title: Parallel Fock matrix construction with distributed shared memory model for the FMO-MO method.
abstract: 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.
authors.affiliation: Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan. umeda@ccs.tsukuba.ac.jp
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Umeda
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Inadomi
authors.forename: Toshio
authors.initials: T
authors.lastname: Watanabe
authors.forename: Toru
authors.initials: T
authors.lastname: Yagi
authors.forename: Takayoshi
authors.initials: T
authors.lastname: Ishimoto
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Ikegami
authors.forename: Hiroto
authors.initials: H
authors.lastname: Tadano
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Umpei
authors.initials: U
authors.lastname: Nagashima
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D066246:ErbB Receptors / Q000737:chemistry*; D008958:Models, Molecular; D010940:Plant Proteins / Q000737:chemistry*; D011789:Quantum Theory
chemical_list: D010940:Plant Proteins; C024934:crambin protein, Crambe abyssinica; D066246:ErbB Receptors