +11,7 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
__global float4* posq, __local float4* local_posq, __global unsigned int* exclusions, __global unsigned int* exclusionIndices,
__global unsigned int* exclusionRowIndices, __local float4* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
#else
unsigned int numTiles
#endif
......@@ -31,9 +31,9 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -195,8 +195,8 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
forceBuffers[offset2].xyz += local_force[get_local_id(0)].xyz;
STORE_DERIVATIVES_1
STORE_DERIVATIVES_2
lasty = y;
}
lasty = y;
pos++;
}
energyBuffer[get_global_id(0)] += energy;
......
platforms/opencl/src/kernels/customGBValueN2_default.cl
View file @ a8fe9cea
......@@ -9,7 +9,7 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
__global unsigned int* exclusionIndices, __global unsigned int* exclusionRowIndices, __global float* global_value, __local float* local_value,
__local float* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
#else
unsigned int numTiles
#endif
......@@ -27,9 +27,9 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -196,8 +196,8 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
global_value[offset1] += value+tempBuffer[get_local_id(0)+TILE_SIZE];
global_value[offset2] += local_value[get_local_id(0)]+local_value[get_local_id(0)+TILE_SIZE];
}
lasty = y;
}
lasty = y;
pos++;
}
}
platforms/opencl/src/kernels/customGBValueN2_nvidia.cl
View file @ a8fe9cea
......@@ -9,7 +9,7 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
__global unsigned int* exclusionIndices, __global unsigned int* exclusionRowIndices, __global float* global_value, __local float* local_value,
__local float* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
#else
unsigned int numTiles
#endif
......@@ -29,9 +29,9 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -233,8 +233,8 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
#endif
global_value[offset1] += value;
global_value[offset2] += local_value[get_local_id(0)];
lasty = y;
}
lasty = y;
pos++;
}
}
platforms/opencl/src/kernels/findInteractingBlocks.cl
View file @ a8fe9cea
#pragma OPENCL EXTENSION cl_khr_global_int32_base_atomics : enable
#pragma OPENCL EXTENSION cl_khr_byte_addressable_store : enable
#define TILE_SIZE 32
#define GROUP_SIZE 64
#define BUFFER_GROUPS 4
......@@ -44,31 +45,34 @@ __kernel void findBlockBounds(int numAtoms, float4 periodicBoxSize, float4 invPe
* This is called by findBlocksWithInteractions(). It compacts the list of blocks and writes them
* to global memory.
*/
void storeInteractionData(__local short2* buffer, __local bool* valid, __local int* sum, __local int* sum2, __local short2* temp, __local int* baseIndex,
__global unsigned int* interactionCount, __global unsigned int* interactingTiles) {
void storeInteractionData(__local ushort2* buffer, __local int* valid, __local short* sum, __local ushort2* temp, __local int* baseIndex,
__global unsigned int* interactionCount, __global ushort2* interactingTiles, float cutoffSquared, float4 periodicBoxSize,
float4 invPeriodicBoxSize, __global float4* posq, __global float4* blockCenter, __global float4* blockBoundingBox) {
// The buffer is full, so we need to compact it and write out results. Start by doing a parallel prefix sum.
for (int i = get_local_id(0); i < BUFFER_SIZE; i += GROUP_SIZE)
sum[i] = (valid[i] ? 1 : 0);
temp[i].x = (valid[i] ? 1 : 0);
barrier(CLK_LOCAL_MEM_FENCE);
int whichBuffer = 0;
for (int offset = 1; offset < BUFFER_SIZE; offset *= 2) {
if (whichBuffer == 0)
for (int i = get_local_id(0); i < BUFFER_SIZE; i += GROUP_SIZE)
sum2[i] = (i < offset ? sum[i] : sum[i]+sum[i-offset]);
temp[i].y = (i < offset ? temp[i].x : temp[i].x+temp[i-offset].x);
else
for (int i = get_local_id(0); i < BUFFER_SIZE; i += GROUP_SIZE)
sum[i] = (i < offset ? sum2[i] : sum2[i]+sum2[i-offset]);
temp[i].x = (i < offset ? temp[i].y : temp[i].y+temp[i-offset].y);
whichBuffer = 1-whichBuffer;
barrier(CLK_LOCAL_MEM_FENCE);
}
if (whichBuffer == 1) {
if (whichBuffer == 0)
for (int i = get_local_id(0); i < BUFFER_SIZE; i += GROUP_SIZE)
sum[i] = sum2[i];
barrier(CLK_LOCAL_MEM_FENCE);
}
sum[i] = temp[i].x;
else
for (int i = get_local_id(0); i < BUFFER_SIZE; i += GROUP_SIZE)
sum[i] = temp[i].y;
barrier(CLK_LOCAL_MEM_FENCE);
// Compact the buffer and store it to global memory.
