Advertisement

Theory of Computing Systems

, Volume 37, Issue 2, pp 295–318 | Cite as

A Note on N-Body Computations with Cutoffs

  • Marc SnirEmail author
Article

Abstract

We provide a theoretical analysis of the communication requirements of parallel algorithms for molecular dynamic simulations. We describe two commonly used algorithms, space decomposition and force decomposition, and analyze their communication requirements; each is better in a distinct computation regime. We next introduce a new hybrid algorithm that further reduces communication. We show that the new algorithm is optimal, by providing a matching lower bound.

Keywords

Theoretical Analysis Molecular Dynamic Simulation Dynamic Simulation Parallel Algorithm Hybrid Algorithm 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    M.P. Allen and D.J. Tildesley. Computer Simulation of Liquid}. Oxford Science Publications, Oxford, 1987. Google Scholar
  2. 2.
    Almasi, G.S., Cascaval, C., Castaños, J.G., Denneau, M.,  et al. 2002Demonstrating the scalability of a molecular dynamics application on a petaflop computerJournal of Parallel Programming30317351CrossRefzbMATHGoogle Scholar
  3. 3.
    A.Bar-Noy and S.Kipnis. Designing broadcasting algorithms in the postal model for message-passing systems. In Proceedings of the 4th Annual Symposium on Parallel Algorithms and Architectures, pages 13–22, 1992. Google Scholar
  4. 4.
    Board, J., Schulten, K. 2000The fast multipole algorithmIEEE Computational Science & Engineering25659Google Scholar
  5. 5.
    Yu.D. Burago and V.A. Zalgaller. \Geometric Inequalities}. Springer-Verlag, Berlin, 1988. Google Scholar
  6. 6.
    Dickerson, M.T., Eppstein, D. 1996Algorithms for proximity problems in higher dimensionsComputational Geometry Theory and Applications5277291Google Scholar
  7. 7.
    Ewald, P. 192Die Berechnung optischer und elektrostatischer GitterpotentialeAnnalen der Physik64253287zbMATHGoogle Scholar
  8. 8.
    L.F. Greengard. The Rapid Evaluation of Potential Fields in Particle Systems. MIT Press, Cambridge, MA, 1988. Google Scholar
  9. 9.
    Greengard, L., Rokhlin, V. 1987A fast algorithm for particle simulationJournal of Computational Physics73325348Google Scholar
  10. 10.
    R. Motwani and P. Raghavan. Randomized Algorithms. Cambridge University Press, Cambridge, 1995.Google Scholar
  11. 11.
    Plimpton, S. 1995Fast parallel algorithms for short-range molecular dynamicsJournal of Computational Physics117119Google Scholar
  12. 12.
    M. Snir. A note on n-body computation with cutoffs. Technical Report RC22059, IBM T. J. Watson Research Center, 2001.Google Scholar
  13. 13.
    Taylor, V.E., Stevens, R., Arnold, K. 1997Parallel molecular dynamics: implications for massively parallel machinesJournal on Parallel and Distributed Computin45166175Google Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  1. 1.Computer Science Department, University of Illinois at Urbana-Champaign, Urbana, IL 61801USA

Personalised recommendations