Abstract :
[en] 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.
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