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Resolving Load Balancing Issues in BWA on NUMA Multicore Architectures

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Parallel Processing and Applied Mathematics (PPAM 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8385))

Abstract

Running BWA in multithreaded mode on a multi-socket server results in poor scaling behaviour. This is because the current parallelisation strategy does not take into account the load imbalance that is inherent to the properties of the data being aligned, e.g. varying read lengths and numbers of mutations. Additional load imbalance is also caused by the BWA code not anticipating certain hardware characteristics of multi-socket multicores, such as the non-uniform memory access time of the different cores. We show that rewriting the parallel section using Cilk removes the load imbalance, resulting in a factor two performance improvement over the original BWA.

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Notes

  1. 1.

    We always refer to the latest version of BWA, i.e. the bwa-0.6.2 download on [2].

  2. 2.

    This is actually configured via the -t parameter.

  3. 3.

    Averages for 5 runs. Same distribution of reads across cores for each run.

  4. 4.

    Graphs omitted due to space restrictions, see our technical report [10].

References

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  2. Burrows-Wheeler Aligner. http://bio-bwa.sourceforge.net/

  3. Leiserson, C.E.: The Cilk++ concurrency platform. J. Supercomput. 51(3), 244–257 (2010). (Kluwer Academic Publishers)

    Article  Google Scholar 

  4. Intel Cilk Plus. http://software.intel.com/en-us/intel-cilk-plus

  5. Farragina, P., Manzini, G.: Opportunistic data structures with applications. In: 41st IEEE Annual Symposium on Foundations of Computer Science, pp. 390–398. IEEE Computer Society, Los Alamitos (2000)

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  6. Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L.: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25:1–R25:10 (2009). (Article: R25)

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  8. Genomes Project. http://www.1000genomes.org/

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  10. Herzeel, C., Costanza, P., Ashby, T., Wuyts, R.: Performance analysis of BWA alignment. Technical report, ExaScience Life Lab (2013)

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Acknowledgments

This work is funded by Intel, Janssen Pharmaceutica and by the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT).

Author information

Authors and Affiliations

  1. imec, Kapeldreef 75, 3001, Leuven, Belgium

    Charlotte Herzeel & Thomas J. Ashby

  2. Software Languages Lab, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussel, Belgium

    Wolfgang De Meuter

  3. Intel, Veldkant 31, 2550, Kontich, Belgium

    Pascal Costanza

  4. ExaScience Life Lab, Kapeldreef 75, 3001, Leuven, Belgium

    Charlotte Herzeel, Thomas J. Ashby & Pascal Costanza

Authors
  1. Charlotte Herzeel
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  2. Thomas J. Ashby
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  3. Pascal Costanza
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  4. Wolfgang De Meuter
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Corresponding author

Correspondence to Charlotte Herzeel .

Editor information

Editors and Affiliations

  1. Institute of Computer and Information Science, Czestochowa University of Technology, Czestochowa, Poland

    Roman Wyrzykowski

  2. University of Tennessee, Department of Computer Science, Knoxville, Tennessee, USA

    Jack Dongarra

  3. Institute of Computer and Information Science, Czestochowa University of Technology, Czestochowa, Poland

    Konrad Karczewski

  4. Technical University of Denmark Informatics and Mathematical Modelling, Kongens Lyngby, Denmark

    Jerzy Waśniewski

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Herzeel, C., Ashby, T.J., Costanza, P., De Meuter, W. (2014). Resolving Load Balancing Issues in BWA on NUMA Multicore Architectures. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Waśniewski, J. (eds) Parallel Processing and Applied Mathematics. PPAM 2013. Lecture Notes in Computer Science(), vol 8385. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-55195-6_21

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  • DOI: https://doi.org/10.1007/978-3-642-55195-6_21

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-55194-9

  • Online ISBN: 978-3-642-55195-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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