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Commit a3464898 authored by Peter Eastman's avatar Peter Eastman
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Continuing CUDA implementation of CustomNonbondedForce

parent 673b555b
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Showing with 79 additions and 18 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ a3464898
......@@ -82,7 +82,6 @@ static double calcEnergy(ContextImpl& context, CudaPlatform::PlatformData& data,
pos[i] = Vec3(posData[3*i], posData[3*i+1], posData[3*i+2]);
delete[] posData;
refContext.setPositions(pos);
// printf("Total CPU energies: %f\n", refContext.getState(State::Energy).getPotentialEnergy());
return refContext.getState(State::Energy).getPotentialEnergy();
}
else
......@@ -97,9 +96,10 @@ static double calcEnergy(ContextImpl& context, CudaPlatform::PlatformData& data,
kReduceObcGbsaBornForces(gpu);
kCalculateObcGbsaForces2(gpu);
}
else if (data.hasNonbonded) {
else if (data.hasNonbonded)
kCalculateCDLJForces(gpu);
}
if (data.hasCustomNonbonded)
kCalculateCustomNonbondedForces(gpu, data.hasNonbonded);
kCalculateLocalForces(gpu);
if (gpu->bIncludeGBSA)
kReduceBornSumAndForces(gpu);
......@@ -389,8 +389,7 @@ CudaCalcCustomNonbondedForceKernel::~CudaCalcCustomNonbondedForceKernel() {
}
void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const CustomNonbondedForce& force) {
if (data.primaryKernel == NULL)
data.primaryKernel = this;
data.primaryKernel = this; // This must always be the primary kernel so it can update the global parameters
data.hasCustomNonbonded = true;
numParticles = force.getNumParticles();
_gpuContext* gpu = data.gpu;
......@@ -452,21 +451,45 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
paramNames.push_back(force.getParameterName(i));
combiningRules.push_back(force.getParameterCombiningRule(i));
}
globalParamNames.resize(force.getNumGlobalParameters());
globalParamValues.resize(force.getNumGlobalParameters());
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParamNames[i] = force.getGlobalParameterName(i);
globalParamValues[i] = force.getGlobalParameterDefaultValue(i);
}
gpuSetCustomNonbondedParameters(gpu, parameters, exclusionList, exceptionParticle1, exceptionParticle2, exceptionParams, method,
(float)force.getCutoffDistance(), force.getEnergyFunction(), combiningRules, paramNames);
(float)force.getCutoffDistance(), force.getEnergyFunction(), combiningRules, paramNames, globalParamNames);
if (globalParamValues.size() > 0)
SetCustomNonbondedGlobalParams(globalParamValues);
}
void CudaCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context) {
if (data.primaryKernel == this)
if (data.primaryKernel == this) {
updateGlobalParams(context);
calcForces(context, data);
}
}
double CudaCalcCustomNonbondedForceKernel::executeEnergy(ContextImpl& context) {
if (data.primaryKernel == this)
if (data.primaryKernel == this) {
updateGlobalParams(context);
return calcEnergy(context, data, system);
}
return 0.0;
}
void CudaCalcCustomNonbondedForceKernel::updateGlobalParams(ContextImpl& context) {
bool changed = false;
for (int i = 0; i < globalParamNames.size(); i++) {
float value = (float) context.getParameter(globalParamNames[i]);
if (value != globalParamValues[i])
changed = true;
globalParamValues[i] = value;
}
if (changed)
SetCustomNonbondedGlobalParams(globalParamValues);
}
CudaCalcGBSAOBCForceKernel::~CudaCalcGBSAOBCForceKernel() {
}
......
platforms/cuda/src/CudaKernels.h
View file @ a3464898
......@@ -289,8 +289,11 @@ public:
*/
double executeEnergy(ContextImpl& context);
private:
void updateGlobalParams(ContextImpl& context);
CudaPlatform::PlatformData& data;
int numParticles;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
System& system;
};
......
