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


   title={Accelerating reaction–diffusion simulations with general-purpose graphics processing units},

   author={Vigelius, M. and Lane, A. and Meyer, B.},






   publisher={Oxford Univ Press}


Source Source   Source codes Source codes




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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