Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units
复制标题
NVIDIA和AMD图形处理单元的量子力学/分子力学模拟
DOI：
10.1021/acs.jcim.2c01505
复制
发表时间：
2023-01
影响因子：
5.6
通讯作者：
M. Manathunga;H. Aktulga;A. Götz;K. Merz
中科院分区：
文献类型：
--
作者：
M. Manathunga;H. Aktulga;A. Götz;K. Merz
我们移植并优化了图形处理单元（GPU）加速的QUICK和基于amber的从头算量子力学/分子力学（QM/MM）在AMD GPU上的实现。这包含了整个Fock矩阵的构建和力的计算，包括单电子积分，双电子排斥积分，交换相关正交和线性代数操作。还介绍了QUICK GPU代码的一般性能改进。在NVIDIA V100和AMD MI100卡上进行的基准测试显示，在两种硬件上使用QUICK进行独立HF/DFT计算和使用QUICK/AMBER进行QM/MM分子动力学模拟的性能相似。此外，对于QUICK/AMBER版本21，在QM/MM分子动力学模拟中观察到显著的加速。这极大地增加了可以在最先进的计算机硬件上使用开源QM/MM软件解决的科学问题的范围。
We have ported and optimized the graphics processing unit (GPU)-accelerated QUICK and AMBER-based ab initio quantum mechanics/molecular mechanics (QM/MM) implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra operations. General performance improvements to the QUICK GPU code are also presented. Benchmarks carried out on NVIDIA V100 and AMD MI100 cards display similar performance on both hardware for standalone HF/DFT calculations with QUICK and QM/MM molecular dynamics simulations with QUICK/AMBER. Furthermore, with respect to the QUICK/AMBER release version 21, significant speedups are observed for QM/MM molecular dynamics simulations. This significantly increases the range of scientific problems that can be addressed with open-source QM/MM software on state-of-the-art computer hardware.