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Efficient Smith-Waterman on Multi-core with FastFlow

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3 Author(s)
Marco Aldinucci ; Comput. Sci. Dept., Univ. of Torino, Turin, Italy ; Massimiliano Meneghin ; Massimo Torquati

Shared memory multiprocessors have returned to popularity thanks to rapid spreading of commodity multi-core architectures. However, little attention has been paid to supporting effective streaming applications on these architectures. In this paper we describe FastFlow, a low-level programming framework based on lock-free queues explicitly designed to support high-level languages for streaming applications. We compare FastFlow with state-of-the-art programming frameworks such as Cilk, OpenMP, and Intel TBB. We experimentally demonstrate that FastFlow is always more efficient than them on a given real world application: the speedup of FastFlow over other solutions may be substantial for fine grain tasks, for example +35% over OpenMP, +226% over Cilk, +96% over TBB for the alignment of protein P01111 against UniProt DB using the Smith-Waterman algorithm.

Published in:

2010 18th Euromicro Conference on Parallel, Distributed and Network-based Processing

Date of Conference:

17-19 Feb. 2010