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
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.