Ontology type: schema:Chapter
2017
AUTHORSEnzo Rucci , Carlos Garcia , Guillermo Botella , Armando De Giusti , Marcelo Naiouf , Manuel Prieto-Matias
ABSTRACTThe 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. More... »
PAGES569-579
Algorithms and Architectures for Parallel Processing
ISBN
978-3-319-65481-2
978-3-319-65482-9
http://scigraph.springernature.com/pub.10.1007/978-3-319-65482-9_42
DOIhttp://dx.doi.org/10.1007/978-3-319-65482-9_42
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