[gmx-users] cluster types supported

Mikko Huhtala mhuhtala at abo.fi
Tue Aug 19 09:40:01 CEST 2003

 > From: "Mike Grommet" 
 > From this group...  I set up openmosix (using clusterknoppix at the time)
 > and couldn't seem to get the processes to migrate around when running them.
 > I asked about my problem and was led to believe that openMosix wouldn't do
 > mpi and that I was barking up the wrong tree... Did I get the wrong
 > impression?
 > I don't discount the high possibility of user error.  I'm open to
 > enlightenment :)

OpenMosix provides process migration and dynamic load balancing across
clustered computers, but there is no added parallelization or
interprocess communication APIs in openMosix. oM looks like a regular
Linux system to the program; the process migration mechanism tries to
be as transparent as possible. Both MPI and PVM *can* be run on top of
openMosix and they run quite well in practice. MPI applications such
as Gromacs can benefit from oM in a case where another user starts
something on the nodes that are running Gromacs. oM can automatically
migrate these processes out of the way at run-time if there is free
capacity somewhere else in the cluster. MPI processes can also
migrated, but in practice I suspect many people run them locked to
their original nodes and let other things migrate freely.

The advantage of oM is that it looks to the casual user almost like a
single-image system (minus shared memory), so they do not need to
learn to use queuing etc. We have been running both MPI (Gromacs) and
PVM applications on top of oM practically without problems. oM's
stability is quite good; I last rebooted the cluster about a month ago
to upgrade the kernel and the uptime was over four months at that


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