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Commit 562cfb39 authored by Peter Eastman's avatar Peter Eastman
Browse files

Created CustomGBForce kernels optimized for CPU. Fixed bugs in CPU GBSA kernels.

parent cbfff447
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Showing with 560 additions and 51 deletions
platforms/opencl/src/OpenCLKernels.cpp
View file @ 562cfb39
......@@ -1715,7 +1715,7 @@ double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeF
computeBornSumKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
computeBornSumKernel.setArg<cl::Buffer>(index++, params->getDeviceBuffer());
computeBornSumKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*13*sizeof(cl_float), NULL);
computeBornSumKernel.setArg(index++, OpenCLContext::ThreadBlockSize*sizeof(cl_float), NULL);
computeBornSumKernel.setArg(index++, (deviceIsCpu ? 1 : OpenCLContext::ThreadBlockSize)*sizeof(cl_float), NULL);
if (nb.getUseCutoff()) {
computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
......@@ -1734,7 +1734,7 @@ double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeF
force1Kernel.setArg<cl::Buffer>(index++, bornRadii->getDeviceBuffer());
force1Kernel.setArg<cl::Buffer>(index++, bornForce->getDeviceBuffer());
force1Kernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*13*sizeof(cl_float), NULL);
force1Kernel.setArg(index++, OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
force1Kernel.setArg(index++, (deviceIsCpu ? 1 : OpenCLContext::ThreadBlockSize)*sizeof(mm_float4), NULL);
if (nb.getUseCutoff()) {
force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
......@@ -1954,6 +1954,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
bool useCutoff = (force.getNonbondedMethod() != CustomGBForce::NoCutoff);
bool usePeriodic = (force.getNonbondedMethod() != CustomGBForce::NoCutoff && force.getNonbondedMethod() != CustomGBForce::CutoffNonPeriodic);
bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
{
// Create the N2 value kernel.
......@@ -1987,8 +1988,8 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
string paramName = "params"+intToString(i+1);
extraArgs << ", __global " << buffer.getType() << "* global_" << paramName << ", __local " << buffer.getType() << "* local_" << paramName;
loadLocal1 << "local_" << paramName << "[get_local_id(0)] = " << paramName << "1;\n";
loadLocal2 << "local_" << paramName << "[get_local_id(0)] = global_" << paramName << "[j];\n";
loadLocal1 << "local_" << paramName << "[localAtomIndex] = " << paramName << "1;\n";
loadLocal2 << "local_" << paramName << "[localAtomIndex] = global_" << paramName << "[j];\n";
load1 << buffer.getType() << " " << paramName << "1 = global_" << paramName << "[atom1];\n";
load2 << buffer.getType() << " " << paramName << "2 = local_" << paramName << "[atom2];\n";
}
......@@ -2010,7 +2011,13 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
defines["NUM_BLOCKS"] = OpenCLExpressionUtilities::intToString(cl.getNumAtomBlocks());
string file = (cl.getSIMDWidth() == 32 ? OpenCLKernelSources::customGBValueN2_nvidia : OpenCLKernelSources::customGBValueN2_default);
string file;
if (deviceIsCpu)
file = OpenCLKernelSources::customGBValueN2_cpu;
else if (cl.getSIMDWidth() == 32)
file = OpenCLKernelSources::customGBValueN2_nvidia;
else
OpenCLKernelSources::customGBValueN2_default;
cl::Program program = cl.createProgram(cl.replaceStrings(file, replacements), defines);
pairValueKernel = cl::Kernel(program, "computeN2Value");
}
......@@ -2106,8 +2113,8 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
string paramName = "params"+intToString(i+1);
extraArgs << ", __global " << buffer.getType() << "* global_" << paramName << ", __local " << buffer.getType() << "* local_" << paramName;
