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Commit 6c6d68d2 authored by peastman's avatar peastman
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Merge pull request #1499 from peastman/reallocneighbors 

Improved method for resizing neighbor list
parents c2be00a6 6cc2edd1
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Showing with 401 additions and 383 deletions
platforms/cuda/include/CudaContext.h
View file @ 6c6d68d2
...@@ -326,6 +326,18 @@ public: ...@@ -326,6 +326,18 @@ public:
void setStepsSinceReorder(int steps) { void setStepsSinceReorder(int steps) {
stepsSinceReorder = steps; stepsSinceReorder = steps;
} }
/**
* Get the flag that marks whether the current force evaluation is valid.
*/
bool getForcesValid() const {
return forcesValid;
}
/**
* Get the flag that marks whether the current force evaluation is valid.
*/
void setForcesValid(bool valid) {
forcesValid = valid;
}
/** /**
* Get the number of atoms. * Get the number of atoms.
*/ */
...@@ -572,7 +584,7 @@ private: ...@@ -572,7 +584,7 @@ private:
int paddedNumAtoms; int paddedNumAtoms;
int numAtomBlocks; int numAtomBlocks;
int numThreadBlocks; int numThreadBlocks;
bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered, boxIsTriclinic, hasCompilerKernel; bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered, boxIsTriclinic, hasCompilerKernel, forcesValid;
std::string compiler, tempDir, cacheDir, gpuArchitecture; std::string compiler, tempDir, cacheDir, gpuArchitecture;
float4 periodicBoxVecXFloat, periodicBoxVecYFloat, periodicBoxVecZFloat, periodicBoxSizeFloat, invPeriodicBoxSizeFloat; float4 periodicBoxVecXFloat, periodicBoxVecYFloat, periodicBoxVecZFloat, periodicBoxSizeFloat, invPeriodicBoxSizeFloat;
double4 periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ, periodicBoxSize, invPeriodicBoxSize; double4 periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ, periodicBoxSize, invPeriodicBoxSize;
......
platforms/cuda/include/CudaNonbondedUtilities.h
View file @ 6c6d68d2
...@@ -269,6 +269,8 @@ private: ...@@ -269,6 +269,8 @@ private:
CudaArray* oldPositions; CudaArray* oldPositions;
CudaArray* rebuildNeighborList; CudaArray* rebuildNeighborList;
CudaSort* blockSorter; CudaSort* blockSorter;
CUevent downloadCountEvent;
int* pinnedCountBuffer;
std::vector<void*> forceArgs, findBlockBoundsArgs, sortBoxDataArgs, findInteractingBlocksArgs; std::vector<void*> forceArgs, findBlockBoundsArgs, sortBoxDataArgs, findInteractingBlocksArgs;
std::vector<std::vector<int> > atomExclusions; std::vector<std::vector<int> > atomExclusions;
std::vector<ParameterInfo> parameters; std::vector<ParameterInfo> parameters;
......
platforms/cuda/src/CudaContext.cpp
View file @ 6c6d68d2
...@@ -1131,7 +1131,6 @@ void CudaContext::reorderAtoms() { ...@@ -1131,7 +1131,6 @@ void CudaContext::reorderAtoms() {
reorderAtomsImpl<float, float4, double, double4>(); reorderAtomsImpl<float, float4, double, double4>();
else else
reorderAtomsImpl<float, float4, float, float4>(); reorderAtomsImpl<float, float4, float, float4>();
nonbonded->updateNeighborListSize();
} }
template <class Real, class Real4, class Mixed, class Mixed4> template <class Real, class Real4, class Mixed, class Mixed4>
......
