A multithreading methodology with OpenMP on multi-core CPUs: SNPHAP case study

Author

Ranok, Udom ; Kittitornkun, Surin ; Tongsima, Sissades

Author_Institution

Sch. of Comput. Eng., King Mongkut´´s Inst. of Technol. Lardkrabang, Bangkok, Thailand

fYear

2011

fDate

17-19 May 2011

Firstpage

459

Lastpage

463

Abstract

This paper presents a multithreading methodology for OpenMP library. The methodology can be applied to convert existing sequential and demanding programs to be multithreaded programs with OpenMP running on the Multi core CPUs. In our experiments, we apply this methodology to SNPHAP, which is one of the best haplotype inference bioinformatics program in terms of speed. The results show that our significant achievement is the maximum Speedup 316% for Intel Xeon E5405 (8-core 2.0 GHz) and 410% for Intel Xeon E5520 (8-Core with HyperThreading 2.66GHz) faster than its own sequential version.

Keywords

bioinformatics; multi-threading; multiprocessing systems; open systems; Intel Xeon E5405; Intel Xeon E5520; OpenMP library; SNPHAP; demanding program; haplotype inference bioinformatics program; multicore CPU; multithreading methodology; sequential program; Bioinformatics; Instruction sets; Optimization; Pipelines; Programming; Runtime;

fLanguage

English

Publisher

ieee

Conference_Titel

Electrical Engineering/Electronics, Computer, Telecommunications and Information Technology (ECTI-CON), 2011 8th International Conference on

Conference_Location

Khon Kaen

Print_ISBN

978-1-4577-0425-3

Type

conf

DOI

10.1109/ECTICON.2011.5947874

Filename

5947874