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

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini
Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX1 3LB
IEEE Transactions on Parallel and Distributed Systems, 2011

@article{klingbeil2011fat,

   title={Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions},

   author={Klingbeil, G. and Erban, R. and Giles, M. and Maini, P.K.},

   journal={IEEE Trans. Parallel Distributed Syst},

   year={2011}

}

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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 minimise data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximises 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 (J. Phys. Chem, Vol. 81, p. 2340-2361, 1977). 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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