loadLocal1 << "local_" << paramName << "[get_local_id(0)] = " << paramName << "1;\n";
loadLocal2 << "local_" << paramName << "[get_local_id(0)] = global_" << paramName << "[j];\n";
loadLocal1 << "local_" << paramName << "[localAtomIndex] = " << paramName << "1;\n";
loadLocal2 << "local_" << paramName << "[localAtomIndex] = global_" << paramName << "[j];\n";
load1 << buffer.getType() << " " << paramName << "1 = global_" << paramName << "[atom1];\n";
load2 << buffer.getType() << " " << paramName << "2 = local_" << paramName << "[atom2];\n";
}
......@@ -2115,8 +2122,8 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
string valueName = "values"+intToString(i+1);
extraArgs << ", __global " << buffer.getType() << "* global_" << valueName << ", __local " << buffer.getType() << "* local_" << valueName;
loadLocal1 << "local_" << valueName << "[get_local_id(0)] = " << valueName << "1;\n";
loadLocal2 << "local_" << valueName << "[get_local_id(0)] = global_" << valueName << "[j];\n";
loadLocal1 << "local_" << valueName << "[localAtomIndex] = " << valueName << "1;\n";
loadLocal2 << "local_" << valueName << "[localAtomIndex] = global_" << valueName << "[j];\n";
load1 << buffer.getType() << " " << valueName << "1 = global_" << valueName << "[atom1];\n";
load2 << buffer.getType() << " " << valueName << "2 = local_" << valueName << "[atom2];\n";
}
......@@ -2124,7 +2131,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
string index = intToString(i+1);
extraArgs << ", __global " << buffer.getType() << "* derivBuffers" << index << ", __local " << buffer.getType() << "* local_deriv" << index;
clearLocal << "local_deriv" << index << "[get_local_id(0)] = 0.0f;\n";
clearLocal << "local_deriv" << index << "[localAtomIndex] = 0.0f;\n";
load1 << buffer.getType() << " deriv" << index << "_1 = 0.0f;\n";
load2 << buffer.getType() << " deriv" << index << "_2 = 0.0f;\n";
recordDeriv << "local_deriv" << index << "[atom2] += deriv" << index << "_2;\n";
......@@ -2157,7 +2164,13 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
defines["NUM_BLOCKS"] = OpenCLExpressionUtilities::intToString(cl.getNumAtomBlocks());
string file = (cl.getSIMDWidth() == 32 ? OpenCLKernelSources::customGBEnergyN2_nvidia : OpenCLKernelSources::customGBEnergyN2_default);
string file;
if (deviceIsCpu)
file = OpenCLKernelSources::customGBEnergyN2_cpu;
else if (cl.getSIMDWidth() == 32)
file = OpenCLKernelSources::customGBEnergyN2_nvidia;
else
file = OpenCLKernelSources::customGBEnergyN2_default;
cl::Program program = cl.createProgram(cl.replaceStrings(file, replacements), defines);
pairEnergyKernel = cl::Kernel(program, "computeN2Energy");
}
......@@ -2408,6 +2421,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
}
double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
if (!hasInitializedKernels) {
hasInitializedKernels = true;
......@@ -2422,14 +2436,14 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionIndices().getDeviceBuffer());
pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionRowIndices().getDeviceBuffer());
pairValueKernel.setArg<cl::Buffer>(index++, valueBuffers->getDeviceBuffer());
pairValueKernel.setArg(index++, OpenCLContext::ThreadBlockSize*sizeof(cl_float), NULL);
pairValueKernel.setArg(index++, OpenCLContext::ThreadBlockSize*sizeof(cl_float), NULL);
pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*sizeof(cl_float), NULL);
pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*sizeof(cl_float), NULL);
if (nb.getUseCutoff()) {
pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
index += 2; // Periodic box size arguments are set when the kernel is executed.
