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Understanding the Scalability of Molecular Simulation Using Empirical Performance Modeling

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Book cover Programming and Performance Visualization Tools (ESPT 2017, ESPT 2018, VPA 2017, VPA 2018)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 11027))

Abstract

Molecular dynamics (MD) simulation allows for the study of static and dynamic properties of molecular ensembles at various molecular scales, from monatomics to macromolecules such as proteins and nucleic acids. It has applications in biology, materials science, biochemistry, and biophysics. Recent developments in simulation techniques spurred the emergence of the computational molecular engineering (CME) field, which focuses specifically on the needs of industrial users in engineering. Within CME, the simulation code ms2 allows users to calculate thermodynamic properties of bulk fluids. It is a parallel code that aims to scale the temporal range of the simulation while keeping the execution time minimal. In this paper, we use empirical performance modeling to study the impact of simulation parameters on the execution time. Our approach is a systematic workflow that can be used as a blue-print in other fields that aim to scale their simulation codes. We show that the generated models can help users better understand how to scale the simulation with minimal increase in execution time.

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Acknowledgements

This work was supported by the German Research Foundation (DFG) through the Program Performance Engineering for Scientific Software and the ExtraPeak project, by the German Federal Ministry of Education and Research (BMBF) through the TaLPas project under Grant No. 01IH16008D, and by the US Department of Energy through the PRIMA-X project under Grant No. DE-SC0015524. The authors would like to thank the partners of the TaLPas project for fruitful discussions. Finally, the authors would also like express their gratitude to the High Performance Computing Center Stuttgart (HLRS) and the University Computing Center (Hochschulrechenzentrum) of Technische Universität Darmstadt for providing access to machines Hazel Hen and Lichtenberg, respectively.

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Authors and Affiliations

  1. Argonne National Laboratory, Lemont, IL, 60439, USA

    Sergei Shudler

  2. Thermodynamics and Process Engineering, Technical University Berlin, 10587, Berlin, Germany

    Jadran Vrabec

  3. Laboratory for Parallel Programming, Technical University Darmstadt, 64289, Darmstadt, Germany

    Felix Wolf

Authors
  1. Sergei Shudler
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  2. Jadran Vrabec
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  3. Felix Wolf
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Corresponding author

Correspondence to Sergei Shudler .

Editor information

Editors and Affiliations

  1. Lawrence Livermore National Laboratory, Livermore, CA, USA

    Abhinav Bhatele

  2. Lawrence Livermore National Laboratory, Livermore, CA, USA

    David Boehme

  3. The University of Arizona, Tucson, AZ, USA

    Joshua A. Levine

  4. University of Oregon, Eugene, OR, USA

    Allen D. Malony

  5. Technical University of Munich, Munich, Germany

    Martin Schulz

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Shudler, S., Vrabec, J., Wolf, F. (2019). Understanding the Scalability of Molecular Simulation Using Empirical Performance Modeling. In: Bhatele, A., Boehme, D., Levine, J., Malony, A., Schulz, M. (eds) Programming and Performance Visualization Tools. ESPT ESPT VPA VPA 2017 2018 2017 2018. Lecture Notes in Computer Science(), vol 11027. Springer, Cham. https://doi.org/10.1007/978-3-030-17872-7_8

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  • DOI: https://doi.org/10.1007/978-3-030-17872-7_8

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  • Online ISBN: 978-3-030-17872-7

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