Practical aspects of computational chemistry calculations through PC networks: The RAMSES-Beowulf implementation

Citation
D. Beuve-mery et al., Practical aspects of computational chemistry calculations through PC networks: The RAMSES-Beowulf implementation, J COMPUT CH, 22(2), 2001, pp. 172-177
Citations number
6
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Chemistry
Journal title
JOURNAL OF COMPUTATIONAL CHEMISTRY
ISSN journal
0192-8651 → ACNP
Volume
22
Issue
2
Year of publication
2001
Pages
172 - 177
Database
ISI
SICI code
0192-8651(20010130)22:2<172:PAOCCC>2.0.ZU;2-F
Abstract
We have built clusters of PC using up to 320 processors in parallel. The fi rst cluster was built in 1996 from 64 computers. The parallel architectures are named RAMSES. In this article, we share our experience and discuss our choices. The architecture is composed of Pentium processors connected by a 100 Mbits/s Ethernet network. Because RAMSES are built of independent comp uters, the system is easily maintained, and can be modified by adding or re moving machines. Two programs, which are dedicated to molecular modeling an d were previously developed on single machines (OSIRIS and IMPALA), have be en adapted. IMPALA models peptide and protein interaction with membranes, O SIRIS simulates an ab initio folding of globular proteins. After paralleliz ation, each program consists of two parts: one is the human/RAMSES interfac e, and the second is the simulation per se. The parallel architecture is tr ansparent for the users. Tests of the IMPALA and OSIRIS efficiencies are sh own and discussed. (C) 2000 John Wiley & Sons, Inc.