pairValueKernel.setArg<cl_uint>(index++, maxTiles);
if (cl.getSIMDWidth() == 32)
if (cl.getSIMDWidth() == 32 || deviceIsCpu)
pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractionFlags().getDeviceBuffer());
}
else
......@@ -2465,19 +2479,19 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
index = 0;
pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
pairEnergyKernel.setArg(index++, OpenCLContext::ThreadBlockSize*sizeof(cl_float4), NULL);
pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*sizeof(cl_float4), NULL);
pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
pairEnergyKernel.setArg(index++, OpenCLContext::ThreadBlockSize*sizeof(cl_float4), NULL);
pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*sizeof(cl_float4), NULL);
pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusions().getDeviceBuffer());
pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionIndices().getDeviceBuffer());
pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionRowIndices().getDeviceBuffer());
pairEnergyKernel.setArg(index++, OpenCLContext::ThreadBlockSize*sizeof(cl_float4), NULL);
pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*sizeof(cl_float4), NULL);
if (nb.getUseCutoff()) {
pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
index += 2; // Periodic box size arguments are set when the kernel is executed.
pairEnergyKernel.setArg<cl_uint>(index++, maxTiles);
if (cl.getSIMDWidth() == 32)
if (cl.getSIMDWidth() == 32 || deviceIsCpu)
pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractionFlags().getDeviceBuffer());
}
else
......@@ -2487,17 +2501,17 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
for (int i = 0; i < (int) params->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
pairEnergyKernel.setArg(index++, OpenCLContext::ThreadBlockSize*buffer.getSize(), NULL);
pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*buffer.getSize(), NULL);
}
for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
pairEnergyKernel.setArg(index++, OpenCLContext::ThreadBlockSize*buffer.getSize(), NULL);
pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*buffer.getSize(), NULL);
}
for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
pairEnergyKernel.setArg(index++, OpenCLContext::ThreadBlockSize*buffer.getSize(), NULL);
pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : OpenCLContext::ThreadBlockSize)*buffer.getSize(), NULL);
}
if (tabulatedFunctionParams != NULL) {
for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
......@@ -2560,9 +2574,9 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
}
}
int numTiles = cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2;
cl.executeKernel(pairValueKernel, numTiles*OpenCLContext::TileSize);
cl.executeKernel(pairValueKernel, numTiles*OpenCLContext::TileSize, deviceIsCpu ? 1 : -1);
cl.executeKernel(perParticleValueKernel, cl.getPaddedNumAtoms());
cl.executeKernel(pairEnergyKernel, numTiles*OpenCLContext::TileSize);
cl.executeKernel(pairEnergyKernel, numTiles*OpenCLContext::TileSize, deviceIsCpu ? 1 : -1);
cl.executeKernel(perParticleEnergyKernel, cl.getPaddedNumAtoms());
if (needParameterGradient)
cl.executeKernel(gradientChainRuleKernel, cl.getPaddedNumAtoms());
......
platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl 0 → 100644
View file @ 562cfb39
#define TILE_SIZE 32
#define STORE_DERIVATIVE_1(INDEX) derivBuffers##INDEX[offset1] += deriv##INDEX##_1;
#define STORE_DERIVATIVE_2(INDEX) derivBuffers##INDEX[offset2] += local_deriv##INDEX[tgx];
/**
* Compute a force based on pair interactions.
*/
__kernel void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer, __local float4* local_force,
__global float4* posq, __local float4* local_posq, __global unsigned int* exclusions, __global unsigned int* exclusionIndices,
__global unsigned int* exclusionRowIndices, __local float4* tempBuffer,
#ifdef USE_CUTOFF
__global ushort2* tiles, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize, unsigned int maxTiles, __global unsigned int* interactionFlags
#else
unsigned int numTiles
#endif
PARAMETER_ARGUMENTS) {
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
unsigned int pos = get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*(NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0);
unsigned int end = (get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*(NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0);
#else
unsigned int pos = get_group_id(0)*numTiles/get_num_groups(0);
unsigned int end = (get_group_id(0)+1)*numTiles/get_num_groups(0);
#endif
float energy = 0.0f;
unsigned int lasty = 0xFFFFFFFF;
while (pos < end) {
// Extract the coordinates of this tile
unsigned int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
ushort2 tileIndices = tiles[pos];
x = tileIndices.x;
y = tileIndices.y;
}
else
#endif
{
y = (unsigned 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 >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y++;
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Locate the exclusion data for this tile.