platforms/cuda/src/CudaKernels.cpp
View file @ 6c6d68d2
...@@ -94,6 +94,7 @@ void CudaCalcForcesAndEnergyKernel::initialize(const System& system) { ...@@ -94,6 +94,7 @@ void CudaCalcForcesAndEnergyKernel::initialize(const System& system) {
} }
void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) { void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
cu.setForcesValid(true);
cu.setAsCurrent(); cu.setAsCurrent();
cu.clearAutoclearBuffers(); cu.clearAutoclearBuffers();
for (vector<CudaContext::ForcePreComputation*>::iterator iter = cu.getPreComputations().begin(); iter != cu.getPreComputations().end(); ++iter) for (vector<CudaContext::ForcePreComputation*>::iterator iter = cu.getPreComputations().begin(); iter != cu.getPreComputations().end(); ++iter)
...@@ -125,6 +126,8 @@ double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bo ...@@ -125,6 +126,8 @@ double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bo
sum += energy[i]; sum += energy[i];
} }
} }
if (!cu.getForcesValid())
valid = false;
return sum; return sum;
} }
......
platforms/cuda/src/CudaNonbondedUtilities.cpp
View file @ 6c6d68d2
...@@ -65,12 +65,14 @@ private: ...@@ -65,12 +65,14 @@ private:
CudaNonbondedUtilities::CudaNonbondedUtilities(CudaContext& context) : context(context), useCutoff(false), usePeriodic(false), anyExclusions(false), usePadding(true), CudaNonbondedUtilities::CudaNonbondedUtilities(CudaContext& context) : context(context), useCutoff(false), usePeriodic(false), anyExclusions(false), usePadding(true),
exclusionIndices(NULL), exclusionRowIndices(NULL), exclusionTiles(NULL), exclusions(NULL), interactingTiles(NULL), interactingAtoms(NULL), exclusionIndices(NULL), exclusionRowIndices(NULL), exclusionTiles(NULL), exclusions(NULL), interactingTiles(NULL), interactingAtoms(NULL),
interactionCount(NULL), blockCenter(NULL), blockBoundingBox(NULL), sortedBlocks(NULL), sortedBlockCenter(NULL), sortedBlockBoundingBox(NULL), interactionCount(NULL), blockCenter(NULL), blockBoundingBox(NULL), sortedBlocks(NULL), sortedBlockCenter(NULL), sortedBlockBoundingBox(NULL),
oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0) { oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), pinnedCountBuffer(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0) {
// Decide how many thread blocks to use. // Decide how many thread blocks to use.
string errorMessage = "Error initializing nonbonded utilities"; string errorMessage = "Error initializing nonbonded utilities";
int multiprocessors; int multiprocessors;
CHECK_RESULT(cuDeviceGetAttribute(&multiprocessors, CU_DEVICE_ATTRIBUTE_MULTIPROCESSOR_COUNT, context.getDevice())); CHECK_RESULT(cuDeviceGetAttribute(&multiprocessors, CU_DEVICE_ATTRIBUTE_MULTIPROCESSOR_COUNT, context.getDevice()));
CHECK_RESULT(cuEventCreate(&downloadCountEvent, 0));
CHECK_RESULT(cuMemHostAlloc((void**) &pinnedCountBuffer, sizeof(int), CU_MEMHOSTALLOC_PORTABLE));
numForceThreadBlocks = 4*multiprocessors; numForceThreadBlocks = 4*multiprocessors;
forceThreadBlockSize = (context.getComputeCapability() < 2.0 ? 128 : 256); forceThreadBlockSize = (context.getComputeCapability() < 2.0 ? 128 : 256);
} }
...@@ -106,6 +108,9 @@ CudaNonbondedUtilities::~CudaNonbondedUtilities() { ...@@ -106,6 +108,9 @@ CudaNonbondedUtilities::~CudaNonbondedUtilities() {
delete rebuildNeighborList; delete rebuildNeighborList;
if (blockSorter != NULL) if (blockSorter != NULL)
delete blockSorter; delete blockSorter;
if (pinnedCountBuffer != NULL)
cuMemFreeHost(pinnedCountBuffer);
cuEventDestroy(downloadCountEvent);
} }
void CudaNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const vector<vector<int> >& exclusionList, const string& kernel, int forceGroup) { void CudaNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const vector<vector<int> >& exclusionList, const string& kernel, int forceGroup) {
