Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture

Author

Ye, Xiaochun ; Nguyen, Van Hoa ; Lavenier, Dominique ; Fan, Dongrui

Author_Institution

Key Lab. of Comput. Syst. & Archit., Chinese Acad. of Sci., Beijing

fYear

2008

fDate

1-4 Dec. 2008

Firstpage

167

Lastpage

170

Abstract

This paper introduces the Godson-T manycore architecture and demonstrates the efficiency of its synchronization mechanism through a computation intensive bioinformatics application: the comparison of protein banks. The parallel part of the protein sequence comparison algorithm can nearly get a linear speed-up thanks to a fine tuning of the synchronization mechanism provided by the Godson-T chip.

Keywords

bioinformatics; microprocessor chips; parallel architectures; proteins; sequences; synchronisation; Godson-T chip; Godson-T manycore architecture; computation intensive bioinformatics application; fine tuning; protein banks; protein sequence comparison algorithm; synchronization mechanism; Application software; Bioinformatics; Computer architecture; Computer displays; Databases; Distributed computing; Genomics; Protein sequence; Scanning probe microscopy; Tiles; Bioinformatics; Manycore; Parallelization; Protein Sequence Comparison;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel and Distributed Computing, Applications and Technologies, 2008. PDCAT 2008. Ninth International Conference on

Conference_Location

Otago

Print_ISBN

978-0-7695-3443-5

Type

conf

DOI

10.1109/PDCAT.2008.28

Filename

4710977