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

被引:24
|
作者
Vigelius, Matthias [1 ]
Lane, Aidan [1 ]
Meyer, Bernd [1 ]
机构
[1] Monash Univ, FIT Ctr Res Intelligent Syst, Clayton, Vic 3800, Australia
基金
澳大利亚研究理事会;
关键词
STOCHASTIC SIMULATION; PATHWAYS; SYSTEMS;
D O I
10.1093/bioinformatics/btq622
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:288 / 290
页数:3
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