...@@ -375,17 +380,14 @@ void CudaNonbondedUtilities::prepareInteractions(int forceGroups) { ...@@ -375,17 +380,14 @@ void CudaNonbondedUtilities::prepareInteractions(int forceGroups) {
if (lastCutoff != kernels.cutoffDistance) if (lastCutoff != kernels.cutoffDistance)
forceRebuildNeighborList = true; forceRebuildNeighborList = true;
bool rebuild = false; context.executeKernel(kernels.findBlockBoundsKernel, &findBlockBoundsArgs[0], context.getNumAtoms());
do { blockSorter->sort(*sortedBlocks);
context.executeKernel(kernels.findBlockBoundsKernel, &findBlockBoundsArgs[0], context.getNumAtoms()); context.executeKernel(kernels.sortBoxDataKernel, &sortBoxDataArgs[0], context.getNumAtoms());
blockSorter->sort(*sortedBlocks); context.executeKernel(kernels.findInteractingBlocksKernel, &findInteractingBlocksArgs[0], context.getNumAtoms(), 256);
context.executeKernel(kernels.sortBoxDataKernel, &sortBoxDataArgs[0], context.getNumAtoms()); forceRebuildNeighborList = false;
context.executeKernel(kernels.findInteractingBlocksKernel, &findInteractingBlocksArgs[0], context.getNumAtoms(), 256);
forceRebuildNeighborList = false;
if (context.getComputeForceCount() == 1)
rebuild = updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
} while(rebuild);
lastCutoff = kernels.cutoffDistance; lastCutoff = kernels.cutoffDistance;
interactionCount->download(pinnedCountBuffer, false);
cuEventRecord(downloadCountEvent, context.getCurrentStream());
} }
void CudaNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) { void CudaNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) {
...@@ -398,20 +400,22 @@ void CudaNonbondedUtilities::computeInteractions(int forceGroups, bool includeFo ...@@ -398,20 +400,22 @@ void CudaNonbondedUtilities::computeInteractions(int forceGroups, bool includeFo
kernel = createInteractionKernel(kernels.source, parameters, arguments, true, true, forceGroups, includeForces, includeEnergy); kernel = createInteractionKernel(kernels.source, parameters, arguments, true, true, forceGroups, includeForces, includeEnergy);
context.executeKernel(kernel, &forceArgs[0], numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize); context.executeKernel(kernel, &forceArgs[0], numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
} }
if (useCutoff && numTiles > 0) {
cuEventSynchronize(downloadCountEvent);
updateNeighborListSize();
}
} }
bool CudaNonbondedUtilities::updateNeighborListSize() { bool CudaNonbondedUtilities::updateNeighborListSize() {
if (!useCutoff) if (!useCutoff)
return false; return false;
unsigned int* pinnedInteractionCount = (unsigned int*) context.getPinnedBuffer(); if (pinnedCountBuffer[0] <= (unsigned int) maxTiles)
interactionCount->download(pinnedInteractionCount);
if (pinnedInteractionCount[0] <= (unsigned int) maxTiles)
return false; return false;
// The most recent timestep had too many interactions to fit in the arrays. Make the arrays bigger to prevent // The most recent timestep had too many interactions to fit in the arrays. Make the arrays bigger to prevent
// this from happening in the future. // this from happening in the future.
maxTiles = (int) (1.2*pinnedInteractionCount[0]); maxTiles = (int) (1.2*pinnedCountBuffer[0]);
int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2; int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
if (maxTiles > totalTiles) if (maxTiles > totalTiles)
maxTiles = totalTiles; maxTiles = totalTiles;
...@@ -428,6 +432,7 @@ bool CudaNonbondedUtilities::updateNeighborListSize() { ...@@ -428,6 +432,7 @@ bool CudaNonbondedUtilities::updateNeighborListSize() {
forceArgs[17] = &interactingAtoms->getDevicePointer(); forceArgs[17] = &interactingAtoms->getDevicePointer();
findInteractingBlocksArgs[7] = &interactingAtoms->getDevicePointer(); findInteractingBlocksArgs[7] = &interactingAtoms->getDevicePointer();
forceRebuildNeighborList = true; forceRebuildNeighborList = true;
context.setForcesValid(false);
return true; return true;
} }
......
