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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

PetaFLOP Molecular Dynamics for Engineering Applications

Authors : Philipp Neumann, Nikola Tchipev, Steffen Seckler, Matthias Heinen, Jadran Vrabec, Hans-Joachim Bungartz

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

Publisher: Springer International Publishing

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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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previous chapter Seasonal Simulation of Weather Extremes (WRFXXXL)
next chapter Load-Balancing and Spatial Adaptivity for Coarse-Grained Molecular Dynamics Applications
Footnotes
4
Molecules that consist of several interaction sites, e.g. two LJ sites.
 
Literature
1.
M. Abraham, T. Murtola, R. Schulz, S. Páll, J. Smith, B. Hess, E. Lindahl, GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015)CrossRef
2.
W. Brown, P. Wang, S. Plimpton, A. Tharrington, Implementing molecular dynamics on hybrid high performance computers—short range forces. Comput. Phys. Commun. 182(4), 898–911 (2011)CrossRef
3.
W. Eckhardt, Efficient HPC implementations for large-scale molecular simulation in process engineering. Dissertation, Dr. Hut, Munich, 2014
4.
W. Eckhardt, A. Heinecke, An efficient vectorization of linked-cell particle simulations, in ACM International Conference on Computing Frontiers, ACM, New York, NY, USA, pp. 241–243 (2012)
5.
W. Eckhardt, A. Heinecke, R. Bader, M. Brehm, N. Hammer, H. Huber, H.G. Kleinhenz, J. Vrabec, H. Hasse, M. Horsch, M. Bernreuther, C. Glass, C. Niethammer, A. Bode, H.J. Bungartz, 591 TFLOPS multi-trillion particles simulation on superMUC (Springer, Berlin, Heidelberg, 2013), pp. 1–12
6.
W. Eckhardt, T. Neckel, Memory-efficient implementation of a rigid-body molecular dynamics simulation, in Proceedings of the 11th International Symposium on Parallel and Distributed Computing—ISPDC 2012 (Munich, 2012). IEEE, pp. 103–110
7.
C. Gray, K. Gubbins, Theory of Molecular Fluids: I: Fundamentals, in International Series of Monogr, vol.1 (Oxford University Press, Oxford, 1984)
8.
S. Grottel, M. Krone, C. Müller, G. Reina, T. Ertl, MegaMol—a prototyping framework for particle-based visualization. IEEE Trans. Vis. Comput. Graph. 21(2), 201–214 (2015)CrossRef
9.
C. Hu, X. Wang, J. Li, X. He, S. Li, Y. Feng, S. Yang, H. Bai, Kernel optimization for short-range molecular dynamics. Comput. Phys. Commun. 211, 31–40 (2017)CrossRef
10.
A. Köster, T. Jiang, G. Rutkai, C. Glass, J. Vrabec, Automatized determination of fundamental equations of state based on molecular simulations in the cloud. Fluid Phase Equilibria 425, 84–92 (2016)CrossRef
11.
K. Langenbach, M. Heilig, M. Horsch, H. Hasse, Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory. J. Chem. Phys. 148(124702) (2018)CrossRef
12.
G. Nagayama, P. Cheng, Effects of interface wettability on microscale flow by molecular dynamics simulation. Int. J. Heat Mass Transf. 47, 501–513 (2004)CrossRef
13.
C. Niethammer, S. Becker, M. Bernreuther, M. Buchholz, W. Eckhardt, A. Heinecke, S. Werth, H.J. Bungartz, C. Glass, H. Hasse, J. Vrabec, M. Horsch, ls1 mardyn: the massively parallel molecular dynamics code for large systems. J. Chem. Theory Comput. 10(10), 4455–4464 (2014)CrossRef
14.
S. Páll, B. Hess, A flexible algorithm for calculating pair interactions on SIMD architectures. Comput. Phys. Commun. 184(12), 2641–2650 (2013)CrossRef
15.
D. Rapaport, The Art of Molecular Dynamics Simulation (Cambridge University Press, Cambridge, 2004)
16.
L. Rekvig, D. Frenkel, Molecular simulations of droplet coalescence in oil/water/surfactant systems. J. Chem. Phys. 127(134701) (2007)CrossRef
17.
S. Seckler, N. Tchipev, H.J. Bungartz, P. Neumann, Load balancing for molecular dynamics simulations on heterogeneous architectures, in 2016 IEEE 23rd International Conference on High Performance Computing (HiPC), pp. 101–110 (2016)
18.
N. Tchipev, S. Seckler, M. Heinen, J. Vrabec, F. Gratl, M. Horsch, M. Bernreuther, C. Glass, C. Niethammer, N. Hammer, B. Krischok, M. Resch, D. Kranzlmüller, H. Hasse, H.J. Bungartz, P. Neumann, TeTRiS: twenty trillion-atom simulation. Int. J. High Perform. Comput. Appl. (2019), https://​doi.​org/​10.​1177%2F10943420188197​41
19.
N. Tchipev, A. Wafai, C. Glass, W. Eckhardt, A. Heinecke, H.J. Bungartz, P. Neumann, Optimized Force Calculation in Molecular Dynamics Simulations for the Intel Xeon Phi (Springer International Publishing, Cham, 2015), pp. 774–785)CrossRef
20.
J. Vrabec, M. Bernreuther, H.J. Bungartz, W.L. Chen, W. Cordes, R. Fingerhut, C. Glass, J. Gmehling, R. Hamburger, M. Heilig, M. Heinen, M. Horsch, C.M. Hsieh, M. Hülsmann, P. Jäger, P. Klein, S. Knauer, T. Köddermann, A. Köster, K. Langenbach, S.T. Lin, P. Neumann, J. Rarey, D. Reith, G. Rutkai, M. Schappals, M. Schenk, A. Schedemann, M. Schönherr, S. Seckler, S. Stephan, K. Stöbener, N. Tchipev, A. Wafai, S. Werth, H. Hasse, Skasim—Scalable hpc software for molecular simulation in the chemical industry. Chem. Ing. Tech. 90(3), 295–306 (2018)CrossRef
21.
X. Wang, J. Li, J. Wang, X. He, N. Nie, Kernel Optimization on Short-Range Potentials Computations in Molecular Dynamics Simulations (Springer, Singapore, 2016), pp. 269–281
Metadata
Title
PetaFLOP Molecular Dynamics for Engineering Applications
Authors
Philipp Neumann
Nikola Tchipev
Steffen Seckler
Matthias Heinen
Jadran Vrabec
Hans-Joachim Bungartz
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_25

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