Paper Info
Title
Multiple biological sequence alignment in heterogeneous multicore clusters with user-selectable task allocation policies
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.
Year
DOI
Venue
2013
10.1007/s11227-012-0768-8
The Journal of Supercomputing
Keywords
Field
DocType
Heterogeneous multicore clusters,Bioinformatics,Multiple sequence alignment,Task allocation policies
Cluster (physics),Heuristic,Computer science,Parallel computing,Concatenation,Execution time,Multiple sequence alignment,Multi-core processor,Biological sequence alignment,Distributed computing
Journal
Volume
Issue
ISSN
63
3
0920-8542
Citations 
PageRank 
References 
2
0.39
16
Authors
4
Name
Order
Citations
PageRank
Emerson Araujo Macedo150.79
Alba Cristina Magalhaes Alves De Melo225333.90
Gerson Henrique Pfitscher351.13
Azzedine Boukerche44301418.60