platforms/cuda/src/kernels/customGBEnergyN2.cu
View file @ 6c6d68d2
...@@ -168,6 +168,8 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc ...@@ -168,6 +168,8 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else #else
...@@ -191,39 +193,35 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc ...@@ -191,39 +193,35 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos]; x = tiles[pos];
real4 blockSizeX = blockSize[x]; real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
} #else
else y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
#endif x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
{ if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos)); y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) { while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx]; ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[threadIdx.x] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/cuda/src/kernels/customGBValueN2.cu
View file @ 6c6d68d2
...@@ -146,6 +146,8 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const ...@@ -146,6 +146,8 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else #else
...@@ -167,39 +169,35 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const ...@@ -167,39 +169,35 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) { while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx]; ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[threadIdx.x] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/cuda/src/kernels/gbsaObc1.cu
View file @ 6c6d68d2
...@@ -204,6 +204,8 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa ...@@ -204,6 +204,8 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else #else
...@@ -225,39 +227,35 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa ...@@ -225,39 +227,35 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos]; x = tiles[pos];
real4 blockSizeX = blockSize[x]; real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
} #else
else y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
#endif x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
{ if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos)); y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) { while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx]; ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[threadIdx.x] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
...@@ -559,6 +557,8 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo ...@@ -559,6 +557,8 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else #else
...@@ -580,39 +580,35 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo ...@@ -580,39 +580,35 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) { while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx]; ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[threadIdx.x] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/cuda/src/kernels/nonbonded.cu
View file @ 6c6d68d2
...@@ -117,7 +117,9 @@ extern "C" __global__ void computeNonbonded( ...@@ -117,7 +117,9 @@ extern "C" __global__ void computeNonbonded(
#ifndef ENABLE_SHUFFLE #ifndef ENABLE_SHUFFLE
__shared__ AtomData localData[THREAD_BLOCK_SIZE]; __shared__ AtomData localData[THREAD_BLOCK_SIZE];
#endif #endif
// First loop: process tiles that contain exclusions. // First loop: process tiles that contain exclusions.
const unsigned int firstExclusionTile = FIRST_EXCLUSION_TILE+warp*(LAST_EXCLUSION_TILE-FIRST_EXCLUSION_TILE)/totalWarps; const unsigned int firstExclusionTile = FIRST_EXCLUSION_TILE+warp*(LAST_EXCLUSION_TILE-FIRST_EXCLUSION_TILE)/totalWarps;
const unsigned int lastExclusionTile = FIRST_EXCLUSION_TILE+(warp+1)*(LAST_EXCLUSION_TILE-FIRST_EXCLUSION_TILE)/totalWarps; const unsigned int lastExclusionTile = FIRST_EXCLUSION_TILE+(warp+1)*(LAST_EXCLUSION_TILE-FIRST_EXCLUSION_TILE)/totalWarps;
for (int pos = firstExclusionTile; pos < lastExclusionTile; pos++) { for (int pos = firstExclusionTile; pos < lastExclusionTile; pos++) {
...@@ -309,8 +311,11 @@ extern "C" __global__ void computeNonbonded( ...@@ -309,8 +311,11 @@ extern "C" __global__ void computeNonbonded(
// Second loop: tiles without exclusions, either from the neighbor list (with cutoff) or just enumerating all // Second loop: tiles without exclusions, either from the neighbor list (with cutoff) or just enumerating all
// of them (no cutoff). // of them (no cutoff).
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0]; const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps); int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps); int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else #else
...@@ -335,39 +340,35 @@ extern "C" __global__ void computeNonbonded( ...@@ -335,39 +340,35 @@ extern "C" __global__ void computeNonbonded(
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) { while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx]; ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[threadIdx.x] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
// Load atom data for this tile. // Load atom data for this tile.
......
platforms/opencl/include/OpenCLContext.h
View file @ 6c6d68d2
...@@ -408,6 +408,18 @@ public: ...@@ -408,6 +408,18 @@ public:
void setStepsSinceReorder(int steps) { void setStepsSinceReorder(int steps) {
stepsSinceReorder = steps; stepsSinceReorder = steps;
} }
/**
* Get the flag that marks whether the current force evaluation is valid.
*/
bool getForcesValid() const {
return forcesValid;
}
/**
* Get the flag that marks whether the current force evaluation is valid.
