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First Experiences Accelerating Smith-Waterman on Intel’s Knights Landing Processor

  • Enzo Rucci
  • Carlos Garcia
  • Guillermo Botella
  • Armando De Giusti
  • Marcelo Naiouf
  • Manuel Prieto-Matias
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10393)

Abstract

The well-known Smith-Waterman (SW) algorithm is the most commonly used method for local sequence alignments. However, SW is very computationally demanding for large protein databases. There are several implementations that take advantage of parallel capacities on many-cores, FPGAs or GPUs, in order to increase the alignment throughtput. In this paper, we have explored SW acceleration on Intel KNL processor. The novelty of this architecture requires the revision of previous programming and optimization techniques on many-core architectures. To the best of authors knowledge, this is the first KNL architecture assessment for SW algorithm. Our evaluation, using the renowned Environmental NR database as benchmark, has shown that multi-threading and SIMD exploitation showed competitive performance (351 GCUPS) in comparison with other implementations.

Keywords

Bioinformatics Smith-Waterman Xeon-Phi Intel-KNL SIMD 

Notes

Acknowledgments

This work has been partially supported by Spanish government through research contract TIN2015-65277-R and CAPAP-H6 network (TIN2016-81840-REDT).

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Enzo Rucci
    • 1
  • Carlos Garcia
    • 2
  • Guillermo Botella
    • 2
  • Armando De Giusti
    • 1
  • Marcelo Naiouf
    • 3
  • Manuel Prieto-Matias
    • 2
  1. 1.III-LIDI, CONICET, Facultad de InformáticaUniversidad Nacional de La PlataLa PlataArgentina
  2. 2.Depto. Arquitectura de Computadores y AutomáticaUniversidad Complutense de MadridMadridSpain
  3. 3.III-LIDI, Facultad de InformáticaUniversidad Nacional de La PlataLa PlataArgentina

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