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

Conference paper (2008)

Authors

Friman Sánchez Universitat Politecnica de Catalunya
G. Gaydadjiev Computer Engineering - EEMCS
Alex Ramirez Barcelona Supercomputing Center, Universitat Politecnica de Catalunya
Mateo Valero Barcelona Supercomputing Center, Universitat Politecnica de Catalunya
Research Group
Computer Engineering (EEMCS) (TU Delft)
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Published Date

2008

Language

English

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Faculty

Electrical Engineering, Mathematics and Computer Science

Department

Quantum & Computer Engineering

Research Group

Computer Engineering

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.