SC13 Denver, CO

The International Conference for High Performance Computing, Networking, Storage and Analysis

Vectorization of Multi-Center, Highly-Parallel Rigid-Body Molecular Dynamics Simulations.

Authors: Wolfgang Eckhardt (Technische Universität München), Alexander Heinecke (Technische Universität München), Wolfgang Hölzl (Technische Universität München), Hans-Joachim Bungartz (Technische Universität München)

Abstract: The molecular dynamics (MD) code 'ls1 mardyn' is being developed for large-scale molecular simulation of e.g. nano- scale flows for fluids composed of simple, small molecules. In contrast to most other MD codes, ls1 mardyn treats molecules as completely rigid bodies with multiple interaction sites, instead of treating all atoms of an molecule individually and applying a constraint motion algorithm. Having previously demonstrated very good results for scalabilty, we present our efficient implementation of the compute kernel in this poster. We focus on the vectorized implementation of the interaction computation for multi-centered molecules using the AVX instruction set and show the performance of the new kernel on SuperMUC hosted at LRZ, Germany. In addition, we include early results for the Intel MIC architecture. On Sandy Bridge, we are able to gain a 3x runtime improvement, while our implementation on KNC achieves the performance of one SuperMUC node.

Poster: pdf
Two-page extended abstract: pdf

Poster Index