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
相关论文
共 50 条
  • [1] GPU-accelerated Kendall distance computation for large or sparse data
    Akhtyamov, Pavel
    Nabi, Ausaaf
    Gafurov, Vladislav
    Sizykh, Alexey
    Favorov, Alexander
    Medvedeva, Yulia
    Stupnikov, Alexey
    GIGASCIENCE, 2024, 13
  • [2] GPU-accelerated computation of electron transfer
    Hoefinger, Siegfried
    Acocella, Angela
    Pop, Sergiu C.
    Narumi, Tetsu
    Yasuoka, Kenji
    Beu, Titus
    Zerbetto, Francesco
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2012, 33 (29) : 2351 - 2356
  • [3] GPU-accelerated Hausdorff distance computation between dynamic deformable NURBS surfaces
    Krishnamurthy, Adarsh
    McMains, Sara
    Hanniel, Iddo
    COMPUTER-AIDED DESIGN, 2011, 43 (11) : 1370 - 1379
  • [4] GPU-Accelerated KV/MV Dose Computation
    Jacques, R.
    Taylor, R.
    Wong, J.
    McNutt, T.
    MEDICAL PHYSICS, 2010, 37 (06)
  • [5] GPU-accelerated Adaptively Sampled Distance Fields
    Bastos, Thiago
    Celes, Waldemar
    IEEE INTERNATIONAL CONFERENCE ON SHAPE MODELING AND APPLICATIONS 2008, PROCEEDINGS, 2008, : 171 - 178
  • [6] GPU-Accelerated Minimum Distance and Clearance Queries
    Krishnamurthy, Adarsh
    McMains, Sara
    Haller, Kirk
    IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2011, 17 (06) : 729 - 742
  • [7] Accurate GPU-accelerated surface integrals for moment computation
    Krishnamurthy, Adarsh
    McMains, Sara
    COMPUTER-AIDED DESIGN, 2011, 43 (10) : 1284 - 1295
  • [8] Efficient GPU-Accelerated Computation of Isosurface Similarity Maps
    Imre, Martin
    Tao, Jun
    Wang, Chaoli
    2017 IEEE PACIFIC VISUALIZATION SYMPOSIUM (PACIFICVIS), 2017, : 180 - 184
  • [9] GPU-accelerated real-time stixel computation
    Hernandez-Juarez, Daniel
    Espinosa, Antonio
    Moure, Juan C.
    Vazquez, David
    Lopez, Antonio M.
    2017 IEEE WINTER CONFERENCE ON APPLICATIONS OF COMPUTER VISION (WACV 2017), 2017, : 1054 - 1062
  • [10] Detecting Anomalous Computation with RNNs on GPU-Accelerated HPC Machines
    Zou, Pengfei
    Li, Ang
    Barker, Kevin
    Ge, Rong
    PROCEEDINGS OF THE 49TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING, ICPP 2020, 2020,
12345