使用通用图形处理单元加速反应-扩散模拟。
Accelerating reaction-diffusion simulations with general-purpose graphics processing units.
机构信息
FIT Centre for Research in Intelligent Systems, Monash University, Clayton, Victoria, Australia.
出版信息
Bioinformatics. 2011 Jan 15;27(2):288-90. doi: 10.1093/bioinformatics/btq622. Epub 2010 Nov 8.
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/.
摘要
我们提出了一种基于图形处理单元（GPU）的大规模并行随机模拟算法（SSA），用于反应扩散系统。这些芯片经过优化，可以并行处理大量浮点数运算，非常适合各种科学高性能计算。新一代 GPU 提供了一个高级编程接口，将其转变为通用图形处理单元（GPGPU）。我们的 SSA 利用 GPGPU 架构，在传统硬件上最快的现有实现的基础上实现了两个数量级的性能提升。
可用性
该软件可在 http://www.csse.monash.edu.au/~berndm/inchman/ 免费获得。
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