Open AccessAccelerating the Gillespie τ-Leaping Method Using Graphics Processing Units
Author(s) -
Ivan Komarov,
Roshan D’Souza,
José-Juan Tapia
Publication year - 2012
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0037370
Subject(s) - computer science , graphics processing unit , graphics , acceleration , parallel computing , implementation , computational science , cuda , computer graphics , general purpose computing on graphics processing units , algorithm , computer engineering , computer graphics (images) , programming language , physics , classical mechanics
The Gillespie τ -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 τ is quite expensive. In this paper, we explore the acceleration of the τ -Leaping Method using Graphics Processing Unit (GPUs) for ultra-large networks (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.