Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture

Xioachun Ye (1) , van Hoa Nguyen (2) , Dominique Lavenier (2) , Dongrui Fan (1)

1 ICT - Key Lab of Computer System and Architecture, Institute of Computing Technology [Beijing]
2 SYMBIOSE - Biological systems and models, bioinformatics and sequences

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.

Domaines: Bio-informatique [q-bio.QM]; Calcul parallèle, distribué et partagé [cs.DC]

Xioachun Ye, van Hoa Nguyen, Dominique Lavenier, Dongrui Fan. Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture. Ninth International Conference on Parallel and Distributed Computing, Applications and Technologies, Dec 2008, France. online proceedings: http://www.cs.otago.ac.nz/pdcat08/. ⟨hal-00322732⟩