Scaling in the context of molecular dynamics simulations with ms2 and ls1 mardyn

Simon Homes (), Robin Fingerhut, Gabriela Guevara-Carrion, Matthias Heinen and Jadran Vrabec
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Simon Homes: Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin
Robin Fingerhut: Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin
Gabriela Guevara-Carrion: Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin
Matthias Heinen: Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin
Jadran Vrabec: Lehrstuhl für Thermodynamik und Thermische Verfahrenstechnik, Technische Universität Berlin

A chapter in High Performance Computing in Science and Engineering '21, 2023, pp 467-479 from Springer

Abstract: Abstract This chapter covers scaling issues related to our recent work in the field of molecular dynamics simulations with a focus on computational details. The first section deals with finite size effects in the context of multicomponent diffusion. Different methods to correct the influence of the finite simulation domain are compared. In the second section, the structure of a fluid near its critical point is discussed in the context of the strong scaling behavior of the code ms2. The third section discusses droplet coalescence dynamics investigated by large molecular dynamics simulations and a macroscopic phase field model, respectively. The performance of the new supercomputer Hawk is compared to that of Hazel Hen. The last section describes the influence of the direct sampling of the energy flux on the performance of the code ls1 mardyn. Various speed tests are carried out and analyzed in detail.

Date: 2023
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DOI: 10.1007/978-3-031-17937-2_29

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