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

Journal of Computational Chemistry
Hiroaki UmedaUmpei Nagashima

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.

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Citations

Jul 29, 2015·The Journal of Physical Chemistry. a·Kushal Shrestha, Elena Jakubikova
Mar 17, 2015·The Journal of Chemical Physics·Edmond ChowJeff R Hammond
Sep 17, 2017·The Journal of Chemical Physics·Dmitri G Fedorov, Kazuo Kitaura
Jan 17, 2020·The Journal of Chemical Physics·Hua HuangEdmond Chow
Jul 18, 2017·Journal of Chemical Theory and Computation·Ayako NakataTsuyoshi Miyazaki

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