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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:
void setStepsSinceReorder(int 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.
*/
......@@ -572,7 +584,7 @@ private:
int paddedNumAtoms;
int numAtomBlocks;
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;
float4 periodicBoxVecXFloat, periodicBoxVecYFloat, periodicBoxVecZFloat, periodicBoxSizeFloat, invPeriodicBoxSizeFloat;
double4 periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ, periodicBoxSize, invPeriodicBoxSize;
......
platforms/cuda/include/CudaNonbondedUtilities.h
View file @ 6c6d68d2
......@@ -269,6 +269,8 @@ private:
CudaArray* oldPositions;
CudaArray* rebuildNeighborList;
CudaSort* blockSorter;
CUevent downloadCountEvent;
int* pinnedCountBuffer;
std::vector<void*> forceArgs, findBlockBoundsArgs, sortBoxDataArgs, findInteractingBlocksArgs;
std::vector<std::vector<int> > atomExclusions;
std::vector<ParameterInfo> parameters;
......
platforms/cuda/src/CudaContext.cpp
View file @ 6c6d68d2
......@@ -1131,7 +1131,6 @@ void CudaContext::reorderAtoms() {
reorderAtomsImpl<float, float4, double, double4>();
else
reorderAtomsImpl<float, float4, float, float4>();
nonbonded->updateNeighborListSize();
}
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) {
}
void CudaCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
cu.setForcesValid(true);
cu.setAsCurrent();
cu.clearAutoclearBuffers();
for (vector<CudaContext::ForcePreComputation*>::iterator iter = cu.getPreComputations().begin(); iter != cu.getPreComputations().end(); ++iter)
......@@ -125,6 +126,8 @@ double CudaCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bo
sum += energy[i];
}
}
if (!cu.getForcesValid())
valid = false;
return sum;
}
......
platforms/cuda/src/CudaNonbondedUtilities.cpp
View file @ 6c6d68d2
......@@ -65,12 +65,14 @@ private:
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),
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.
string errorMessage = "Error initializing nonbonded utilities";
int multiprocessors;
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;
forceThreadBlockSize = (context.getComputeCapability() < 2.0 ? 128 : 256);
}
......@@ -106,6 +108,9 @@ CudaNonbondedUtilities::~CudaNonbondedUtilities() {
delete rebuildNeighborList;
if (blockSorter != NULL)
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) {
......@@ -375,17 +380,14 @@ void CudaNonbondedUtilities::prepareInteractions(int forceGroups) {
if (lastCutoff != kernels.cutoffDistance)
forceRebuildNeighborList = true;
bool rebuild = false;
do {
context.executeKernel(kernels.findBlockBoundsKernel, &findBlockBoundsArgs[0], context.getNumAtoms());
blockSorter->sort(*sortedBlocks);
context.executeKernel(kernels.sortBoxDataKernel, &sortBoxDataArgs[0], context.getNumAtoms());
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;
interactionCount->download(pinnedCountBuffer, false);
cuEventRecord(downloadCountEvent, context.getCurrentStream());
}
void CudaNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) {
......@@ -398,20 +400,22 @@ void CudaNonbondedUtilities::computeInteractions(int forceGroups, bool includeFo
kernel = createInteractionKernel(kernels.source, parameters, arguments, true, true, forceGroups, includeForces, includeEnergy);
context.executeKernel(kernel, &forceArgs[0], numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
}
if (useCutoff && numTiles > 0) {
cuEventSynchronize(downloadCountEvent);
updateNeighborListSize();
}
}
bool CudaNonbondedUtilities::updateNeighborListSize() {
if (!useCutoff)
return false;
unsigned int* pinnedInteractionCount = (unsigned int*) context.getPinnedBuffer();
interactionCount->download(pinnedInteractionCount);
if (pinnedInteractionCount[0] <= (unsigned int) maxTiles)
if (pinnedCountBuffer[0] <= (unsigned int) maxTiles)
return false;
// 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.
