Code modernization strategies for short-range non-bonded molecular dynamics simulations
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Code modernization strategies for short-range non-bonded molecular dynamics simulations
Modern HPC systems are increasingly relying on greater core counts and wider vector registers thus applications need to be adapted to fully utilize these hardware capabilities. A class of applications that can benefit from this increase in parallelism are molecular dynamics simulations. Scientists, including GL Christoph Junghans of Applied Computer Science (CCS-7), describe their efforts at modernizing the ESPResSo++ molecular dynamics simulation package by restructuring its particle data layout for efficient memory accesses and applying vectorization techniques to benefit the calculation of short-range non-bonded forces, which results in an overall three times speedup and serves as a baseline for further optimizations.
The paper, which was an international collaboration of LANL with the Max-Planck Society and U Mainz (Germany), is available on arXiv at: https://arxiv.org/pdf/2109.10876.pdf
