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International Workshop on Applied Parallel Computing

PARA 1995: Applied Parallel Computing Computations in Physics, Chemistry and Engineering Science pp 391–407Cite as

Multi-million particle molecular dynamics on MPPs

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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1041))

Abstract

We discuss the computational difficulties associated with performing large-scale molecular dynamics simulations involving more than 100 million atoms on modern massively parallel supercomputers. We discuss various performance and memory optimization strategies along with the method we have used to write a highly portable parallel application. Finally, we discuss some recent work addressing the problems associated with analyzing and visualizing the data generated from multi-million particle MD simulations.

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References

  1. D.M. Beazley, P.S. Lomdahl, N. Grønbech-Jensen, R. Giles, and P. Tamayo, Parallel Algorithms for Short-range Molecular Dynamics, Review article to appear in World Scientific's Annual Reviews in Computational Physics, vol. 3 (1995).

    Google Scholar 

  2. P. Tamayo, J.P. Mesirov and B.M. Boghosian, Proc. of Supercomputing 91, IEEE Computer Society, 1991, pp: 462.

    Google Scholar 

  3. D.M. Beazley and P.S. Lomdahl, Parall. Comp. 20 (1994) 173–195.

    Google Scholar 

  4. P.S. Lomdahl, D.M. Beazley, P. Tamayo, and N. Grønbech-Jensen, Multimillion Particle Molecular Dynamics on the CM-5, International Journal of Modern Physics C, World Scientific (1993), p. 1075–1084.

    Google Scholar 

  5. P.S. Lomdahl, P. Tamayo, N. Grønbech-Jensen and D.M. Beazley, Proc. of Supercomputing 93, IEEE Computer Society (1993), pp: 520–527.

    Google Scholar 

  6. D.M. Beazley and P.S. Lomdahl, Optimizing Large-Scale Molecular Dynamics Simulations for RISC-based MPPs and Workstations, Submitted to IPPS'96, LA-UR-95-xxxx.

    Google Scholar 

  7. S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, Sandia National Laboratory Report, SAND91-1144, UC-705 (1993).

    Google Scholar 

  8. S. Chynoweth, Y. Michopoulos, and U.C. Klomp, A Fast Algorithm for the Computation of Interparticle Forces in Molecular Dynamics Simulations. Parallel Computing and Transputer Applications, IOS Press/CIMNE, (1992), p. 128–137.

    Google Scholar 

  9. E.F. D'Azevedo, C.H. Romine, and D.W. Walker, Shared-Memory Emulation Is Key to Billion-Atom Molecular Dynamics Simulation, SIAM News, May/June, (1995).

    Google Scholar 

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Author information

Authors and Affiliations

  1. Theoretical Division, Los Alamos National Laboratory, 87545, Los Alamos, NM

    Peter S. Lomdahl

  2. Department of Computer Science, University of Utah, 84112, Salt Lake City, UT

    David M. Beazley

Authors
  1. Peter S. Lomdahl
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  2. David M. Beazley
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Editor information

Jack Dongarra Kaj Madsen Jerzy Waśniewski

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© 1996 Springer-Verlag Berlin Heidelberg

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Lomdahl, P.S., Beazley, D.M. (1996). Multi-million particle molecular dynamics on MPPs. In: Dongarra, J., Madsen, K., Waśniewski, J. (eds) Applied Parallel Computing Computations in Physics, Chemistry and Engineering Science. PARA 1995. Lecture Notes in Computer Science, vol 1041. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-60902-4_42

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  • DOI: https://doi.org/10.1007/3-540-60902-4_42

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-60902-5

  • Online ISBN: 978-3-540-49670-0

  • eBook Packages: Springer Book Archive

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