Practical aspects of computational chemistry calculations through PC networks: the RAMSES–Beowulf implementation

Abstract

We have built clusters of PC using up to 320 processors in parallel. The first 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 computers, the system is easily maintained, and can be modified by adding or removing machines. Two programs, which are dedicated to molecular modeling and were previously developed on single machines (OSIRIS and IMPALA), have been adapted. IMPALA models peptide and protein interaction with membranes, OSIRIS simulates an ab initio folding of globular proteins. After parallelization, each program consists of two parts: one is the human/RAMSES interface, and the second is the simulation per se. The parallel architecture is transparent for the users. Tests of the IMPALA and OSIRIS efficiencies are shown and discussed. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 172–177, 2001