Accelerating reaction–diffusion simulations with general-purpose graphics processing units

descriptionPublicationkeyboard_double_arrow_right Article 08 Nov 2010 English Publisher:Oxford University Press (OUP)Journal:Bioinformatics, volume 27, pages 288-290 (issn: 1367-4803, eissn: 1367-4811,

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Authors: Matthias Vigelius; Aidan Lane; Bernd Meyer 0001;

doi: 10.1093/bioinformatics/btq622

pmid: 21062761

Accelerating reaction–diffusion simulations with general-purpose graphics processing units

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Abstract

Abstract 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/. Contact: matthias.vigelius@monash.edu Supplementary Information: Supplementary data are available at Bioinformatics online.

Related Organizations

Monash University
Australia
Monash University, Clayton campus
Australia

Keywords

Stochastic Processes, Computer Graphics, Computing Methodologies, Algorithms, Software

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