#ifdef USE_EXCLUSIONS
unsigned int exclusionStart = exclusionRowIndices[x];
unsigned int exclusionEnd = exclusionRowIndices[x+1];
int exclusionIndex = -1;
for (int i = exclusionStart; i < exclusionEnd; i++)
if (exclusionIndices[i] == y) {
exclusionIndex = i*TILE_SIZE;
break;
}
bool hasExclusions = (exclusionIndex > -1);
#else
bool hasExclusions = false;
#endif
// Load the data for this tile if we don't already have it cached.
if (lasty != y) {
for (int localAtomIndex = 0; localAtomIndex < TILE_SIZE; localAtomIndex++) {
unsigned int j = y*TILE_SIZE + localAtomIndex;
local_posq[localAtomIndex] = posq[j];
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
}
}
if (x == y) {
// This tile is on the diagonal.
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
#ifdef USE_EXCLUSIONS
unsigned int excl = exclusions[exclusionIndex+tgx];
#endif
unsigned int atom1 = x*TILE_SIZE+tgx;
float4 force = 0.0f;
float4 posq1 = posq[atom1];
LOAD_ATOM1_PARAMETERS
for (unsigned int j = 0; j < TILE_SIZE; j++) {
#ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1);
#endif
float4 posq2 = local_posq[j];
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
#endif
float r2 = dot(delta.xyz, delta.xyz);
#ifdef USE_CUTOFF
if (r2 < CUTOFF_SQUARED) {
#endif
float r = SQRT(r2);
unsigned int atom2 = j;
LOAD_ATOM2_PARAMETERS
atom2 = y*TILE_SIZE+j;
float dEdR = 0.0f;
float tempEnergy = 0.0f;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS && atom1 != atom2) {
COMPUTE_INTERACTION
dEdR /= -r;
}
energy += 0.5f*tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
#ifdef USE_CUTOFF
}
#endif
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
}
// Write results
unsigned int offset1 = x*TILE_SIZE + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
forceBuffers[offset1].xyz += force.xyz;
STORE_DERIVATIVES_1
}
}
else {
// This is an off-diagonal tile.
for (int localAtomIndex = 0; localAtomIndex < TILE_SIZE; localAtomIndex++) {
local_force[localAtomIndex] = 0.0f;
CLEAR_LOCAL_DERIVATIVES
}
#if defined(USE_CUTOFF) && defined(USE_EXCLUSIONS)
unsigned int flags1 = (numTiles <= maxTiles ? interactionFlags[2*pos] : 0xFFFFFFFF);
unsigned int flags2 = (numTiles <= maxTiles ? interactionFlags[2*pos+1] : 0xFFFFFFFF);
if (!hasExclusions && (flags1 != 0xFFFFFFFF || flags2 != 0xFFFFFFFF)) {
// Compute only a subset of the interactions in this tile.
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
if ((flags2&(1<<tgx)) != 0) {
unsigned int atom1 = x*TILE_SIZE+tgx;
float value = 0.0f;
float4 posq1 = posq[atom1];
LOAD_ATOM1_PARAMETERS
for (unsigned int j = 0; j < TILE_SIZE; j++) {
if ((flags&(1<<j)) != 0) {
float4 posq2 = local_posq[j];
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
#endif
float r2 = dot(delta.xyz, delta.xyz);
if (r2 < CUTOFF_SQUARED) {
float r = SQRT(r2);
unsigned int atom2 = j;
LOAD_ATOM2_PARAMETERS
atom2 = y*TILE_SIZE+j;
float dEdR = 0.0f;
float tempEnergy = 0.0f;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
COMPUTE_INTERACTION
dEdR /= -r;
}
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
atom2 = j;
local_force[atom2].xyz += delta.xyz;
RECORD_DERIVATIVE_2
}
}
}
// Write results for atom1.
