Parallel Implementation of the Quantum Mechanics Force Field Program of Biosystem Using Tens of Millions of Cores on the New-Generation Sunway Supercomputer

doi:10.11871/jfdc.issn.2096-742X.2025.06.015

Abstract

Abstract:

[Objective] This paper aims to achieve efficient parallelization of the explicit polarization (X-Pol) model, a quantum mechanical force field method, on a new generation of domestic supercomputers. [Methods] The PyXPOL program, a Python implementation of the quantum mechanical force field method, is developed. It adopts a two-level parallel architecture of MPI+Athread. By introducing the neighbor list method, the parallel computation of non-bonded interactions is achieved. An S-shaped sorting optimization method for computational workload is employed to achieve load balancing. Considering the characteristics of the SW26010-Pro processor, the quantum chemical calculation program in the X-Pol model is optimized. [Results] The results indicate that the PyXPOL program demonstrates weak scalability on ten million cores. Compared with the calculation using 50,050 cores, the parallel efficiency of the ten-million-core calculation can reach 75%. Moreover, it also achieves large-scale parallel calculations for a biological system with 170,788 atoms. The parallel efficiency of 3 million cores compared to 50,050 cores reaches 82%. [Conclusions] The PyXPOL program achieves efficient parallelization of the X-Pol quantum mechanical force field method on the new generation of domestic supercomputers, significantly improving the computational efficiency for large-scale biological molecular systems. It provides a powerful tool for the application of quantum mechanical force field methods in large-scale parallel computing.

Key words: Explicit polarization (X-Pol) model, two-level parallel, quantum mechanical force field

GUO Jianping,MAO Ruichao,ZHANG Han,ZHANG Yong,GAO Jun. Parallel Implementation of the Quantum Mechanics Force Field Program of Biosystem Using Tens of Millions of Cores on the New-Generation Sunway Supercomputer[J]. Frontiers of Data and Computing, 2025, 7(6): 158-169, https://cstr.cn/32002.14.jfdc.CN10-1649/TP.2025.06.015.

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计算函数	运行时间/s	时间占比
DIIS	710	48.0%
DENSITY_CALCULATE	289	20.0%
SYMMETRIC_UPPER	478	32.0%
其他	5	0.3%
总计	1,482	100%

核数	帧数
50,050	1
500,500	10
1,001,000	20
3,003,000	60
5,005,000	100
7,507,500	150
10,010,000	200