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hLCS. A Hybrid GPGPU Approach for Solving Multiple Short and Unbalanced LCS Problems

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Computational Science and Its Applications – ICCSA 2014 (ICCSA 2014)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8584))

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Abstract

The “Longest Common Subsequence” is one of the most widely used and well-known methods within the similarity search community, applicable to a wide range of fields. Currently, modern multicore CPU and GPU-based systems offer an impressive cost/performance ratio and are an attractive test platform to accelerate response time and increase the number of problems solved per second. The use of GPUs for carrying out sequences alignment is widely extended for bioinformatics applications. However, we focus on the use of this algorithm applied to other problems which supposes a new and different approach. In particular, the most important difference is found in the pattern of the sequences. While, on one hand, the size of the biological sequences are large and similar, on the other hand, the sequences in other applications are short and unbalanced. Furthermore, this work aims to use one multicore CPU and GPU system for computing multiple problems simultaneously instead of computing only one. The main contribution of this work is a new hybrid approach which combines the two classical parallel techniques for our problem in two different phases. This new implementation is up to 80× and 25× faster, in terms of speedup, over the sequential and multicore counterpart respectively for our particular problem, that is, solving multiple “Longest Common Subsequence” problems on short and unbalanced sequences with a high ratio of problems solved per second.

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Author information

Authors and Affiliations

  1. Research Center for Energy, Environment and Technology, CIEMAT, Numerical Simulation Unit, Madrid, Spain

    Pedro Valero-Lara

  2. School of Computer Science, The Complutense University of Madrid, Spain

    Pedro Valero-Lara

Authors
  1. Pedro Valero-Lara
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Editor information

Editors and Affiliations

  1. School of Engineering, University of Basilicata, 85100, Potenza, Italy

    Beniamino Murgante

  2. Department of Computer and Information Sciences, Covenant University, Ota, Nigeria

    Sanjay Misra

  3. Department of Production and Systems, University of Minho, 4710-057, Braga, Portugal

    Ana Maria A. C. Rocha

  4. DICAR, Polytecnico di Bari, 70125, Bari, Italy

    Carmelo Torre

  5. University of Minho, Braga, Portugal

    Jorge Gustavo Rocha  & Maria Irene Falcão  & 

  6. Monash University, 3800, Clayton, VIC, Australia

    David Taniar

  7. Department of Intelligent Informatics, Kyushu Sangyo University, 2-3-1 Matsukadai, 813-8503, Higashi-ku, Fukuoka, Japan

    Bernady O. Apduhan

  8. Department of Mathematics and Computer Science, University of Perugia, Via Vanvitelli, 1, 06123, Perugia, Italy

    Osvaldo Gervasi

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Valero-Lara, P. (2014). hLCS. A Hybrid GPGPU Approach for Solving Multiple Short and Unbalanced LCS Problems. In: Murgante, B., et al. Computational Science and Its Applications – ICCSA 2014. ICCSA 2014. Lecture Notes in Computer Science, vol 8584. Springer, Cham. https://doi.org/10.1007/978-3-319-09153-2_8

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  • DOI: https://doi.org/10.1007/978-3-319-09153-2_8

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-09152-5

  • Online ISBN: 978-3-319-09153-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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