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value;
}
}
}
else
#endif
{
// Compute the full set of interactions in this tile.
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
unsigned int atom1 = x*TILE_SIZE+tgx;
float4 force = 0.0f;
float4 posq1 = posq[atom1];
LOAD_ATOM1_PARAMETERS
#ifdef USE_EXCLUSIONS
unsigned int excl = (hasExclusions ? exclusions[exclusionIndex+tgx] : 0xFFFFFFFF);
#endif
for (unsigned int j = 0; j < TILE_SIZE; j++) {
#ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1);
#endif
float4 posq2 = local_posq[j];
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
#endif
float r2 = dot(delta.xyz, delta.xyz);
#ifdef USE_CUTOFF
if (r2 < CUTOFF_SQUARED) {
#endif
float r = SQRT(r2);
unsigned int atom2 = j;
LOAD_ATOM2_PARAMETERS
atom2 = y*TILE_SIZE+j;
float dEdR = 0.0f;
float tempEnergy = 0.0f;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
COMPUTE_INTERACTION
dEdR /= -r;
}
energy += tempEnergy;
delta.xyz *= dEdR;
force.xyz -= delta.xyz;
atom2 = j;
local_force[atom2].xyz += delta.xyz;
RECORD_DERIVATIVE_2
#ifdef USE_CUTOFF
}
#endif
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
}
// Write results for atom1.
unsigned int offset1 = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
forceBuffers[offset1].xyz += force.xyz;
STORE_DERIVATIVES_1
}
}
// Write results
for (int tgx = 0; tgx < TILE_SIZE; tgx++) {
unsigned int offset2 = y*TILE_SIZE+tgx + get_group_id(0)*PADDED_NUM_ATOMS;
forceBuffers[offset2].xyz += local_force[tgx].xyz;
STORE_DERIVATIVES_2
}
}
lasty = y;
pos++;
}
energyBuffer[get_global_id(0)] += energy;
}
platforms/opencl/src/kernels/customGBEnergyN2_default.cl
View file @ 562cfb39
......@@ -74,7 +74,8 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
if (x == y) {
// This tile is on the diagonal.
local_posq[get_local_id(0)] = posq1;
const unsigned int localAtomIndex = get_local_id(0);
local_posq[localAtomIndex] = posq1;
LOAD_LOCAL_PARAMETERS_FROM_1
barrier(CLK_LOCAL_MEM_FENCE);
#ifdef USE_EXCLUSIONS
......@@ -136,12 +137,13 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
else {
// This is an off-diagonal tile.
const unsigned int localAtomIndex = get_local_id(0);
if (lasty != y && get_local_id(0) < TILE_SIZE) {
unsigned int j = y*TILE_SIZE + tgx;
local_posq[get_local_id(0)] = posq[j];
local_posq[localAtomIndex] = posq[j];
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
}
local_force[get_local_id(0)] = 0.0f;
local_force[localAtomIndex] = 0.0f;
CLEAR_LOCAL_DERIVATIVES
barrier(CLK_LOCAL_MEM_FENCE);
......
platforms/opencl/src/kernels/customGBEnergyN2_nvidia.cl
View file @ 562cfb39
......@@ -75,7 +75,8 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
if (x == y) {
// This tile is on the diagonal.
local_posq[get_local_id(0)] = posq1;
const unsigned int localAtomIndex = get_local_id(0);
local_posq[localAtomIndex] = posq1;
LOAD_LOCAL_PARAMETERS_FROM_1
#ifdef USE_EXCLUSIONS
unsigned int excl = exclusions[exclusionIndex[localGroupIndex]+tgx];
......@@ -128,12 +129,13 @@ void computeN2Energy(__global float4* forceBuffers, __global float* energyBuffer
else {
// This is an off-diagonal tile.
