Bioinformatics Performance Comparison of Many-core Tile64 vs. Multi-core Intel Xeon

Authors

  • Myriam Kurtz
  • Francisco J. Esteban
  • Pilar Hernández
  • Juan Antonio Caballero
  • Antonio Guevara
  • Gabriel Dorado
  • Sergio Gálvez

DOI:

https://doi.org/10.19153/cleiej.17.1.4

Abstract

The performance of the many-core Tile64 versus the multi-core Xeon x86 architecture on bioinformatics has been compared. We have used the pairwise algorithm MC64-NW/SW that we have previously developed to align nucleic acid (DNA and RNA) and peptide (protein) sequences for the benchmarking, being an enhanced and parallel implementation of the Needleman-Wunsch and Smith-Waterman algorithms. We have ported the MC64-NW/SW (originally developed for the Tile64 processor), to the x86 architecture (Intel Xeon Quad Core and Intel i7 Quad Core processors) with excellent results. Hence, the evolution of the x86-based architectures towards coprocessors like the Xeon Phi should represent significant performance improvements for bioinformatics.

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Published

2014-04-01

Issue

Vol. 17 No. 1 (2014): HPCLatAm 2013 Special Issue

Section

Articles

License

CLEIej is supported by its home institution, CLEI, and by the contribution of the Latin American and international researchers community, and it does not apply any author charges whatsoever for submitting and publishing. Since its creation in 1998, all contents are made publicly accesibly. The current license being applied is a (CC)-BY license (effective October 2015; between 2011 and 2015 a (CC)-BY-NC license was used).