FM-index on GPU : a cooperative scheme to reduce memory footprint
Chacón, Alejandro (Universitat Autònoma de Barcelona)
Marco-Sola, Santiago (Centre Nacional d'Anàlisi Genòmica)

Date:	2014
Abstract:	The FM-index is a data structure which is seeing more and more pervasive use, in particular in the field of highthroughput 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.
Grants:	Ministerio de Ciencia e Innovación TIN2011-28689-C02-01
Rights:	Tots els drets reservats.
Language:	Anglès
Document:	Comunicació de congrés
Subject:	GPGPU ; Bioinformatics ; FM-index ; Fine-Grain Parallelism ; Memory-Level Parallelism
Published in:	ISPA : IEEE International Symposium on Parallel and Distributed Processing with Applications. Milà, Itàlia, 12è : 2014

DOI: 10.1109/ISPA.2014.10

Accepted document 9 p, 645.7 KB

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