Computational Molecular Science Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan.
J Comput Chem. 2017 Mar 30;38(8):489-507. doi: 10.1002/jcc.24701.
A massively parallel algorithm of the analytical energy gradient calculations based the resolution of identity Møller-Plesset perturbation (RI-MP2) method from the restricted Hartree-Fock reference is presented for geometry optimization calculations and one-electron property calculations of large molecules. This algorithm is designed for massively parallel computation on multicore supercomputers applying the Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) hybrid parallel programming model. In this algorithm, the two-dimensional hierarchical MP2 parallelization scheme is applied using a huge number of MPI processes (more than 1000 MPI processes) for acceleration of the computationally demanding O(N ) step such as calculations of occupied-occupied and virtual-virtual blocks of MP2 one-particle density matrix and MP2 two-particle density matrices. The new parallel algorithm performance is assessed using test calculations of several large molecules such as buckycatcher C @C H (144 atoms, 1820 atomic orbitals (AOs) for def2-SVP basis set, and 3888 AOs for def2-TZVP), nanographene dimer (C H ) (240 atoms, 2928 AOs for def2-SVP, and 6432 AOs for cc-pVTZ), and trp-cage protein 1L2Y (304 atoms and 2906 AOs for def2-SVP) using up to 32,768 nodes and 262,144 central processing unit (CPU) cores of the K computer. The results of geometry optimization calculations of trp-cage protein 1L2Y at the RI-MP2/def2-SVP level using the 3072 nodes and 24,576 cores of the K computer are presented and discussed to assess the efficiency of the proposed algorithm. © 2017 Wiley Periodicals, Inc.
本文提出了一种基于完全哈密顿量微扰(RI-MP2)方法的解析能量梯度计算的大规模并行算法,用于大型分子的几何优化计算和单电子性质计算。该算法是为多核超级计算机上的大规模并行计算而设计的,采用消息传递接口(MPI)和开放式多处理(OpenMP)混合并行编程模型。在该算法中,应用二维层次 MP2 并行化方案,使用大量 MPI 进程(超过 1000 个 MPI 进程)加速计算量较大的 O(N)步骤,例如 MP2 单粒子密度矩阵和 MP2 双粒子密度矩阵的占据-占据和虚拟-虚拟块的计算。使用 buckycatcher C @C H(144 个原子,1820 个原子轨道(AOs)用于 def2-SVP 基组,3888 AOs 用于 def2-TZVP)、纳米石墨烯二聚体(C H )(240 个原子,2928 AOs 用于 def2-SVP,6432 AOs 用于 cc-pVTZ)和 trp-cage 蛋白 1L2Y(304 个原子和 2906 AOs 用于 def2-SVP)等几个大分子的测试计算来评估新的并行算法性能,使用多达 32768 个节点和 K 计算机的 262144 个中央处理单元(CPU)核。展示并讨论了使用 K 计算机的 3072 个节点和 24576 个核在 RI-MP2/def2-SVP 水平上对 trp-cage 蛋白 1L2Y 进行几何优化计算的结果,以评估所提出算法的效率。© 2017 威利父子公司