Performance enhancement of smith-waterman algorithm using hybrid model: Comparing the MPI and hybrid programming paradigm on SMP clusters

Author(s):  
Mahdi Noorian ◽  
Hamidreza Pooshfam ◽  
Zeinab Noorian ◽  
Rosni Abdullah
Author(s):  
G. Mahinthakumar ◽  
F. Saied

Summary The hybrid MPI-OpenMP model is a natural parallel programming paradigm for emerging parallel architectures that are based on symmetric multiprocessor (SMP) clusters. This paper presents a hybrid implementation adapted for an implicit finite-element code developed for groundwater transport simulations. The original code was parallelized for distributed memory architectures using MPI (Message Passing Interface) using a domain decomposition strategy. OpenMP directives were then added to the code (a straightforward loop-level implementation) to use multiple threads within each MPI process. To improve the OpenMP performance, several loop modifications were adopted. The parallel performance results are compared for four modern parallel architectures. The results show that for most of the cases tested, the pure MPI approach outperforms the hybrid model. The exceptions to this observation were mainly due to a limitation in the MPI library implementation on one of the architectures. A general conclusion is that while the hybrid model is a promising approach for SMP cluster architectures, at the time of this writing, the payoff may not be justified for converting all existing MPI codes to hybrid codes. However, improvements in OpenMP compilers combined with potential MPI limitations in SMP nodes may make the hybrid approach more attractive for a broader set of applications in the future.


2005 ◽  
Vol 65 (4) ◽  
pp. 414-423 ◽  
Author(s):  
M.J. Berger ◽  
M.J. Aftosmis ◽  
D.D. Marshall ◽  
S.M. Murman

2003 ◽  
Author(s):  
M. Bar-Eli ◽  
O. Lowengart ◽  
J. Goldberg ◽  
S. Epstein ◽  
R. D. Fosbury

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