[gmx-users] OpenMosix and Gromacs
aeszter at gwdg.de
Mon Jul 2 11:15:53 CEST 2007
On Fri, Jun 29, 2007 at 03:49:01PM -0600, Nicolas Sapay wrote:
> I wonder if someone has some experience with Gromacs and OpenMosix. Has
> someone tried recently to run Gromacs in parallel with an OpenMosix
> cluster? I have read some messages about that on the mailing-list but
I have not tried that; but I do have some experience with OpenMosix
development, and I would not expect that combination to work well.
oM copes very well with dynamic loads since it distributed
processes on the fly, but Gromacs is more likely to generate a static
load that does not change at all during the simulation run.
However, some spurious migrations will likely take place even during a
static load scenario, taking away quite some time (on the order of seconds).
Moreover, oM does not in itself provide any inter-process communication,
so MPI is needed anyway. There might be a problem with shared memory
(which is not supported by oM).
Finally, most syscalls are very slow under oM since they are executed on
the home node. This pertains especially to file operations, which go
through the network unbuffered.
All in all, oM was written to solve a problem that usually does not
occur when running programs like Gromacs, so there seem to be many
potential problems but little benefit from combining those two.
Researcher & Sysadmin
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