Skip to main content
SpringerLink
Log in

Molecular dynamics using P-threads

  • 5. Posters
  • Conference paper
  • First Online:
High-Performance Computing and Networking (HPCN-Europe 1998)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1401))

Included in the following conference series:

  • 205 Accesses

Abstract

In this paper we report our work on a SM-MIMD architecture clustered as four SMP machines of the MPI version of the GROMACS V1.5.1. We used a cluster of Digital AS4100 interconnected with Memory Channel and Digital MPI V1.4 as hardware testbed. We developed a new threaded version of MPI GROMACS and it permitted us to measure perfomance and scalability of the new code in real MD simulation runs. The new code open a way to further improve the MD simulations to date giving a way to estimate its scalability on M-SMP clustered machine and similar parallel architectures.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  1. D. Roccatano, R. Bizzarri, G. Chillemi, N. Sanna and A. Di Nola, J. Comp. Chem., in printing.

    Google Scholar 

  2. D. G. Green, K. E. Meacham, M. Surridge, F. van Hoesel and H. J. C. Berendsen, Parallelization of Molecular Dynamics Code. GROMOS87 parallelization for distributed memory architecture in “Methods and Techniques in Computational Chemistry: METECC-95”, STEF (1995).

    Google Scholar 

  3. S. Plimpton, J. Comp. Phys., 117 (1995) 1.

    Google Scholar 

  4. H. J. C. Berendsen et al. Chapter 6: Selected parallel applications and pratical elements in “Aspects of computational science”, NCF (1995)

    Google Scholar 

  5. W. Gropp, E. Lusk and A. Skjellum, “Using MPI: Portable Parallel Programming with the Message Passing”, MIT press (1994).

    Google Scholar 

  6. H. J. C. Berendsen, D. van der Spoel R. van Drunen, Comp. Phys. Comm., 95 (1995) 43.

    Google Scholar 

  7. See http://www.caspur.it/progetti/4venti/home.html for additional configuration details.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CASPUR, c/o Universitä “La Sapienza”, P.le Aldo Moro 5, 00185, Rome, Italy

    G. Chillemi & N. Sanna

Authors
  1. G. Chillemi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. Sanna
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Peter Sloot Marian Bubak Bob Hertzberger

Rights and permissions

Reprints and permissions

Copyright information

© 1998 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Chillemi, G., Sanna, N. (1998). Molecular dynamics using P-threads. In: Sloot, P., Bubak, M., Hertzberger, B. (eds) High-Performance Computing and Networking. HPCN-Europe 1998. Lecture Notes in Computer Science, vol 1401. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0037218

Download citation

  • DOI: https://doi.org/10.1007/BFb0037218

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-64443-9

  • Online ISBN: 978-3-540-69783-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation