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 ...
Get GPU Computing Gems Emerald Edition now with the O’Reilly learning platform.
O’Reilly members experience books, live events, courses curated by job role, and more from O’Reilly and nearly 200 top publishers.
