Performance Evaluation of Partially Direct SCF Method

Yuichi INADOMIa,b*, Tohru SASAKIc, Umpei NAGASHIMAa,b and Kazuaki MURAKAMId

aNational Institute of Advanced Science and Technology, Grid Technology Research Center
Central 2, 1-1-1 Umezono, Tsukuba, 305-8568, JAPAN
bCore Research for Evolutional Science and Technology, Japan Science and Technology Agency
Kawaguchi Center building, 4-1-8 Honcho, Kawaguchi, 332-0012, JAPAN
cA priori Microsystems, Inc. Keio University
3-14-1 Hiyoshi, Kohoku-ku, Yokohama, JAPAN
dGraduate School of Information Science and Electrical Engineering
6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, JAPAN

(Received: July 4, 2005; Accepted for publication: August 12, 2005; Published on Web: November 18, 2005)

The partially direct SCF-MO method was developed to improve the parallelization efficiency in the Fock matrix generation using a PC cluster without secondary storage on each processor. Some of the electron repulsion integrals are stored in buffer (unused memory) with their four indices at the first SCF cycle, and they are reused at the later SCF cycles. This simple method achieved super-linear scalability, for example, the parallelization efficiency became ca. 1.13 in the Fock matrix generation of the Crambin molecule (1974 basis functions), equipped by the 128 Xeon processors (2.8GHz) with 16GB buffer area (See Figure 4). This algorithm is suitable for the special purpose computers for fast evaluation of the electron repulsion integrals because the recent special purpose processor has usually no secondary storage and has a relatively large main memory.

Keywords: Molecular Orbital Method, Two-Electron Integral, Special purpose machine, Parallelization, Partially direct SCF method

Abstract in Japanese

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