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

Matthias Vigelius, Aidan Lane, Bernd Meyer
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}

}

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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.
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