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Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions
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DOI：10.1109/TPDS.2021.3091408.png)
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Abstract
En 中文
Molecular dynamics (MD) simulations are playing an increasingly important role in many areas ranging from chemical materials to biological molecules. With the continuing development of MD models, the potentials are getting larger and more complex. In this article, we focus on the reactive force field (ReaxFF) potential from LAMMPS to optimize the computation of interactions. We present our efforts on refactoring for neighbor list building, bond order computation, as well as valence angles and torsion angles computation. After redesigning these kernels, we develop a vectorized implementation for non-bonded interactions, which is nearly 100x faster than the management processing element (MPE) on the Sunway TaihuLight supercomputer. Furthermore, we have implemented the three-body-list free torsion angles computation, and propose a line-locked software cache method to eliminate write conflicts in the torsion angle and valence angle interactions resulting in an order-of-magnitude speedup on a single Sunway TaihuLight node. In addition, we achieve a speedup of up to 3.5 compared to the KOKKOS package on an Intel Xeon Gold 6148 core. When executed on 1,024 processes, our implementation enables the simulation of 21,233,664 atoms on 66,560 cores with a performance of 0.032 ns/day and a weak scaling efficiency of 95.71 percent.
Keywords:
High performance computing
molecular dynamics
computational science
Sunway TaihuLight supercomputer (TaihuLight)
Journal
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6
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5.2K
Citations:
1.1W