platforms/cuda/src/kernels/cudaKernels.h
View file @ a3464898
......@@ -96,3 +96,4 @@ extern void GetRandomSim(gpuContext gpu);
extern void SetCustomNonbondedForceExpression(const Expression<128>& expression);
extern void SetCustomNonbondedEnergyExpression(const Expression<128>& expression);
extern void SetCustomNonbondedCombiningRules(const Expression<64>* expressions);
extern void SetCustomNonbondedGlobalParams(const std::vector<float>& paramValues);
platforms/cuda/src/kernels/cudatypes.h
View file @ a3464898
......@@ -244,7 +244,7 @@ enum CudaNonbondedMethod
};
enum ExpressionOp {
CONSTANT = 0, VARIABLE0, VARIABLE1, VARIABLE2, VARIABLE3, VARIABLE4, VARIABLE5, VARIABLE6, VARIABLE7, VARIABLE8, CUSTOM, ADD, SUBTRACT, MULTIPLY, DIVIDE,
CONSTANT = 0, VARIABLE0, VARIABLE1, VARIABLE2, VARIABLE3, VARIABLE4, VARIABLE5, VARIABLE6, VARIABLE7, VARIABLE8, GLOBAL, CUSTOM, ADD, SUBTRACT, MULTIPLY, DIVIDE,
POWER, NEGATE, SQRT, EXP, LOG, SIN, COS, SEC, CSC, TAN, COT, ASIN, ACOS, ATAN, SQUARE, CUBE, RECIPROCAL, INCREMENT, DECREMENT
};
......
platforms/cuda/src/kernels/gpu.cpp
View file @ a3464898
......@@ -132,7 +132,7 @@ static const float BOLTZ = (RGAS / KILO); // (k
#define DUMP_PARAMETERS 0
template <int SIZE>
static Expression<SIZE> createExpression(const string& expression, const Lepton::ExpressionProgram& program, const vector<string>& variables) {
static Expression<SIZE> createExpression(const string& expression, const Lepton::ExpressionProgram& program, const vector<string>& variables, const vector<string>& globalParamNames) {
Expression<SIZE> exp;
if (program.getNumOperations() > SIZE)
throw OpenMMException("Expression contains too many operations: "+expression);
......@@ -164,8 +164,14 @@ static Expression<SIZE> createExpression(const string& expression, const Lepton:
exp.op[i] = VARIABLE7;
else if (variables.size() > 8 && op.getName() == variables[8])
exp.op[i] = VARIABLE8;
else
throw OpenMMException("Unknown variable '"+op.getName()+"' in expression: "+expression);
else {
int j;
for (j = 0; j < globalParamNames.size() && op.getName() != globalParamNames[j]; j++);
if (j == globalParamNames.size())
throw OpenMMException("Unknown variable '"+op.getName()+"' in expression: "+expression);
exp.op[i] = GLOBAL;
exp.arg[i] = j;
}
break;
case Operation::ADD:
exp.op[i] = ADD;
......@@ -560,12 +566,15 @@ void gpuSetNonbondedCutoff(gpuContext gpu, float cutoffDistance, float solventDi
extern "C"
void gpuSetCustomNonbondedParameters(gpuContext gpu, const vector<vector<double> >& parameters, const vector<vector<int> >& exclusions,
const vector<int>& exceptionAtom1, const vector<int>& exceptionAtom2, const vector<vector<double> >& exceptionParams,
CudaNonbondedMethod method, float cutoffDistance, const string& energyExp, const vector<string>& combiningRules, const vector<string>& paramNames)
CudaNonbondedMethod method, float cutoffDistance, const string& energyExp, const vector<string>& combiningRules,
const vector<string>& paramNames, const vector<string>& globalParamNames)
{
if (gpu->sim.nonbondedCutoff != 0.0f && gpu->sim.nonbondedCutoff != cutoffDistance)
throw OpenMMException("All nonbonded forces must use the same cutoff");
if (paramNames.size() > 4)
throw OpenMMException("CudaPlatform only supports four per-atom parameters for custom nonbonded forces");
if (globalParamNames.size() > 8)
throw OpenMMException("CudaPlatform only supports eight global parameters for custom nonbonded forces");
gpu->sim.nonbondedCutoff = cutoffDistance;
gpu->sim.nonbondedCutoffSqr = cutoffDistance*cutoffDistance;
gpu->sim.customNonbondedMethod = method;
