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Commit 74efa95f authored by peastman's avatar peastman
Browse files

OpenCL implementation of parameter derivatives for CustomGBForce

parent df07fbe9
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Showing with 251 additions and 58 deletions
platforms/opencl/include/OpenCLKernels.h
View file @ 74efa95f
...@@ -808,13 +808,15 @@ public: ...@@ -808,13 +808,15 @@ public:
void copyParametersToContext(ContextImpl& context, const CustomGBForce& force); void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
private: private:
double cutoff; double cutoff;
bool hasInitializedKernels, needParameterGradient; bool hasInitializedKernels, needParameterGradient, needEnergyParamDerivs;
int maxTiles, numComputedValues; int maxTiles, numComputedValues;
OpenCLContext& cl; OpenCLContext& cl;
OpenCLParameterSet* params; OpenCLParameterSet* params;
OpenCLParameterSet* computedValues; OpenCLParameterSet* computedValues;
OpenCLParameterSet* energyDerivs; OpenCLParameterSet* energyDerivs;
OpenCLParameterSet* energyDerivChain; OpenCLParameterSet* energyDerivChain;
std::vector<OpenCLParameterSet*> dValuedParam;
std::vector<OpenCLArray*> dValue0dParam;
OpenCLArray* longEnergyDerivs; OpenCLArray* longEnergyDerivs;
OpenCLArray* globals; OpenCLArray* globals;
OpenCLArray* valueBuffers; OpenCLArray* valueBuffers;
......
platforms/opencl/src/OpenCLBondedUtilities.cpp
View file @ 74efa95f
...@@ -204,7 +204,7 @@ void OpenCLBondedUtilities::initialize(const System& system) { ...@@ -204,7 +204,7 @@ void OpenCLBondedUtilities::initialize(const System& system) {
for (int i = 0; i < (int) arguments.size(); i++) for (int i = 0; i < (int) arguments.size(); i++)
s<<", __global "<<argTypes[i]<<"* customArg"<<(i+1); s<<", __global "<<argTypes[i]<<"* customArg"<<(i+1);
if (energyParameterDerivatives.size() > 0) if (energyParameterDerivatives.size() > 0)
s<<", __global mixed* energyParamDerivs"; s<<", __global mixed* restrict energyParamDerivs";
s<<") {\n"; s<<") {\n";
s<<"mixed energy = 0;\n"; s<<"mixed energy = 0;\n";
for (int i = 0; i < energyParameterDerivatives.size(); i++) for (int i = 0; i < energyParameterDerivatives.size(); i++)
...@@ -219,7 +219,7 @@ void OpenCLBondedUtilities::initialize(const System& system) { ...@@ -219,7 +219,7 @@ void OpenCLBondedUtilities::initialize(const System& system) {
for (int i = 0; i < energyParameterDerivatives.size(); i++) for (int i = 0; i < energyParameterDerivatives.size(); i++)
for (int index = 0; index < numDerivs; index++) for (int index = 0; index < numDerivs; index++)
if (allParamDerivNames[index] == energyParameterDerivatives[i]) if (allParamDerivNames[index] == energyParameterDerivatives[i])
s<<"energyParamDerivs[get_global_id(0)*"<<numDerivs<<"+"<<i<<"] += energyParamDeriv"<<i<<";\n"; s<<"energyParamDerivs[get_global_id(0)*"<<numDerivs<<"+"<<index<<"] += energyParamDeriv"<<i<<";\n";
s<<"}\n"; s<<"}\n";
map<string, string> defines; map<string, string> defines;
defines["PADDED_NUM_ATOMS"] = context.intToString(context.getPaddedNumAtoms()); defines["PADDED_NUM_ATOMS"] = context.intToString(context.getPaddedNumAtoms());
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 74efa95f
This diff is collapsed.
platforms/opencl/src/OpenCLNonbondedUtilities.cpp
View file @ 74efa95f
...@@ -605,7 +605,7 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc ...@@ -605,7 +605,7 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc
} }
} }
if (energyParameterDerivatives.size() > 0) if (energyParameterDerivatives.size() > 0)
args << ", __global mixed* energyParamDerivs"; args << ", __global mixed* restrict energyParamDerivs";
replacements["PARAMETER_ARGUMENTS"] = args.str(); replacements["PARAMETER_ARGUMENTS"] = args.str();
stringstream loadLocal1; stringstream loadLocal1;
for (int i = 0; i < (int) params.size(); i++) { for (int i = 0; i < (int) params.size(); i++) {
...@@ -666,7 +666,7 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc ...@@ -666,7 +666,7 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc
for (int i = 0; i < energyParameterDerivatives.size(); i++) for (int i = 0; i < energyParameterDerivatives.size(); i++)
for (int index = 0; index < numDerivs; index++) for (int index = 0; index < numDerivs; index++)
if (allParamDerivNames[index] == energyParameterDerivatives[i]) if (allParamDerivNames[index] == energyParameterDerivatives[i])
saveDerivs<<"energyParamDerivs[get_global_id(0)*"<<numDerivs<<"+"<<i<<"] += energyParamDeriv"<<i<<";\n"; saveDerivs<<"energyParamDerivs[get_global_id(0)*"<<numDerivs<<"+"<<index<<"] += energyParamDeriv"<<i<<";\n";
replacements["SAVE_DERIVATIVES"] = saveDerivs.str(); replacements["SAVE_DERIVATIVES"] = saveDerivs.str();
map<string, string> defines; map<string, string> defines;
if (useCutoff) if (useCutoff)
......