*/
void setForcesValid(bool valid) {
forcesValid = valid;
}
/** /**
* Get the number of atoms. * Get the number of atoms.
*/ */
...@@ -684,7 +696,7 @@ private: ...@@ -684,7 +696,7 @@ private:
int numThreadBlocks; int numThreadBlocks;
int numForceBuffers; int numForceBuffers;
int simdWidth; int simdWidth;
bool supports64BitGlobalAtomics, supportsDoublePrecision, useDoublePrecision, useMixedPrecision, atomsWereReordered, boxIsTriclinic; bool supports64BitGlobalAtomics, supportsDoublePrecision, useDoublePrecision, useMixedPrecision, atomsWereReordered, boxIsTriclinic, forcesValid;
mm_float4 periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ; mm_float4 periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ;
mm_double4 periodicBoxSizeDouble, invPeriodicBoxSizeDouble, periodicBoxVecXDouble, periodicBoxVecYDouble, periodicBoxVecZDouble; mm_double4 periodicBoxSizeDouble, invPeriodicBoxSizeDouble, periodicBoxVecXDouble, periodicBoxVecYDouble, periodicBoxVecZDouble;
std::string defaultOptimizationOptions; std::string defaultOptimizationOptions;
......
platforms/opencl/include/OpenCLNonbondedUtilities.h
View file @ 6c6d68d2
...@@ -281,6 +281,9 @@ private: ...@@ -281,6 +281,9 @@ private:
OpenCLArray* oldPositions; OpenCLArray* oldPositions;
OpenCLArray* rebuildNeighborList; OpenCLArray* rebuildNeighborList;
OpenCLSort* blockSorter; OpenCLSort* blockSorter;
cl::Event downloadCountEvent;
cl::Buffer* pinnedCountBuffer;
int* pinnedCountMemory;
std::vector<std::vector<int> > atomExclusions; std::vector<std::vector<int> > atomExclusions;
std::vector<ParameterInfo> parameters; std::vector<ParameterInfo> parameters;
std::vector<ParameterInfo> arguments; std::vector<ParameterInfo> arguments;
......
platforms/opencl/src/OpenCLContext.cpp
View file @ 6c6d68d2
...@@ -1052,7 +1052,6 @@ void OpenCLContext::reorderAtoms() { ...@@ -1052,7 +1052,6 @@ void OpenCLContext::reorderAtoms() {
reorderAtomsImpl<cl_float, mm_float4, cl_double, mm_double4>(); reorderAtomsImpl<cl_float, mm_float4, cl_double, mm_double4>();
else else
reorderAtomsImpl<cl_float, mm_float4, cl_float, mm_float4>(); reorderAtomsImpl<cl_float, mm_float4, cl_float, mm_float4>();
nonbonded->updateNeighborListSize();
} }
template <class Real, class Real4, class Mixed, class Mixed4> template <class Real, class Real4, class Mixed, class Mixed4>
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 6c6d68d2
...@@ -118,6 +118,7 @@ void OpenCLCalcForcesAndEnergyKernel::initialize(const System& system) { ...@@ -118,6 +118,7 @@ void OpenCLCalcForcesAndEnergyKernel::initialize(const System& system) {
} }
void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) { void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
cl.setForcesValid(true);
cl.clearAutoclearBuffers(); cl.clearAutoclearBuffers();
for (vector<OpenCLContext::ForcePreComputation*>::iterator iter = cl.getPreComputations().begin(); iter != cl.getPreComputations().end(); ++iter) for (vector<OpenCLContext::ForcePreComputation*>::iterator iter = cl.getPreComputations().begin(); iter != cl.getPreComputations().end(); ++iter)
(*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups); (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
...@@ -149,6 +150,8 @@ double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, ...@@ -149,6 +150,8 @@ double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context,
sum += energy[i]; sum += energy[i];
} }
} }
if (!cl.getForcesValid())
valid = false;
return sum; return sum;
} }
......
