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.
 
 
Highlights
The current computer engineering and High-Performance Computing (HPC) are evolving very fast towards new Chip MultiProcessor (CMP) architectures, using different approaches
The TilExpress-20G is a Peripheral Component Interconnect express (PCIe) card that can be used on any desktop Personal Computer (PC) running the Linux operating system, being controlled from such a host using a Command-Line Interface (CLI)
The total theoretical computing power of the Tile64 should be 59 × 0.866 GHz = 51.09 GHz. This provides a measure for the power of the processors, but it does not take into account some other features, like the cache memories, bridges to the main memory, RAM specifications, etc
Summary
The current computer engineering and High-Performance Computing (HPC) are evolving very fast towards new Chip MultiProcessor (CMP) architectures, using different approaches. We are developing and testing other algorithms, like the ClustalW [5], and the Basic Local Alignment Search Tool (BLAST) adapted to the Tile but, MC64-NW/SW is the one with the best gain in performance. This RISC hardware technology from Tilera has not evolved significantly over the last four years, whereas other companies like Intel have developed advanced commercial products. Any aspects relative to the power consumption or operating voltages are out of the scope of this work, and have not been considered
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