GPU-Accelerated DNA Distance Matrix Computation

Zhi Ying, Xinhua Lin, Simon Chong-Wee See, Minglu Li
Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
The 6th ChinaGrid Annual Conference, ChinaGrid 2011, 2011


   title={GPU-Accelerated DNA Distance Matrix Computation},

   author={Ying, Z. and Lin, X. and See123, S.C.W. and Li14, M.},

   booktitle={The 6th ChinaGrid Annual Conference, ChinaGrid 2011},



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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 GPUaccelerated 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.
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