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The Performance of Different Communication Mechanisms and Algorithms Used for Parallelization of Molecular Dynamics Code

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Parallel Processing and Applied Mathematics (PPAM 2001)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2328))

Abstract

Communication performance appears to have the most important influence on parallelization efficiency of large scientific applications. Different communication algorithms and communication mechanisms were used in parallelization of molecular dynamics code. In is shown that in the case of fast communication hardware well scaling algorithm must be used. Presented data shows that MD code can be also run efficiently on the pentium cluster but low latency communication mechanism must be used.

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References

  1. S. T. Wlodek, Terry Clark, L. Ridgway Scott, and J. Andrew McCammon. Molecular dynamics of Acetylcholinesterase dimer complexed with Tacrine. Journal of the American Chemical Society, 119(40):9513–952, 1997.

    Article  Google Scholar 

  2. T. W. Clark and J. A. McCammon. Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architecture. Computers & Chemistry, 14(3):219–24, 1990.

    Article  Google Scholar 

  3. T. Clark, R. von Hanxleden, J. A. McCammon, and L. R. Scott. Parallelizing molecular dynamics using spatial decomposition. In Scalable High Performance Computing Conference, pages 95–102, Knoxville, TN, May 1994. IEEE Computer Society. Available via anonymous ftp from softlib.rice.eduaspub/CRPC-TRs/reports/CRPC-TR93356-S

    Google Scholar 

  4. S. Plimpton. Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics, 117:1–19, March 1995.

    Google Scholar 

  5. T. Clark, R. von Hanxleden, K. Kennedy, C. Koelbel, and L. R. Scott. Evaluating parallel languages for molecular dynamics computations. In Scalable High Performance Computing Conference, Williamsburg, VA, 1992. IEEE. Available via anonymous ftp from oftlib.rice.edu as pub/CRPC-TRs/reports/CRPC-TR992202-S.

    Google Scholar 

  6. R. von Hanxleden. Compiler Support for Machine-Independent Parallelization of Irregular Problems. PhD thesis, Rice University, December 1994. Available via anonymous ftp from softlib.rice.edu as pub/CRPC-TRs/reports/CRPC-TR94495-S.

    Google Scholar 

  7. P. Bała, T. W. Clark, and L. R. Scott. Application of Pfortran and Co-Array fortran in the parallelization of the GROMOS96 molecular dynamics module. In M. Bubak, J. Moűciñski, and Marian Noga, editors, SGI Users’ Conference-Conference Processdings, pages 194–204. Academic Computer Centre CYFRONET AGH, 2000.

    Google Scholar 

  8. P. Bała, T. W. Clark, and L. R. Scott. Application of Pfortran and Co-Array fortran in the parallelization of the GROMOS96 molecular dynamics module. Su-percomputing Journal 2001 (in press)

    Google Scholar 

  9. W. Van Gunsteren and H. J. C. Berendsen. GROMOS (Groningen Molecular Simulation Computer Program Package). Biomos, Laboratory of Physical Chemistry, ETH Zentrum, Zurich, 1996.

    Google Scholar 

  10. B. Bagheri, T. W. Clark, and L. R. Scott. Pfortran: a parallel dialect of fortran. ACM Fortran Forum, 11(3):20–31, 1992.

    Article  Google Scholar 

  11. M. P. Allen and D. J. Tildesley. Computer simulations of liquids. Clarendon, Oxford, 1987.

    Google Scholar 

  12. W. F. van Gunsteren and H. J. C. Berendsen. A leap-frog algorithm for stochastic dynamics. Molecular Simulation, 1(3):173–182, 1988.

    Article  Google Scholar 

  13. W. F. van Gunsteren and H. J. C. Berendsen. Algorithms for brownian dynamics. Molecular Physics, 45:637–647, 1982.

    Article  Google Scholar 

  14. J. W. Eastwood R. W. Hockney. Computer Simulation Using Particles. Cambridge University Press, Cambridge, 1987.

    Google Scholar 

  15. USA NERSC, Lawrance Research Laboratory. MVICH-MPI for virtual interface architecture. http://www.nersc.gov/research/FTG/mvich, 2000.

  16. USA NERSC, Lawrance Research Laboratory. M-VIA: A high performance modular via for linux. http://www.nersc.gov/research/FTG/via, 2000.

  17. R. W. Numrich. F—: a parallel extension to Cray fortran. Scientific Programming, 6(3):275–84, 1997.

    Google Scholar 

  18. R. W. Numrich, J. Reid, and K. Kim. Writing a multigrid solver using Co-Array fortran. In B. Kågström, J. Dongarra, E. Elmroth, and J. Waśniewski, editors, Recent Advances in Applied Parallel Computing, Lecture Notes in Computer Science 1541, pages 390–399. Springer-Verlag Berlin, 1998.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Faculty of Mathematics and Computer Science, N. Copernicus University, Chopina 12/18, 87-100, Toruń, Poland

    Rafał Metkowski & Piotr Bała

  2. Department of Computer Science, The University of Chicago and Computation Institute, 1100 E. 58th Street, Chicago, IL, 60637, USA

    Terry Clark

Authors
  1. Rafał Metkowski
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  2. Piotr Bała
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  3. Terry Clark
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Editor information

Editors and Affiliations

  1. Institute of Mathematics and Computer Science, Technical University of Czestochowa, Dabrowskiego 73, 42-200, Czestochowa, Poland

    Roman Wyrzykowski

  2. Computer Science Department, University of Tennessee, 122 Volunteer Blvd, Knoxville, TN, 37996-3450, USA

    Jack Dongarra

  3. Computer Science Department, Oklahoma State University, 700 N. Greenwood Ave., Tulsa, OK, 74106, USA

    Marcin Paprzycki

  4. DTU, UNI-C, Danish Computing Centre for Research and Education, Bldg. 304, 2800, Lyngby, Denmark

    Jerzy Waśniewski

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© 2002 Springer-Verlag Berlin Heidelberg

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Metkowski, R., Bała, P., Clark, T. (2002). The Performance of Different Communication Mechanisms and Algorithms Used for Parallelization of Molecular Dynamics Code. In: Wyrzykowski, R., Dongarra, J., Paprzycki, M., Waśniewski, J. (eds) Parallel Processing and Applied Mathematics. PPAM 2001. Lecture Notes in Computer Science, vol 2328. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-48086-2_17

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  • DOI: https://doi.org/10.1007/3-540-48086-2_17

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43792-5

  • Online ISBN: 978-3-540-48086-0

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