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Improved GROMACS Scaling on Ethernet Switched Clusters

  • Conference paper
Recent Advances in Parallel Virtual Machine and Message Passing Interface (EuroPVM/MPI 2006)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 4192))

Abstract

We investigated the prerequisites for decent scaling of the GROMACS 3.3 molecular dynamics (MD) code [1] on Ethernet Beowulf clusters. The code uses the MPI standard for communication between the processors and scales well on shared memory supercomputers like the IBM p690 (Regatta) and on Linux clusters with a high-bandwidth/low latency network. On Ethernet switched clusters, however, the scaling typically breaks down as soon as more than two computational nodes are involved. For an 80k atom MD test system, exemplary speedups Sp N on N CPUs are Sp 8 = 6.2, Sp 16 = 10 on a Myrinet dual-CPU 3 GHz Xeon cluster, Sp 16 = 11 on an Infiniband dual-CPU 2.2 GHz Opteron cluster, and Sp 32 = 21 on one Regatta node. However, the maximum speedup we could initially reach on our Gbit Ethernet 2 GHz Opteron cluster was Sp 4 = 3 using two dual-CPU nodes. Employing more CPUs only led to slower execution (Table 1).

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References

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Author information

Authors and Affiliations

  1. Department of Theoretical and Computational Biophysics, Max-Planck-Institute of Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany

    Carsten Kutzner, Martin Fechner, Udo W. Schmitt, Bert L. de Groot & Helmut Grubmüller

  2. Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, S-75124, Uppsala, Sweden

    David van der Spoel

  3. Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE-10691, Stockholm, Sweden

    Erik Lindahl

Authors
  1. Carsten Kutzner
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  2. David van der Spoel
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  3. Martin Fechner
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  4. Erik Lindahl
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  5. Udo W. Schmitt
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  6. Bert L. de Groot
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  7. Helmut Grubmüller
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Editor information

Editors and Affiliations

  1. Forschungszentrum Jülich, ZAM, 52425, Jülich, Germany

    Bernd Mohr

  2. NEC Europe Ltd., NEC Laboratories Europe, Rathausallee 10, D-53757, Sankt Augustin, Germany

    Jesper Larsson Träff

  3. Dolphin Interconnect Solutions ASA R&D Germany, Siebengebirgsblick 26, 53343, Wachtberg, Germany

    Joachim Worringen

  4. Computer Science Department, University of Tennessee, 37996-3450, Knoxville, TN, USA

    Jack Dongarra

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© 2006 Springer-Verlag Berlin Heidelberg

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Kutzner, C. et al. (2006). Improved GROMACS Scaling on Ethernet Switched Clusters. In: Mohr, B., Träff, J.L., Worringen, J., Dongarra, J. (eds) Recent Advances in Parallel Virtual Machine and Message Passing Interface. EuroPVM/MPI 2006. Lecture Notes in Computer Science, vol 4192. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11846802_57

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  • DOI: https://doi.org/10.1007/11846802_57

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-39110-4

  • Online ISBN: 978-3-540-39112-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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