Optimizing and multithreading SNPHAP on a multi-core APU with OpenCL

Rattanatranurak, Apisit; Kittitornkun, Surin; Tongsima, Sissades

doi:10.1109/JCSSE.2012.6261947

Optimizing and multithreading SNPHAP on a multi-core APU with OpenCL

Author(s)

Rattanatranurak, Apisit

Kittitornkun, Surin

Tongsima, Sissades

Date Issued

September 24, 2012

Type

Conference Paper

DOI

10.1109/JCSSE.2012.6261947

Abstract

In this paper, we have optimized and multithreaded SNPHAP, a bioinformatics program, with OpenCL to reduce the computation time and thus accelerate the execution. Our method is called Radix Comparison algorithm running in sequential and parallel (multithreading). Based on the recent multi-core AMD A6-3650 APU (Accelerated Processing Unit), the achieveable Speedups of Sequential Radix and Parallel Radix SNPHAP compared with the original SNPHAP are 260% and 271%, respectively. © 2012 IEEE.

Citation

Jcsse 2012 9th International Joint Conference on Computer Science and Software Engineering, 174-179, 2012