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Commit f15f591b authored by Peter Eastman's avatar Peter Eastman
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Continuing to convert CudaArrays.

parent b8c86406
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Showing with 430 additions and 598 deletions
platforms/cuda/include/CudaKernels.h
View file @ f15f591b
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2017 Stanford University and the Authors. *
* Portions copyright (c) 2008-2018 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -265,9 +265,8 @@ private:
class CudaCalcHarmonicBondForceKernel : public CalcHarmonicBondForceKernel {
public:
CudaCalcHarmonicBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcHarmonicBondForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
hasInitializedKernel(false), cu(cu), system(system) {
}
~CudaCalcHarmonicBondForceKernel();
/**
* Initialize the kernel.
*
......@@ -298,7 +297,7 @@ private:
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaArray* params;
CudaArray params;
};
/**
......@@ -307,7 +306,7 @@ private:
class CudaCalcCustomBondForceKernel : public CalcCustomBondForceKernel {
public:
CudaCalcCustomBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomBondForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), params(NULL), globals(NULL) {
hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
}
~CudaCalcCustomBondForceKernel();
/**
......@@ -341,7 +340,7 @@ private:
ForceInfo* info;
const System& system;
CudaParameterSet* params;
CudaArray* globals;
CudaArray globals;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
};
......@@ -352,9 +351,8 @@ private:
class CudaCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
public:
CudaCalcHarmonicAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcHarmonicAngleForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
hasInitializedKernel(false), cu(cu), system(system) {
}
~CudaCalcHarmonicAngleForceKernel();
/**
* Initialize the kernel.
*
......@@ -385,7 +383,7 @@ private:
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaArray* params;
CudaArray params;
};
/**
......@@ -394,7 +392,7 @@ private:
class CudaCalcCustomAngleForceKernel : public CalcCustomAngleForceKernel {
public:
CudaCalcCustomAngleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomAngleForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), params(NULL), globals(NULL) {
hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
}
~CudaCalcCustomAngleForceKernel();
/**
......@@ -428,7 +426,7 @@ private:
ForceInfo* info;
const System& system;
CudaParameterSet* params;
CudaArray* globals;
CudaArray globals;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
};
......@@ -439,9 +437,8 @@ private:
class CudaCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
public:
CudaCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcPeriodicTorsionForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
hasInitializedKernel(false), cu(cu), system(system) {
}
~CudaCalcPeriodicTorsionForceKernel();
/**
* Initialize the kernel.
*
......@@ -472,7 +469,7 @@ private:
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaArray* params;
CudaArray params;
};
/**
......@@ -481,9 +478,8 @@ private:
class CudaCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
public:
CudaCalcRBTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcRBTorsionForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), params1(NULL), params2(NULL) {
hasInitializedKernel(false), cu(cu), system(system) {
}
~CudaCalcRBTorsionForceKernel();
/**
* Initialize the kernel.
*
......@@ -514,8 +510,8 @@ private:
CudaContext& cu;
ForceInfo* info;
const System& system;
CudaArray* params1;
CudaArray* params2;
CudaArray params1;
CudaArray params2;
};
/**
......@@ -524,9 +520,8 @@ private:
class CudaCalcCMAPTorsionForceKernel : public CalcCMAPTorsionForceKernel {
public:
CudaCalcCMAPTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCMAPTorsionForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), coefficients(NULL), mapPositions(NULL), torsionMaps(NULL) {
hasInitializedKernel(false), cu(cu), system(system) {
}
~CudaCalcCMAPTorsionForceKernel();
/**
* Initialize the kernel.
