Title :
Optimizing and multithreading SNPHAP on a multi-core APU with OpenCL
Author :
Rattanatranurak, Apisit ; Kittitornkun, Surin ; Tongsima, Sissades
Author_Institution :
Dept. of Comput. Eng., KMITL Bangkok, Bangkok, Thailand
fDate :
May 30 2012-June 1 2012
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.
Keywords :
bioinformatics; digital arithmetic; multi-threading; multiprocessing systems; OpenCL; SNPHAP multithreading; SNPHAP optimization; accelerated processing unit; bioinformatics program; multicore AMD A6-3650 APU; parallel radix SNPHAP; radix comparison algorithm; sequential radix SNPHAP; Acceleration; Arrays; Computational modeling; Indexes; Instruction sets; Kernel; Multithreading;
Conference_Titel :
Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on
Conference_Location :
Bangkok
Print_ISBN :
978-1-4673-1920-1
DOI :
10.1109/JCSSE.2012.6261947
