Node-Level Performance of Adaptive Resolution in ls1 Mardyn

Escobar, Jose Alfonso Pinzon; Neumann, Philipp; Hocks, Alex

doi:10.1007/978-3-031-97570-7_4

Contribution to a conference proceedings/Contribution to a book

PUBDB-2025-05335

Node-Level Performance of Adaptive Resolution in ls1 Mardyn

Escobar, J. A. P. ; Hocks, A. ; Neumann, P.Extern*DESY*

2025
Springer Nature Switzerland Cham
ISBN: 978-3-031-97569-1, 978-3-031-97570-7 (electronic)

Computational Science – ICCS 2025 Workshops / Paszynski, Maciej (Editor) [https://orcid.org/0000-0001-7766-6052] ; Cham : Springer Nature Switzerland, 2025, Chapter 4 ; ISSN: 0302-9743=1611-3349 ; ISBN: 978-3-031-97569-1=978-3-031-97570-7 ; doi:10.1007/978-3-031-97570-7
International Conference on Computational Science, Singapore, Singapore, 7 Jul 2025 - 9 Jul 2025 Cham : Springer Nature Switzerland, Lecture Notes in Computer Science 15911, 33 - 47 (2025) [10.1007/978-3-031-97570-7_4]

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Abstract: In this work we present a node-level performance analysis of an adaptive resolution scheme (AdResS) implemented in ls1 mardyn . This is relevant in simulations involving a very large number of particles or long timescales, because it lowers the computational effort required to calculate short-range interactions in molecular dynamics. An introduction to AdResS is given, together with an explanation of the coarsening technique used to obtain an effective potential for the coarse molecular model, i.e., the Iterative Boltzmann Inversion (IBI). This is accompanied by details of the implementation in our software package, as well as an algorithmic description of the IBI method and the simulation workflow used to generate results. This will be of interest for practitioners. Results are provided for a pure Lennard-Jones tetrahedral molecule coarsened to a single site, validated by verifying the correct reproduction of structural correlation functions, e.g. the radial distribution function. The performance analysis builds upon a literature-driven methodology, which provides a theoretical estimate for the speedup based on a reference simulation and the size of the full particle region. Additionally, a strong scaling study was performed at node level. In this sense, several configurations with vertical interfaces between the resolution regions are tested, where different resolution widths are benchmarked. A comparison between several linked cell traversal routines, which are provided in ls1 mardyn , was performed to showcase the effect of algorithmic aspects on the adaptive resolution simulation and on the estimated performance.

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