platforms/opencl/src/OpenCLNonbondedUtilities.cpp
View file @ 6c6d68d2
...@@ -57,7 +57,7 @@ private: ...@@ -57,7 +57,7 @@ private:
OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : context(context), useCutoff(false), usePeriodic(false), anyExclusions(false), usePadding(true), OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : context(context), useCutoff(false), usePeriodic(false), anyExclusions(false), usePadding(true),
numForceBuffers(0), exclusionIndices(NULL), exclusionRowIndices(NULL), exclusionTiles(NULL), exclusions(NULL), interactingTiles(NULL), interactingAtoms(NULL), numForceBuffers(0), exclusionIndices(NULL), exclusionRowIndices(NULL), exclusionTiles(NULL), exclusions(NULL), interactingTiles(NULL), interactingAtoms(NULL),
interactionCount(NULL), blockCenter(NULL), blockBoundingBox(NULL), sortedBlocks(NULL), sortedBlockCenter(NULL), sortedBlockBoundingBox(NULL), interactionCount(NULL), blockCenter(NULL), blockBoundingBox(NULL), sortedBlocks(NULL), sortedBlockCenter(NULL), sortedBlockBoundingBox(NULL),
oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0) { oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), pinnedCountBuffer(NULL), pinnedCountMemory(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0) {
// Decide how many thread blocks and force buffers to use. // Decide how many thread blocks and force buffers to use.
deviceIsCpu = (context.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU); deviceIsCpu = (context.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
...@@ -90,6 +90,8 @@ OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : con ...@@ -90,6 +90,8 @@ OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : con
numForceBuffers = numForceThreadBlocks*forceThreadBlockSize/OpenCLContext::TileSize; numForceBuffers = numForceThreadBlocks*forceThreadBlockSize/OpenCLContext::TileSize;
} }
} }
pinnedCountBuffer = new cl::Buffer(context.getContext(), CL_MEM_ALLOC_HOST_PTR, sizeof(int));
pinnedCountMemory = (int*) context.getQueue().enqueueMapBuffer(*pinnedCountBuffer, CL_TRUE, CL_MAP_READ, 0, sizeof(int));
} }
OpenCLNonbondedUtilities::~OpenCLNonbondedUtilities() { OpenCLNonbondedUtilities::~OpenCLNonbondedUtilities() {
...@@ -123,6 +125,8 @@ OpenCLNonbondedUtilities::~OpenCLNonbondedUtilities() { ...@@ -123,6 +125,8 @@ OpenCLNonbondedUtilities::~OpenCLNonbondedUtilities() {
delete rebuildNeighborList; delete rebuildNeighborList;
if (blockSorter != NULL) if (blockSorter != NULL)
delete blockSorter; delete blockSorter;
if (pinnedCountBuffer != NULL)
delete pinnedCountBuffer;
} }
void OpenCLNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const vector<vector<int> >& exclusionList, const string& kernel, int forceGroup) { void OpenCLNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const vector<vector<int> >& exclusionList, const string& kernel, int forceGroup) {
...@@ -357,20 +361,16 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) { ...@@ -357,20 +361,16 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
if (lastCutoff != kernels.cutoffDistance) if (lastCutoff != kernels.cutoffDistance)
forceRebuildNeighborList = true; forceRebuildNeighborList = true;
bool rebuild = false; setPeriodicBoxArgs(context, kernels.findBlockBoundsKernel, 1);
do { context.executeKernel(kernels.findBlockBoundsKernel, context.getNumAtoms());
setPeriodicBoxArgs(context, kernels.findBlockBoundsKernel, 1); blockSorter->sort(*sortedBlocks);
context.executeKernel(kernels.findBlockBoundsKernel, context.getNumAtoms()); kernels.sortBoxDataKernel.setArg<cl_int>(9, forceRebuildNeighborList);
blockSorter->sort(*sortedBlocks); context.executeKernel(kernels.sortBoxDataKernel, context.getNumAtoms());
kernels.sortBoxDataKernel.setArg<cl_int>(9, forceRebuildNeighborList); setPeriodicBoxArgs(context, kernels.findInteractingBlocksKernel, 0);
context.executeKernel(kernels.sortBoxDataKernel, context.getNumAtoms()); context.executeKernel(kernels.findInteractingBlocksKernel, context.getNumAtoms(), interactingBlocksThreadBlockSize);
setPeriodicBoxArgs(context, kernels.findInteractingBlocksKernel, 0); forceRebuildNeighborList = false;
context.executeKernel(kernels.findInteractingBlocksKernel, context.getNumAtoms(), interactingBlocksThreadBlockSize);
