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

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 x6.7 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.. © 2010 Springer-Verlag.