GPU accelerated RNA folding algorithm

pages 199-210In 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