const unsigned int localAtomIndex = get_local_id(0);
if (lasty != y) {
unsigned int j = y*TILE_SIZE + tgx;
local_posq[get_local_id(0)] = posq[j];
local_posq[localAtomIndex] = posq[j];
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
}
local_force[get_local_id(0)] = 0.0f;
local_force[localAtomIndex] = 0.0f;
CLEAR_LOCAL_DERIVATIVES
#ifdef USE_CUTOFF
unsigned int flags = (numTiles <= maxTiles ? interactionFlags[pos] : 0xFFFFFFFF);
......
platforms/opencl/src/kernels/customGBValueN2_cpu.cl 0 → 100644
View file @ 562cfb39
#define TILE_SIZE 32
/**
* Compute a value based on pair interactions.
*/
__kernel void computeN2Value(__global float4* posq, __local float4* local_posq, __global unsigned int* exclusions,
__global unsigned int* exclusionIndices, __global unsigned int* exclusionRowIndices, __global float* global_value, __local float* local_value,
__local float* tempBuffer,
#ifdef USE_CUTOFF
__global ushort2* tiles, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize, unsigned int maxTiles, __global unsigned int* interactionFlags
#else
unsigned int numTiles
#endif
PARAMETER_ARGUMENTS) {
#ifdef USE_CUTOFF
unsigned int numTiles = interactionCount[0];
unsigned int pos = get_group_id(0)*(numTiles > maxTiles ? NUM_BLOCKS*(NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0);
unsigned int end = (get_group_id(0)+1)*(numTiles > maxTiles ? NUM_BLOCKS*(NUM_BLOCKS+1)/2 : numTiles)/get_num_groups(0);
#else
unsigned int pos = get_group_id(0)*numTiles/get_num_groups(0);
unsigned int end = (get_group_id(0)+1)*numTiles/get_num_groups(0);
#endif
unsigned int lasty = 0xFFFFFFFF;
while (pos < end) {
// Extract the coordinates of this tile
unsigned int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles) {
ushort2 tileIndices = tiles[pos];
x = tileIndices.x;
y = tileIndices.y;
}
else
#endif
{
y = (unsigned 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 >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y++;
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Locate the exclusion data for this tile.
#ifdef USE_EXCLUSIONS
unsigned int exclusionStart = exclusionRowIndices[x];
unsigned int exclusionEnd = exclusionRowIndices[x+1];
int exclusionIndex = -1;
for (int i = exclusionStart; i < exclusionEnd; i++)
if (exclusionIndices[i] == y) {
exclusionIndex = i*TILE_SIZE;
break;
}
bool hasExclusions = (exclusionIndex > -1);
#else
bool hasExclusions = false;
#endif
// Load the data for this tile if we don't already have it cached.
if (lasty != y) {
for (int localAtomIndex = 0; localAtomIndex < TILE_SIZE; localAtomIndex++) {
unsigned int j = y*TILE_SIZE + localAtomIndex;
local_posq[localAtomIndex] = posq[j];
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
}
}
if (x == y) {
// This tile is on the diagonal.
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
#ifdef USE_EXCLUSIONS
unsigned int excl = exclusions[exclusionIndex+tgx];
#endif
unsigned int atom1 = x*TILE_SIZE+tgx;
float value = 0.0f;
float4 posq1 = posq[atom1];
LOAD_ATOM1_PARAMETERS
for (unsigned int j = 0; j < TILE_SIZE; j++) {
#ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1);
#endif
float4 posq2 = local_posq[j];
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
#endif
float r2 = dot(delta.xyz, delta.xyz);
#ifdef USE_CUTOFF
if (r2 < CUTOFF_SQUARED) {
#endif
float r = SQRT(r2);
unsigned int atom2 = j;
LOAD_ATOM2_PARAMETERS
atom2 = y*TILE_SIZE+j;
float tempValue1 = 0.0f;
float tempValue2 = 0.0f;
#ifdef USE_EXCLUSIONS
if (!isExcluded && atom1 < NUM_ATOMS && atom2 < NUM_ATOMS && atom1 != atom2) {
#else
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS && atom1 != atom2) {
#endif
COMPUTE_VALUE
}
value += tempValue1;
#ifdef USE_CUTOFF
}
#endif
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
}
// Write results
unsigned int offset = x*TILE_SIZE + tgx + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value;
}
}
else {
// This is an off-diagonal tile.
