Abstract
This paper presents the design and evaluation of a task allocation framework for Biological Sequence Comparison applications that use dynamic programming and run in heterogeneous environments. The framework is composed by four modules and either task allocation policies or applications can be integrated to it. The results obtained with four different task allocation policies in a 10-machine heterogeneous environment show that, for some sequence sizes, we were able to reduce the execution time of the parallel application in 54.2%, with the appropriate allocation policy.
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References
Batista, R.B., Melo, A.C.M.A.: Z-align: An Exact Parallel Strategy for Biological Sequence Alignment in User-Restricted Memory Space. In: Proc. of the IEEE Int. Conf. on Cluster Computing, Barcelona, IEEE Digital Library, Los Alamitos (2006)
Boukerche, A., Melo, A.C.M.A., Ayala-Rincon, M., Santana, T.M.: Parallel Smith-Waterman Algorithm for Local DNA Comparison in a Cluster of Workstations. In: Nikoletseas, S.E. (ed.) WEA 2005. LNCS, vol. 3503, pp. 464–475. Springer, Heidelberg (2005)
Boukerche, A., Melo, A.C.M.A., Sandes, E.S.F., Ayala-Rincon, M.: A Parallel Exact Algorithm to Compare Very Long Biological Sequences in Clusters of Workstations. Cluster Computing 10(2), 187–202 (2007)
Chen, C., Schmidt, B.: Computing large-scale alignments on a multi-cluster. In: IEEE International Conference on Cluster Computing, IEEE Digital Library, Los Alamitos (2003)
Cuenca, J., Gimenez, D., Martinez, J.P.: Heuristics for work distribution of a homogeneous parallel dynamic programming scheme on heterogeneous systems. In: Proc. of HeteroPar, pp. 354–360. IEEE Computer Society Press, Los Alamitos (2004)
Driga, A., et al.: Fastlsa: a fast, linear-space, parallel and sequential algorithm for sequence alignment. In: International Conference Parallel Processing, pp. 48–56 (2003)
Hwang, K., Xu, Z.: Scalable Parallel Computing: Technology, Architecture, Programming, 1st edn. McGraw-Hill, New York (1998)
Legrand, A., et al.: Mapping and Load Balancing of Iterative Applications. IEEE Transactions on Parallel and Distributed Systems 15(6), 546–558 (2004)
Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970)
Papadimitri, C.H., Steiglitz, K.: Combinatorial Optimization: Algorithms and Complexity. Dover Publications Inc., Mineola, NY (1998)
Rajko, S., Aluru, S.: Space and Time Optimal Parallel Sequence Alignments. IEEE Transactions on Parallel and Distributed Systems 15(2), 1070–1081 (2004)
Setubal, J.C., Meidanis, J.: Introduction to Computational Molecular Biology. PWS Pub. Co. (1997)
Sinnen, O., Sousa, L.: Communication Contention in Task Scheduling. IEEE Transactions on Parallel and Distributed Systems 16(6), 503–515 (2005)
Smith, T.F., Waterman, M.S.: Identification of Common molecular subsequences. Journal of Mol. Biol. 147(1), 195–197 (1981)
Taura, K., Chien, A.: A Heuristic Algorithm for Mapping Communicating Tasks on Heterogeneous Resources. In: Proc of the 9th Heterogeneous Computing Workshop, IEEE Computer Society Press, IEEE Digital Library, Los Alamitos (2000)
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Santana, M.N.P., Melo, A.C.M.A. (2007). Biological Sequence Comparison Application in Heterogeneous Environments with Dynamic Programming Algorithms. In: Sagot, MF., Walter, M.E.M.T. (eds) Advances in Bioinformatics and Computational Biology. BSB 2007. Lecture Notes in Computer Science(), vol 4643. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73731-5_5
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DOI: https://doi.org/10.1007/978-3-540-73731-5_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73730-8
Online ISBN: 978-3-540-73731-5
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