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Many-core Tile64 vs. Multi-core Intel Xeon: Bioinformatics Performance Comparison 1

Myriam Kurtz, Francisco J. Esteban, Pilar Hernández, Juan Antonio Caballero, Antonio Jesús Guevara Plaza, Gabriel Dorado, Sergio Gálvez, Edificio Ramón

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Abstract

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

About this research paper

What this paper is about

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

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Available abstract

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

Key concepts: Xeon Phi, x86, Porting, Xeon, Computer science, Coprocessor, Parallel computing, Benchmark (surveying)

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