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Optimal Worksharing of DNA Sequence Analysis on Accelerated Platforms
Linnaeus University, Faculty of Technology, Department of Computer Science. (Parallel Computing)
Linnaeus University, Faculty of Technology, Department of Computer Science. (Parallel Computing)
Cracow University of Technology, Poland.
2016 (English)In: Resource Management for Big Data Platforms: Algorithms, Modelling, and High-Performance Computing Techniques, Springer, 2016, 279-309 p.Chapter in book (Refereed)
Abstract [en]

In this chapter, we describe an optimized approach for DNA sequence analysis on a heterogeneous platform that is accelerated with the Intel Xeon Phi. Such platforms commonly comprise one or two general purpose CPUs and one (or more) Xeon Phi coprocessors. Our parallel DNA sequence analysis algorithm is based on Finite Automata and finds patterns in large-scale DNA sequences. To determine the optimal worksharing (that is, DNA sequence fractions for the host and accelerating device) we propose a solution that combines combinatorial optimization and machine learning. The objective function that we aim to minimize is the execution time of the DNA sequence analysis. We use combinatorial optimization to efficiently explore the system configuration space and determine with machine learning the near-optimal system configuration for execution of the DNA sequence analysis. We evaluate our approach empirically using real-world DNA segments of various organisms. For experimentation, we use an accelerated platform that comprises two 12-core Intel Xeon E5 CPUs and an Intel Xeon Phi 7120P accelerator with 61 cores.

Place, publisher, year, edition, pages
Springer, 2016. 279-309 p.
Series
Computer Communications and Networks, ISSN 1617-7975
National Category
Computer Systems
Identifiers
URN: urn:nbn:se:lnu:diva-57765DOI: 10.1007/978-3-319-44881-7_14ISBN: 978-3-319-44880-0 (print)ISBN: 978-3-319-44881-7 (print)OAI: oai:DiVA.org:lnu-57765DiVA: diva2:1044068
Available from: 2016-11-01 Created: 2016-11-01 Last updated: 2016-11-15Bibliographically approved

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CiteExportLink to record
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Citation style
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