吉林大学学报(工学版) ›› 2015, Vol. 45 ›› Issue (4): 1253-1259.doi: 10.13229/j.cnki.jdxbgxb201504033

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Dynamic task migration optimization for molecule docking

DONG Yue-li, GUO Quan, SUN Bin, KANG Ling   

  1. Dalian Neusoft University of Information, Dalian 116023,China
  • Received:2013-09-28 Online:2015-07-01 Published:2015-07-01

Abstract: In this paper an optimization strategy of dynamic task migration for molecule docking is proposed based traditional task migration method. The mean and variance of the number of sequential jobs of each node are analyzed to obtain the coefficient of variation reliability, thus, to increase the efficiency and security of molecule docking tasks. An incremental data migration is carried out from the source node to a high reliable target node, and the time of downtime copy is shortened. The results of case study show that the efficiency and security of molecule docking tasks are improved.

Key words: computer architecture, computer network, virtual machine, task migration, molecule docking, ligand, receptor

CLC Number: 

  • TP393.1
[1] 陈凯先,蒋华良,嵇汝运. 计算机辅助药物设计——原理、方法及应用[M]. 上海:上海科学技术出版社,2000:25-33.
[2] Abagyan R, Totrov M, Kuznetsov D. ICM-a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation[J]. J Comput Chem, 1994,15(5):488-506.
[3] Goodsell D S, Morris G M, Olson A J. Distributed automated docking of flexible ligands to proteins: parallel applications of autodock 2.4[J]. J Comput-Aided Mol Des, 1996,10(4):293-304.
[4] 李纯莲,王希诚,赵金城. 应用改进型遗传算法进行药物分子对接设计[J]. 计算机工程与应用,2003,39(36):31-33. Li Chun-lian, Wang Xi-cheng, Zhao Jin-cheng. Drug molecular design using a modified genetic algorithm[J]. Computer Engineering and Applications, 2003, 39(36):31-33.
[5] Ewing T J, Makino S, Skillman A G, et al. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases[J]. J Comput Aided Mol Des, 2001,15(5):411-428.
[6] Baek S, Park S, Yand S, et al. Efficient server virtualization using grid service infrastructure[J]. J Inf Process Syst, 2010,6(4):553-562.
[7] 张彬彬,罗英伟,汪小林,等. 虚拟机全系统在线迁移[J]. 电子学报,2009,37(4):894-899. Zhang Bin-bin, Luo Ying-wei, Wang Xiao-lin, et al. Whole-system live migration mechanism for virtual machines[J]. Acta Electronica Sinica, 2009, 37(4):894-899.
[8] Kivity A, Kamay Y, Laor D, et al. KVM: the Linux virtual machine monitor[C]∥Proceedings of the Linux Symposium,Ottawa, Ontario, Canada, 2007: 225-230.
[9] Tao Peng, Lai Lu-hua. Protein ligand docking based on empirical method for binding affinity estimation[J]. Journal of Computer-Aided Molecular Design, 2001,15(5): 429-446.
[10] 康玲,李洪林,王希诚. 一种考虑蛋白质柔性的分子对接方法[J]. 大连理工大学学报,2008,48(2):282-286. Kang Ling, Li Hong-lin, Wang Xi-cheng. A molecular docking method considering protein flexibility[J]. Journal of Dalian University of Technology, 2008, 48(2):282-286.
[11] Rodriguez P, Biersack E W. Dynamic parallel access to replicated content in the Internet[J].IEEE/ACM Transactions on Networking, 2002, 10(4): 455-465.
[12] Cully B, Lefebvre G, Meyer D, et al. Remus: High availability via asynchronous virtual machine replication[C]∥NSDI'08 Proceedings of the 5th USENIX Symposium on Networked Systems Design and Implementation,Berkeley, CA, USA, 2008:161-174.
[13] Hirofuchi T, Ogawa H, Nakada H, et al. A live storage migration mechanism over WAN for relocatable virtual machine services on clouds cluster computing and the grid[C]∥IEEE/ACM International Symposium on Cluster Computing and the Grid, Shanghai, China, 2009:460-465.
[14] 陈阳,怀进鹏,胡春明. 基于内存混合复制方式的虚拟机在线迁移机制[J]. 计算机学报,2011,34(12):2278-2290. Chen Yang, Huai Jin-peng, Hu Chun-ming. Live migration of virtual machines based on hybrid memory copy approach[J]. Chinese Journal of Computer, 2011, 34(12):2278-2290.
[15] 郭权,王希诚. 网格环境下具有可靠性的任务调度策略[J]. 南京理工大学学报:自然科学版,2006,30(5):592-598. Guo Quan, Wang Xi-cheng. Reliable and cost-considered task scheduling for grid computing[J]. Journal of Nanjing University of Science and Technology(Natural Science Edition), 2006, 30(5):592-598.
[16] Topcuoglu H, Hariri S. Performance-effective and low-complexity task scheduling for heterogeneous computing[J]. IEEE Trans Parallel and Distributed Systems, 2002, 13(3):260-274.
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