for (int tgx = 0; tgx < TILE_SIZE; tgx++)
local_value[tgx] = 0.0f;
#if defined(USE_CUTOFF) && defined(USE_EXCLUSIONS)
unsigned int flags1 = (numTiles <= maxTiles ? interactionFlags[2*pos] : 0xFFFFFFFF);
unsigned int flags2 = (numTiles <= maxTiles ? interactionFlags[2*pos+1] : 0xFFFFFFFF);
if (!hasExclusions && (flags1 != 0xFFFFFFFF || flags2 != 0xFFFFFFFF)) {
// Compute only a subset of the interactions in this tile.
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
if ((flags2&(1<<tgx)) != 0) {
unsigned int atom1 = x*TILE_SIZE+tgx;
float value = 0.0f;
float4 posq1 = posq[atom1];
LOAD_ATOM1_PARAMETERS
for (unsigned int j = 0; j < TILE_SIZE; j++) {
if ((flags&(1<<j)) != 0) {
float4 posq2 = local_posq[j];
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
#endif
float r2 = dot(delta.xyz, delta.xyz);
float tempValue1 = 0.0f;
float tempValue2 = 0.0f;
if (r2 < CUTOFF_SQUARED) {
float r = SQRT(r2);
unsigned int atom2 = j;
LOAD_ATOM2_PARAMETERS
atom2 = y*TILE_SIZE+j;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
COMPUTE_VALUE
}
value += tempValue1;
local_value[j] += tempValue2;
}
}
}
// Write results for atom1.
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value;
}
}
}
else
#endif
{
// Compute the full set of interactions in this tile.
for (unsigned int tgx = 0; tgx < TILE_SIZE; tgx++) {
unsigned int atom1 = x*TILE_SIZE+tgx;
float value = 0.0f;
float4 posq1 = posq[atom1];
LOAD_ATOM1_PARAMETERS
#ifdef USE_EXCLUSIONS
unsigned int excl = (hasExclusions ? exclusions[exclusionIndex+tgx] : 0xFFFFFFFF);
#endif
for (unsigned int j = 0; j < TILE_SIZE; j++) {
#ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1);
#endif
float4 posq2 = local_posq[j];
float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
#ifdef USE_PERIODIC
delta.xyz -= floor(delta.xyz*invPeriodicBoxSize.xyz+0.5f)*periodicBoxSize.xyz;
#endif
float r2 = dot(delta.xyz, delta.xyz);
#ifdef USE_CUTOFF
if (r2 < CUTOFF_SQUARED) {
#endif
float r = SQRT(r2);
unsigned int atom2 = j;
LOAD_ATOM2_PARAMETERS
atom2 = y*TILE_SIZE+j;
float tempValue1 = 0.0f;
float tempValue2 = 0.0f;
#ifdef USE_EXCLUSIONS
if (!isExcluded && atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
#else
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
#endif
COMPUTE_VALUE
}
value += tempValue1;
local_value[j] += tempValue2;
#ifdef USE_CUTOFF
}
#endif
#ifdef USE_EXCLUSIONS
excl >>= 1;
#endif
}
// Write results for atom1.