*
......@@ -558,9 +553,9 @@ private:
ForceInfo* info;
const System& system;
std::vector<int2> mapPositionsVec;
CudaArray* coefficients;
CudaArray* mapPositions;
CudaArray* torsionMaps;
CudaArray coefficients;
CudaArray mapPositions;
CudaArray torsionMaps;
};
/**
......@@ -569,7 +564,7 @@ private:
class CudaCalcCustomTorsionForceKernel : public CalcCustomTorsionForceKernel {
public:
CudaCalcCustomTorsionForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomTorsionForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), params(NULL), globals(NULL) {
hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
}
~CudaCalcCustomTorsionForceKernel();
/**
......@@ -603,7 +598,7 @@ private:
ForceInfo* info;
const System& system;
CudaParameterSet* params;
CudaArray* globals;
CudaArray globals;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
};
......@@ -614,9 +609,7 @@ private:
class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
CudaCalcNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcNonbondedForceKernel(name, platform),
cu(cu), hasInitializedFFT(false), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), directPmeGrid(NULL), reciprocalPmeGrid(NULL),
pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeDispersionBsplineModuliX(NULL), pmeDispersionBsplineModuliY(NULL),
pmeDispersionBsplineModuliZ(NULL), pmeAtomRange(NULL), pmeAtomGridIndex(NULL), pmeEnergyBuffer(NULL), sort(NULL), dispersionFft(NULL), fft(NULL), pmeio(NULL) {
cu(cu), hasInitializedFFT(false), sort(NULL), dispersionFft(NULL), fft(NULL), pmeio(NULL) {
}
~CudaCalcNonbondedForceKernel();
/**
......@@ -682,20 +675,20 @@ private:
CudaContext& cu;
ForceInfo* info;
bool hasInitializedFFT;
CudaArray* sigmaEpsilon;
CudaArray* exceptionParams;
CudaArray* cosSinSums;
CudaArray* directPmeGrid;
CudaArray* reciprocalPmeGrid;
CudaArray* pmeBsplineModuliX;
CudaArray* pmeBsplineModuliY;
CudaArray* pmeBsplineModuliZ;
CudaArray* pmeDispersionBsplineModuliX;
CudaArray* pmeDispersionBsplineModuliY;
CudaArray* pmeDispersionBsplineModuliZ;
CudaArray* pmeAtomRange;
CudaArray* pmeAtomGridIndex;
CudaArray* pmeEnergyBuffer;
CudaArray sigmaEpsilon;
CudaArray exceptionParams;
CudaArray cosSinSums;
CudaArray directPmeGrid;
CudaArray reciprocalPmeGrid;
CudaArray pmeBsplineModuliX;
CudaArray pmeBsplineModuliY;
CudaArray pmeBsplineModuliZ;
CudaArray pmeDispersionBsplineModuliX;
CudaArray pmeDispersionBsplineModuliY;
CudaArray pmeDispersionBsplineModuliZ;
CudaArray pmeAtomRange;
CudaArray pmeAtomGridIndex;
CudaArray pmeEnergyBuffer;
CudaSort* sort;
Kernel cpuPme;
PmeIO* pmeio;
......@@ -737,7 +730,7 @@ private:
class CudaCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
public:
CudaCalcCustomNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomNonbondedForceKernel(name, platform),
cu(cu), params(NULL), globals(NULL), interactionGroupData(NULL), forceCopy(NULL), system(system), hasInitializedKernel(false) {
cu(cu), params(NULL), forceCopy(NULL), system(system), hasInitializedKernel(false) {
}
~CudaCalcCustomNonbondedForceKernel();
/**
......@@ -769,13 +762,13 @@ private:
CudaContext& cu;
ForceInfo* info;
CudaParameterSet* params;
CudaArray* globals;
CudaArray* interactionGroupData;
CudaArray globals;
CudaArray interactionGroupData;
CUfunction interactionGroupKernel;
std::vector<void*> interactionGroupArgs;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
std::vector<CudaArray> tabulatedFunctions;
double longRangeCoefficient;
std::vector<double> longRangeCoefficientDerivs;
bool hasInitializedLongRangeCorrection, hasInitializedKernel, hasParamDerivs;
......@@ -790,9 +783,8 @@ private:
class CudaCalcGBSAOBCForceKernel : public CalcGBSAOBCForceKernel {
public:
CudaCalcGBSAOBCForceKernel(std::string name, const Platform& platform, CudaContext& cu) : CalcGBSAOBCForceKernel(name, platform), cu(cu),
hasCreatedKernels(false), params(NULL), bornSum(NULL), bornRadii(NULL), bornForce(NULL), obcChain(NULL) {
hasCreatedKernels(false) {
}
~CudaCalcGBSAOBCForceKernel();
/**
* Initialize the kernel.