forceRebuildNeighborList = false;
if (context.getComputeForceCount() == 1)
rebuild = updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
} while (rebuild);
lastCutoff = kernels.cutoffDistance; lastCutoff = kernels.cutoffDistance;
context.getQueue().enqueueReadBuffer(interactionCount->getDeviceBuffer(), CL_FALSE, 0, sizeof(int), pinnedCountMemory, NULL, &downloadCountEvent);
} }
void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) { void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) {
...@@ -385,20 +385,22 @@ void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool include ...@@ -385,20 +385,22 @@ void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool include
setPeriodicBoxArgs(context, kernel, 9); setPeriodicBoxArgs(context, kernel, 9);
context.executeKernel(kernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize); context.executeKernel(kernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
} }
if (useCutoff && numTiles > 0) {
downloadCountEvent.wait();
updateNeighborListSize();
}
} }
bool OpenCLNonbondedUtilities::updateNeighborListSize() { bool OpenCLNonbondedUtilities::updateNeighborListSize() {
if (!useCutoff) if (!useCutoff)
return false; return false;
unsigned int* pinnedInteractionCount = (unsigned int*) context.getPinnedBuffer(); if (pinnedCountMemory[0] <= (unsigned int) interactingTiles->getSize())
interactionCount->download(pinnedInteractionCount);
if (pinnedInteractionCount[0] <= (unsigned int) interactingTiles->getSize())
return false; return false;
// The most recent timestep had too many interactions to fit in the arrays. Make the arrays bigger to prevent // The most recent timestep had too many interactions to fit in the arrays. Make the arrays bigger to prevent
// this from happening in the future. // this from happening in the future.
int maxTiles = (int) (1.2*pinnedInteractionCount[0]); int maxTiles = (int) (1.2*pinnedCountMemory[0]);
int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2; int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
if (maxTiles > totalTiles) if (maxTiles > totalTiles)
maxTiles = totalTiles; maxTiles = totalTiles;
...@@ -430,6 +432,7 @@ bool OpenCLNonbondedUtilities::updateNeighborListSize() { ...@@ -430,6 +432,7 @@ bool OpenCLNonbondedUtilities::updateNeighborListSize() {
kernels.findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles); kernels.findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
} }
forceRebuildNeighborList = true; forceRebuildNeighborList = true;
context.setForcesValid(false);
return true; return true;
} }
......
platforms/opencl/src/kernels/customGBEnergyN2.cl
View file @ 6c6d68d2
...@@ -181,6 +181,8 @@ __kernel void computeN2Energy( ...@@ -181,6 +181,8 @@ __kernel void computeN2Energy(
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else #else
...@@ -204,42 +206,38 @@ __kernel void computeN2Energy( ...@@ -204,42 +206,38 @@ __kernel void computeN2Energy(
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS; SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
SYNC_WARPS; ushort2 tile = exclusionTiles[skipBase+tgx];
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[get_local_id(0)] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
View file @ 6c6d68d2
...@@ -201,6 +201,8 @@ __kernel void computeN2Energy( ...@@ -201,6 +201,8 @@ __kernel void computeN2Energy(
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0]; const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0)); int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0)); int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else #else
...@@ -220,35 +222,31 @@ __kernel void computeN2Energy( ...@@ -220,35 +222,31 @@ __kernel void computeN2Energy(
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) { while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) { if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++]; ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
} }
includeTile = (nextToSkip != pos); else
nextToSkip = end;
} }
includeTile = (nextToSkip != pos);
#endif
if (includeTile) { if (includeTile) {
// Load the data for this tile. // Load the data for this tile.