......@@ -612,8 +621,8 @@ void gpuSetCustomNonbondedParameters(gpuContext gpu, const vector<vector<double>
variables.push_back("r");
for (int i = 0; i < paramNames.size(); i++)
variables.push_back(paramNames[i]);
SetCustomNonbondedEnergyExpression(createExpression<128>(energyExp, Lepton::Parser::parse(energyExp).optimize().createProgram(), variables));
SetCustomNonbondedForceExpression(createExpression<128>(energyExp, Lepton::Parser::parse(energyExp).differentiate("r").optimize().createProgram(), variables));
SetCustomNonbondedEnergyExpression(createExpression<128>(energyExp, Lepton::Parser::parse(energyExp).optimize().createProgram(), variables, globalParamNames));
SetCustomNonbondedForceExpression(createExpression<128>(energyExp, Lepton::Parser::parse(energyExp).differentiate("r").optimize().createProgram(), variables, globalParamNames));
Expression<64> paramExpressions[4];
vector<string> combiningRuleParams;
combiningRuleParams.push_back("");
......@@ -627,7 +636,7 @@ void gpuSetCustomNonbondedParameters(gpuContext gpu, const vector<vector<double>
combiningRuleParams.push_back("");
}
for (int i = 0; i < paramNames.size(); i++)
paramExpressions[i] = createExpression<64>(combiningRules[i], Lepton::Parser::parse(combiningRules[i]).optimize().createProgram(), combiningRuleParams);
paramExpressions[i] = createExpression<64>(combiningRules[i], Lepton::Parser::parse(combiningRules[i]).optimize().createProgram(), combiningRuleParams, globalParamNames);
SetCustomNonbondedCombiningRules(paramExpressions);
}
......
platforms/cuda/src/kernels/gputypes.h
View file @ a3464898
......@@ -186,7 +186,7 @@ extern "C"
void gpuSetCustomNonbondedParameters(gpuContext gpu, const std::vector<std::vector<double> >& parameters, const std::vector<std::vector<int> >& exclusions,
const std::vector<int>& exceptionAtom1, const std::vector<int>& exceptionAtom2, const std::vector<std::vector<double> >& exceptionParams,
CudaNonbondedMethod method, float cutoffDistance, const std::string& energyExp, const std::vector<std::string>& combiningRules,
const std::vector<std::string>& paramNames);
const std::vector<std::string>& paramNames, const std::vector<std::string>& globalParamNames);
extern "C"
void gpuSetEwaldParameters(gpuContext gpu, float alpha, int kmaxx, int kmaxy, int kmaxz);
......
platforms/cuda/src/kernels/kCalculateCustomNonbondedForces.cu
View file @ a3464898
......@@ -53,6 +53,7 @@ static __constant__ cudaGmxSimulation cSim;
static __constant__ Expression<128> forceExp;
static __constant__ Expression<128> energyExp;
static __constant__ Expression<64> combiningRules[4];
static __constant__ float globalParams[8];
void SetCalculateCustomNonbondedForcesSim(gpuContext gpu)
{
......@@ -89,6 +90,13 @@ void SetCustomNonbondedCombiningRules(const Expression<64>* expressions)
RTERROR(status, "SetCustomNonbondedCombiningRules: cudaMemcpyToSymbol failed");
}
void SetCustomNonbondedGlobalParams(const vector<float>& paramValues)
{
cudaError_t status;
status = cudaMemcpyToSymbol(globalParams, &paramValues[0], sizeof(globalParams));
RTERROR(status, "SetCustomNonbondedGlobalParams: cudaMemcpyToSymbol failed");
}
template<int SIZE>
__device__ float kEvaluateExpression_kernel(Expression<SIZE>* expression, float* stack, float var0, float4 vars1, float4 vars2)
{
......@@ -127,6 +135,9 @@ __device__ float kEvaluateExpression_kernel(Expression<SIZE>* expression, float*
case VARIABLE8:
stack[++stackPointer] = vars2.w;
break;
case GLOBAL:
stack[++stackPointer] = globalParams[(int) expression->arg[i]];
break;
case ADD:
{
float temp = stack[stackPointer];
......
