Literature DB >> 21062761

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

Matthias Vigelius1, Aidan Lane, Bernd Meyer.   

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/.

Mesh：

Year:  2010        PMID： 21062761     DOI： 10.1093/bioinformatics/btq622

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  13 in total

1.  Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation.

Authors:  Elijah Roberts; John E Stone; Zaida Luthey-Schulten
Journal:  J Comput Chem       Date:  2012-09-25       Impact factor: 3.376

2.  Multi-dimensional, mesoscopic Monte Carlo simulations of inhomogeneous reaction-drift-diffusion systems on graphics-processing units.

Authors:  Matthias Vigelius; Bernd Meyer
Journal:  PLoS One       Date:  2012-04-10       Impact factor: 3.240

3.  Accelerating the Gillespie τ-Leaping Method using graphics processing units.

Authors:  Ivan Komarov; Roshan M D'Souza; Jose-Juan Tapia
Journal:  PLoS One       Date:  2012-06-08       Impact factor: 3.240

4.  High-performance biocomputing for simulating the spread of contagion over large contact networks.

Authors:  Keith R Bisset; Ashwin M Aji; Madhav V Marathe; Wu-chun Feng
Journal:  BMC Genomics       Date:  2012-04-12       Impact factor: 3.969

5.  Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization.

Authors:  Paolo Cazzaniga; Marco S Nobile; Daniela Besozzi; Matteo Bellini; Giancarlo Mauri
Journal:  Biomed Res Int       Date:  2014-06-16       Impact factor: 3.411

6.  Multiscale modelling and analysis of collective decision making in swarm robotics.

Authors:  Matthias Vigelius; Bernd Meyer; Geoffrey Pascoe
Journal:  PLoS One       Date:  2014-11-04       Impact factor: 3.240

7.  Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers.

Authors:  Weiliang Chen; Erik De Schutter
Journal:  Front Neuroinform       Date:  2017-02-10       Impact factor: 4.081

8.  Stochastic simulations of pattern formation in excitable media.

Authors:  Matthias Vigelius; Bernd Meyer
Journal:  PLoS One       Date:  2012-08-10       Impact factor: 3.240

9.  cuTauLeaping: a GPU-powered tau-leaping stochastic simulator for massive parallel analyses of biological systems.

Authors:  Marco S Nobile; Paolo Cazzaniga; Daniela Besozzi; Dario Pescini; Giancarlo Mauri
Journal:  PLoS One       Date:  2014-03-24       Impact factor: 3.240

Review 10.  Discovering epistasis in large scale genetic association studies by exploiting graphics cards.

Authors:  Gary K Chen; Yunfei Guo
Journal:  Front Genet       Date:  2013-12-03       Impact factor: 4.599
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