Abstract
Implementing a parallel molecular dynamics as a parallel application presents some unique load balancing challenges. Non-uniform distribution of atoms in space, along with the need to avoid symmetric redundant computations, produces a highly irregular computational load. Scalability and efficiency considerations produce further irregularity. Also, as the simulation evolves, the movement of atoms causes changes in the load distributions. This paper describes the use of an object-based, measurement-based load balancing strategy for a parallel molecular dynamics application, and its impact on performance.
This work was supported in part by National Institute of Health (NIH PHS 5 P41 RR05969-04 and NIH HL 16059) and National Science Foundation (NSF/GCAG BIR 93-18159 and NSF BIR 94-23827EQ).
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
References
Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4(2):187–217, 1983
Axel T. Briinger. Brünger. A System for X-ray Crystallography and NMR. Yale University Press, 1992.
Terry W. Clark, Reinhard v. Hanxleden, J. Andrew McCammon, and L. Ridgeway Scott. Parallelizing molecular dynamics using spatial decomposition. Technical report, Center for Research on Parallel Comutation, Rice University, P.O. Box 1892, Houston, TX 77251-1892, November 1993.
H. Heller, H. GrubMuller, and K. Schulten. Molecular dynamics simulation on a parallel computer. Molecular Simulation, 5, 1990.
L. V. Kalé, Milind Bhandarkar, Robert Brunner, Neal Krawetz, James Phillips, and Aritomo Shinozaki. A case study in multilingual parallel programming. In 10th International Workshop on Languages and Compilers for Parallel Computing, Minneapolis, Minnesota, June 1997.
L. V. KaIé, Milind Bhandarkar, Narain Jagathesan, Sanjeev Krishnan, and Joshua Yelon. Converse: An Interoperable Framework for Parallel Programming. In Proceedings of the 10th International Parallel Processing Symposium, pages 212–217, Honolulu, Hawaii, April 1996.
L.V. Kale and S. Krishnan. Charm++: A portable concurrent object oriented system based on C++. In Proceedings of the Conference on Object Oriented Programming Systems, Languages and Applications, September 1993.
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. NAMD-A parallel, object-oriented molecular dynamics program. Intl. J. Supercomput. Applies. High Performance Computing, 10(4):251–268, Winter 1996.
W. Rankin and J. Board. A portable distributed implementation of the parallel multipole tree algorithm. IEEE Symposium on High Performance Distributed Computing, 1995. [Duke University Technical Report 95-002].
W. F. van Gunsteren and H. J. C. Berendsen. GROMOS Manual. BIOMOS b. v., Lab. of Phys. Chem., Univ. of Groningen, 1987.
P. K. Weiner and P. A. Kollman. AMBER: Assisted model building with energy refinement. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2:287, 1981.
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 1998 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kalé, L.V., Bhandarkar, M., Brunner, R. (1998). Load balancing in parallel molecular dynamics. In: Ferreira, A., Rolim, J., Simon, H., Teng, SH. (eds) Solving Irregularly Structured Problems in Parallel. IRREGULAR 1998. Lecture Notes in Computer Science, vol 1457. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0018544
Download citation
DOI: https://doi.org/10.1007/BFb0018544
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-64809-3
Online ISBN: 978-3-540-68533-3
eBook Packages: Springer Book Archive