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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Vydáno v:	The Journal of supercomputing Ročník 78; číslo 7; s. 9184 - 9215
Hlavní autoři:	Morillo, Julian, Vassaux, Maxime, Coveney, Peter V., Garcia-Gasulla, Marta
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	New York Springer US 01.05.2022 Springer Nature B.V
Témata:	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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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.
AbstractList	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. 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.
Author	Morillo, Julian Vassaux, Maxime Coveney, Peter V. Garcia-Gasulla, Marta
Author_xml	– sequence: 1 givenname: Julian orcidid: 0000-0002-8448-9995 surname: Morillo fullname: Morillo, Julian email: julian.morillo@bsc.es organization: Barcelona Supercomputing Center - Centro Nacional de Supercomputacion – sequence: 2 givenname: Maxime surname: Vassaux fullname: Vassaux, Maxime organization: Centre for Computational Sciences - University College London – sequence: 3 givenname: Peter V. surname: Coveney fullname: Coveney, Peter V. organization: Centre for Computational Sciences - University College London – sequence: 4 givenname: Marta surname: Garcia-Gasulla fullname: Garcia-Gasulla, Marta organization: Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
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Cites_doi	10.1006/jcph.1995.1039 10.1002/adts.201800168 10.1007/s11227-013-0915-x 10.1016/j.jpdc.2013.12.008 10.1109/ICPP.2009.56 10.1002/(SICI)1096-987X 10.1177/1094342003017001005 10.1016/j.cpc.2021.108171 10.1109/SC.2014.58 10.1002/jcc.23591 10.1002/adma.202003213 10.1007/978-3-540-24644-2_20 10.1109/IPDPS.2009.5160973 10.1007/978-3-642-11261-4_11 10.1006/jcph.2000.6501 10.1109/IPDPSW.2012.207 10.1109/SC.2000.10035 10.1016/j.powtec.2015.03.019 10.1137/S1064827595287997 10.1109/PDP50117.2020.00032 10.1080/08927028708080929 10.1016/0010-4655(91)90097-5 10.1016/j.apnum.2004.08.028 10.1177/1094342019842919 10.1007/978-3-030-11987-4_1 10.1109/PDP.2009.43 10.1016/j.parco.2013.05.004 10.1137/S1064827598337373
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References_xml	– reference: Rabenseifner R, Hager G, Jost G (2009) Hybrid mpi/openmp parallel programming on clusters of multi-core smp nodes. In: 2009 17th Euromicro International Conference on Parallel, Distributed and Network-Based Processing, pp 427–436. IEEE – reference: RabenseifnerRWelleinGCommunication and optimization aspects of parallel programming models on hybrid architecturesInt J High Performance Comput Appl2003171496210.1177/1094342003017001005 – reference: ServatHFramework for a productive performance optimizationParallel Comput201339833635310.1016/j.parco.2013.05.004 – reference: FinchamDParallel computers and molecular simulationMol Simul198711–214510.1080/08927028708080929 – reference: Schloegel K, Karypis G, Kumar V (2000) A unified algorithm for load-balancing adaptive scientific simulations. In: SC’00: Proceedings of the 2000 ACM/IEEE Conference on Supercomputing, pp 59–59. 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Title	Hybrid parallelization of molecular dynamics simulations to reduce load imbalance
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