*
......@@ -823,11 +815,11 @@ private:
int maxTiles;
CudaContext& cu;
ForceInfo* info;
CudaArray* params;
CudaArray* bornSum;
CudaArray* bornRadii;
CudaArray* bornForce;
CudaArray* obcChain;
CudaArray params;
CudaArray bornSum;
CudaArray bornRadii;
CudaArray bornForce;
CudaArray obcChain;
CUfunction computeBornSumKernel;
CUfunction reduceBornSumKernel;
CUfunction force1Kernel;
......@@ -841,8 +833,7 @@ private:
class CudaCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
public:
CudaCalcCustomGBForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomGBForceKernel(name, platform),
hasInitializedKernels(false), cu(cu), params(NULL), computedValues(NULL), energyDerivs(NULL), energyDerivChain(NULL), longEnergyDerivs(NULL), globals(NULL),
valueBuffers(NULL), system(system) {
hasInitializedKernels(false), cu(cu), params(NULL), computedValues(NULL), energyDerivs(NULL), energyDerivChain(NULL), system(system) {
}
~CudaCalcCustomGBForceKernel();
/**
......@@ -880,13 +871,13 @@ private:
CudaParameterSet* energyDerivs;
CudaParameterSet* energyDerivChain;
std::vector<CudaParameterSet*> dValuedParam;
std::vector<CudaArray*> dValue0dParam;
CudaArray* longEnergyDerivs;
CudaArray* globals;
CudaArray* valueBuffers;
std::vector<CudaArray> dValue0dParam;
CudaArray longEnergyDerivs;
CudaArray globals;
CudaArray valueBuffers;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
std::vector<CudaArray> tabulatedFunctions;
std::vector<bool> pairValueUsesParam, pairEnergyUsesParam, pairEnergyUsesValue;
const System& system;
CUfunction pairValueKernel, perParticleValueKernel, pairEnergyKernel, perParticleEnergyKernel, gradientChainRuleKernel;
......@@ -901,7 +892,7 @@ private:
class CudaCalcCustomExternalForceKernel : public CalcCustomExternalForceKernel {
public:
CudaCalcCustomExternalForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomExternalForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), system(system), params(NULL), globals(NULL) {
hasInitializedKernel(false), cu(cu), system(system), params(NULL) {
}
~CudaCalcCustomExternalForceKernel();
/**
......@@ -935,7 +926,7 @@ private:
ForceInfo* info;
const System& system;
CudaParameterSet* params;
CudaArray* globals;
CudaArray globals;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
};
......@@ -946,8 +937,7 @@ private:
class CudaCalcCustomHbondForceKernel : public CalcCustomHbondForceKernel {
public:
CudaCalcCustomHbondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomHbondForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), donorParams(NULL), acceptorParams(NULL), donors(NULL), acceptors(NULL),
globals(NULL), donorExclusions(NULL), acceptorExclusions(NULL), system(system) {
hasInitializedKernel(false), cu(cu), donorParams(NULL), acceptorParams(NULL), system(system) {
}
~CudaCalcCustomHbondForceKernel();
/**
......@@ -981,14 +971,14 @@ private:
ForceInfo* info;
CudaParameterSet* donorParams;
CudaParameterSet* acceptorParams;
CudaArray* globals;
CudaArray* donors;
CudaArray* acceptors;
CudaArray* donorExclusions;
CudaArray* acceptorExclusions;
CudaArray globals;
CudaArray donors;
CudaArray acceptors;
CudaArray donorExclusions;
CudaArray acceptorExclusions;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
std::vector<CudaArray> tabulatedFunctions;
std::vector<void*> donorArgs, acceptorArgs;
const System& system;
CUfunction donorKernel, acceptorKernel;
......@@ -1000,7 +990,7 @@ private:
class CudaCalcCustomCentroidBondForceKernel : public CalcCustomCentroidBondForceKernel {
public:
CudaCalcCustomCentroidBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomCentroidBondForceKernel(name, platform),
cu(cu), params(NULL), globals(NULL), groupParticles(NULL), groupWeights(NULL), groupOffsets(NULL), groupForces(NULL), bondGroups(NULL), centerPositions(NULL), system(system) {
cu(cu), params(NULL), system(system) {
}
~CudaCalcCustomCentroidBondForceKernel();
/**
......@@ -1034,16 +1024,16 @@ private:
CudaContext& cu;
ForceInfo* info;
CudaParameterSet* params;
CudaArray* globals;
CudaArray* groupParticles;
CudaArray* groupWeights;
CudaArray* groupOffsets;
CudaArray* groupForces;
