Hybrid Parallel Multiple Sequence Alignment Based on Artificial Bee Colony on the Supercomputer JUQUEEN

The paper 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 investigation 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, performed on JUQUEEN. The experimental results show that the hybrid parallel implementation provides considerably better performance than the original code.