Parallel Fock matrix construction with distributed shared memory model for the FMO-MO method.
A parallel Fock matrix construction program for FMO-MO method has been developed with the distributed shared memory model. To construct a large-sized Fock matrix during FMO-MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO-MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6-31G level of theory, with the frontier orbitals being extracted by a Sakurai-Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen-components on a PC cluster system using 256 processors.
Umeda
Hiroaki
H
Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan. umeda@ccs.tsukuba.ac.jp
Inadomi
Yuichi
Y
Watanabe
Toshio
T
Yagi
Toru
T
Ishimoto
Takayoshi
T
Ikegami
Tsutomu
T
Tadano
Hiroto
H
Sakurai
Tetsuya
T
Nagashima
Umpei
U
D019295:Computational Biology; D003198:Computer Simulation; D066246:ErbB Receptors / Q000737:chemistry*; D008958:Models, Molecular; D010940:Plant Proteins / Q000737:chemistry*; D011789:Quantum Theory
D010940:Plant Proteins; C024934:crambin protein, Crambe abyssinica; D066246:ErbB Receptors