Abstract
Grid provides a promising platform for the efficient execution of drug molecular docking design. Scheduling such applications is challenging for the heterogeneity, autonomy, and dynamic adaptability of grid resources. Assuming resource owners have a preemptive priority, we propose an adaptive algorithm of jobs scheduling based on time balancing strategy, which solves parallel molecular docking task by using the idle resources in the Grid. A mathematical model is developed to predict performance, which also considers systems with heterogeneous machine utilization and heterogeneous service distribution. According to the time balancing policy, ligands are partitioned into several subtasks and scheduled. The expected value of molecular docking completion time is predicted with performance model. To get better parallel computing performance, an optimal subset of heterogeneous resources with the shortest parallel executing time of tasks can be selected with the algorithm.
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References
McFadden, G.: The smallpox research project (2004), http://www.grid.org/projects/smallpox
Bonnie, E.: The Drug Design and optimization Lab (2004), http://www.d2ol.com/dOL/download_instructions.html
Jun, Z., Yan, C., Xiang-Hui, X., et al.: Realization of Multi-Level Parallel Load-Balance P2P Computation in the DDG. Journal of Computer Research and Development 41(12) (December 2004)
Ackerman, F., Herrmann, G., Posch, S.: Estimation and filtering of potential protein-protein docking positions. Bio-informatics 14(2), 196–205 (1998)
Braun, T.D., Siegek, H.J., Beck, N.: A Comparison of Eleven Static Heuristics for Mapping a Class of Independent Tasks onto Heterogeneous Distributed Computing Systems. Journal of Parallel and Distributed Computing, 810–837 (2001)
Braun, T.D., Siegel, H.J., et al.: A Comparison Study of Static Heuristics for a Class of Meta-tasks on Heterogeneous Computing Systems. Journal of Parallel and Distributed Computing, 723–751 (2002)
Maheswaran, M., Ali, S., et al.: Dynamic Matching and Scheduling of a Class of Independent Tasks onto Heterogeneous Computing Systems. In: Proceedings of the 8th IEEE Heterogeneous Computing Workshop (HCW 1999), pp. 30–44. IEEE Computer Society Press, Los Alamitos (1999)
Maheswaran, M., Siegel, H.J.: A Dynamic Matching and Scheduling Algorithm for Heterogeneous Computing Systems. In: Proceedings of the 7th IEEE Heterogeneous Computing Workshop (HCW 1998), pp. 57–69. IEEE Computer Society Press, Los Alamitos (1998)
Maheswaran, M., Ali, S., et al.: Dynamic mapping of a class of independent tasks onto heterogeneous Computing systems. Journal of Parallel and Distributed Computing 59(2), 107–131 (1999)
Casanova, H., Legrand, A.: Heuristics for Scheduling Parameter Sweep Applications in Grid Environments, 609–630 (2003)
Buyya, R., Branson, K., Giddy, J., Abramson, D.: The Virtual Laboratory: Enabling On-Demand Drug Design with the World Wide Grid. In: Proceedings of the IEEE International Symposium on Cluster Computing and the Grid, May 21-24 (2002)
Buyya, R., Branson, K., Giddy, J., Abramson, D.: The Virtual Laboratory: Enabling Molecular Modeling for Drug Design on the World Wide Grid. In: Proceedings of the IEEE International Symposium on Cluster Computing and the Grid, May 12-15 (2003)
Chien, A.A., Calder, B., Elbert, S., Bhatia, K.: Entropia: architecture and performance of an enterprise desktop grid system. Journal of Parallel and Distributed Computing 63(5), 597–610 (2003)
Gong, L., Sun, X.-H. (Senior Member, IEEE), Watson, E.F.: Performance Modeling and Prediction of Nondedicated Network Computing. IEEE Transaction on Computers 51(9) (September 2002)
Foster, I., Kesselman, C.: The Grid2:Blueprint for a New Computing Infrastructure. Publishing House Electronics Industry, Beijing (2004)
Kubinyi, H.: Burger‘s medicinal chemistry and drug discovery. In: Wolff, M.E. (ed.) Principles and Practice, vol. 1, pp. 497–571. John Wiley &Sons, News York (1995)
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Hu, YL., Bai, L., Zhang, WM., Xiao, WD., Liu, Z. (2005). An Adaptive Scheduling Algorithm for Molecule Docking Design on Grid. In: Zhuge, H., Fox, G.C. (eds) Grid and Cooperative Computing - GCC 2005. GCC 2005. Lecture Notes in Computer Science, vol 3795. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11590354_42
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DOI: https://doi.org/10.1007/11590354_42
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-30510-1
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