FM-index on GPU: A cooperative scheme to reduce memory footprint

A. Chacon, S. Marco-Sola, A. Espinosa, P. Ribeca, J.C. Moure

Research output: Chapter in BookChapterResearchpeer-review

5 Citations (Scopus)

Abstract

The FM-index is a data structure which is seeing more and more pervasive use, in particular in the field of high-throughput bioinformatics. Algorithms based on it show a pseudo-random memory access pattern. As a consequence, they are usually bound by memory bandwidth rather than CPU usage. Naive GPU implementations are no exception. Here we show that the combination of a compact design of the FM-index and a thread-cooperative approach can be used to restore a proper balance. The resulting solution is less memory-bandwidth intensive, and allows full exploitation of the computational resources of the GPU across several GPU architectures.
Original languageEnglish
Title of host publicationProceedings - 2014 IEEE International Symposium on Parallel and Distributed Processing with Applications, ISPA 2014
ISBN (Electronic)2158-9208
DOIs
Publication statusPublished - 2014

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