Parallelizing the Smith-Waterman Algorithm using OpenSHMEM and MPI-3 One-Sided Interfaces

Title: Parallelizing the Smith-Waterman Algorithm using OpenSHMEM and MPI-3 One-Sided Interfaces

Conference · Thu Jan 01 00:00:00 EST 2015

DOI:https://doi.org/10.1007/978-3-319-26428-8_12· OSTI ID:1311222

Baker, Matthew B ^[1]; Welch, Donald A ^[1]; Gorentla Venkata, Manjunath ^[1]

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Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)

Sponsoring Organization:: USDOE Office of Science (SC); Work for Others (WFO)

Resource Relation:: Journal Volume: 9397; Conference: OpenSHMEM 2015, Annapolis, MD, USA, 20150804, 20150806

Identification of common molecular subsequences Smith, T. F.; Waterman, M. S. Journal of Molecular Biology, Vol. 147, Issue 1, p. 195-197 https://doi.org/10.1016/0022-2836(81)90087-5	journal	March 1981
An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data Wang, Y.; Lu, J.; Yu, J. Genome Research, Vol. 23, Issue 5 https://doi.org/10.1101/gr.146084.112	journal	January 2013
Parallel Smith-Waterman Comparison on Multicore and Manycore Computing Platforms with BSP++ Hamidouche, Khaled; Mendonca, Fernando Machado; Falcou, Joel International Journal of Parallel Programming, Vol. 41, Issue 1 https://doi.org/10.1007/s10766-012-0209-6	journal	August 2012
Performance enhancement of smith-waterman algorithm using hybrid model: Comparing the MPI and hybrid programming paradigm on SMP clusters Noorian, Mahdi; Pooshfam, Hamidreza; Noorian, Zeinab 2009 IEEE International Conference on Systems, Man and Cybernetics - SMC https://doi.org/10.1109/ICSMC.2009.5346845	conference	October 2009
Acceleration of the Smith–Waterman algorithm using single and multiple graphics processors Khajeh-Saeed, Ali; Poole, Stephen; Blair Perot, J. Journal of Computational Physics, Vol. 229, Issue 11 https://doi.org/10.1016/j.jcp.2010.02.009	journal	June 2010
An improved algorithm for matching biological sequences Gotoh, Osamu Journal of Molecular Biology, Vol. 162, Issue 3 https://doi.org/10.1016/0022-2836(82)90398-9	journal	December 1982

Leveraging MPI's One-Sided Communication Interface for Shared-Memory Programming.

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