Accelerating reaction-diffusion simulations with general-purpose graphics processing units.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 21062761.
- Also identified by DOI 10.1093/bioinformatics/btq622.
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Abstract
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. The software is freely available at http://www.csse.monash.edu.au/~berndm/inchman/.
Medical subject headings
- Algorithms
- Computer Graphics