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Load-Balancing and Spatial Adaptivity for Coarse-Grained Molecular Dynamics Applications

In: High Performance Computing in Science and Engineering ' 18

Author

Listed:
  • Steffen Hirschmann

    (Institute for Parallel and Distributed Systems, University of Stuttgart)

  • Michael Lahnert

    (Institute for Parallel and Distributed Systems, University of Stuttgart)

  • Carolin Schober

    (Institute for Parallel and Distributed Systems, University of Stuttgart)

  • Malte Brunn

    (Institute for Parallel and Distributed Systems, University of Stuttgart)

  • Miriam Mehl

    (Institute for Parallel and Distributed Systems, University of Stuttgart)

  • Dirk Pflüger

    (Institute for Parallel and Distributed Systems, University of Stuttgart)

Abstract

We present our approach for a scalable implementation of coupled soft matter simulations for inhomogeneous applications based on the simulation package ESPResSo and an extended version of the adaptive grid framework p4est. Our main contribution in this paper is the development and implementation of a joint partitioning of two or more distinct octree-based grids based on the concept of a finest common tree. This concept guarantees that, on all grids, the same process is responsible for each point in space and, thus, avoids communication of data in overlapping volumes handled in different partitions. We achieve up to 85% parallel efficiency in a weak scaling setting. Our proposed algorithms take only a small fraction of the overall runtime of grid adaption.

Suggested Citation

  • Steffen Hirschmann & Michael Lahnert & Carolin Schober & Malte Brunn & Miriam Mehl & Dirk Pflüger, 2019. "Load-Balancing and Spatial Adaptivity for Coarse-Grained Molecular Dynamics Applications," Springer Books, in: Wolfgang E. Nagel & Dietmar H. Kröner & Michael M. Resch (ed.), High Performance Computing in Science and Engineering ' 18, pages 409-423, Springer.
    • Handle: RePEc:spr:sprchp:978-3-030-13325-2_26
    DOI: 10.1007/978-3-030-13325-2_26
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