Accelerating reaction-diffusion simulations with general-purpose graphics processing units
FIT Centre for Research in Intelligent Systems, Monash University, Clayton Victoria 3800, Australia
Bioinformatics, Volume 27 Issue 2, January 2011
@article{vigelius2011accelerating,
title={Accelerating reaction–diffusion simulations with general-purpose graphics processing units},
author={Vigelius, M. and Lane, A. and Meyer, B.},
journal={Bioinformatics},
volume={27},
number={2},
pages={288},
year={2011},
publisher={Oxford Univ Press}
}
SUMMARY: We present a massively parallel stochastic simulation algorithm (SSA) for reaction-diffusion systems implemented on Graphics Processing Units (GPUs). These are designated chips optimized to process a high number of floating point operations in parallel, rendering them well-suited for a range of scientific high-performance computations. Newer GPU generations provide a high-level programming interface which turns them into General-Purpose Graphics Processing Units (GPGPUs). Our SSA exploits GPGPU architecture to achieve a performance gain of two orders of magnitude over the fastest existing implementations on conventional hardware. AVAILABILITY: The software is freely available at http://www.csse.monash.edu.au/~berndm/inchman/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
September 23, 2011 by hgpu
