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Nanos Group, Barcelona Supercomputing Centre
Contact: Alex Duran (alex@bsc.es)
Protein Alignment
All protein sequences from an input file are aligned against every other sequence using the Myers and Miller algorithm. The alignments are scored and the best score for each pair is provided as a result. The scoring method is a full dynamic programming algorithm. It uses a weight matrix to score mismatches, and assigns penalties for opening and extending gaps. The output is the best score for each pair of them.
The outer loop is parallelized with an omp for worksharing directive with tasks created inside this parallel loop. This allows the implementation to break the iterations when the number of threads is large compared to the number of iterations and when there is imbalance. To be able to use untied tasks several global variables, used as temporal space, were moved to local variables.
The program takes an input of proteins to align in the FASTA format. The reference data set uses 3000 sequences, the train data set uses 100 sequences and the train data set uses 20 sequences.
For benchmarking purposes, where the SPEC tools are used to validate the solution, the computed results are only stored.
A portion of the matching weight file is produced.
ANSI C
None
A. Duran, X. Teruel, R. Ferrer, X. Martorell and E. Ayguadé: Barcelona OpenMP Tasks Suite: A Set of Benchmarks Targeting the Exploitation of Task Parallelism in OpenMP , in: Proceedings of ICPP-2009, The 38th International Conference on Parallel Processing, Copyright 2009 The Institute of Electrical and Electronics Engineers, Inc. DOI
Last Updated: March 15, 2012