tinyMD: Mapping Molecular Dynamics Simulations to Heterogeneous Hardware using Partial Evaluation

In Journal of Computational Science (JOCS), 54(101425): 1-11, 2021

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.

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BibTeX

@article{ravedutti2021tinymd,
  author          = {Ravedutti Lucio Machado, Rafael and Schmitt, Jonas and Eibl, Sebastian and Eitzinger, Jan and Leißa, Roland and Hack, Sebastian and Pérard-Gayot, Arsène and Membarth, Richard and Köstler, Harald},
  title           = {{tinyMD}: Mapping Molecular Dynamics Simulations to Heterogeneous Hardware using Partial Evaluation},
  journal         = {Journal of Computational Science (JOCS)},
  pages           = {1--11},
  volume          = {54},
  number          = {101425},
  year            = 2021,
  month           = jul,
  date            = {2021-07-10},
  doi             = {10.1016/j.jocs.2021.101425},
  publisher       = {Elsevier}
}

tinyMD: Mapping Molecular Dynamics Simulations to Heterogeneous Hardware using Partial Evaluation

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