Towards auto-tuning Multi-Site Molecular Dynamics simulations with AutoPas
Publication date
2023-12-01
Document type
Research article
Author
Organisational unit
Scopus ID
ISSN
Series or journal
Journal of Computational and Applied Mathematics
Periodical volume
433
First page
115278
Last page
115278
Peer-reviewed
✅
Part of the university bibliography
✅
Keyword
Auto-tuning
AutoPass
High performance computing
Molecular Dynamics
Multi-Site Molecular Dynamics
Abstract
There exists an extensive literature of algorithms for short-range pairwise interactions in particle simulations, however, there is no single algorithm that performs the most optimally in every scenario, motivating the use of auto-tuning to select the optimal pairwise interaction algorithm. Previous efforts to auto-tune Molecular Dynamics have focused on Single-Site Molecular Dynamics, where the computational cost for the intermolecular force calculation is constant. Alternatively, for Multi-Site Molecular Dynamics, the cost of this calculation varies with the number of sites, which, as we show in this paper, can result in different optimal algorithms. Despite this further benefit for auto-tuning, it has yet to be applied to Multi-Site Molecules. In this paper, we introduce an implementation of Multi-Site Molecular Dynamics that is integrated with AutoPas. Using this implementation, we analyse how the relative performance between these algorithms varies as the number of sites varies, for both homogeneous and heterogeneous molecule distributions, and for two different hardware. Furthermore, we demonstrate the advantage of auto-tuning in the context of Multi-Site Molecular Dynamics using the node-level short-range particle simulation library, AutoPas.
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