Performance analysis & improvement of SNPHAP on Multi-core CPUs

Author

Ranokphanuwat, Ratthaslip ; Kittitornkun, Surin ; Tongsima, Sissades

Author_Institution

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

fYear

2013

fDate

15-17 May 2013

Firstpage

1

Lastpage

6

Abstract

In this paper, we attempt to analyse this highly computational problem by parallelizing a haplotype inference algorithm, called SNPHAP. The analysis is based on both the orignal (sequential) algorithm and its corresponding run time complexity in Big-O notations. Then, we improve its performance using OpenMP 3.0 and test on a 4-core Intel Core i7-2600 (Hyper-Threading), an 8-core Intel XeonE5405, an 8-core Intel Xeon E5520 (Hyper-Threading) and a 32-core AMD Opteron 8356 Linux machines. The achievements in terms of maximum speedups are 260%, 316%, 410% and 488%, respectively. The factors that affect the speedup of SNPHAP are the specific parallelized code fraction, the suitable OpenMP constructs, the number of physical cores, the sizes of cache memories within/among CPU cores, the clock frequency and finally the memory technology.

Keywords

Linux; cache storage; computational complexity; inference mechanisms; message passing; multiprocessing systems; 32-core AMD Opteron 8356 Linux machines; 4-core Intel Core i7-2600; 8-core Intel Xeon E5520; 8-core Intel XeonE5405; OpenMP; OpenMP 3.0; SNPHAP; big-O notations; cache memories; expectation maximization algorithm; haplotype inference algorithm; multicore CPU; run time complexity; Algorithm design and analysis; Computational complexity; Equations; Instruction sets; Multicore processing; Sockets;

fLanguage

English

Publisher

ieee

Conference_Titel

Electrical Engineering/Electronics, Computer, Telecommunications and Information Technology (ECTI-CON), 2013 10th International Conference on

Conference_Location

Krabi

Print_ISBN

978-1-4799-0546-1

Type

conf

DOI

10.1109/ECTICon.2013.6559572

Filename

6559572