A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs

Autor(en)

Lorenzo Rovigatti, Petr Sulc, Istvan Z. Reguly, Flavio Romano

Abstrakt

We test the relative performances of two different approaches to the computation of forces for molecular dynamics simulations on graphics processing units. A vertex-based approach, where a computing thread is started per particle, is compared to an edge-based approach, where a thread is started per each potentially non-zero interaction. We find that the former is more efficient for systems with many simple interactions per particle while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent graphics processing unit technology, we predict that, if the current trend of increasing the number of processing coresas opposed to their computing powerremains, the edge-based approach will gradually become the most efficient choice in an increasing number of cases.

Organisation(en)

Computergestützte Physik und Physik der Weichen Materie

Externe Organisation(en)

Università degli Studi di Roma La Sapienza, University of Oxford

Journal

Journal of Computational Chemistry

Band

36

Seiten

1-8

Anzahl der Seiten

8

ISSN

0192-8651

DOI

https://doi.org/10.1002/jcc.23763

Publikationsdatum

01-2015

Peer-reviewed

Ja

ÖFOS 2012

103036 Theoretische Physik, 104017 Physikalische Chemie, 103023 Polymerphysik, 103029 Statistische Physik

Schlagwörter

ASJC Scopus Sachgebiete

Computational Mathematics, Allgemeine Chemie

Link zum Portal

https://ucrisportal.univie.ac.at/de/publications/b24842bf-88e8-4549-aed5-4e13e4b583ef