Parallel Fock matrix construction with distributed shared memory model for the FMO-MO method

✍ Scribed by Hiroaki Umeda; Yuichi Inadomi; Toshio Watanabe; Toru Yagi; Takayoshi Ishimoto; Tsutomu Ikegami; Hiroto Tadano; Tetsuya Sakurai; Umpei Nagashima

• Publisher: John Wiley and Sons
• Year: 2010
• Tongue: English
• Weight: 706 KB
• Volume: 31
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.21531

✦ Synopsis

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. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010