Title :
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
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;
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
DOI :
10.1109/ECTICON.2011.5947874
