Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST

YL Zhu and D Pan and ZW Li and H Liu and HJ Qian and Y Zhao and ZY Lu and ZY Sun, MOLECULAR PHYSICS, 116, 1065-1077 (2018).

DOI: 10.1080/00268976.2018.1434904

We describe the algorithm of employing multi-GPU power on the basis of Message Passing Interface (MPI) domain decomposition in a molecular dynamics code, GALAMOST, which is designed for the coarse-grained simulation of soft matters. The code of multi-GPU version is developed based on our previous single-GPU version. In multi-GPU runs, one GPU takes charge of one domain and runs single-GPU code path. The communication between neighbouring domains takes a similar algorithm of CPU-based code of LAMMPS, but is optimised specifically for GPUs. We employ a memory-saving design which can enlarge maximum system size at the same device condition. An optimisation algorithm is employed to prolong the update period of neighbour list. We demonstrate good performance of multi-GPU runs on the simulation of Lennard-Jones liquid, dissipative particle dynamics liquid, polymer and nanoparticle composite, and two-patch particles on workstation. A good scaling of many nodes on cluster for two-patch particles is presented.

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