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Chapitre D'ouvrage Année : 2011

GPU accelerated RNA folding algorithm

Résumé

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 with optimized CPU implementation that also uses the same approach to tile and vectorize the code.

Dates et versions

hal-00637827 , version 1 (03-11-2011)

Identifiants

Citer

Dominique Lavenier, Guillaume Rizk, Sanjay Rajopadhye. GPU accelerated RNA folding algorithm. Wen-mei W. Hwu. GPU Computing Gems, ELSEVIER, pp.560, 2011, ⟨10.1016/B978-0-12-384988-5.00014-0⟩. ⟨hal-00637827⟩
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