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 () |