maxTiles = (int) (1.2*pinnedInteractionCount[0]);
maxTiles = (int) (1.2*pinnedCountBuffer[0]);
int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
if (maxTiles > totalTiles)
maxTiles = totalTiles;
......@@ -428,6 +432,7 @@ bool CudaNonbondedUtilities::updateNeighborListSize() {
forceArgs[17] = &interactingAtoms->getDevicePointer();
findInteractingBlocksArgs[7] = &interactingAtoms->getDevicePointer();
forceRebuildNeighborList = true;
context.setForcesValid(false);
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
#ifdef USE_CUTOFF
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 end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -191,16 +193,12 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -223,7 +221,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
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
#ifdef USE_CUTOFF
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 end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -167,16 +169,12 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -199,7 +197,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
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
#ifdef USE_CUTOFF
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 end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -225,16 +227,12 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -257,7 +255,7 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......@@ -559,6 +557,8 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
#ifdef USE_CUTOFF
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 end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -580,16 +580,12 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -612,7 +608,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
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(
#ifndef ENABLE_SHUFFLE
__shared__ AtomData localData[THREAD_BLOCK_SIZE];
#endif
// 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 lastExclusionTile = FIRST_EXCLUSION_TILE+(warp+1)*(LAST_EXCLUSION_TILE-FIRST_EXCLUSION_TILE)/totalWarps;
for (int pos = firstExclusionTile; pos < lastExclusionTile; pos++) {
......@@ -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
// of them (no cutoff).
#ifdef USE_CUTOFF
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 end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -335,16 +340,12 @@ extern "C" __global__ void computeNonbonded(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -367,7 +368,7 @@ extern "C" __global__ void computeNonbonded(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
// Load atom data for this tile.
......
platforms/opencl/include/OpenCLContext.h
View file @ 6c6d68d2
......@@ -408,6 +408,18 @@ public:
void setStepsSinceReorder(int 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.
*/
......@@ -684,7 +696,7 @@ private:
int numThreadBlocks;
int numForceBuffers;
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_double4 periodicBoxSizeDouble, invPeriodicBoxSizeDouble, periodicBoxVecXDouble, periodicBoxVecYDouble, periodicBoxVecZDouble;
std::string defaultOptimizationOptions;
......
platforms/opencl/include/OpenCLNonbondedUtilities.h
View file @ 6c6d68d2
......@@ -281,6 +281,9 @@ private:
OpenCLArray* oldPositions;
OpenCLArray* rebuildNeighborList;
OpenCLSort* blockSorter;
cl::Event downloadCountEvent;
cl::Buffer* pinnedCountBuffer;
int* pinnedCountMemory;
std::vector<std::vector<int> > atomExclusions;
std::vector<ParameterInfo> parameters;
std::vector<ParameterInfo> arguments;
......
platforms/opencl/src/OpenCLContext.cpp
View file @ 6c6d68d2
......@@ -1052,7 +1052,6 @@ void OpenCLContext::reorderAtoms() {
reorderAtomsImpl<cl_float, mm_float4, cl_double, mm_double4>();
else
reorderAtomsImpl<cl_float, mm_float4, cl_float, mm_float4>();
nonbonded->updateNeighborListSize();
}
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) {
}
void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
cl.setForcesValid(true);
cl.clearAutoclearBuffers();
for (vector<OpenCLContext::ForcePreComputation*>::iterator iter = cl.getPreComputations().begin(); iter != cl.getPreComputations().end(); ++iter)
(*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
......@@ -149,6 +150,8 @@ double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context,
sum += energy[i];
}
}
if (!cl.getForcesValid())
valid = false;
return sum;
}
......
platforms/opencl/src/OpenCLNonbondedUtilities.cpp
View file @ 6c6d68d2
......@@ -57,7 +57,7 @@ private:
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),
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.
