title: Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations.
abstract: Simulation ofin vivocellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel e ciency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system inE. coli. Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems.
authors.affiliation: School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Hallock
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave., Urbana, IL 61801.
authors.forename: John E
authors.initials: JE
authors.lastname: Stone
authors.affiliation: Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218.
authors.forename: Elijah
authors.initials: E
authors.lastname: Roberts
authors.affiliation: Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801.
authors.forename: Corey
authors.initials: C
authors.lastname: Fry
authors.affiliation: Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801.
authors.forename: Zaida
authors.initials: Z
authors.lastname: Luthey-Schulten
keywords: GPU Computing; Gillespie algorithm; biological cells; distributed memory parallel computing; reaction-diffusion master equation; stochastic simulation