Source-to-source optimization of CUDA C for GPU accelerated cardiac cell modeling

Authors:
Fred V. Lionetti;Andrew D. McCulloch;Scott B. Baden
Affiliations:
Departments of Computer Science and Engineering, University of California, San Diego, La Jolla, CA;Departments of Bioengineering, University of California, San Diego, La Jolla, CA;Departments of Computer Science and Engineering, University of California, San Diego, La Jolla, CA
Venue:
EuroPar'10 Proceedings of the 16th international Euro-Par conference on Parallel processing: Part I
Year:
2010

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Abstract

Large and complex systems of ordinary differential equations (ODEs) arise in diverse areas of science and engineering, and pose special challenges on a streaming processor owing to the large amount of state they manipulate. We describe a set of domain-specific source transformations on CUDA C that improved performance by ×6.7 on a system of ODEs arising in cardiac electrophysiology running on the nVidia GTX- 295, without requiring expert knowledge of the GPU. Our transformations should apply to a wide range of reaction-diffusion systems.