GPU-accelerated DNA distance matrix computation

被引：4
作者：
Ying Z. [1 ]
Lin X. [1 ]
See S.C.-W. [1 ,2 ,3 ]
Li M. [1 ,4 ]
机构：
[1] Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai
[2] Institute of High Performance Computing, AStar, Singapore
来源：
Proceedings - 2011 6th Annual ChinaGrid Conference, ChinaGrid 2011 | 2011年
关键词：
distance matrix; GPU; OpenCL; phylogeny;
D O I：
10.1109/ChinaGrid.2011.11
中图分类号：
学科分类号：
摘要：
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. © 2011 IEEE.
引用
收藏
页码：42 / 47
页数：5
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