......
platforms/opencl/src/kernels/customGBValueN2.cl
View file @ 6c6d68d2
...@@ -157,6 +157,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -157,6 +157,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else #else
...@@ -178,42 +180,38 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -178,42 +180,38 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS; SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
SYNC_WARPS; ushort2 tile = exclusionTiles[skipBase+tgx];
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[get_local_id(0)] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/customGBValueN2_cpu.cl
View file @ 6c6d68d2
...@@ -170,6 +170,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -170,6 +170,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0]; const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0)); int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0)); int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else #else
...@@ -188,35 +190,31 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -188,35 +190,31 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) { while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) { if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++]; ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
} }
includeTile = (nextToSkip != pos); else
nextToSkip = end;
} }
includeTile = (nextToSkip != pos);
#endif
if (includeTile) { if (includeTile) {
// Load the data for this tile. // Load the data for this tile.
......
platforms/opencl/src/kernels/gbsaObc.cl
View file @ 6c6d68d2
...@@ -169,6 +169,8 @@ __kernel void computeBornSum( ...@@ -169,6 +169,8 @@ __kernel void computeBornSum(
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else #else
...@@ -190,42 +192,38 @@ __kernel void computeBornSum( ...@@ -190,42 +192,38 @@ __kernel void computeBornSum(
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS; SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
SYNC_WARPS; ushort2 tile = exclusionTiles[skipBase+tgx];
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[get_local_id(0)] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
...@@ -556,6 +554,8 @@ __kernel void computeGBSAForce1( ...@@ -556,6 +554,8 @@ __kernel void computeGBSAForce1(
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int pos = (int) (warp*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps); int end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else #else
...@@ -577,42 +577,38 @@ __kernel void computeGBSAForce1( ...@@ -577,42 +577,38 @@ __kernel void computeGBSAForce1(
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
SYNC_WARPS; SYNC_WARPS;
while (skipTiles[tbx+TILE_SIZE-1] < pos) { if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
SYNC_WARPS; ushort2 tile = exclusionTiles[skipBase+tgx];
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) { skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[get_local_id(0)] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
} }
while (skipTiles[currentSkipIndex] < pos) else
currentSkipIndex++; skipTiles[get_local_id(0)] = end;
includeTile = (skipTiles[currentSkipIndex] != pos); skipBase += TILE_SIZE;
currentSkipIndex = tbx;
SYNC_WARPS;
} }
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) { if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx; unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/gbsaObc_cpu.cl
View file @ 6c6d68d2
...@@ -178,6 +178,8 @@ __kernel void computeBornSum( ...@@ -178,6 +178,8 @@ __kernel void computeBornSum(
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0)); int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0)); int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else #else
...@@ -196,35 +198,31 @@ __kernel void computeBornSum( ...@@ -196,35 +198,31 @@ __kernel void computeBornSum(
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) { while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) { if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++]; ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
} }
includeTile = (nextToSkip != pos); else
nextToSkip = end;
} }
includeTile = (nextToSkip != pos);
#endif
if (includeTile) { if (includeTile) {
// Load the data for this tile. // Load the data for this tile.
...@@ -593,6 +591,8 @@ __kernel void computeGBSAForce1( ...@@ -593,6 +591,8 @@ __kernel void computeGBSAForce1(
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0]; unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0)); int pos = (int) (get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0)); int end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else #else
...@@ -611,35 +611,31 @@ __kernel void computeGBSAForce1( ...@@ -611,35 +611,31 @@ __kernel void computeGBSAForce1(
int x, y; int x, y;
bool singlePeriodicCopy = false; bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { x = tiles[pos];
x = tiles[pos]; real4 blockSizeX = blockSize[x];
real4 blockSizeX = blockSize[x]; singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF && 0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF && 0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF); #else
} y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
else x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
#endif if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
{ y += (x < y ? -1 : 1);
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2); x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error. }
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
// Skip over tiles that have exclusions, since they were already processed. // Skip over tiles that have exclusions, since they were already processed.
while (nextToSkip < pos) { while (nextToSkip < pos) {
if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) { if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[currentSkipIndex++]; ushort2 tile = exclusionTiles[currentSkipIndex++];
nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2; nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
nextToSkip = end;
} }
includeTile = (nextToSkip != pos); else
nextToSkip = end;
} }
includeTile = (nextToSkip != pos);
#endif
if (includeTile) { if (includeTile) {
// Load the data for this tile. // Load the data for this tile.
......
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