// Compact the buffer.
for (int i = get_local_id(0); i < BUFFER_SIZE; i += GROUP_SIZE)
if (valid[i]) {
......@@ -77,14 +81,74 @@ void storeInteractionData(__local short2* buffer, __local bool* valid, __local i
}
barrier(CLK_LOCAL_MEM_FENCE);
int numValid = sum[BUFFER_SIZE-1];
if (get_local_id(0) == 0)
*baseIndex = atom_add(interactionCount, numValid);
barrier(CLK_LOCAL_MEM_FENCE);
// Filter the list of tiles by comparing the distance from each atom to the other bounding box.
int tile;
int index = get_local_id(0)&(TILE_SIZE-1);
int group = get_local_id(0)/TILE_SIZE;
__local int* flag = sum;
int lasty = -1;
float4 center, boxSize, pos;
for (tile = 0; tile < numValid; tile++) {
int x = temp[tile].x;
int y = temp[tile].y;
if (x == y) {
tile++;
continue;
}
if (index == 0)
flag[group] = true;
barrier(CLK_LOCAL_MEM_FENCE);
// Load an atom position and the bounding box the other block.
if (group == 0) {
center = blockCenter[x];
boxSize = blockBoundingBox[x];
if (y != lasty)
pos = posq[y*TILE_SIZE+index];
}
else {
if (y != lasty) {
center = blockCenter[y];
boxSize = blockBoundingBox[y];
}
pos = posq[x*TILE_SIZE+index];
}
lasty = y;
// Find the distance of the atom from the bounding box.
float4 delta = pos-center;
#ifdef USE_PERIODIC
delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
#endif
delta = max((float4) 0.0f, fabs(delta)-boxSize);
if (delta.x*delta.x+delta.y*delta.y+delta.z*delta.z < cutoffSquared)
flag[group] = false;
barrier(CLK_LOCAL_MEM_FENCE);
if (flag[0] || flag[1]) {
// This tile contains no interactions.
numValid--;
if (get_local_id(0) == 0)
temp[tile] = temp[numValid];
}
else
tile++;
barrier(CLK_LOCAL_MEM_FENCE);
}
// Store it to global memory.
if (get_local_id(0) == 0)
*baseIndex = atom_add(interactionCount, numValid);
barrier(CLK_LOCAL_MEM_FENCE);
for (int i = get_local_id(0); i < numValid; i += GROUP_SIZE)
interactingTiles[*baseIndex+i] = (temp[i].x<<17)+(temp[i].y<<2);
interactingTiles[*baseIndex+i] = temp[i];
barrier(CLK_LOCAL_MEM_FENCE);
}
......@@ -93,12 +157,11 @@ void storeInteractionData(__local short2* buffer, __local bool* valid, __local i
* mark them as non-interacting.
