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Parallelizing a multiobjective swarm intelligence approach to phylogenetics using hybrid MPI/OpenMP schemes

Published: 15 September 2013 Publication History

Abstract

Phylogenetic inference is one of the most challenging problems in Computational Biology. As recent research lines aim to introduce multiobjective optimization techniques to resolve incongruences in Phylogenetics, parallel multiobjective metaheuristics can be useful to address the computational complexity required to perform phylogenetic analyses according to multiple criteria simultaneously. In this work, we propose several master-worker hybrid approaches based on MPI and OpenMP to parallelize a multiobjective algorithm inspired by the behaviour of fireflies for inferring phylogenies on multicore cluster architectures. Experiments on four real biological data sets suggest that this algorithm can achieve significant speedup and efficiency values by using a proper hybrid model designed to exploit parallelism at the inference and assessment levels.

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cover image ACM Other conferences
EuroMPI '13: Proceedings of the 20th European MPI Users' Group Meeting
September 2013
289 pages
ISBN:9781450319034
DOI:10.1145/2488551
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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  • ARCOS: Computer Architecture and Technology Area, Universidad Carlos III de Madrid

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 15 September 2013

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Author Tags

  1. cluster computing
  2. firefly algorithm
  3. multiobjective optimization
  4. phylogenetic inference
  5. swarm intelligence

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EuroMPI '13
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  • ARCOS
EuroMPI '13: 20th European MPI Users's Group Meeting
September 15 - 18, 2013
Madrid, Spain

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EuroMPI '13 Paper Acceptance Rate 22 of 47 submissions, 47%;
Overall Acceptance Rate 66 of 139 submissions, 47%

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