dc.contributor.author |
Chacón, Alejandro |
dc.contributor.author |
Marco-Sola, Santiago |
dc.date |
2014 |
dc.identifier |
https://ddd.uab.cat/record/131866 |
dc.identifier |
urn:10.1109/ISPA.2014.10 |
dc.identifier |
urn:oai:ddd.uab.cat:131866 |
dc.identifier |
urn:scopus_id:84911439685 |
dc.identifier |
urn:wos_id:000364951700001 |
dc.identifier |
urn:oai:egreta.uab.cat:publications/471ab7ed-af95-4474-bf55-b618854b1802 |
dc.format |
application/pdf |
dc.language |
eng |
dc.publisher |
|
dc.relation |
Ministerio de Ciencia e Innovación TIN2011-28689-C02-01 |
dc.relation |
ISPA : IEEE International Symposium on Parallel and Distributed Processing with Applications ; 12è : 2014 |
dc.rights |
open access |
dc.rights |
Tots els drets reservats. |
dc.rights |
https://rightsstatements.org/vocab/InC/1.0/ |
dc.subject |
GPGPU |
dc.subject |
Bioinformatics |
dc.subject |
FM-index |
dc.subject |
Fine-Grain Parallelism |
dc.subject |
Memory-Level Parallelism |
dc.title |
FM-index on GPU : a cooperative scheme to reduce memory footprint |
dc.type |
Comunicació de congrés |
dc.description.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. |