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

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

doi:10.1007/978-3-540-70550-5_7

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

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

^*Corresponding author for this work

Computer Engineering

Research output: Chapter in Book/Conference proceedings/Edited volume › Conference contribution › Scientific › peer-review

3 Citations (Scopus)

Abstract

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.

Original language	English
Title of host publication	Embedded Computer Systems
Subtitle of host publication	Architectures, Modeling, and Simulation - 8th International Workshop, SAMOS 2008, Proceedings
Pages	53-64
Number of pages	12
DOIs	https://doi.org/10.1007/978-3-540-70550-5_7
Publication status	Published - 2008
Event	8th International Workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2008 - Samos, Greece Duration: 21 Jul 2008 → 24 Jul 2008

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5114 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	8th International Workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2008
Country/Territory	Greece
City	Samos
Period	21/07/08 → 24/07/08

Access to Document

10.1007/978-3-540-70550-5_7

Cite this

Isaza, S., Sánchez, F., Gaydadjiev, G., Ramirez, A., & Valero, M. (2008). Preliminary analysis of the cell BE processor limitations for sequence alignment applications. In Embedded Computer Systems: Architectures, Modeling, and Simulation - 8th International Workshop, SAMOS 2008, Proceedings (pp. 53-64). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5114 LNCS). https://doi.org/10.1007/978-3-540-70550-5_7

Isaza, Sebastian ; Sánchez, Friman ; Gaydadjiev, Georgi et al. / Preliminary analysis of the cell BE processor limitations for sequence alignment applications. Embedded Computer Systems: Architectures, Modeling, and Simulation - 8th International Workshop, SAMOS 2008, Proceedings. 2008. pp. 53-64 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Isaza, S, Sánchez, F, Gaydadjiev, G, Ramirez, A & Valero, M 2008, Preliminary analysis of the cell BE processor limitations for sequence alignment applications. in Embedded Computer Systems: Architectures, Modeling, and Simulation - 8th International Workshop, SAMOS 2008, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5114 LNCS, pp. 53-64, 8th International Workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2008, Samos, Greece, 21/07/08. https://doi.org/10.1007/978-3-540-70550-5_7

Preliminary analysis of the cell BE processor limitations for sequence alignment applications. / Isaza, Sebastian; Sánchez, Friman; Gaydadjiev, Georgi et al.
Embedded Computer Systems: Architectures, Modeling, and Simulation - 8th International Workshop, SAMOS 2008, Proceedings. 2008. p. 53-64 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5114 LNCS).

Research output: Chapter in Book/Conference proceedings/Edited volume › Conference contribution › Scientific › peer-review

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AB - 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.

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Isaza S, Sánchez F, Gaydadjiev G, Ramirez A, Valero M. Preliminary analysis of the cell BE processor limitations for sequence alignment applications. In Embedded Computer Systems: Architectures, Modeling, and Simulation - 8th International Workshop, SAMOS 2008, Proceedings. 2008. p. 53-64. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-70550-5_7

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

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