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Pàgina inicial > Contribucions a jornades i congressos > Ponències i comunicacions > FM-index on GPU : |
Data: | 2014 |
Resum: | 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. |
Ajuts: | Ministerio de Ciencia e Innovación TIN2011-28689-C02-01 |
Drets: | Tots els drets reservats. |
Llengua: | Anglès |
Document: | Comunicació de congrés |
Matèria: | GPGPU ; Bioinformatics ; FM-index ; Fine-Grain Parallelism ; Memory-Level Parallelism |
Publicat a: | ISPA : IEEE International Symposium on Parallel and Distributed Processing with Applications. Milà, Itàlia, 12è : 2014 |
Accepted document 9 p, 645.7 KB |