Exploring SIMD for Molecular Dynamics, Using Intel® Xeon® Processors and Intel® Xeon Phi Coprocessors

@article{Pennycook2013ExploringSF,
  title={Exploring SIMD for Molecular Dynamics, Using Intel® Xeon® Processors and Intel® Xeon Phi Coprocessors},
  author={Simon J. Pennycook and Christopher J. Hughes and Mikhail Smelyanskiy and Stephen A. Jarvis},
  journal={2013 IEEE 27th International Symposium on Parallel and Distributed Processing},
  year={2013},
  pages={1085-1097}
}
We analyse gather-scatter performance bottlenecks in molecular dynamics codes and the challenges that they pose for obtaining benefits from SIMD execution. This analysis informs a number of novel code-level and algorithmic improvements to Sandia's miniMD benchmark, which we demonstrate using three SIMD widths (128-, 256and 512bit). The applicability of these optimisations to wider SIMD is discussed, and we show that the conventional approach of exposing more parallelism through redundant… CONTINUE READING
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