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Parallel and Distributed Processing Symposium, International (2008)
Miami, FL, USA
Apr. 14, 2008 to Apr. 18, 2008
ISBN: 978-1-4244-1693-6
pp: 1-8
Byung-Hoon Park , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
Nagiza F. Samatova , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
Tatiana Karpinets , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
Kevin Thomas , Cray Inc., USA
Matthew Schmidt , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
ABSTRACT
Data-driven modeling of biological systems such as protein-protein interaction networks is data-intensive and combinatorially challenging. Backtracking can constrain a combinatorial search space. Yet, its recursive nature, exacerbated by data-intensity, limits its applicability for large-scale systems. Parallel, scalable, and memory-efficient backtracking is a promising approach. Parallel backtracking suffers from unbalanced loads. Load rebalancing via synchronization and data movement is prohibitively expensive. Balancing these discrepancies, while minimizing end-to-end execution time and memory requirements, is desirable. This paper introduces such a framework. Its scalability and efficiency, demonstrated on the maximal clique enumeration problem, are attributed to the proposed: (a) representation of search tree decomposition to enable parallelization; (b) depth-first parallel search to minimize memory requirement; (c) least stringent synchronization to minimize data movement; and (d) on-demand work stealing with stack splitting to minimize processors’ idle time. The applications of this framework to real biological problems related to bioethanol production are discussed.
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CITATION
Byung-Hoon Park, Nagiza F. Samatova, Tatiana Karpinets, Kevin Thomas, Matthew Schmidt, "Parallel, scalable, memory-efficient backtracking for combinatoria modeling of large-scale biological systems", Parallel and Distributed Processing Symposium, International, vol. 00, no. , pp. 1-8, 2008, doi:10.1109/IPDPS.2008.4536180
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