Title :
GPU-accelerated DNA Distance Matrix Computation
Author :
Ying, Zhi ; Lin, Xinhua ; See, Simon Chong-Wee ; Li, Minglu
Author_Institution :
Dept. of Comput. Sci. & Eng., Shanghai Jiao Tong Univ., Shanghai, China
Abstract :
Distance matrix calculation used in phylogeny analysis is computational intensive. The growing sequences data sets necessitate fast computation method. This paper accelerate Felsenstein´s DNADIST program by using OpenCL to exploit the great computation capability of graphic card. The GPU-accelerated DNADIST program achieves more than 12-fold speedup over the serial CPU program on a personal workstation with a 2.66GHz quad-core Intel CPU and an AMD HD5850 graphics card. And dual HD5850 cards on the same platform perform linear improvement of 24-fold speedup. The program also shows good performance portability by achieving 16-fold speedup with a NVIDIA Tesla C2050 card.
Keywords :
DNA; biology computing; computer graphic equipment; coprocessors; evolution (biological); genetics; matrix algebra; AMD HD5850 graphics card; GPU-accelerated DNA distance matrix computation; GPU-accelerated DNADIST program; NVIDIA Tesla C2050 card; OpenCL; phylogeny analysis; quad-core Intel CPU; sequences data sets; serial CPU program; Acceleration; Central Processing Unit; Computational modeling; Computer architecture; Graphics processing unit; Newton method; Phylogeny; GPU; OpenCL; distance matrix; phylogeny;
Conference_Titel :
Chinagrid Conference (ChinaGrid), 2011 Sixth Annual
Conference_Location :
Liaoning
Print_ISBN :
978-1-4577-0885-5
DOI :
10.1109/ChinaGrid.2011.11
