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The TNG50 Simulation of the IllustrisTNG Project: Bridging the Gap Between Large Cosmological Volumes and Resolved Galaxies Read chapter Read first chapter

2019 | OriginalPaper | Chapter

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

Authors : Steffen Hirschmann, Michael Lahnert, Carolin Schober, Malte Brunn, Miriam Mehl, Dirk Pflüger

Published in: High Performance Computing in Science and Engineering ' 18

Publisher: Springer International Publishing

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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.

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previous chapter PetaFLOP Molecular Dynamics for Engineering Applications
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Footnotes
1
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Literature
1.
P. Ahlrichs, B. Dünweg, Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics. J. Chem. Phys. 111(17), 8225–8239 (1999)CrossRef
2.
A. Arnold et al., ESPResSo 3.1: molecular dynamics software for coarse-grained models, in Meshfree Methods for Partial Differential Equations VI, ed. by M. Griebel, M.A. Schweitzer. Lecture Notes in Computational Science and Engineering, vol. 89 (Springer, Berlin, Heidelberg, 2012), pp. 1–23MATH
3.
M. Brunn, Coupling of particle simulation and lattice Boltzmann background flow on adaptive grids. M.A. thesis, University of Stuttgart, Germany, 2017
4.
M. Buchholz, Framework zur Parallelisierung von Molekulardynamiksimulationen in verfahrenstechnischen Anwendungen. Ph.D. thesis (2010)
5.
C. Burstedde et al., p4est: scalable algorithms for parallel adaptive mesh refinement on forests of octrees. SIAM J. Sci. Comput. 33(3), 1103–1133 (2011)MathSciNetCrossRef
6.
P.M. Campbell et al., Dynamic octree load balancing using space-filling curves. In: Williams College Department of Computer Science, Technical Report (2003), pp. 1–26
7.
B. Dünweg, A.J.C. Ladd, Lattice Boltzmann simulations of soft matter systems, in Advanced Computer Simulation Approaches for Soft Matter Sciences III (2009), pp. 89–166
8.
B. Dünweg et al., Statistical mechanics of the fluctuating lattice Boltzmann equation. Phys. Rev. E 76(3), 036704 (2007)
9.
B. Forsyth et al., Particle charge distribution measurement for commonly generated laboratory aerosols. Aerosol Sci. Technol. 28(6), 489–501 (1998)CrossRef
10.
C. Helsper, W. Mölter, Determination and neutralization of the charge produced by the dispersion of powders. J. Aerosol Sci. 18(6), 877–880 (1987)CrossRef
11.
S. Hirschmann et al., Towards understanding optimal load-balancing of heterogeneous short-range molecular dynamics, in Workshop on High Performance Computing and Big Data in Molecular Engineering 2016. Hyderabad, India (2016)
12.
S. Hirschmann et al., Load balancing with p4est for short-range molecular dynamics with ESPResSo, in Advances in Parallel Computing, ed. by S. Bassini et al., vol. 32 (IOS Press, 2017), pp. 455–464
13.
R.W. Hockney, J.W. Eastwood, Computer Simulation Using Particles (Taylor & Francis, Inc., Bristol, PA, USA, 1988)
14.
T. Isaac et al., Recursive algorithms for distributed forests of octrees. SIAM J. Sci. Comput. 37(5), C497–C531 (2015)MathSciNetCrossRef
15.
A.M. Johnston et al., Electrical charge characteristics of dry aerosols produced by a number of laboratory mechanical dispensers. Aerosol Sci. Technol. 6(2), 115–127 (1987)MathSciNetCrossRef
16.
M. Lahnert et al., Minimally-invasive integration of p4est in ESPResSo for adaptive Lattice-Boltzmann, in The 30th Computational Fluid Dynamics Symposium (Japan Society of Fluid Mechanics, 2016)
17.
M. Lahnert et al., Towards Lattice-Boltzmann on dynamically adaptive grids - minimally-invasive grid exchange in ESPResSo, in VII European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS, ed. by M. Papadrakakis et al. (2016)
18.
H.J. Limbach et al., ESPResSo - an extensible simulation package for research on soft matter systems. Comput. Phys. Commun. 174(9), 704–727 (2006)CrossRef
19.
M. Mehl et al., Navier-Stokes and Lattice-Boltzmann on octree-like grids in the Peano framework. Int. J. Numer. Methods Fluids 65(1–3), 67–86 (2010)MathSciNetCrossRef
20.
W.F. Mitchell, A refinement-tree based partitioning method for dynamic load balancing with adaptively refined grids. J. Parallel Distrib. Comput. 67(4), 417–429 (2007)CrossRef
21.
G.M. Morton, A computer oriented geodetic data base; and a new technique in file sequencing. Technical report IBM Ltd., 1966
22.
A. Pınar, C. Aykanat, Fast optimal load balancing algorithms for 1D partitioning. J. Parallel Distrib. Comput. 64(8), 974–996 (2004)CrossRef
23.
M. Rohde et al., A generic, mass conservative local grid refinement technique for lattice-Boltzmann schemes. Int. J. Numer. Methods Fluids 51(4), 439–468 (2006)MathSciNetCrossRef
24.
U.D. Schiller, Thermal fluctuations and boundary conditions in the lattice Boltzmann method. PhD thesis. Johannes Gutenberg-Universität, Mainz, 2008
25.
C. Schober et al., Simulating the interaction of electrostatically charged particles in the inflow area of cabin air filters using a fully coupled system, in Coupled Problems in Science and Engineering VII, ed. by M. Papadrakakis et al. (2017)
26.
F. Schornbaum, U. Rüde, Massively parallel algorithms for the lattice Boltzmann method on nonuniform grids. SIAM J. Sci. Comput. 38(2), C96–C126 (2016)MathSciNetCrossRef
27.
I. Tischler, Implementing adaptive electrokinetics in ESPResSo. MA thesis. University of Stuttgart, Germany (2018)
28.
C. Xiaolin, M. Zeyao, A new scalable parallel method for molecular dynamics based on cell-block data structure, in Parallel and Distributed Processing and Applications, ed. by J. Cao et al., vol. 3358. Lecture Notes in Computer Science (Springer, Berlin, 2005), pp. 757–764
Metadata
Title
Load-Balancing and Spatial Adaptivity for Coarse-Grained Molecular Dynamics Applications
Authors
Steffen Hirschmann
Michael Lahnert
Carolin Schober
Malte Brunn
Miriam Mehl
Dirk Pflüger
Copyright Year
2019
Book
High Performance Computing in Science and Engineering ' 18

Print ISBN: 978-3-030-13324-5

Electronic ISBN: 978-3-030-13325-2

Copyright Year: 2019

DOI
https://doi.org/10.1007/978-3-030-13325-2_26

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