Multiple biological sequence alignment in heterogeneous multicore clusters with user-selectable task allocation policies

Authors:
Emerson Araujo Macedo;Alba Cristina Magalhaes Alves De Melo;Gerson Henrique Pfitscher;Azzedine Boukerche
Affiliations:
Department of Computer Science, University of Brasilia (UnB), Brasilia, Brazil;Department of Computer Science, University of Brasilia (UnB), Brasilia, Brazil;Department of Computer Science, University of Brasilia (UnB), Brasilia, Brazil;School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, Canada and Kuwait University, Kuwait City, Kuwait
Venue:
The Journal of Supercomputing
Year:
2013

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Abstract

Multiple Sequence Alignment (MSA) is an important problem in Bioinformatics that aims to align more than two sequences in order to emphasize similarity regions. This problem is known to be NP-Hard, so heuristic methods are used to solve it. DIALIGN-TX is an iterative heuristic method for MSA that generates alignments by concatenating ungapped regions with high similarity. Usually, the first phase of MSA algorithms is parallelized by distributing several independent tasks among the nodes. Even though heterogeneous multicore clusters are becoming very common nowadays, very few task allocation policies were proposed for this type of architecture. This paper proposes an MPI/OpenMP master/slave parallel strategy to run DIALIGN-TX in heterogeneous multicore clusters, with several allocation policies. We show that an appropriate choice of the master node has great impact on the overall system performance. Also, the results obtained in a heterogeneous multicore cluster composed of 4 nodes (30 cores), with real sequence sets show that the execution time can be drastically reduced when the appropriate allocation policy is used.