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

Authors:
Matthias Vigelius;Aidan Lane;Bernd Meyer
Affiliations:
-;-;-
Venue:
Bioinformatics
Year:
2011

Citing 0
Cited 2

Parallel implementation of the diffusion-drift algorithm for modeling the electrophysiological activity of breast tumors

Journal of Parallel and Distributed Computing
The Relevance of Topology in Parallel Simulation of Biological Networks

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

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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.