Accelerating Reaction-Diffusion Simulations with General-Purpose Graphics Processing Units.

Accelerating Reaction-Diffusion Simulations with General-Purpose Graphics Processing Units.: "Publication Date: 2010 Nov 9 PMID: 21062761
Authors: Vigelius, M. - Lane, A. - Meyer, B.
Journal: Bioinformatics

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 information is available at Bioinformatics online.

post to: CiteULike"