*/
__kernel void findBlocksWithInteractions(float cutoffSquared, float4 periodicBoxSize, float4 invPeriodicBoxSize, __global float4* blockCenter,
__global float4* blockBoundingBox, __global unsigned int* interactionCount, __global unsigned int* interactingTiles) {
__local short2 buffer[BUFFER_SIZE];
__local bool valid[BUFFER_SIZE];
__local int sum[BUFFER_SIZE];
__local int sum2[BUFFER_SIZE];
__local short2 temp[BUFFER_SIZE];
__global float4* blockBoundingBox, __global unsigned int* interactionCount, __global ushort2* interactingTiles, __global float4* posq) {
__local ushort2 buffer[BUFFER_SIZE];
__local int valid[BUFFER_SIZE];
__local short sum[BUFFER_SIZE];
__local ushort2 temp[BUFFER_SIZE];
__local int bufferFull;
__local int globalIndex;
int valuesInBuffer = 0;
......@@ -138,7 +201,7 @@ __kernel void findBlocksWithInteractions(float cutoffSquared, float4 periodicBox
int bufferIndex = valuesInBuffer*GROUP_SIZE+get_local_id(0);
valid[bufferIndex] = true;
buffer[bufferIndex] = (short2) (x, y);
buffer[bufferIndex] = (ushort2) (x, y);
valuesInBuffer++;
if (!bufferFull && valuesInBuffer == BUFFER_GROUPS)
bufferFull = true;
......@@ -146,21 +209,21 @@ __kernel void findBlocksWithInteractions(float cutoffSquared, float4 periodicBox
}
barrier(CLK_LOCAL_MEM_FENCE);
if (bufferFull) {
storeInteractionData(buffer, valid, sum, sum2, temp, &globalIndex, interactionCount, interactingTiles);
storeInteractionData(buffer, valid, sum, temp, &globalIndex, interactionCount, interactingTiles, cutoffSquared, periodicBoxSize, invPeriodicBoxSize, posq, blockCenter, blockBoundingBox);
valuesInBuffer = 0;
if (get_local_id(0) == 0)
bufferFull = false;
barrier(CLK_LOCAL_MEM_FENCE);
}
}
storeInteractionData(buffer, valid, sum, sum2, temp, &globalIndex, interactionCount, interactingTiles);
storeInteractionData(buffer, valid, sum, temp, &globalIndex, interactionCount, interactingTiles, cutoffSquared, periodicBoxSize, invPeriodicBoxSize, posq, blockCenter, blockBoundingBox);
}
/**
* Compare each atom in one block to the bounding box of another block, and set
* flags for which ones are interacting.
*/
__kernel void findInteractionsWithinBlocks(float cutoffSquared, float4 periodicBoxSize, float4 invPeriodicBoxSize, __global float4* posq, __global unsigned int* tiles, __global float4* blockCenter,
__kernel void findInteractionsWithinBlocks(float cutoffSquared, float4 periodicBoxSize, float4 invPeriodicBoxSize, __global float4* posq, __global ushort2* tiles, __global float4* blockCenter,
__global float4* blockBoundingBox, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, __local unsigned int* flags) {
unsigned int totalWarps = get_global_size(0)/TILE_SIZE;
unsigned int warp = get_global_id(0)/TILE_SIZE;
......@@ -173,13 +236,10 @@ __kernel void findInteractionsWithinBlocks(float cutoffSquared, float4 periodicB
float4 apos;
while (pos < end) {
// Extract the coordinates of this tile
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
bool hasExclusions = (x & 0x1);
x = (x >> 17);
if (x == y || hasExclusions) {
// Assume this tile will be dense.
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
if (x == y) {
if (index == 0)
interactionFlags[pos] = 0xFFFFFFFF;
}
......
platforms/opencl/src/kernels/gbsaObc_default.cl
View file @ a8fe9cea
......@@ -17,7 +17,7 @@ typedef struct {
__kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1)))
void computeBornSum(__global float* global_bornSum, __global float4* posq, __global float2* global_params, __local AtomData* localData, __local float* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
#else
unsigned int numTiles) {
#endif
......@@ -32,9 +32,9 @@ void computeBornSum(__global float* global_bornSum, __global float4* posq, __glo
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -181,8 +181,8 @@ void computeBornSum(__global float* global_bornSum, __global float4* posq, __glo
global_bornSum[offset1] += bornSum+tempBuffer[get_local_id(0)+TILE_SIZE];
global_bornSum[offset2] += localData[get_local_id(0)].bornSum+localData[get_local_id(0)+TILE_SIZE].bornSum;
}
lasty = y;
}
lasty = y;
pos++;
}
}
......@@ -196,7 +196,7 @@ void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuff
__global float4* posq, __global float* global_bornRadii,
__global float* global_bornForce, __local AtomData* localData, __local float4* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
#else
unsigned int numTiles) {
#endif
......@@ -211,9 +211,9 @@ void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuff
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -366,8 +366,8 @@ void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuff
global_bornForce[offset1] += force.w+tempBuffer[get_local_id(0)+TILE_SIZE].w;
global_bornForce[offset2] += sum.w;
}
lasty = y;
}
lasty = y;
pos++;
}
energyBuffer[get_global_id(0)] += energy;
......
