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Reseach Article

Applying Parallel Design Patterns on Molecular Dynamics Simulation

by Nilesh Maltare, Vithal N. Kamat
International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 181 - Number 50
Year of Publication: 2019
Authors: Nilesh Maltare, Vithal N. Kamat
10.5120/ijca2019918674

Nilesh Maltare, Vithal N. Kamat . Applying Parallel Design Patterns on Molecular Dynamics Simulation. International Journal of Computer Applications. 181, 50 ( Apr 2019), 21-24. DOI=10.5120/ijca2019918674

@article{ 10.5120/ijca2019918674,
author = { Nilesh Maltare, Vithal N. Kamat },
title = { Applying Parallel Design Patterns on Molecular Dynamics Simulation },
journal = { International Journal of Computer Applications },
issue_date = { Apr 2019 },
volume = { 181 },
number = { 50 },
month = { Apr },
year = { 2019 },
issn = { 0975-8887 },
pages = { 21-24 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume181/number50/30499-2019918674/ },
doi = { 10.5120/ijca2019918674 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-07T01:09:44.298526+05:30
%A Nilesh Maltare
%A Vithal N. Kamat
%T Applying Parallel Design Patterns on Molecular Dynamics Simulation
%J International Journal of Computer Applications
%@ 0975-8887
%V 181
%N 50
%P 21-24
%D 2019
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Molecular dynamics simulates behavior of atoms and molecules. Molecular dynamics Simulation demonstrates and derives macroscopic properties by atomic interactions. In this experiment we have redesigned Molecular Dynamics (MD) Simulation by applying different parallel design pattern. Redesigned MD Simulation focuses on adaptability to different architectures and scalability to use with large number of atoms and long duration simulation. The paper demonstrates performance of MD on different architectures.

References
  1. A Rahman, "Correlations in the motion of atoms in liquid argon", Physical Review, 1964 – APS.
  2. W. G. Hoover, A. J. C. Ladd, and V. N. Hoover,” Historical Development and Recent Applications of Molecular Dynamics Simulation”, Advances in Chemistry Series 1983.
  3. Raymond Kapral, Giovanni Ciccotti, "Molecular dynamics: an account of its evolution", Theory and Applications of Computational Chemistry Elsevier 2005
  4. Adam Hospital, Josep Ramon Goni, Modesto Orozco, Josep L Gelpi, “Molecular dynamics simulations: Advances and applications”, Advances and Applications in Bioinformatics and Chemistry, November 2015
  5. DOI: 10.2147/AABC.S70333
  6. K. Asanovic, R. Bodik, J. Demmel, T. Keaveny, K. Keutzer, J. Kubiatowicz,N. Morgan, D. Patterson, K. Sen, J. Wawrzynek, et al. “A view of the parallel computing landscape. Communications of the ACM”, 52(10):56–67, 2009.
  7. Culler, D. E., Singh, J. P., & Gupta, A. (1999). Parallel computer architecture: a hardware/software approach. San Francisco, CA: Morgan Kaufman Publishers, Inc
  8. Diaz, J., Muoz-Caro, C., & Nio, A. (2012). A survey of parallel programming models and tools in the multi and many-core era. IEEE Transactions on Parallel and Distributed Systems, 23(8), 1369-1386. doi:10.1109/TPDS.2011.308
  9. Erich Gamma, Richard Helm, Ralph Johnson, John Vlissides. “Design patterns: Abstraction and reuse of object-oriented design”, ECOOP1993 pages: 406-431, Springer-Verlag.
  10. Frank Buschmann et al., “Pattern-Oriented Software Architecture - A System of Patterns” , Wiley, 1996.
  11. S. Siu, A. Singh,"Design patterns for parallel computing using a network of processors" Proceedings. The Sixth IEEE International Symposium on High Performance Distributed Computing, DOI: 10.1109/HPDC.1997.626434
  12. D. M. Beazley, “Parallel Algorithm for Short-Range Molecular Dynamics”, World Scientific’s Annual Reviews in Computational Physics, 3, 119 (1995).
  13. Timothy G. Mattson,Beverly A. Sanders, Berna L. Massingill. “Patterns for Parallel Programming”, 2005 ISBN-10: 0321228111, ISBN-13: 9780321228116, Addison-Wesley Professional.
  14. D. Goswami, A. Singh, and B. Priess. “Architectural skeletons: The reusable building-blocks for parallel applications”. In Proceedings of the 1999 International Conference on Parallel and Distributed Processing Techniques and Applciations (PDPTA’99), pages 1250–1256, 1999..
  15. S. MacDonald, D. Szafron, J. Schaeffer, and S. Bromling. “From patterns to frameworks to parallel programs”. Journal of Parallel and Distributed Computing, 2001. .
  16. J.L. Ortega,”Arjona Design Patterns for Communication Components”, Proceedings of the 12th European Conference on Pattern Languages of Programming and Computing (EuroPLoP2007), Kloster Irsee, Germany, 2007
  17. J. Anvik, J. Schaeffer, D. Szafron, K. Tan. “Asserting the utility of CO2P3S using the Cowichan Problem Set”, Journal of Parallel and Distributed Computing, Volume 65 Issue 12, December 2005.
  18. S. Plimpton, “Fast Parallel Algorithms for Short-Range Molecular Dynamics,” J. Computational Physics, vol. 117, no-1, 1995, pp. 1–19.
  19. K.B. Tarmyshov and F. Muller-Plathe, “Parallelizing a Molecular Dynamics Algorithm on a Multiprocessor Workstation Using OpenMP,” J. Chemical Information and Modeling, vol. 45, no. 6, 2005, pp. 1943–1952.
  20. Zia Ul Huda, Rohit Atre, Ali Jannesari and Felix Wolf,"Automatic Parallel Pattern Detection in the Algorithm Structure Design Space", IEEE International Parallel and Distributed Processing Symposium 2016, doi:10.1109/ipdps.2016.60.
  21. Nilesh Maltare, Chetan Chudasama, "Applying parallel design patterns to embarassingly parallel problem", 2016 Symposium on Colossal Data Analysis and Networking (CDAN), 2016.
Index Terms

Computer Science
Information Sciences

Keywords

Parallel Programming Patterns Threads.