Preliminary analysis of the cell BE processor limitations for sequence alignment applications

Sebastian Isaza, Friman Sánchez, Georgi Gaydadjiev, Alex Ramirez, Mateo Valero

Producción científica: Capítulo en Libro/ReporteContribución a la conferencia

3 Citas (Scopus)

Resumen

The fast growth of bioinformatics field has attracted the attention of computer scientists in the last few years. At the same time the increasing database sizes require greater efforts to improve the computational performance. From a computer architecture point of view, we intend to investigate how bioinformatics applications can benefit from future multi-core processors. In this paper we present a preliminary study of the Cell BE processor limitations when executing two representative sequence alignment applications (Ssearch and ClustalW). The inherent large parallelism of the targeted algorithms makes them ideal for architectures supporting multiple dimensions of parallelism (TLP and DLP). However, in the case of Cell BE we identified several architectural limitations that need a careful study and quantification.

Idioma originalInglés estadounidense
Título de la publicación alojadaEmbedded Computer Systems
Subtítulo de la publicación alojadaArchitectures, Modeling, and Simulation - 8th International Workshop, SAMOS 2008, Proceedings
Páginas53-64
Número de páginas12
DOI
EstadoPublicada - 2008
Publicado de forma externa
Evento8th International Workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2008 - Samos, Grecia
Duración: jul. 21 2008jul. 24 2008

Serie de la publicación

NombreLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volumen5114 LNCS
ISSN (versión impresa)0302-9743
ISSN (versión digital)1611-3349

Conferencia

Conferencia8th International Workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2008
País/TerritorioGrecia
CiudadSamos
Período7/21/087/24/08

Áreas temáticas de ASJC Scopus

  • Ciencia computacional teórica
  • Ciencia de la Computación General

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