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Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini
Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX1 3LB
IEEE Transactions on Parallel and Distributed Systems, Vol. 23, No. 2, 2012

@article{klinbeil2011fat,

   title={Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions},

   author={Klingbeil, Guido and Erban, Radek and Giles, Mike and Maini, Philip K.},

   journal={IEEE Transactions on Parallel and Distributed Systems},

   volume={23},

   year={2012}

}

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We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimize data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximizes parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie [14]. In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system’s size.
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