TCB Publications - Paper Request

Michael J. Hallock, John E. Stone, Elijah Roberts, Corey Fry, and Zaida Luthey-Schulten. Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. Parallel Computing, 40:86-99, 2014.

HALL2014-ZLS 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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