Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units 英文参考文献.docVIP

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Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units 英文参考文献.doc

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Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units 英文参考文献

AcceleratingtheGillespieExactStochasticSimulation AlgorithmUsingHybridParallelExecutiononGraphics ProcessingUnits IvanKomarov,RoshanM.D’Souza* DepartmentofMechanicalEngineering,ComplexSystemsSimulationLab,UniversityofWisconsin-Milwaukee,Milwaukee,Wisconsin,UnitedStatesofAmerica Abstract The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differentialequations.TheinherentlimitationsoftheGSSAincludethetimerequiredforexecutingasinglerunandthe needfor multipleruns forparameter sweepexercises duetothestochastic natureof thesimulation. Evenveryefficient variantsofGSSAareprohibitivelyexpensivetocomputeandperformparametersweeps.Herewepresentanovelvariantof theexactGSSAthatisamenabletoaccelerationbyusinggraphicsprocessingunits(GPUs).Weparallelizetheexecutionofa single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, whichisthebottleneckincomputingtheGSSA.Ourbenchmarksshowan8621206performancegainovervariousstate- of-the-artserialalgorithmswhensimulatingdifferenttypesofmodels. Citation:KomarovI,D’SouzaRM(2012)AcceleratingtheGillespieExactStochasticSimulationAlgorithmUsingHybridParallelExecutiononGraphicsProcessing Units.PLoSONE7(11):e46693.doi:10.1371/journal.pone.0046693 Editor:MariaSchilstra,UniversityofHertfordshire,UnitedKingdom ReceivedJune1,2012;AcceptedSeptember3,2012;PublishedNovember9,2012 Copyright:?2012Komarov,D’Souza.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermits unrestricteduse,distribution,andreproductioninanymedium,providedth