title: A comparison between parallelization approaches in molecular dynamics simulations on GPUs.
abstract: 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 cores--as opposed to their computing power--remains, the "edge-based" approach will gradually become the most efficient choice in an increasing number of cases.
authors.affiliation: Dipartimento di Fisica, Sapienza-Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy; Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090, Vienna, Austria.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Rovigatti
authors.forename: Petr
authors.initials: P
authors.lastname: Sulc
authors.forename: István Z
authors.initials: IZ
authors.lastname: Reguly
authors.forename: Flavio
authors.initials: F
authors.lastname: Romano
keywords: graphics processing unit; molecular dynamics; parallelization; soft matter