A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs

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. (c) 2014 Wiley Periodicals, Inc.