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Large-Scale Neo-Heterogeneous Programming and Optimization of SNP Detection on Tianhe-2

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High Performance Computing (ISC High Performance 2015)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9137))

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Abstract

SNP detection is a fundamental procedure in genome analysis. A popular SNP detection tool SOAPsnp can take more than one week to analyze one human genome with a 20-fold coverage. To improve the efficiency, we developed mSNP, a parallel version of SOAPsnp. mSNP utilizes CPU cooperated with Intel® Xeon PhiTM for large-scale SNP detection. Firstly, we redesigned the key data structure of SOAPsnp, which significantly reduces the overhead of memory operations. Secondly, we devised a coordinated parallel framework, in which CPU collaborates with Xeon Phi for higher hardware utilization. Thirdly, we proposed a read-based window division strategy to improve throughput and parallel scale on multiple nodes. To the best of our knowledge, mSNP is the first SNP detection tool empowered by Xeon Phi. We achieved a 45x speedup on a single node of Tianhe-2, without any loss in precision. Moreover, mSNP showed promising scalability on 4,096 nodes on Tianhe-2.

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Notes

  1. 1.

    SOAPsnp website: http://soap.genomics.org.cn/soapsnp.html.

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Acknowledgments

We would like to thank Mr. Yingrui Li from BGI for providing the source code of SOAPsnp and Dr. Jun Wang from BGI for providing related test data. We would also like to thank Prof. Hans V. Westerhoff from University of Manchester for discussions of the human genome re-sequencing analysis problem and thus improving our own understanding. This work is supported by NSFC Grant 61272056, U1435222, 61133005, 61120106005, 91430218 and 61303191.

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Authors and Affiliations

  1. School of Computer Science, National University of Defense Technology, Changsha, China

    Yingbo Cui, **angke Liao, Shaoliang Peng, Yutong Lu, Canqun Yang & Chengkun Wu

  2. National Supercomputing Center in Shenzhen, Shenzhen, China

    Bingqiang Wang

Authors
  1. Yingbo Cui
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  2. **angke Liao
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  3. Shaoliang Peng
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  4. Yutong Lu
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  5. Canqun Yang
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  6. Bingqiang Wang
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  7. Chengkun Wu
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Corresponding author

Correspondence to Shaoliang Peng .

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Editors and Affiliations

  1. Deutsches Klimarechenzentrum (DKRZ), Hamburg, Germany

    Julian M. Kunkel

  2. Deutsches Klimarechenzentrum (DKRZ), Hamburg, Germany

    Thomas Ludwig

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Cui, Y. et al. (2015). Large-Scale Neo-Heterogeneous Programming and Optimization of SNP Detection on Tianhe-2. In: Kunkel, J., Ludwig, T. (eds) High Performance Computing. ISC High Performance 2015. Lecture Notes in Computer Science(), vol 9137. Springer, Cham. https://doi.org/10.1007/978-3-319-20119-1_6

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  • DOI: https://doi.org/10.1007/978-3-319-20119-1_6

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-20118-4

  • Online ISBN: 978-3-319-20119-1

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