MOE: A special-purpose parallel computer for high-speed, large-scale molecular orbital calculation

Koji Hashimoto, Hiroto Tomita, Inoue Koji, Katsuhiko Metsugi, Kazuaki Murakami, Shinjiro Inabata, So Yamada, Nobuaki Miyakawa, Hajime Takashima, Kunihiro Kitamura, Shigeru Obara, Takashi Amisaki, Kazutoshi Tanabe, Umpei Nagashima

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

We are constructing a high-performance, special-purpose parallel machine for ab initio Molecular Orbital calculations, called MOE (Molecular Orbital calculation Engine). The sequential execution time is O(N4) where N is the number of basis functions, and most of time is spent to the calculations of electron repulsion integrals (ERIs). The calculation of ERIs have a lot of parallelism of O(N4), and therefore MOE tries to exploit the parallelism. This paper discuss the MOE architecture and examines important aspects of architecture design, which is required to calculate ERIs according to the "Obara method". We conclude that n-way parallelization is the most cost-effective, hence we designed the MOE prototype system with a host computer and many processing nodes. The processing node includes a 76 bit oating-point MULTIPLY-and-ADD unit and internal memory, etc., and it performs ERI computations efficiently. We estimate that the prototype system with 100 processing nodes calculate the energy of proteins in a few days.

Original languageEnglish
Title of host publicationACM/IEEE SC 1999 Conference, SC 1999
PublisherInstitute of Electrical and Electronics Engineers Inc.
Number of pages1
ISBN (Electronic)1581130910, 9781581130911
DOIs
Publication statusPublished - Jan 1 1999
Event1999 ACM/IEEE Conference on Supercomputing, SC 1999 - Portland, United States
Duration: Nov 13 1999Nov 19 1999

Publication series

NameACM/IEEE SC 1999 Conference, SC 1999

Other

Other1999 ACM/IEEE Conference on Supercomputing, SC 1999
CountryUnited States
CityPortland
Period11/13/9911/19/99

All Science Journal Classification (ASJC) codes

  • Hardware and Architecture

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    Hashimoto, K., Tomita, H., Koji, I., Metsugi, K., Murakami, K., Inabata, S., Yamada, S., Miyakawa, N., Takashima, H., Kitamura, K., Obara, S., Amisaki, T., Tanabe, K., & Nagashima, U. (1999). MOE: A special-purpose parallel computer for high-speed, large-scale molecular orbital calculation. In ACM/IEEE SC 1999 Conference, SC 1999 [1592701] (ACM/IEEE SC 1999 Conference, SC 1999). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/SC.1999.10000