Efficient parallel algorithm for compound comparisons on multi-GPUs

Chun Yuan Lin, Chung Hung Wang, Che Lun Hung*, Yu Shiang Lin

*此作品的通信作者

研究成果: Conference contribution同行評審

2 引文 斯高帕斯(Scopus)

摘要

Compound comparison is an important task for computational chemistry. By the comparison reulsts, potential inhibitors can be found and then used for the following experiments. The time complexity of a pairwise compound comparison is O(n2), where n is the maximal length of compounds. In general, the compound length is small, and the cost of computation time is short. However, more and more compounds have been synthesized and extracted now, even more than ten of millions. Therefore, it still will be time-consuming when comparing with a large amount of compounds (multiple compound comparisons). In this paper, we propose a parallel algorithm for multiple compound comparisons on multi-GPUs. Four load-balancing strategies were considered in the proposed algorithm in order to accelerate the computation speed among thread blocks on GPUs. The proposed algorithm was implemented by C+OpenMP+CUDA, and achieved more than 50 times speedup by comparing with its CPU version under the experiemtal results.

原文English
主出版物標題Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
編輯Huiru Zheng, Xiaohua Tony Hu, Daniel Berrar, Yadong Wang, Werner Dubitzky, Jin-Kao Hao, Kwang-Hyun Cho, David Gilbert
發行者Institute of Electrical and Electronics Engineers Inc.
頁面30-35
頁數6
ISBN(電子)9781479956692
DOIs
出版狀態Published - 29 12月 2014
事件2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 - Belfast, United Kingdom
持續時間: 2 11月 20145 11月 2014

出版系列

名字Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014

Conference

Conference2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
國家/地區United Kingdom
城市Belfast
期間2/11/145/11/14

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