headerlogo
scyourway

SC Conference - Activity Details



Molecular Orbital Calculation with 100,000 Bases using FMO-MO Method: Distributed Parallel Construction and Diagonalization of Semi-sparse Fock Matrix

Authors:
Hiroaki Umeda  (National Institute of Advanced Industrial Science & Technology)
Hiroto Tadano  (University of Tsukuba)
Toshio Watanabe  (National Institute of Advanced Industrial Science & Technology)
Tetsuya Sakurai  (University of Tsukuba)
Tsutomu Ikegami  (National Institute of Advanced Industrial Science & Technology)
Umpei Nagashima  (National Institute of Advanced Industrial Science & Technology)
Posters Session
Tuesday,  05:15PM - 07:00PM
Room Rotunda Lobby
Abstract:
Molecular orbital calculation for the 17,246 atomic protein, EGFR, is performed using FMO-MO method at the HF/6-31G level of theory, which involves 96,234 basis functions. A 96,234 dimensional Fock matrix is constructed based on the preceding FMO calculation and is diagonalized to obtain desired orbitals. For the Fock matrix construction, a distributed parallel algorithm is designed to make full use of local memory to reduce communication, and has been implemented on the Global Array toolkit. The resulting Fock matrix is incorporated in a generalized eigenvalue problem, fill rate of which is about 5 % and 457 million non-zero elements exist. To extract a few desired eigen-components, a highly parallel contour integral method is employed. It takes 49 hours to construct the Fock matrix with 96,234 basis functions, and 10 minutes to extract 94 eigen-components on an Opteron cluster system using 256 processors.
   IEEE Computer Society  /  ACM     2 0   Y E A R S   -   U N L E A S H I N G   T H E   P O W E R   O F   H P C