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- W2912422172 abstract "Highly-optimized parallel molecular dynamics programs have allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: a significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup, we assess key accelerating programming components of four different best-performing molecular dynamics programs-- GROMACS, NAMD, LAMMPS and CP2K-- each having a particular scope of application, for contribution to performance and for portability. We use builds with and without these components, tested on HPC systems. We also analyze the code-bases to determine compliance with portability recommendations. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. This characterizes the performance efficiency that must be approached for good performance portability on a programmatic level, suggesting solutions to this difficult problem, which should come from developers, industry and funding institutions, and possibly new research in programming languages." @default.
- W2912422172 created "2019-02-21" @default.
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- W2912422172 date "2018-11-01" @default.
- W2912422172 modified "2023-10-16" @default.
- W2912422172 title "High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability" @default.
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- W2912422172 doi "https://doi.org/10.1109/p3hpc.2018.00004" @default.
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