Performance optimization of reactive molecular dynamics simulations with dynamic charge distribution models on distributed memory platforms
Performance optimization of reactive molecular dynamics simulations with dynamic charge distribution models on distributed memory platforms
复制标题
分布式存储平台上动态电荷分布模型的反应分子动力学模拟的性能优化
DOI：
10.1145/3330345.3330359
复制
发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Aktulga, Hasan Metin
中科院分区：
文献类型：
--
作者：
O'Hearn, Kurt A.;Alperen, Abdullah;Aktulga, Hasan Metin
反应分子动力学（MD）模拟对于具有化学反应的大型系统的高保真模拟是重要的。迭代线性求解器用于动态确定原子极化反应分子动力学模型和冗余相关的键序计算构成显着的瓶颈，在时间的解决方案和反应力场的整体可扩展性。这项工作的目标是解决这些瓶颈问题。为了实现这一目标，探索了几个优化，包括加速的电荷模型求解器通过一个有效的预处理技术和一个数值方法，减少通信开销，以及初始化和数据结构的变化，键序计算。这些优化及其整体影响的详细可扩展性分析。一个单一的allreduce流水线非阻塞共轭梯度（PIPECG）求解器与稀疏近似逆（SAI）的预处理器耦合已被观察到产生显着的加速比基线标准CG求解器与雅可比预处理器。这些结果是显着的，因为它们可以促进可扩展的模拟大型反应系统，并提出的技术可以用于其他极化MD模型。
Reactive molecular dynamics (MD) simulations are important for high-fidelity simulations of large systems with chemical reactions. Iterative linear solvers used to dynamically determine atom polarizations in reactive MD models and redundancies related to bond order calculations constitute significant bottlenecks in terms of time-to-solution and the overall scalability of reactive force fields. The objective of this work is to address these bottlenecks. To accomplish this goal, several optimizations are explored including acceleration of the charge model solver through an effective preconditioning technique and a numerical method with reduced communication overheads, as well as initialization and data structure changes for bond order calculations. Detailed scalability analysis of these optimizations and their overall impact is presented. A single-allreduce pipelined non-blocking conjugate gradient (PIPECG) solver coupled with a sparse approximate inverse (SAI) based preconditioner has been observed to yield significant speedups over the baseline standard CG solver with Jacobi preconditioner. These results are significant as they can facilitate scalable simulations of large reactive systems, and presented techniques can be used in other polarizable MD models.
分子动力学模拟中 Si/Ge/Si 纳米棒的应变松弛
DOI：
--
发表时间：
2009
期刊：
影响因子：
--
作者：
Y. Park;Hasan Metin Atkulga;A. Grama;A. Strachan
通讯作者：
A. Strachan
影响因子：
4.1
作者：
Kylasa, S. B.;Aktulga, H. M.;Grama, A. Y.
通讯作者：
Grama, A. Y.
影响因子：
4.4
作者：
Fogarty, Joseph C.;Aktulga, Hasan Metin;Pandit, Sagar A.
通讯作者：
Pandit, Sagar A.