platforms/opencl/src/kernels/customGBEnergyN2.cl
View file @ 74efa95f
...@@ -32,6 +32,7 @@ __kernel void computeN2Energy( ...@@ -32,6 +32,7 @@ __kernel void computeN2Energy(
const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1); const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1);
const unsigned int tbx = get_local_id(0) - tgx; const unsigned int tbx = get_local_id(0) - tgx;
mixed energy = 0; mixed energy = 0;
INIT_PARAM_DERIVS
// First loop: process tiles that contain exclusions. // First loop: process tiles that contain exclusions.
...@@ -73,6 +74,7 @@ __kernel void computeN2Energy( ...@@ -73,6 +74,7 @@ __kernel void computeN2Energy(
atom2 = y*TILE_SIZE+j; atom2 = y*TILE_SIZE+j;
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 0.5f;
#ifdef USE_EXCLUSIONS #ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1); bool isExcluded = !(excl & 0x1);
#endif #endif
...@@ -123,6 +125,7 @@ __kernel void computeN2Energy( ...@@ -123,6 +125,7 @@ __kernel void computeN2Energy(
atom2 = y*TILE_SIZE+tj; atom2 = y*TILE_SIZE+tj;
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
#ifdef USE_EXCLUSIONS #ifdef USE_EXCLUSIONS
bool isExcluded = !(excl & 0x1); bool isExcluded = !(excl & 0x1);
#endif #endif
...@@ -281,6 +284,7 @@ __kernel void computeN2Energy( ...@@ -281,6 +284,7 @@ __kernel void computeN2Energy(
atom2 = atomIndices[tbx+tj]; atom2 = atomIndices[tbx+tj];
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) { if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
COMPUTE_INTERACTION COMPUTE_INTERACTION
dEdR /= -r; dEdR /= -r;
...@@ -319,6 +323,7 @@ __kernel void computeN2Energy( ...@@ -319,6 +323,7 @@ __kernel void computeN2Energy(
atom2 = atomIndices[tbx+tj]; atom2 = atomIndices[tbx+tj];
real dEdR = 0; real dEdR = 0;
real tempEnergy = 0; real tempEnergy = 0;
const real interactionScale = 1.0f;
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) { if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
COMPUTE_INTERACTION COMPUTE_INTERACTION
dEdR /= -r; dEdR /= -r;
...@@ -373,4 +378,5 @@ __kernel void computeN2Energy( ...@@ -373,4 +378,5 @@ __kernel void computeN2Energy(
pos++; pos++;
} }
energyBuffer[get_global_id(0)] += energy; energyBuffer[get_global_id(0)] += energy;
SAVE_PARAM_DERIVS
} }
platforms/opencl/src/kernels/customGBEnergyPerParticle.cl
View file @ 74efa95f
...@@ -12,6 +12,7 @@ ...@@ -12,6 +12,7 @@
__kernel void computePerParticleEnergy(int bufferSize, int numBuffers, __global real4* restrict forceBuffers, __global mixed* restrict energyBuffer, __global const real4* restrict posq __kernel void computePerParticleEnergy(int bufferSize, int numBuffers, __global real4* restrict forceBuffers, __global mixed* restrict energyBuffer, __global const real4* restrict posq
PARAMETER_ARGUMENTS) { PARAMETER_ARGUMENTS) {
mixed energy = 0; mixed energy = 0;
INIT_PARAM_DERIVS
unsigned int index = get_global_id(0); unsigned int index = get_global_id(0);
while (index < NUM_ATOMS) { while (index < NUM_ATOMS) {
// Reduce the derivatives // Reduce the derivatives
...@@ -27,4 +28,5 @@ __kernel void computePerParticleEnergy(int bufferSize, int numBuffers, __global ...@@ -27,4 +28,5 @@ __kernel void computePerParticleEnergy(int bufferSize, int numBuffers, __global
index += get_global_size(0); index += get_global_size(0);
} }
energyBuffer[get_global_id(0)] += energy; energyBuffer[get_global_id(0)] += energy;
SAVE_PARAM_DERIVS
} }
platforms/opencl/src/kernels/customGBGradientChainRule.cl
View file @ 74efa95f
...@@ -4,6 +4,7 @@ ...@@ -4,6 +4,7 @@
__kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffers, __global const real4* restrict posq __kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffers, __global const real4* restrict posq
PARAMETER_ARGUMENTS) { PARAMETER_ARGUMENTS) {
INIT_PARAM_DERIVS
unsigned int index = get_global_id(0); unsigned int index = get_global_id(0);
while (index < NUM_ATOMS) { while (index < NUM_ATOMS) {
real4 pos = posq[index]; real4 pos = posq[index];
