research-article

Combining Task-based Parallelism and Adaptive Mesh Refinement Techniques in Molecular Dynamics Simulations

Authors:

Laurent Colombet,

Raymond NamystAuthors Info & Claims

ICPP '18: Proceedings of the 47th International Conference on Parallel Processing

Article No.: 48, Pages 1 - 10

https://doi.org/10.1145/3225058.3225085

Published: 13 August 2018 Publication History

Abstract

Modern parallel architectures require applications to generate massive parallelism so as to feed their large number of cores and their wide vector units. We revisit the extensively studied classical Molecular Dynamics N-body problem in the light of these hardware constraints. We use Adaptive Mesh Refinement techniques to store particles in memory, and to optimize the force computation loop using multi-threading and vectorization-friendly data structures. Our design is guided by the need for load balancing and adaptivity raised by highly dynamic particle sets, as typically observed in simulations of strong shocks resulting in material micro-jetting. We analyze performance results on several simulation scenarios, over nodes equipped by Intel Xeon Phi Knights Landing (KNL) or Intel Xeon Skylake (SKL) processors. Performance obtained with our OpenMP implementation outperforms state-of-the-art implementations (LAMMPS) on both steady and micro-jetting particles simulations. In the latter case, our implementation is 4.7 times faster on KNL, and 2 times faster on SKL.

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cover image ACM Other conferences

ICPP '18: Proceedings of the 47th International Conference on Parallel Processing

August 2018

945 pages

ISBN:9781450365109

DOI:10.1145/3225058

Copyright © 2018 ACM.

Publication rights licensed to ACM. ACM acknowledges that this contribution was authored or co-authored by an employee, contractor or affiliate of a national government. As such, the Government retains a nonexclusive, royalty-free right to publish or reproduce this article, or to allow others to do so, for Government purposes only.

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University of Oregon: University of Oregon

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Publication History

Published: 13 August 2018

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ICPP 2018

ICPP 2018: 47th International Conference on Parallel Processing

August 13 - 16, 2018

OR, Eugene, USA

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ICPP '18 Paper Acceptance Rate 91 of 313 submissions, 29%;

Overall Acceptance Rate 91 of 313 submissions, 29%

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https://doi.org/10.21105/joss.07484
Carrard TPrat RLatu GBabilotte KLafourcade PAmarsid LSoulard L(2024)ExaNBody: A HPC Framework for N-Body ApplicationsEuro-Par 2023: Parallel Processing Workshops10.1007/978-3-031-50684-0_27(342-354)Online publication date: 16-Apr-2024
https://doi.org/10.1007/978-3-031-50684-0_27
Soulard L(2023)Micro-jetting: A semi-analytical model to calculate the velocity and density of the jet from a triangular grooveJournal of Applied Physics10.1063/5.0142057133:8Online publication date: 22-Feb-2023
https://doi.org/10.1063/5.0142057
Massimo FLobet MDerouillat JBeck ABouchard GGrech MPérez FVinci TRobinson T(2022)A task programming implementation for the particle in cell code smileiProceedings of the Platform for Advanced Scientific Computing Conference10.1145/3539781.3539788(1-13)Online publication date: 27-Jun-2022
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Soulard LCarrard TDurand O(2022)Molecular dynamics study of the impact of a solid drop on a solid targetJournal of Applied Physics10.1063/5.0083266131:13Online publication date: 1-Apr-2022
https://doi.org/10.1063/5.0083266
Guidotti NCeyrat PBarreto JMonteiro JRodrigues RFonseca RMartorell XPeña A(2021)Particle-In-Cell Simulation Using Asynchronous TaskingEuro-Par 2021: Parallel Processing10.1007/978-3-030-85665-6_30(482-498)Online publication date: 1-Sep-2021
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Sala KRico ABeltran V(2020)Towards Data-Flow Parallelization for Adaptive Mesh Refinement Applications2020 IEEE International Conference on Cluster Computing (CLUSTER)10.1109/CLUSTER49012.2020.00042(314-325)Online publication date: Sep-2020
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Durand OSoulard LColombet LPrat R(2020)Influence of the phase transitions of shock-loaded tin on microjetting and ejecta production using molecular dynamics simulationsJournal of Applied Physics10.1063/5.0003744127:17Online publication date: 1-May-2020
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Soulard LDurand O(2020)Observation of phase transitions in shocked tin by molecular dynamicsJournal of Applied Physics10.1063/5.0003089127:16Online publication date: 23-Apr-2020
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Rucci EMoreno EPousa AChichizola F(2020)Optimization of the N-Body Simulation on Intel’s Architectures Based on AVX-512 Instruction SetComputer Science – CACIC 201910.1007/978-3-030-48325-8_3(37-52)Online publication date: 14-May-2020
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