Meyer, Ralf

Permanent URI for this communityhttps://laurentian.scholaris.ca/handle/10219/2695

Browse

Browsing Meyer, Ralf by Subject "parallel computing"

Filter results by typing the first few letters
Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Efficient parallelization of molecular dynamics simulations with short-ranged forces
    (IOP Publishing Ltd., 2014) Meyer, Ralf
    Recently, an alternative strategy for the parallelization of molecular dynamics simulations with short-ranged forces has been proposed. In this work, this algorithm is tested on a variety of multi-core systems using three types of benchmark simulations. The results show that the new algorithm gives consistent speedups which are depending on the properties of the simulated system either comparable or superior to those obtained with spatial decomposition. Comparisons of the parallel speedup on different systems indicates that on multi-core machines the parallel efficiency of the method is mainly limited by memory access speed.
  • Thumbnail Image
    Item
    Efficient parallelization of short-range molecular dynamics simulations on many-core systems
    (American Physical Society, 2013-11) Meyer, Ralf
    This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly inhomogeneous systems like nanodevices or nanostructured materials. In the proposed scheme the calculation of the forces and the generation of neighbor lists are divided into small tasks. The tasks are then executed by a thread pool according to a dependent task schedule. This schedule is constructed in such a way that a particle is never accessed by two threads at the same time. Benchmark simulations on a typical 12-core machine show that the described algorithm achieves excellent parallel efficiencies above 80% for different kinds of systems and all numbers of cores. For inhomogeneous systems the speedups are strongly superior to those obtained with spatial decomposition. Further benchmarks were performed on an Intel Xeon Phi coprocessor. These simulations demonstrate that the algorithm scales well to large numbers of cores.
  • Thumbnail Image
    Item
    Parallelization of Molecular-Dynamics Simulations Using Tasks
    (Cambridge University Press, 2015-02) Meyer, Ralf; Mangiardi, Chris M.
    This article discusses novel algorithms for molecular-dynamics (MD) simulations with short-ranged forces on modern multi- and many-core processors like the Intel Xeon Phi. A task-based approach to the parallelization of MD on shared-memory computers and a tiling scheme to facilitate the SIMD vectorization of the force calculations is described. The algorithms have been tested with three different potentials and the resulting speed-ups on Intel Xeon Phi coprocessors are shown.