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High Performance Computing in Science and Engineering ' 18 pp 397–407Cite as

PetaFLOP Molecular Dynamics for Engineering Applications

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Abstract

Molecular dynamics (MD) simulations enable the investigation of multicomponent and multiphase processes relevant to engineering applications, such as droplet coalescence or bubble formation. These scenarios require the simulation of ensembles containing a large number of molecules. We present recent advances within the MD framework ls1 mardyn which is being developed with particular regard to this class of problems. We discuss several OpenMP schemes that deliver optimal performance at node-level. We have further introduced nonblocking communication and communication hiding for global collective operations. Together with revised data structures and vectorization, these improvements unleash PetaFLOP performance and enable multi-trillion atom simulations on the HLRS supercomputer Hazel Hen. We further present preliminary results achieved for droplet coalescence scenarios at a smaller scale.

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Notes

  1. 1.

    www.gromacs.org.

  2. 2.

    www.lammps.org.

  3. 3.

    http://www.ks.uiuc.edu/Research/namd/.

  4. 4.

    Molecules that consist of several interaction sites, e.g. two LJ sites.

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Acknowledgements

The presented work was carried out in the scope of the Large-Scale Project Extreme-Scale Molecular Dynamics Simulation of Droplet Coalescence, acronym GCS-MDDC, of the Gauss Centre for Supercomputing; the authors thank Bernd Krischok, Dr.-Ing. Martin Bernreuther and Prof. Dr. Michael Resch for their support throughout the project. Financial support by the Federal Ministry of Education and Research, project Task-based load balancing and auto-tuning in particle simulations (TaLPas), grant numbers 01IH16008A/B/E, is acknowledged.

Author information

Authors and Affiliations

  1. Department of Informatics, Universität Hamburg, Bundesstr. 45a, 20146, Hamburg, Germany

    Philipp Neumann

  2. Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748, Garching, Germany

    Nikola Tchipev, Steffen Seckler & Hans-Joachim Bungartz

  3. Thermodynamics and Process Engineering, Technical University of Berlin, Ernst-Reuter-Platz 1, 10587, Berlin, Germany

    Matthias Heinen & Jadran Vrabec

Authors
  1. Philipp Neumann
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  2. Nikola Tchipev
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  3. Steffen Seckler
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  4. Matthias Heinen
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  5. Jadran Vrabec
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  6. Hans-Joachim Bungartz
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Corresponding author

Correspondence to Philipp Neumann .

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Editors and Affiliations

  1. Zentrum für Informationsdienste und Hochleistungsrechnen (ZIH), Technische Universität Dresden, Dresden, Germany

    Wolfgang E. Nagel

  2. Abteilung für Angewandte Mathematik, Universität Freiburg, Freiburg, Germany

    Dietmar H. Kröner

  3. Höchstleistungsrechenzentrum Stuttgart (HLRS), Universität Stuttgart, Stuttgart, Germany

    Michael M. Resch

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Neumann, P., Tchipev, N., Seckler, S., Heinen, M., Vrabec, J., Bungartz, HJ. (2019). PetaFLOP Molecular Dynamics for Engineering Applications. In: Nagel, W., Kröner, D., Resch, M. (eds) High Performance Computing in Science and Engineering ' 18. Springer, Cham. https://doi.org/10.1007/978-3-030-13325-2_25

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