platforms/opencl/src/kernels/gbsaObc_nvidia.cl
View file @ a8fe9cea
......@@ -17,7 +17,7 @@ typedef struct {
__kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1)))
void computeBornSum(__global float* global_bornSum, __global float4* posq, __global float2* global_params, __local AtomData* localData, __local float* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
#else
unsigned int numTiles) {
#endif
......@@ -34,9 +34,9 @@ void computeBornSum(__global float* global_bornSum, __global float4* posq, __glo
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -247,8 +247,8 @@ void computeBornSum(__global float* global_bornSum, __global float4* posq, __glo
#endif
global_bornSum[offset1] += bornSum;
global_bornSum[offset2] += localData[get_local_id(0)].bornSum;
lasty = y;
}
lasty = y;
pos++;
}
}
......@@ -262,7 +262,7 @@ void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuff
__global float4* posq, __global float* global_bornRadii,
__global float* global_bornForce, __local AtomData* localData, __local float4* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize) {
#else
unsigned int numTiles) {
#endif
......@@ -279,9 +279,9 @@ void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuff
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -489,8 +489,8 @@ void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuff
forceBuffers[offset2] += (float4) (localData[get_local_id(0)].fx, localData[get_local_id(0)].fy, localData[get_local_id(0)].fz, 0);
global_bornForce[offset1] += force.w;
global_bornForce[offset2] += localData[get_local_id(0)].fw;
lasty = y;
}
lasty = y;
pos++;
}
energyBuffer[get_global_id(0)] += energy;
......
platforms/opencl/src/kernels/nonbonded_default.cl
View file @ a8fe9cea
......@@ -15,7 +15,7 @@ __kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1)))
void computeNonbonded(__global float4* forceBuffers, __global float* energyBuffer, __global float4* posq, __global unsigned int* exclusions,
__global unsigned int* exclusionIndices, __global unsigned int* exclusionRowIndices, __local AtomData* localData, __local float4* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
#else
unsigned int numTiles
#endif
......@@ -33,9 +33,9 @@ void computeNonbonded(__global float4* forceBuffers, __global float* energyBuffe
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -212,8 +212,8 @@ void computeNonbonded(__global float4* forceBuffers, __global float* energyBuffe
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;
}
lasty = y;
pos++;
}
energyBuffer[get_global_id(0)] += energy;
......
platforms/opencl/src/kernels/nonbonded_nvidia.cl
View file @ a8fe9cea
......@@ -15,7 +15,7 @@ __kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1)))
void computeNonbonded(__global float4* forceBuffers, __global float* energyBuffer, __global float4* posq, __global unsigned int* exclusions,
__global unsigned int* exclusionIndices, __global unsigned int* exclusionRowIndices, __local AtomData* localData, __local float4* tempBuffer,
#ifdef USE_CUTOFF
__global unsigned int* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
__global ushort2* tiles, __global unsigned int* interactionFlags, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize
#else
unsigned int numTiles
#endif
......@@ -35,9 +35,9 @@ void computeNonbonded(__global float4* forceBuffers, __global float* energyBuffe
while (pos < end) {
// Extract the coordinates of this tile
#ifdef USE_CUTOFF
unsigned int x = tiles[pos];
unsigned int y = ((x >> 2) & 0x7fff);
x = (x>>17);
ushort2 tileIndices = tiles[pos];
unsigned int x = tileIndices.x;
unsigned int y = tileIndices.y;
#else
unsigned int y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
unsigned int x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
......@@ -261,8 +261,8 @@ void computeNonbonded(__global float4* forceBuffers, __global float* energyBuffe
#endif
forceBuffers[offset1].xyz += 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;
}
lasty = y;
pos++;
}
energyBuffer[get_global_id(0)] += energy;
......
platforms/opencl/tests/TestOpenCLNonbondedForce.cpp
View file @ a8fe9cea
......@@ -517,7 +517,7 @@ void testBlockInteractions(bool periodic) {
// Verify that interactions were identified correctly.
vector<cl_uint> interactionCount;
vector<cl_uint> interactingTiles;
vector<mm_ushort2> interactingTiles;
vector<cl_uint> interactionFlags;
nb.getInteractionCount().download(interactionCount);
int numWithInteractions = interactionCount[0];
......@@ -528,9 +528,8 @@ void testBlockInteractions(bool periodic) {
const unsigned int grid = OpenCLContext::TileSize;
const unsigned int dim = clcontext.getNumAtomBlocks();
for (int i = 0; i < numWithInteractions; i++) {
unsigned int tile = interactingTiles[i];
unsigned int x = (tile >> 17);
unsigned int y = ((tile >> 2) & 0x7fff);
unsigned int x = interactingTiles[i].x;
unsigned int y = interactingTiles[i].y;
int index = (x > y ? x+y*dim-y*(y+1)/2 : y+x*dim-x*(x+1)/2);
hasInteractions[index] = true;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment