Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs
Joint Authors
Hung, Che-Lun
Wang, Chung-Hung
Lin, Yu-Shiang
Lin, Chun-Yuan
Source
International Journal of Genomics
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-13
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
Compound comparison is an important task for the computational chemistry.
By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments.
The time complexity of a pairwise compound comparison is O(n2), where n is the maximal length of compounds.
In general, the length of compounds is tens to hundreds, and the computation time is small.
However, more and more compounds have been synthesized and extracted now, even more than tens of millions.
Therefore, it still will be time-consuming when comparing with a large amount of compounds (seen as a multiple compound comparison problem, abbreviated to MCC).
The intrinsic time complexity of MCC problem is O(k2n2) with k compounds of maximal length n.
In this paper, we propose a GPU-based algorithm for MCC problem, called CUDA-MCC, on single- and multi-GPUs.
Four LINGO-based load-balancing strategies are considered in CUDA-MCC in order to accelerate the computation speed among thread blocks on GPUs.
CUDA-MCC was implemented by C+OpenMP+CUDA.
CUDA-MCC achieved 45 times and 391 times faster than its CPU version on a single NVIDIA Tesla K20m GPU card and a dual-NVIDIA Tesla K20m GPU card, respectively, under the experimental results.
American Psychological Association (APA)
Lin, Chun-Yuan& Wang, Chung-Hung& Hung, Che-Lun& Lin, Yu-Shiang. 2015. Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs. International Journal of Genomics،Vol. 2015, no. 2015, pp.1-9.
https://search.emarefa.net/detail/BIM-1066051
Modern Language Association (MLA)
Lin, Chun-Yuan…[et al.]. Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs. International Journal of Genomics No. 2015 (2015), pp.1-9.
https://search.emarefa.net/detail/BIM-1066051
American Medical Association (AMA)
Lin, Chun-Yuan& Wang, Chung-Hung& Hung, Che-Lun& Lin, Yu-Shiang. Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs. International Journal of Genomics. 2015. Vol. 2015, no. 2015, pp.1-9.
https://search.emarefa.net/detail/BIM-1066051
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1066051