tinyMD: Mapping molecular dynamics simulations to heterogeneous hardware using partial evaluation

Ravedutti Lucio Machado R, Schmitt J, Eibl S, Eitzinger J, Leißa R, Hack S, Pérard-Gayot A, Membarth R, Köstler H (2021)

Publication Type: Journal article

Publication year: 2021

Journal

Book Volume: 54

Article Number: 101425

DOI: 10.1016/j.jocs.2021.101425

Abstract

This paper investigates the suitability of the AnyDSL partial evaluation framework to implement tinyMD: an efficient, scalable, and portable simulation of pairwise interactions among particles. We compare tinyMD with the miniMD proxy application that scales very well on parallel supercomputers. We discuss the differences between both implementations and contrast miniMD's performance for single-node CPU and GPU targets, as well as its scalability on SuperMUC-NG and Piz Daint supercomputers. Additionally, we demonstrate tinyMD's flexibility by coupling it with the waLBerla multi-physics framework. This allow us to execute tinyMD simulations using the load-balancing mechanism implemented in waLBerla.

Authors with CRIS profile

Involved external institutions

Technische Hochschule Ingolstadt Germany (DE) Universität des Saarlandes (UdS) Germany (DE)

How to cite

APA:

Ravedutti Lucio Machado, R., Schmitt, J., Eibl, S., Eitzinger, J., Leißa, R., Hack, S.,... Köstler, H. (2021). tinyMD: Mapping molecular dynamics simulations to heterogeneous hardware using partial evaluation. Journal of Computational Science, 54. https://dx.doi.org/10.1016/j.jocs.2021.101425

MLA:

Ravedutti Lucio Machado, Rafael, et al. "tinyMD: Mapping molecular dynamics simulations to heterogeneous hardware using partial evaluation." Journal of Computational Science 54 (2021).

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