NAME¶
KernelLauncher -
SYNOPSIS¶
Public Member Functions¶
KernelLauncher (
GPUInterface *inGpu)
void
GetTransitionProbabilitiesSquare (GPUPtr dPtr, GPUPtr dEvec, GPUPtr
dIevc, GPUPtr dEigenValues, GPUPtr distanceQueue, unsigned int totalMatrix,
unsigned int index)
void
PartialsPartialsPruningDynamicCheckScaling (GPUPtr partials1, GPUPtr
partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, int
writeScalingIndex, int readScalingIndex, int cumulativeScalingIndex, GPUPtr
*dScalingFactors, GPUPtr *dScalingFactorsMaster, unsigned int patternCount,
unsigned int categoryCount, int doRescaling, int *hRescalingTrigger, GPUPtr
dRescalingTrigger, int sizeReal)
void
PartialsPartialsPruningDynamicScaling (GPUPtr partials1, GPUPtr
partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr
scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned
int categoryCount, int doRescaling)
void
StatesPartialsPruningDynamicScaling (GPUPtr states1, GPUPtr
partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr
scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned
int categoryCount, int doRescaling)
void
StatesStatesPruningDynamicScaling (GPUPtr states1, GPUPtr states2,
GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr scalingFactors,
GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int
categoryCount, int doRescaling)
void
IntegrateLikelihoodsDynamicScaling (GPUPtr dResult, GPUPtr
dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr
dRootScalingFactors, unsigned int patternCount, unsigned int categoryCount)
void
IntegrateLikelihoodsAutoScaling (GPUPtr dResult, GPUPtr
dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr
dRootScalingFactors, unsigned int patternCount, unsigned int categoryCount)
void
IntegrateLikelihoodsDynamicScalingSecondDeriv (GPUPtr dResult,
GPUPtr dFirstDerivResult, GPUPtr dSecondDerivResult, GPUPtr dRootPartials,
GPUPtr dRootFirstDeriv, GPUPtr dRootSecondDeriv, GPUPtr dWeights, GPUPtr
dFrequencies, GPUPtr dRootScalingFactors, unsigned int patternCount, unsigned
int categoryCount)
void
PartialsPartialsEdgeLikelihoods (GPUPtr dPartialsTmp, GPUPtr
dParentPartials, GPUPtr dChildParials, GPUPtr dTransMatrix, unsigned int
patternCount, unsigned int categoryCount)
void
PartialsPartialsEdgeLikelihoodsSecondDeriv (GPUPtr dPartialsTmp,
GPUPtr dFirstDerivTmp, GPUPtr dSecondDerivTmp, GPUPtr dParentPartials, GPUPtr
dChildParials, GPUPtr dTransMatrix, GPUPtr dFirstDerivMatrix, GPUPtr
dSecondDerivMatrix, unsigned int patternCount, unsigned int categoryCount)
void
StatesPartialsEdgeLikelihoods (GPUPtr dPartialsTmp, GPUPtr
dParentPartials, GPUPtr dChildStates, GPUPtr dTransMatrix, unsigned int
patternCount, unsigned int categoryCount)
void
StatesPartialsEdgeLikelihoodsSecondDeriv (GPUPtr dPartialsTmp,
GPUPtr dFirstDerivTmp, GPUPtr dSecondDerivTmp, GPUPtr dParentPartials, GPUPtr
dChildStates, GPUPtr dTransMatrix, GPUPtr dFirstDerivMatrix, GPUPtr
dSecondDerivMatrix, unsigned int patternCount, unsigned int categoryCount)
void
AccumulateFactorsDynamicScaling (GPUPtr dScalingFactors, GPUPtr
dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned
int patternCount)
void
AccumulateFactorsAutoScaling (GPUPtr dScalingFactors, GPUPtr
dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned
int patternCount, unsigned int scaleBufferSize)
void
RemoveFactorsDynamicScaling (GPUPtr dScalingFactors, GPUPtr
dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned
int patternCount)
void
RescalePartials (GPUPtr partials3, GPUPtr scalingFactors, GPUPtr
cumulativeScaling, unsigned int patternCount, unsigned int categoryCount,
unsigned int fillWithOnes)
void
IntegrateLikelihoods (GPUPtr dResult, GPUPtr dRootPartials, GPUPtr
dWeights, GPUPtr dFrequencies, unsigned int patternCount, unsigned int
categoryCount)
void
IntegrateLikelihoodsSecondDeriv (GPUPtr dResult, GPUPtr
dFirstDerivResult, GPUPtr dSecondDerivResult, GPUPtr dRootPartials, GPUPtr
dRootFirstDeriv, GPUPtr dRootSecondDeriv, GPUPtr dWeights, GPUPtr
dFrequencies, unsigned int patternCount, unsigned int categoryCount)
void
IntegrateLikelihoodsMulti (GPUPtr dResult, GPUPtr dRootPartials,
GPUPtr dWeights, GPUPtr dFrequencies, unsigned int patternCount, unsigned int
categoryCount, unsigned int takeLog)
void
IntegrateLikelihoodsFixedScaleMulti (GPUPtr dResult, GPUPtr
dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dScalingFactors,
GPUPtr dPtrQueue, GPUPtr dMaxScalingFactors, GPUPtr dIndexMaxScalingFactors,
unsigned int patternCount, unsigned int categoryCount, unsigned int
subsetCount, unsigned int subsetIndex)
void
SumSites1 (GPUPtr dArray1, GPUPtr dSum1, GPUPtr dPatternWeights,
unsigned int patternCount)
void
SumSites2 (GPUPtr dArray1, GPUPtr dSum1, GPUPtr dArray2, GPUPtr
dSum2, GPUPtr dPatternWeights, unsigned int patternCount)
void
SumSites3 (GPUPtr dArray1, GPUPtr dSum1, GPUPtr dArray2, GPUPtr
dSum2, GPUPtr dArray3, GPUPtr dSum3, GPUPtr dPatternWeights, unsigned int
patternCount)
void
SetupKernelBlocksAndGrids ()
Protected Member Functions¶
void
LoadKernels ()
Author¶
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