platforms/cuda/src/kernels/kCalculateCustomNonbondedForces.h
View file @ a3464898
......@@ -39,6 +39,7 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
unsigned int numWorkUnits = cSim.pInteractionCount[0];
unsigned int pos = warp*numWorkUnits/totalWarps;
unsigned int end = (warp+1)*numWorkUnits/totalWarps;
float totalEnergy = 0.0f;
#ifdef USE_CUTOFF
float3* tempBuffer = (float3*) &sA[cSim.nonbond_threads_per_block];
#endif
......@@ -112,6 +113,7 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
float r = sqrt(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r;
float dEdR = -kEvaluateExpression_kernel(&forceExp, &stack[MAX_STACK_SIZE*threadIdx.x], r, combinedParams, combinedParams)*invR;
float energy = kEvaluateExpression_kernel(&energyExp, &stack[MAX_STACK_SIZE*threadIdx.x], r, combinedParams, combinedParams);
#ifdef USE_CUTOFF
if (!(excl & 0x1) || r > cSim.nonbondedCutoff)
#else
......@@ -119,7 +121,9 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
#endif
{
dEdR = 0.0f;
energy = 0.0f;
}
totalEnergy += 0.5f*energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
......@@ -213,12 +217,15 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
float r = sqrt(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r;
float dEdR = -kEvaluateExpression_kernel(&forceExp, &stack[MAX_STACK_SIZE*threadIdx.x], r, combinedParams, combinedParams)*invR;
float energy = kEvaluateExpression_kernel(&energyExp, &stack[MAX_STACK_SIZE*threadIdx.x], r, combinedParams, combinedParams);
#ifdef USE_CUTOFF
if (r > cSim.nonbondedCutoff)
{
dEdR = 0.0f;
energy = 0.0f;
}
#endif
totalEnergy += energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
......@@ -276,12 +283,15 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
float r = sqrt(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r;
float dEdR = -kEvaluateExpression_kernel(&forceExp, &stack[MAX_STACK_SIZE*threadIdx.x], r, combinedParams, combinedParams)*invR;
float energy = kEvaluateExpression_kernel(&energyExp, &stack[MAX_STACK_SIZE*threadIdx.x], r, combinedParams, combinedParams);
#ifdef USE_CUTOFF
if (r > cSim.nonbondedCutoff)
{
dEdR = 0.0f;
energy = 0.0f;
}
#endif
totalEnergy += energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
......@@ -375,6 +385,7 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
float r = sqrt(dx*dx + dy*dy + dz*dz);
float invR = 1.0f/r;
float dEdR = -kEvaluateExpression_kernel(&forceExp, &stack[MAX_STACK_SIZE*threadIdx.x], r, combinedParams, combinedParams)*invR;
float energy = kEvaluateExpression_kernel(&energyExp, &stack[MAX_STACK_SIZE*threadIdx.x], r, combinedParams, combinedParams);
#ifdef USE_CUTOFF
if (!(excl & 0x1) || r > cSim.nonbondedCutoff)
#else
......@@ -382,7 +393,9 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
#endif
{
dEdR = 0.0f;
energy = 0.0f;
}
totalEnergy += energy;
dx *= dEdR;
dy *= dEdR;
dz *= dEdR;
......@@ -430,4 +443,5 @@ __global__ void METHOD_NAME(kCalculateCustomNonbonded, Forces_kernel)(unsigned i
pos++;
}
cSim.pEnergy[blockIdx.x*blockDim.x+threadIdx.x] += totalEnergy;
}
platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp
View file @ a3464898
......@@ -205,7 +205,7 @@ void testPeriodic() {
int main() {
try {
testSimpleExpression();
// testParameters();
testParameters();
// testExceptions();
testCutoff();
testPeriodic();
......
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