Hybrid parallelization of molecular dynamics simulations to reduce load imbalance

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 pa...

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Vydané v:The Journal of supercomputing Ročník 78; číslo 7; s. 9184 - 9215
Hlavní autori: Morillo, Julian, Vassaux, Maxime, Coveney, Peter V., Garcia-Gasulla, Marta
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: New York Springer US 01.05.2022
Springer Nature B.V
Predmet:
Compilers
Computer Science
Computing costs
Domain decomposition methods
Interpreters
Microprocessors
Molecular dynamics
Processor Architectures
Programming Languages
Simulation
Spatial distribution
Molecular dynamics
Parallel computing
Hybrid programming model
OpenMP
Load Balance
MPI
ISSN:0920-8542, 1573-0484
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Shrnutí: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.
Bibliografia:ObjectType-Article-1
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ISSN:0920-8542
1573-0484
DOI:10.1007/s11227-021-04214-4