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 proceedingConference contribution

1 Citation (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 languageEnglish
Title of host publication2nd International Conference on Computer Research and Development, ICCRD 2010
Pages25-29
Number of pages5
DOIs
Publication statusPublished - 09-08-2010
Externally publishedYes
Event2nd International Conference on Computer Research and Development, ICCRD 2010 - Kuala Lumpur, Malaysia
Duration: 07-05-201010-05-2010

Conference

Conference2nd International Conference on Computer Research and Development, ICCRD 2010
CountryMalaysia
CityKuala Lumpur
Period07-05-1010-05-10

Fingerprint

Proteins
Processing
Experiments

All Science Journal Classification (ASJC) codes

  • Computer Science (miscellaneous)

Cite this

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 (pp. 25-29). [5489419] https://doi.org/10.1109/ICCRD.2010.58
Othman, Fazilah ; Umar, Ibrahim ; Abdullah, Rosni ; Rathi, Abhishek. / Parallel bipartite graph algorithm for protein structure matching using OpenMP. 2nd International Conference on Computer Research and Development, ICCRD 2010. 2010. pp. 25-29
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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

Parallel bipartite graph algorithm for protein structure matching using OpenMP. / Othman, Fazilah; Umar, Ibrahim; Abdullah, Rosni; Rathi, Abhishek.

2nd International Conference on Computer Research and Development, ICCRD 2010. 2010. p. 25-29 5489419.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Othman F, Umar I, Abdullah R, Rathi A. Parallel bipartite graph algorithm for protein structure matching using OpenMP. In 2nd International Conference on Computer Research and Development, ICCRD 2010. 2010. p. 25-29. 5489419 https://doi.org/10.1109/ICCRD.2010.58