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Source-to-Source Optimization of CUDA C for GPU Accelerated Cardiac Cell Modeling

Fred V. Lionetti, Andrew D. McCulloch, Scott B. Baden
Departments of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0404 USA
Euro-Par 2010 – Parallel Processing, Lecture Notes in Computer Science, 2010, Volume 6271/2010, 38-49

@article{lionetti2010source,

   title={Source-to-Source Optimization of CUDA C for GPU Accelerated Cardiac Cell Modeling},

   author={Lionetti, F. and McCulloch, A. and Baden, S.},

   journal={Euro-Par 2010-Parallel Processing},

   pages={38–49},

   year={2010},

   publisher={Springer}

}

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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.
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