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Hybrid parallelization of molecular dynamics simulations to reduce load imbalance

Morillo, Julian; Vassaux, Maxime; Coveney, Peter V; Garcia-Gasulla, Marta; (2022) Hybrid parallelization of molecular dynamics simulations to reduce load imbalance. Journal of Supercomputing , 78 (7) pp. 9184-9215. 10.1007/s11227-021-04214-4. Green open access

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Abstract

The most widely used technique to allow for parallel simulations in molecular dynamics is spatial domain decomposition, where the physical geometry is divided into boxes, one per processor. This technique can inherently produce computational load imbalance when either the spatial distribution of particles or the computational cost per particle is not uniform. This paper shows the benefits of using a hybrid MPI+OpenMP model to deal with this load imbalance. We consider LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator), a prototypical molecular dynamics simulator that provides its own balancing mechanism and an OpenMP implementation for many of its modules, allowing for a hybrid setup. In this work, we extend the current OpenMP implementation of LAMMPS and optimize it and evaluate three different setups: MPI-only, MPI with the LAMMPS balance mechanism, and hybrid setup using our improved OpenMP version. This comparison is made using the five standard benchmarks included in the LAMMPS distribution plus two additional test cases. Results show that the hybrid approach can deal with load balancing problems better and more effectively (50% improvement versus MPI-only for a highly imbalanced test case) than the LAMMPS balance mechanism (only 43% improvement) and improve simulations with issues other than load imbalance.

Type: Article
Title: Hybrid parallelization of molecular dynamics simulations to reduce load imbalance
Open access status: An open access version is available from UCL Discovery
DOI: 10.1007/s11227-021-04214-4
Publisher version: https://doi.org/10.1007/s11227-021-04214-4
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Science & Technology, Technology, Computer Science, Hardware & Architecture, Computer Science, Theory & Methods, Engineering, Electrical & Electronic, Computer Science, Engineering, Load Balance, Parallel computing, Molecular dynamics, MPI, OpenMP, Hybrid programming model
UCL classification: UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Chemistry
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL
URI: https://discovery.ucl.ac.uk/id/eprint/10151087
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