...@@ -12,4 +13,5 @@ __kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffer ...@@ -12,4 +13,5 @@ __kernel void computeGradientChainRuleTerms(__global real4* restrict forceBuffer
forceBuffers[index] = force; forceBuffers[index] = force;
index += get_global_size(0); index += get_global_size(0);
} }
SAVE_PARAM_DERIVS
} }
platforms/opencl/src/kernels/customGBValueN2.cl
View file @ 74efa95f
...@@ -74,6 +74,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -74,6 +74,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
COMPUTE_VALUE COMPUTE_VALUE
} }
value += tempValue1; value += tempValue1;
ADD_TEMP_DERIVS1
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
} }
#endif #endif
...@@ -123,6 +124,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -123,6 +124,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
} }
value += tempValue1; value += tempValue1;
local_value[tbx+tj] += tempValue2; local_value[tbx+tj] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
} }
#endif #endif
...@@ -137,18 +140,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -137,18 +140,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
// Write results. // Write results.
#ifdef SUPPORTS_64_BIT_ATOMICS #ifdef SUPPORTS_64_BIT_ATOMICS
unsigned int offset = x*TILE_SIZE + tgx; unsigned int offset1 = x*TILE_SIZE + tgx;
atom_add(&global_value[offset], (long) (value*0x100000000)); atom_add(&global_value[offset1], (long) (value*0x100000000));
STORE_PARAM_DERIVS1
if (x != y) { if (x != y) {
offset = y*TILE_SIZE + tgx; unsigned int offset2 = y*TILE_SIZE + tgx;
atom_add(&global_value[offset], (long) (local_value[get_local_id(0)]*0x100000000)); atom_add(&global_value[offset2], (long) (local_value[get_local_id(0)]*0x100000000));
STORE_PARAM_DERIVS2
} }
#else #else
unsigned int offset1 = x*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS; unsigned int offset1 = x*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
unsigned int offset2 = y*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS; unsigned int offset2 = y*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
global_value[offset1] += value; global_value[offset1] += value;
if (x != y) STORE_PARAM_DERIVS1
if (x != y) {
global_value[offset2] += local_value[get_local_id(0)]; global_value[offset2] += local_value[get_local_id(0)];
STORE_PARAM_DERIVS2
}
#endif #endif
} }
...@@ -292,6 +300,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -292,6 +300,8 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
} }
value += tempValue1; value += tempValue1;
local_value[tbx+tj] += tempValue2; local_value[tbx+tj] += tempValue2;
ADD_TEMP_DERIVS1
ADD_TEMP_DERIVS2
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
} }
#endif #endif
...@@ -308,15 +318,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4* ...@@ -308,15 +318,23 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
unsigned int atom2 = y*TILE_SIZE + tgx; unsigned int atom2 = y*TILE_SIZE + tgx;
#endif #endif
#ifdef SUPPORTS_64_BIT_ATOMICS #ifdef SUPPORTS_64_BIT_ATOMICS
atom_add(&global_value[atom1], (long) (value*0x100000000)); unsigned in offset1 = atom1;
if (atom2 < PADDED_NUM_ATOMS) atom_add(&global_value[offset1], (long) (value*0x100000000));
atom_add(&global_value[atom2], (long) (local_value[get_local_id(0)]*0x100000000)); STORE_PARAM_DERIVS1
if (atom2 < PADDED_NUM_ATOMS) {
unsigned int offset2 = atom2;
atom_add(&global_value[offset2], (long) (local_value[get_local_id(0)]*0x100000000));
STORE_PARAM_DERIVS2
}
#else #else
unsigned int offset1 = atom1 + warp*PADDED_NUM_ATOMS; unsigned int offset1 = atom1 + warp*PADDED_NUM_ATOMS;
unsigned int offset2 = atom2 + warp*PADDED_NUM_ATOMS;
global_value[offset1] += value; global_value[offset1] += value;
if (atom2 < PADDED_NUM_ATOMS) STORE_PARAM_DERIVS1
if (atom2 < PADDED_NUM_ATOMS) {
unsigned int offset2 = atom2 + warp*PADDED_NUM_ATOMS;
global_value[offset2] += local_value[get_local_id(0)]; global_value[offset2] += local_value[get_local_id(0)];
STORE_PARAM_DERIVS2
}
#endif #endif
} }
pos++; pos++;
......
