GPU-accelerated DNA Distance Matrix Computation

GPU-accelerated DNA Distance Matrix Computation

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-accele...

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Bibliographische Detailangaben
Hauptverfasser: Zhi Ying, Xinhua Lin, See, Simon Chong-Wee, Minglu Li
Format: Tagungsbericht
Sprache:eng
Schlagworte:
Acceleration
Central Processing Unit
Computational modeling
Computer architecture
distance matrix
GPU
Graphics processing unit
Newton method
OpenCL
Phylogeny
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Beschreibung
Zusammenfassung: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.
ISSN:1949-131X
1949-1328
DOI:10.1109/ChinaGrid.2011.11