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Reseach Article

Load Balancing for Parallel Motif Discoveries

by Angkul Kongmunvattana
International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 124 - Number 13
Year of Publication: 2015
Authors: Angkul Kongmunvattana
10.5120/ijca2015905745

Angkul Kongmunvattana . Load Balancing for Parallel Motif Discoveries. International Journal of Computer Applications. 124, 13 ( August 2015), 29-34. DOI=10.5120/ijca2015905745

@article{ 10.5120/ijca2015905745,
author = { Angkul Kongmunvattana },
title = { Load Balancing for Parallel Motif Discoveries },
journal = { International Journal of Computer Applications },
issue_date = { August 2015 },
volume = { 124 },
number = { 13 },
month = { August },
year = { 2015 },
issn = { 0975-8887 },
pages = { 29-34 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume124/number13/22166-2015905745/ },
doi = { 10.5120/ijca2015905745 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T23:14:20.226624+05:30
%A Angkul Kongmunvattana
%T Load Balancing for Parallel Motif Discoveries
%J International Journal of Computer Applications
%@ 0975-8887
%V 124
%N 13
%P 29-34
%D 2015
%I Foundation of Computer Science (FCS), NY, USA
Abstract

The problem of motif discovery has been studied extensively over the last few decades. Many sequential and parallel algorithms have been proposed and studied. A significant runtime is still required for several challenging instances of the motif search problem. This paper studies parameter spaces to find an optimal point for load balancing between the master and the worker processes, which are collaboratively and concurrently searching for motifs. Extensive experiments have been carried out on the state-of-the-art TACC Stampede System. The results demonstrated that a workload from the parallel motif discovery problem is best divided between the master and worker processes by having the master process worked on the first ((l-4))/2 nucleotides in the DNA sequences, where l is the total length of the input DNA sequences, before passing the remaining work to the worker process. In addition, the results also shown that the latency tolerance techniques used in the implementation of this work is effective because of the almost linear speedup obtained.

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Index Terms

Computer Science
Information Sciences

Keywords

Latency Tolerance Load Balancing Message Passing Motif Discovery