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += value;
}
}
// Write results
for (int tgx = 0; tgx < TILE_SIZE; tgx++) {
unsigned int offset = y*TILE_SIZE+tgx + get_group_id(0)*PADDED_NUM_ATOMS;
global_value[offset] += local_value[tgx];
}
}
lasty = y;
pos++;
}
}
platforms/opencl/src/kernels/customGBValueN2_default.cl
View file @ 562cfb39
......@@ -71,7 +71,8 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
if (x == y) {
// This tile is on the diagonal.
local_posq[get_local_id(0)] = posq1;
const unsigned int localAtomIndex = get_local_id(0);
local_posq[localAtomIndex] = posq1;
LOAD_LOCAL_PARAMETERS_FROM_1
barrier(CLK_LOCAL_MEM_FENCE);
#ifdef USE_EXCLUSIONS
......@@ -134,6 +135,7 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
if (lasty != y && get_local_id(0) < TILE_SIZE) {
unsigned int j = y*TILE_SIZE + tgx;
local_posq[get_local_id(0)] = posq[j];
const unsigned int localAtomIndex = get_local_id(0);
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
}
local_value[get_local_id(0)] = 0.0f;
......
platforms/opencl/src/kernels/customGBValueN2_nvidia.cl
View file @ 562cfb39
......@@ -73,7 +73,8 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
if (x == y) {
// This tile is on the diagonal.
local_posq[get_local_id(0)] = posq1;
const unsigned int localAtomIndex = get_local_id(0);
local_posq[localAtomIndex] = posq1;
LOAD_LOCAL_PARAMETERS_FROM_1
#ifdef USE_EXCLUSIONS
unsigned int excl = exclusions[exclusionIndex[localGroupIndex]+tgx];
......@@ -129,6 +130,7 @@ void computeN2Value(__global float4* posq, __local float4* local_posq, __global
if (lasty != y) {
unsigned int j = y*TILE_SIZE + tgx;
local_posq[get_local_id(0)] = posq[j];
const unsigned int localAtomIndex = get_local_id(0);
LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
}
local_value[get_local_id(0)] = 0.0f;
......
platforms/opencl/src/kernels/gbsaObc_cpu.cl
View file @ 562cfb39
......@@ -14,8 +14,7 @@ typedef struct {
* Compute the Born sum.
*/
__kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1)))
void computeBornSum(__global float* global_bornSum, __global float4* posq, __global float2* global_params, __local AtomData* localData, __local float* tempBuffer,
__kernel void computeBornSum(__global float* global_bornSum, __global float4* posq, __global float2* global_params, __local AtomData* localData, __local float* tempBuffer,
#ifdef USE_CUTOFF
__global ushort2* tiles, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize, unsigned int maxTiles, __global unsigned int* interactionFlags) {
#else
......@@ -171,8 +170,7 @@ void computeBornSum(__global float* global_bornSum, __global float4* posq, __glo
// Write results for atom1.
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
global_bornSum[offset] += localData[tgx].bornSum;
}
global_bornSum[offset] += bornSum;
}
// Write results
......@@ -181,6 +179,7 @@ void computeBornSum(__global float* global_bornSum, __global float4* posq, __glo
unsigned int offset = y*TILE_SIZE+tgx + get_group_id(0)*PADDED_NUM_ATOMS;
global_bornSum[offset] += localData[tgx].bornSum;
}
}
lasty = y;
pos++;
}
......@@ -190,8 +189,7 @@ void computeBornSum(__global float* global_bornSum, __global float4* posq, __glo
* First part of computing the GBSA interaction.
*/
__kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1)))
void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuffer,
__kernel void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global float* global_bornRadii,
__global float* global_bornForce, __local AtomData* localData, __local float4* tempBuffer,
#ifdef USE_CUTOFF
......@@ -344,7 +342,7 @@ void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuff
unsigned int offset = atom1 + get_group_id(0)*PADDED_NUM_ATOMS;
forceBuffers[offset].xyz = forceBuffers[offset].xyz+force.xyz;
}
global_bornForce[offset] += force.w;
}
// Write results
......@@ -358,6 +356,7 @@ void computeGBSAForce1(__global float4* forceBuffers, __global float* energyBuff
forceBuffers[offset] = f;
global_bornForce[offset] += localData[tgx].fw;
}
}
lasty = y;
pos++;
}
......
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