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
来源：
BIOINFORMATICS | 2011年 / 27卷 / 02期
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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