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Parallel Fock matrix construction with distributed shared memory model for the FMO‐MO method
Author(s) -
Umeda Hiroaki,
Inadomi Yuichi,
Watanabe Toshio,
Yagi Toru,
Ishimoto Takayoshi,
Ikegami Tsutomu,
Tadano Hiroto,
Sakurai Tetsuya,
Nagashima Umpei
Publication year - 2010
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21531
Subject(s) - fock matrix , benchmark (surveying) , computer science , atomic orbital , matrix (chemical analysis) , molecular orbital , construct (python library) , coupled cluster , parallel computing , basis (linear algebra) , cluster (spacecraft) , fock space , distributed memory , generator matrix , computational science , shared memory , hartree–fock method , chemistry , computational chemistry , algorithm , physics , mathematics , molecule , quantum mechanics , organic chemistry , programming language , geometry , geodesy , chromatography , electron , geography , decoding methods
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