A symmetric transformation for 3-body potential molecular dynamics using force-decomposition in a heterogeneous distributed environment

J. V. Sumanth, David R Swanson, Hong Jiang

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

4 Citations (Scopus)

Abstract

Evaluating the Force Matrix constitutes the most computationally intensive part of a Classical Molecular Dynamics (MD) simulation. In three-body MD simulations, the total energy of the system is determined by the energy of every unique triple in the system and the force matrix is three-dimensional. The execution time of a three-body MD algorithm is thus proportional to the cube of the number of atoms in the system. Fortunately, there exist symmetries in the Force Matrix that can be exploited to improve the running time of the algorithm. While this optimization is straight forward to implement in the case of sequential code, it has proven to be nontrivial for parallel code even in a homogeneous environment. In this paper, we present two force matrix transformations that are capable of exploiting the symmetries in a 3-body force matrix in both a homogeneous and a heterogeneous environment while balancing the load among all the participating processors. The first transformation distributes the number of interactions to be computed uniformly among all the slices of the force matrix along any of the axes. The transformed matrix can be scheduled using any well known heterogeneous slice-level scheduling technique. The second transformation distributes interactions to be computed uniformly over the entire volume of the force matrix allowing us to perform a block decomposition of the force matrix. The transformed force matrix can be scheduled by any block level scheduling algorithm. We also derive theoretical bounds for efficiency and load balance for our transformations and prove some interesting and useful properties of our transformations and evaluate their advantages and disadvantages. The performance of an MPI implementation of the transformations is studied in terms of the Step Time Variation Ratio (STVR) in a homogeneous and heterogeneous environment.

Original languageEnglish (US)
Title of host publicationProceedings of ICS07
Subtitle of host publication21st ACM International Conference on Supercomputing
Pages105-115
Number of pages11
DOIs
StatePublished - Aug 24 2007
Event21st ACM International Conference on Supercomputing, ICS07 - Seattle, WA, United States
Duration: Jun 17 2007Jun 21 2007

Publication series

NameProceedings of the International Conference on Supercomputing

Conference

Conference21st ACM International Conference on Supercomputing, ICS07
CountryUnited States
CitySeattle, WA
Period6/17/076/21/07

Fingerprint

Molecular dynamics
Decomposition
Computer simulation
Scheduling algorithms
Scheduling
Atoms

Keywords

  • Grid computing
  • Load balancing
  • Molecular dynamics

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Sumanth, J. V., Swanson, D. R., & Jiang, H. (2007). A symmetric transformation for 3-body potential molecular dynamics using force-decomposition in a heterogeneous distributed environment. In Proceedings of ICS07: 21st ACM International Conference on Supercomputing (pp. 105-115). (Proceedings of the International Conference on Supercomputing). https://doi.org/10.1145/1274971.1274988

A symmetric transformation for 3-body potential molecular dynamics using force-decomposition in a heterogeneous distributed environment. / Sumanth, J. V.; Swanson, David R; Jiang, Hong.

Proceedings of ICS07: 21st ACM International Conference on Supercomputing. 2007. p. 105-115 (Proceedings of the International Conference on Supercomputing).

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

Sumanth, JV, Swanson, DR & Jiang, H 2007, A symmetric transformation for 3-body potential molecular dynamics using force-decomposition in a heterogeneous distributed environment. in Proceedings of ICS07: 21st ACM International Conference on Supercomputing. Proceedings of the International Conference on Supercomputing, pp. 105-115, 21st ACM International Conference on Supercomputing, ICS07, Seattle, WA, United States, 6/17/07. https://doi.org/10.1145/1274971.1274988
Sumanth JV, Swanson DR, Jiang H. A symmetric transformation for 3-body potential molecular dynamics using force-decomposition in a heterogeneous distributed environment. In Proceedings of ICS07: 21st ACM International Conference on Supercomputing. 2007. p. 105-115. (Proceedings of the International Conference on Supercomputing). https://doi.org/10.1145/1274971.1274988
Sumanth, J. V. ; Swanson, David R ; Jiang, Hong. / A symmetric transformation for 3-body potential molecular dynamics using force-decomposition in a heterogeneous distributed environment. Proceedings of ICS07: 21st ACM International Conference on Supercomputing. 2007. pp. 105-115 (Proceedings of the International Conference on Supercomputing).
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