Node-level performance of adaptive resolution in ls1 mardyn
Publication date
2025-07-05
Document type
Konferenzbeitrag
Author
Organisational unit
Conference
25th International Conference on Computational Science (ICCS 2025) ; Singapore ; July 7–9, 2025
Project
Publisher
Springer
Series or journal
Lecture Notes in Computer Science
Periodical volume
15911
Book title
Computational Science – ICCS 2025 Workshops
Volume (part of multivolume book)
5
First page
33
Last page
47
Peer-reviewed
✅
Part of the university bibliography
✅
Language
English
Keyword
Molecular dynamics
Adaptive resolution
Iterative Boltzmann Inversion
dtec.bw
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.
Version
Published version
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