Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations |
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Affiliation: | 1. School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, United States;2. Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave., Urbana, IL 61801, United States;3. Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States;4. Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, United States |
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Abstract: | Simulation of in vivo cellular 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 efficiency 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 in E. coli. Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems. |
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Keywords: | GPU Computing Reaction–diffusion master equation Gillespie algorithm Stochastic simulation Distributed memory parallel computing Biological cells |
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