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Journal Article

Code modernization strategies for short-range non-bonded molecular dynamics simulations


Rampp,  Markus
Max Planck Computing and Data Facility, Max Planck Society;


Eibl,  Sebastian
Max Planck Computing and Data Facility, Max Planck Society;

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Vance, J., Xu, Z.-H., Tretyakov, N., Stuehn, T., Rampp, M., Eibl, S., et al. (2023). Code modernization strategies for short-range non-bonded molecular dynamics simulations. Computer Physics Communications, 290: 108760. doi:10.1016/j.cpc.2023.108760.

Cite as: https://hdl.handle.net/21.11116/0000-000D-318A-0
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. One class of applications that can benefit from this increase in parallelism are molecular dynamics simulations. In this paper, we describe our efforts at modernizing the ESPResSo++ simulation package for molecular dynamics 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. We also implement fine-grained parallelism for multi-core CPUs through HPX, a C++ runtime system which uses lightweight threads and an asynchronous many-task approach to maximize concurrency. Our goal is to evaluate the performance of an HPX-based approach compared to the bulk-synchronous MPI-based implementation. This requires the introduction of an additional layer to the domain decomposition scheme that defines the task granularity. On spatially inhomogeneous systems, which impose a corresponding load-imbalance in traditional MPI-based approaches, we demonstrate that by choosing an optimal task size, the efficient work-stealing mechanisms of HPX can overcome the overhead of communication resulting in an overall 1.4 times speedup compared to the baseline MPI version.