SC13 Home > SC13 Schedule > SC13 Presentation - Vectorization of Multi-Center, Highly-Parallel Rigid-Body Molecular Dynamics Simulations

SCHEDULE: NOV 16-22, 2013

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

SESSION: Research Poster Reception

EVENT TYPE: Posters, Electronic Posters, and Education Posters

TIME: 5:15PM - 7:00PM

AUTHOR(S):Wolfgang Eckhardt, Alexander Heinecke, Wolfgang Hölzl, Hans-Joachim Bungartz

ROOM:Mile High Pre-Function

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.

Chair/Author Details:

Wolfgang Eckhardt - Technische Universität München

Alexander Heinecke - Technische Universität München

Wolfgang Hölzl - Technische Universität München

Hans-Joachim Bungartz - Technische Universität München

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