Preliminary Analysis of the Cell BE Processor Limitations for Sequence Alignment Applications

Authors:
Sebastian Isaza;Friman Sánchez;Georgi Gaydadjiev;Alex Ramirez;Mateo Valero
Affiliations:
Computer Engineering Lab, Delft University of Technology, The Netherlands;Computer Architecture Department, Technical University of Catalonia, Spain;Computer Engineering Lab, Delft University of Technology, The Netherlands;Computer Architecture Department, Technical University of Catalonia, Spain and Barcelona Supercomputing Center-CNS, Spain;Computer Architecture Department, Technical University of Catalonia, Spain and Barcelona Supercomputing Center-CNS, Spain
Venue:
SAMOS '08 Proceedings of the 8th international workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation
Year:
2008

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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.