Paper Citing NAMD - Abstract
Umeda, Hiroaki; Inadomi, Yuichi; Watanabe, Toshio; Yagi, Toru; Ishimoto, Takayoshi; Ikegami, Tsutomu; Tadano, Hiroto; Sakurai, Tetsuya; Nagashima, Umpei
Parallel Fock Matrix Construction with Distributed Shared Memory Model for the FMO-MO Method
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:2381-2388, OCT 2010
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/6-3IG 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. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 2381-2388, 2010
