A Hybrid Implementation of Massively Parallel Multiple Sequence Alignment Method Based on Artificial Bee Colony Algorithm
Creators
- 1. Greek Research and Technology Network, Athens, Greece; Scientific Computing Center, Aristotle University of Thessaloniki, Greece
Contributors
- 1. Greek Research and Technology Network, Athens, Greece; Scientific Computing Center, Aristotle University of Thessaloniki, Greece
- 2. National Centre for Supercomputing Applications, Bulgaria; Department of Computer Systems, Technical University of Sofia, Bulgaria
- 3. National Centre for Supercomputing Applications, Bulgaria; Department of Programming and Computer Technologies, Technical University of Sofia, Bulgaria
Description
The project focuses on performance investigation and improvement of multiple biological sequence alignment software
MSA_BG on the BlueGene/Q supercomputer JUQUEEN. For this purpose, scientific experiments in the area of
bioinformatics have been carried out, using as case study influenza virus sequences. The objectives of the project are code
optimization, porting, scaling, profiling and performance evaluation of MSA_BG software. To this end we have developed
hybrid MPI/OpenMP parallelization on the top of the MPI only code and we showcase the advantages of this approach
through the results of benchmark tests that were performed on JUQUEEN. The experimental results show that the hybrid
parallel implementation provides considerably better performance than the original code.
Files
WP127.pdf
Files
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