A novel parallel algorithm for large-scale Fock matrix construction with small locally distributed memory architectures: RT parallel algorithm

We developed a novel parallel algorithm for large‐scale Fock matrix calculation with small locally distributed memory architectures, and named it the “RT parallel algorithm.” The RT parallel algorithm actively involves the concept of integral screening, which is indispensable for reduction of comput...

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Vydáno v:Journal of computational chemistry Ročník 23; číslo 14; s. 1337 - 1346
Hlavní autoři: Takashima, Hajime, Yamada, So, Obara, Shigeru, Kitamura, Kunihiro, Inabata, Shinjiro, Miyakawa, Nobuaki, Tanabe, Kazutoshi, Nagashima, Umpei
Médium: Journal Article
Jazyk:angličtina
Vydáno: New York Wiley Subscription Services, Inc., A Wiley Company 15.11.2002
Témata:
Algorithms
Biological materials
Calculations
Combinatorial Chemistry Techniques
Computer Simulation
Functions
integral screening
Large scale systems
large-scale SCF
massively parallel and distributed Fock matrix construction
Matrix algebra
Models, Theoretical
Molecules
parallel efficiency
RT parallel algorithm
Time Factors
ISSN:0192-8651, 1096-987X
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Shrnutí:We developed a novel parallel algorithm for large‐scale Fock matrix calculation with small locally distributed memory architectures, and named it the “RT parallel algorithm.” The RT parallel algorithm actively involves the concept of integral screening, which is indispensable for reduction of computing times with large‐scale biological molecules. The primary characteristic of this algorithm is parallel efficiency, which is achieved by well‐balanced reduction of both communicating and computing volume. Only the density matrix data necessary for Fock matrix calculations are communicated, and the data once communicated are reutilized for calculations as many times as possible. The RT parallel algorithm is a scalable method because required memory volume does not depend on the number of basis functions. This algorithm automatically includes a partial summing technique that is indispensable for maintaining computing accuracy, and can also include some conventional methods to reduce calculation times. In our analysis, the RT parallel algorithm had better performance than other methods for massively parallel processors. The RT parallel algorithm is most suitable for massively parallel and distributed Fock matrix calculations for large‐scale biological molecules with more than thousands of basis functions. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1337–1346, 2002
Bibliografie:ArticleID:JCC10133
Grant-in-Aid for the Scientific Research from the Ministry of Education, Science, and Culture
Science and Technology Agency
istex:82F8C3B9FB1C130D027E5567BD80ABE663B17CCA
ark:/67375/WNG-HH3N3RD2-7
New Energy and Industrial Technology Development Organization
ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 23
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.10133