• Hybrid parallelization of mole...

*Result*: Hybrid parallelization of molecular dynamics simulations to reduce load imbalance

Title:
Hybrid parallelization of molecular dynamics simulations to reduce load imbalance
Authors:
Morillo, Julian, Vassaux, Maxime, Coveney, Peter V., Garcia Gasulla, Marta
Contributors:
Barcelona Supercomputing Center
Publisher Information:
Springer
Publication Year:
2022
Collection:
Universitat Politècnica de Catalunya, BarcelonaTech: UPCommons - Global access to UPC knowledge
Subject Terms:
Àrees temàtiques de la UPC::Informàtica::Enginyeria del software, OpenMP (Application program interface), Molecular dynamics, Load Balance, Parallel computing, MPI, OpenMP, Hybrid programming model, Simulació per ordinador
Document Type:
*Academic Journal* article in journal/newspaper
File Description:
application/pdf
Language:
English
Relation:
https://link.springer.com/article/10.1007/s11227-021-04214-4; info:eu-repo/grantAgreement/EC/H2020/824080/EU/Performance Optimisation and Productivity 2/POP2; Morillo, J. [et al.]. Hybrid parallelization of molecular dynamics simulations to reduce load imbalance. "Journal of Supercomputing", 2022; https://rdcu.be/cE8iB; https://hdl.handle.net/2117/364810
DOI:
10.1007/s11227-021-04214-4
Availability:
https://hdl.handle.net/2117/364810
https://rdcu.be/cE8iB
https://doi.org/10.1007/s11227-021-04214-4
Rights:
Open Access
Accession Number:
edsbas.C3FCF340
Database:
BASE

*Further Information*

*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. ; This work is partially supported by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European POP CoE (GA n. 824080). This work is also funded as part of the European Union Horizon 2020 research and innovation program under grant agreement nos. 800925 (VECMA project; www.vecma.eu) and 823712 (CompBioMed2 Centre of Excellence; www.compbiomed.eu), as well as the UK EPSRC for the UK High-End Computing Consortium (grant no. EP/R029598/1). ; Peer Reviewed ; Postprint (author's final draft)*