Accelerating the Gillespie t-Leaping Method Using Graphics Processing Units

The Gillespie t-Leaping Method is an approximate algorithm that is faster than the exact Direct Method (DM) due to the progression of the simulation with larger time steps. However, the procedure to compute the time leap t is quite expensive. In this paper, we explore the acceleration of the t-Leaping Method using Graphics Processing Unit (GPUs) for ultra-large networks (w0:5e reaction channels). We have developed data structures and algorithms that take advantage of the unique hardware architecture and available libraries. Our results show that we obtain a performance gain of over 60x when compared with the best conventional implementations. Citation: Komarov I, D’Souza RM, Tapia J-J (2012) Accelerating the Gillespie t-Leaping Method Using Graphics Processing Units. PLoS ONE 7(6): e37370. doi:10.1371/journal.pone.0037370 Editor: Jörg Langowski, German Cancer Research Center, Germany Received November 29, 2011; Accepted April 19, 2012; Published June 8, 2012 Copyright: 2012 Komarov et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by the grants CNS 0968519 and CCF 1013278 from the National Science Foundation (NSF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected]