Parallel bipartite graph algorithm for protein structure matching using OpenMP

Fazilah Othman; Ibrahim Umar; Rosni Abdullah; Abhishek Rathi

doi:10.1109/ICCRD.2010.58

Parallel bipartite graph algorithm for protein structure matching using OpenMP

Fazilah Othman, Ibrahim Umar, Rosni Abdullah, Abhishek Rathi

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2 Citations (Scopus)

Abstract

Current work on bipartite graph-based algorithm for protein tertiary structure matching shows that the algorithm demands heavy computation and extensive processing time during graph preparation and matching. In this work, we deployed multithreading approach using OpenMP to enhance the performance of the algorithm. The experiment on dual quad core machines shows that the speedup is 4.9 on 8 threads with the minimum execution time of 121.39 seconds, before it gradually increases as more threads are added. The parallel code has successfully utilized the available multi-cores resources and it extends the capability of the algorithm to match more structures in a given time.

Original language	English
Title of host publication	2nd International Conference on Computer Research and Development, ICCRD 2010
Pages	25-29
Number of pages	5
DOIs	https://doi.org/10.1109/ICCRD.2010.58
Publication status	Published - 09-08-2010
Externally published	Yes
Event	2nd International Conference on Computer Research and Development, ICCRD 2010 - Kuala Lumpur, Malaysia Duration: 07-05-2010 → 10-05-2010

Conference

Conference	2nd International Conference on Computer Research and Development, ICCRD 2010
Country/Territory	Malaysia
City	Kuala Lumpur
Period	07-05-10 → 10-05-10

All Science Journal Classification (ASJC) codes

Computer Science (miscellaneous)

Access to Document

10.1109/ICCRD.2010.58

Cite this

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title = "Parallel bipartite graph algorithm for protein structure matching using OpenMP",

abstract = "Current work on bipartite graph-based algorithm for protein tertiary structure matching shows that the algorithm demands heavy computation and extensive processing time during graph preparation and matching. In this work, we deployed multithreading approach using OpenMP to enhance the performance of the algorithm. The experiment on dual quad core machines shows that the speedup is 4.9 on 8 threads with the minimum execution time of 121.39 seconds, before it gradually increases as more threads are added. The parallel code has successfully utilized the available multi-cores resources and it extends the capability of the algorithm to match more structures in a given time.",

author = "Fazilah Othman and Ibrahim Umar and Rosni Abdullah and Abhishek Rathi",

year = "2010",

month = aug,

day = "9",

doi = "10.1109/ICCRD.2010.58",

language = "English",

isbn = "9780769540436",

pages = "25--29",

booktitle = "2nd International Conference on Computer Research and Development, ICCRD 2010",

note = "2nd International Conference on Computer Research and Development, ICCRD 2010 ; Conference date: 07-05-2010 Through 10-05-2010",

}

Othman, F, Umar, I, Abdullah, R & Rathi, A 2010, Parallel bipartite graph algorithm for protein structure matching using OpenMP. in 2nd International Conference on Computer Research and Development, ICCRD 2010., 5489419, pp. 25-29, 2nd International Conference on Computer Research and Development, ICCRD 2010, Kuala Lumpur, Malaysia, 07-05-10. https://doi.org/10.1109/ICCRD.2010.58

TY - GEN

T1 - Parallel bipartite graph algorithm for protein structure matching using OpenMP

AU - Othman, Fazilah

AU - Umar, Ibrahim

AU - Abdullah, Rosni

AU - Rathi, Abhishek

PY - 2010/8/9

Y1 - 2010/8/9

N2 - Current work on bipartite graph-based algorithm for protein tertiary structure matching shows that the algorithm demands heavy computation and extensive processing time during graph preparation and matching. In this work, we deployed multithreading approach using OpenMP to enhance the performance of the algorithm. The experiment on dual quad core machines shows that the speedup is 4.9 on 8 threads with the minimum execution time of 121.39 seconds, before it gradually increases as more threads are added. The parallel code has successfully utilized the available multi-cores resources and it extends the capability of the algorithm to match more structures in a given time.

AB - Current work on bipartite graph-based algorithm for protein tertiary structure matching shows that the algorithm demands heavy computation and extensive processing time during graph preparation and matching. In this work, we deployed multithreading approach using OpenMP to enhance the performance of the algorithm. The experiment on dual quad core machines shows that the speedup is 4.9 on 8 threads with the minimum execution time of 121.39 seconds, before it gradually increases as more threads are added. The parallel code has successfully utilized the available multi-cores resources and it extends the capability of the algorithm to match more structures in a given time.

UR - http://www.scopus.com/inward/record.url?scp=77955210194&partnerID=8YFLogxK

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U2 - 10.1109/ICCRD.2010.58

DO - 10.1109/ICCRD.2010.58

M3 - Conference contribution

AN - SCOPUS:77955210194

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SP - 25

EP - 29

BT - 2nd International Conference on Computer Research and Development, ICCRD 2010

T2 - 2nd International Conference on Computer Research and Development, ICCRD 2010

Y2 - 7 May 2010 through 10 May 2010

ER -

Parallel bipartite graph algorithm for protein structure matching using OpenMP

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