The Mathematical Institute, University of Oxford, Eprints Archive

Fat versus thin threading approach on GPUs: application to stochastic simulation of chemical reactions

Klingbeil, G. and Erban, R. and Giles, M. B. and Maini, P. K. (2012) Fat versus thin threading approach on GPUs: application to stochastic simulation of chemical reactions. IEEE Transactions on Parallel & Distributed Systems, 23 (2). pp. 280-287.

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Abstract

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.

Item Type:Article
Uncontrolled Keywords:Parallel processing , compute unified device architecture (CUDA) , graphics processing unit (GPU)
Subjects:A - C > Biology and other natural sciences
ID Code:1458
Deposited By:Philip Maini
Deposited On:07 Jan 2012 09:10
Last Modified:08 Oct 2012 14:20

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