MPI versus MPI+OpenMP on IBM SP for the NAS benchmarks
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Sequence comparison on a cluster of workstations using the PVM system
IPPS '95 Proceedings of the 9th International Symposium on Parallel Processing
Experiments with Parallelizing a Tribology Application
ICPPW '02 Proceedings of the 2002 International Conference on Parallel Processing Workshops
Exploiting Multi-level Parallelism for Homology Search using General Purpose Processors
ICPADS '05 Proceedings of the 11th International Conference on Parallel and Distributed Systems - Workshops - Volume 02
Performance Modeling of Communication and Computation in Hybrid MPI and OpenMP Applications
ICPADS '06 Proceedings of the 12th International Conference on Parallel and Distributed Systems - Volume 2
Parallel homologous search with Hirschberg algorithm: a hybrid MPI-Pthreads solution
ICCOMP'07 Proceedings of the 11th WSEAS International Conference on Computers
Parallelisation of sequence comparison algorithms using hybridised parallel techniques
HONET'09 Proceedings of the 6th international conference on High capacity optical networks and enabling technologies
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Nowadays, database pattern searching is the most heavily used operation in computational biology. Indeed, sequence alignment algorithm plays an important role to find the homologous groups of sequences which may help to determine the function of new sequences. Meanwhile Smith-Waterman algorithm is one of the most prominent pattern matching algorithms. However, it cost the large quantity of time and resource power. By the aid of parallel hardware and software architecture it becomes more feasible to get the fast and accurate result in efficient time. In this paper, Smith-Waterman algorithm is parallelized base on various types of parallel programming, pure MPI, pure OpenMP and Hybrid MPI-OpenMP model. In addition, based on the experiments it will be proved that hybrid programming which employ the coarse grain and fine grain parallelization, is more efficient compare with pure MPI and pure OpenMP in cluster of SMP machines.