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GPU Computing Gems Emerald Edition by Wen-mei W. Hwu

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Chapter 14. GPU Accelerated RNA Folding Algorithm *
* Work performed while the first author was visiting Colorado State University and supported in part by NSF grant CCF-0917319, “Simplifying Reductions,” and in part by French ANR BioWIC: ANR-08-SEGI-005.
Guillaume Rizk, Dominique Lavenier and Sanjay Rajopadhye
In this chapter, we present an implementation of the main kernel in the widely used RNA folding package Unafold. Its key computation is a dynamic programming algorithm with complex dependency patterns, making it an a priori bad match for GPU computing. This study, however, shows that reordering computations in such a way to enable tiled computations and good data reuse can significantly improve GPU performance and yields good speedup compared ...

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