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

ABSTRACT

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.

KEYWORDS:

• GALAMOST
• molecular dynamics
• multi-GPU
• coarse-graining
• soft matter

Acknowledgments

Zhong-Yuan Lu thanks to the support of JLU-STIRT program at Jilin University. You-Liang Zhu gratefully acknowledges the support of NVIDIA Corporation with the donation of the Tesla K40 GPU used for this research. In this research, we have used the TianHe-1(A) supercomputer at National Supercomputer Center in Tianjin, TianHe-2 supercomputer at National Supercomputer Center in Guangzhou for program debugging, and the high-performance cluster at Dalian Institute of Chemical Physics, Chinese Academy of Sciences for performance benchmarking. We thank Guo-Hui Li and Yue-Bin Zhang for their help on the tests at the cluster of Dalian Institute of Chemical Physics, Chinese Academy of Sciences.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work is supported by the National Natural Science Foundation of China [21404102], [21774129], [21534004], [21474111], [21674116].