platforms/opencl/src/kernels/customGBValuePerParticle.cl
View file @ 74efa95f
...@@ -21,6 +21,7 @@ __kernel void computePerParticleValues(int bufferSize, int numBuffers, __global ...@@ -21,6 +21,7 @@ __kernel void computePerParticleValues(int bufferSize, int numBuffers, __global
for (int i = index+bufferSize; i < totalSize; i += bufferSize) for (int i = index+bufferSize; i < totalSize; i += bufferSize)
sum += valueBuffers[i]; sum += valueBuffers[i];
#endif #endif
REDUCE_PARAM0_DERIV
// Now calculate other values // Now calculate other values
......
tests/TestCustomBondForce.h
View file @ 74efa95f
...@@ -187,8 +187,8 @@ void testEnergyParameterDerivatives() { ...@@ -187,8 +187,8 @@ void testEnergyParameterDerivatives() {
CustomBondForce* bonds = new CustomBondForce("k*(r-r0)^2"); CustomBondForce* bonds = new CustomBondForce("k*(r-r0)^2");
bonds->addGlobalParameter("r0", 0.0); bonds->addGlobalParameter("r0", 0.0);
bonds->addGlobalParameter("k", 0.0); bonds->addGlobalParameter("k", 0.0);
bonds->addEnergyParameterDerivative("r0");
bonds->addEnergyParameterDerivative("k"); bonds->addEnergyParameterDerivative("k");
bonds->addEnergyParameterDerivative("r0");
vector<double> parameters; vector<double> parameters;
bonds->addBond(0, 1, parameters); bonds->addBond(0, 1, parameters);
bonds->addBond(1, 2, parameters); bonds->addBond(1, 2, parameters);
......
tests/TestCustomGBForce.h
View file @ 74efa95f
...@@ -505,10 +505,10 @@ void testEnergyParameterDerivatives() { ...@@ -505,10 +505,10 @@ void testEnergyParameterDerivatives() {
force->addComputedValue("b", "a+B", CustomGBForce::SingleParticle); force->addComputedValue("b", "a+B", CustomGBForce::SingleParticle);
force->addEnergyTerm("C*(a1+b1+a2+b2+r)^0.8", CustomGBForce::ParticlePair); force->addEnergyTerm("C*(a1+b1+a2+b2+r)^0.8", CustomGBForce::ParticlePair);
force->addEnergyTerm("(D-B)*b", CustomGBForce::SingleParticle); force->addEnergyTerm("(D-B)*b", CustomGBForce::SingleParticle);
for (int i = 0; i < numParameters; i++) { for (int i = 0; i < numParameters; i++)
force->addGlobalParameter(paramNames[i], paramValues[i]); force->addGlobalParameter(paramNames[i], paramValues[i]);
for (int i = numParameters-1; i >= 0; i--)
force->addEnergyParameterDerivative(paramNames[i]); force->addEnergyParameterDerivative(paramNames[i]);
}
force->setNonbondedMethod(CustomGBForce::CutoffPeriodic); force->setNonbondedMethod(CustomGBForce::CutoffPeriodic);
force->setCutoffDistance(1.0); force->setCutoffDistance(1.0);
vector<Vec3> positions; vector<Vec3> positions;
......
tests/TestCustomNonbondedForce.h
View file @ 74efa95f
...@@ -1050,8 +1050,8 @@ void testEnergyParameterDerivatives() { ...@@ -1050,8 +1050,8 @@ void testEnergyParameterDerivatives() {
CustomNonbondedForce* nonbonded = new CustomNonbondedForce("k*(r-r0)^2"); CustomNonbondedForce* nonbonded = new CustomNonbondedForce("k*(r-r0)^2");
nonbonded->addGlobalParameter("r0", 0.0); nonbonded->addGlobalParameter("r0", 0.0);
nonbonded->addGlobalParameter("k", 0.0); nonbonded->addGlobalParameter("k", 0.0);
nonbonded->addEnergyParameterDerivative("r0");
nonbonded->addEnergyParameterDerivative("k"); nonbonded->addEnergyParameterDerivative("k");
nonbonded->addEnergyParameterDerivative("r0");
vector<double> parameters; vector<double> parameters;
nonbonded->addParticle(parameters); nonbonded->addParticle(parameters);
nonbonded->addParticle(parameters); nonbonded->addParticle(parameters);
......
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