CudaArray* bondGroups;
CudaArray* centerPositions;
CudaArray globals;
CudaArray groupParticles;
CudaArray groupWeights;
CudaArray groupOffsets;
CudaArray groupForces;
CudaArray bondGroups;
CudaArray centerPositions;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
std::vector<CudaArray> tabulatedFunctions;
std::vector<void*> groupForcesArgs;
CUfunction computeCentersKernel, groupForcesKernel, applyForcesKernel;
const System& system;
......@@ -1055,7 +1045,7 @@ private:
class CudaCalcCustomCompoundBondForceKernel : public CalcCustomCompoundBondForceKernel {
public:
CudaCalcCustomCompoundBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomCompoundBondForceKernel(name, platform),
cu(cu), params(NULL), globals(NULL), system(system) {
cu(cu), params(NULL), system(system) {
}
~CudaCalcCustomCompoundBondForceKernel();
/**
......@@ -1088,10 +1078,10 @@ private:
CudaContext& cu;
ForceInfo* info;
CudaParameterSet* params;
CudaArray* globals;
CudaArray globals;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
std::vector<CudaArray> tabulatedFunctions;
const System& system;
};
......@@ -1101,9 +1091,7 @@ private:
class CudaCalcCustomManyParticleForceKernel : public CalcCustomManyParticleForceKernel {
public:
CudaCalcCustomManyParticleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomManyParticleForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), params(NULL), particleTypes(NULL), orderIndex(NULL), particleOrder(NULL), exclusions(NULL),
exclusionStartIndex(NULL), blockCenter(NULL), blockBoundingBox(NULL), neighborPairs(NULL), numNeighborPairs(NULL), neighborStartIndex(NULL),
numNeighborsForAtom(NULL), neighbors(NULL), system(system) {
hasInitializedKernel(false), cu(cu), params(NULL), system(system) {
}
~CudaCalcCustomManyParticleForceKernel();
/**
......@@ -1138,21 +1126,21 @@ private:
NonbondedMethod nonbondedMethod;
int maxNeighborPairs, forceWorkgroupSize, findNeighborsWorkgroupSize;
CudaParameterSet* params;
CudaArray* particleTypes;
CudaArray* orderIndex;
CudaArray* particleOrder;
CudaArray* exclusions;
CudaArray* exclusionStartIndex;
CudaArray* blockCenter;
CudaArray* blockBoundingBox;
CudaArray* neighborPairs;
CudaArray* numNeighborPairs;
CudaArray* neighborStartIndex;
CudaArray* numNeighborsForAtom;
CudaArray* neighbors;
CudaArray particleTypes;
CudaArray orderIndex;
CudaArray particleOrder;
CudaArray exclusions;
CudaArray exclusionStartIndex;
CudaArray blockCenter;
CudaArray blockBoundingBox;
CudaArray neighborPairs;
CudaArray numNeighborPairs;
CudaArray neighborStartIndex;
CudaArray numNeighborsForAtom;
CudaArray neighbors;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
std::vector<CudaArray> tabulatedFunctions;
std::vector<void*> forceArgs, blockBoundsArgs, neighborsArgs, startIndicesArgs, copyPairsArgs;
const System& system;
CUfunction forceKernel, blockBoundsKernel, neighborsKernel, startIndicesKernel, copyPairsKernel;
......
platforms/cuda/src/CudaBondedUtilities.cpp
View file @ f15f591b
......@@ -84,8 +84,10 @@ void CudaBondedUtilities::initialize(const System& system) {
for (int i = 0; i < numForces; i++) {
int numBonds = forceAtoms[i].size();
int numAtoms = forceAtoms[i][0].size();
int numArrays = (numAtoms+3)/4;
int startAtom = 0;
while (startAtom < numAtoms) {
atomIndices[i].resize(numArrays);
for (int j = 0; j < numArrays; j++) {
int width = min(numAtoms-startAtom, 4);
int paddedWidth = (width == 3 ? 4 : width);
vector<unsigned int> indexVec(paddedWidth*numBonds);
......@@ -93,9 +95,8 @@ void CudaBondedUtilities::initialize(const System& system) {
for (int atom = 0; atom < width; atom++)
indexVec[bond*paddedWidth+atom] = forceAtoms[i][bond][startAtom+atom];
}
atomIndices[i].push_back(CudaArray());
atomIndices[i].back().initialize(context, numBonds, 4*paddedWidth, "bondedIndices");
atomIndices[i].back().upload(&indexVec[0]);
atomIndices[i][j].initialize(context, numBonds, 4*paddedWidth, "bondedIndices");
atomIndices[i][j].upload(&indexVec[0]);
startAtom += width;
}
}
......
platforms/cuda/src/CudaKernels.cpp
View file @ f15f591b
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