Title :
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
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;
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
DOI :
10.1109/PDCAT.2008.28
