Please use this identifier to cite or link to this item: http://dx.doi.org/10.14279/depositonce-9116
Main Title: TweTriS: Twenty trillion-atom simulation
Author(s): Tchipev, Nikola
Seckler, Steffen
Heinen, Matthias
Vrabec, Jadran
Gratl, Fabio
Horsch, Martin
Bernreuther, Martin
Glass, Colin W.
Niethammer, Christoph
Hammer, Nicolay
Krischok, Bernd
Resch, Michael
Kranzlmüller, Dieter
Hasse, Hans
Bungartz, Hans-Joachim
Neumann, Philipp
Type: Article
Language Code: en
Abstract: Significant improvements are presented for the molecular dynamics code ls1 mardyn — a linked cell-based code for simulating a large number of small, rigid molecules with application areas in chemical engineering. The changes consist of a redesign of the SIMD vectorization via wrappers, MPI improvements and a software redesign to allow memory-efficient execution with the production trunk to increase portability and extensibility. Two novel, memory-efficient OpenMP schemes for the linked cell-based force calculation are presented, which are able to retain Newton’s third law optimization. Comparisons to well-optimized Verlet list-based codes, such as LAMMPS and GROMACS, demonstrate the viability of the linked cell-based approach. The present version of ls1 mardyn is used to run simulations on entire supercomputers, maximizing the number of sampled atoms. Compared to the preceding version of ls1 mardyn on the entire set of 9216 nodes of SuperMUC, Phase 1, 27% more atoms are simulated. Weak scaling performance is increased by up to 40% and strong scaling performance by up to more than 220%. On Hazel Hen, strong scaling efficiency of up to 81% and 189 billion molecule updates per second is attained, when scaling from 8 to 7168 nodes. Moreover, a total of 20 trillion atoms is simulated at up to 88% weak scaling efficiency running at up to 1.33 PFLOPS. This represents a fivefold increase in terms of the number of atoms simulated to date.
URI: https://depositonce.tu-berlin.de/handle/11303/10127
http://dx.doi.org/10.14279/depositonce-9116
Issue Date: 6-Jan-2019
Date Available: 17-Oct-2019
DDC Class: 004 Datenverarbeitung; Informatik
530 Physik
Subject(s): molecular dynamics
SIMD vectorization
OpenMP
MPI
coloring
memory-efficient
SuperMUC
Hazel Hen
Sponsor/Funder: BMBF, 01IH16008, Verbundprojekt: TaLPas - Task-basierte Lastverteilung und Auto-Tuning in der Partikelsimulation
License: http://rightsstatements.org/vocab/InC/1.0/
Journal Title: The international journal of high performance computing applications
Publisher: Sage Publications
Publisher Place: Thousand Oaks, Calif.
Volume: 33
Issue: 5
Publisher DOI: 10.1177/1094342018819741
Page Start: 838
Page End: 854
EISSN: 1741-2846
ISSN: 1094-3420
Appears in Collections:FG Thermodynamik und Thermische Verfahrenstechnik » Publications

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