Scaling of parallel multiple sequence alignment on the supercomputer JUQUEEN

Author

Borovska, Plamenka ; Gancheva, Veska ; Soon-Heum Ko

Author_Institution

Comput. Syst. Dept., Tech. Univ. of Sofia, Sofia, Bulgaria

Volume

02

fYear

2013

fDate

12-14 Sept. 2013

Firstpage

687

Lastpage

691

Abstract

In this paper is proposed optimization, scaling, performance evaluation and profiling of parallel multiple sequence alignment based on ClustalW algorithm on the supercomputer BlueGene/Q, so-called JUQUEEN, for the case study of the influenza virus sequences. For this purpose a parallel I/O interface for simultaneous and independent access to single file collectively has been designed and verified on the basis of parallel program implementation on the supercomputer JUQUEEN.

Keywords

biology computing; optimisation; parallel machines; parallel programming; performance evaluation; BlueGene/Q supercomputer; ClustalW algorithm; JUQUEEN supercomputer; influenza virus sequences; optimization; parallel IO interface; parallel multiple sequence alignment; parallel program implementation; performance evaluation; Algorithm design and analysis; Influenza; Optimization; Performance evaluation; Program processors; Supercomputers; ClustalW algorithm; biocomputing; high performance computing; multiple sequence alignment; parallel performance;

fLanguage

English

Publisher

ieee

Conference_Titel

Intelligent Data Acquisition and Advanced Computing Systems (IDAACS), 2013 IEEE 7th International Conference on

Conference_Location

Berlin

Print_ISBN

978-1-4799-1426-5

Type

conf

DOI

10.1109/IDAACS.2013.6663013

Filename

6663013