deviceIsCpu = (context.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
......@@ -90,6 +90,8 @@ OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : con
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() {
......@@ -123,6 +125,8 @@ OpenCLNonbondedUtilities::~OpenCLNonbondedUtilities() {
delete rebuildNeighborList;
if (blockSorter != NULL)
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) {
......@@ -357,8 +361,6 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
if (lastCutoff != kernels.cutoffDistance)
forceRebuildNeighborList = true;
bool rebuild = false;
do {
setPeriodicBoxArgs(context, kernels.findBlockBoundsKernel, 1);
context.executeKernel(kernels.findBlockBoundsKernel, context.getNumAtoms());
blockSorter->sort(*sortedBlocks);
......@@ -367,10 +369,8 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
setPeriodicBoxArgs(context, kernels.findInteractingBlocksKernel, 0);
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;
context.getQueue().enqueueReadBuffer(interactionCount->getDeviceBuffer(), CL_FALSE, 0, sizeof(int), pinnedCountMemory, NULL, &downloadCountEvent);
}
void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool includeForces, bool includeEnergy) {
......@@ -385,20 +385,22 @@ void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool include
setPeriodicBoxArgs(context, kernel, 9);
context.executeKernel(kernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
}
if (useCutoff && numTiles > 0) {
downloadCountEvent.wait();
updateNeighborListSize();
}
}
bool OpenCLNonbondedUtilities::updateNeighborListSize() {
if (!useCutoff)
return false;
unsigned int* pinnedInteractionCount = (unsigned int*) context.getPinnedBuffer();
interactionCount->download(pinnedInteractionCount);
if (pinnedInteractionCount[0] <= (unsigned int) interactingTiles->getSize())
if (pinnedCountMemory[0] <= (unsigned int) interactingTiles->getSize())
return false;
// 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.
int maxTiles = (int) (1.2*pinnedInteractionCount[0]);
int maxTiles = (int) (1.2*pinnedCountMemory[0]);
int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
if (maxTiles > totalTiles)
maxTiles = totalTiles;
......@@ -430,6 +432,7 @@ bool OpenCLNonbondedUtilities::updateNeighborListSize() {
kernels.findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
}
forceRebuildNeighborList = true;
context.setForcesValid(false);
return true;
}
......
platforms/opencl/src/kernels/customGBEnergyN2.cl
View file @ 6c6d68d2
......@@ -181,6 +181,8 @@ __kernel void computeN2Energy(
#ifdef USE_CUTOFF
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 end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -204,16 +206,12 @@ __kernel void computeN2Energy(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -239,7 +237,7 @@ __kernel void computeN2Energy(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
View file @ 6c6d68d2
......@@ -201,6 +201,8 @@ __kernel void computeN2Energy(
#ifdef USE_CUTOFF
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 end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else
......@@ -220,16 +222,12 @@ __kernel void computeN2Energy(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -248,7 +246,7 @@ __kernel void computeN2Energy(
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// 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*
#ifdef USE_CUTOFF
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 end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -178,16 +180,12 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -213,7 +211,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
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*
#ifdef USE_CUTOFF
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 end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else
......@@ -188,16 +190,12 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -216,7 +214,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// Load the data for this tile.
......
platforms/opencl/src/kernels/gbsaObc.cl
View file @ 6c6d68d2
......@@ -169,6 +169,8 @@ __kernel void computeBornSum(
#ifdef USE_CUTOFF
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 end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -190,16 +192,12 @@ __kernel void computeBornSum(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -225,7 +223,7 @@ __kernel void computeBornSum(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......@@ -556,6 +554,8 @@ __kernel void computeGBSAForce1(
#ifdef USE_CUTOFF
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 end = (int) ((warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : (long)numTiles)/totalWarps);
#else
......@@ -577,16 +577,12 @@ __kernel void computeGBSAForce1(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -612,7 +608,7 @@ __kernel void computeGBSAForce1(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
platforms/opencl/src/kernels/gbsaObc_cpu.cl
View file @ 6c6d68d2
......@@ -178,6 +178,8 @@ __kernel void computeBornSum(
#ifdef USE_CUTOFF
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 end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else
......@@ -196,16 +198,12 @@ __kernel void computeBornSum(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -224,7 +222,7 @@ __kernel void computeBornSum(
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// Load the data for this tile.
......@@ -593,6 +591,8 @@ __kernel void computeGBSAForce1(
#ifdef USE_CUTOFF
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 end = (int) ((get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*((long)NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0));
#else
......@@ -611,16 +611,12 @@ __kernel void computeGBSAForce1(
int x, y;
bool singlePeriodicCopy = false;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
x = tiles[pos];
real4 blockSizeX = blockSize[x];
singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
}
else
#endif
{
#else
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);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -639,7 +635,7 @@ __kernel void computeGBSAForce1(
nextToSkip = end;
}
includeTile = (nextToSkip != pos);
}
#endif
if (includeTile) {
// Load the data for this tile.
......
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