AW: Multi core problem

From: Norman Geist (
Date: Tue Jul 10 2012 - 00:38:51 CDT

Hi flavio,

if you are sure this is a multicore version without network support, there
must be something else what the nodes share. Maybe check if your output
frequencies like restart and dcd are too slow so that you mess up your
shared filesystem. That would also worsen with every node that start

If you have a NAMD version with network support, check how the jobs are
distributed. Use the for instance the top command for that to see what
processes are running on the nodes.

If that also doesn't help, think about what else the nodes could share and
if they are real independent nodes and not kind of virtual machine etc. As
we don't know your setup, it's hard to make more precise advice.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von flavio seixas
> Gesendet: Sonntag, 8. Juli 2012 21:48
> An: undefined undefined
> Betreff: namd-l: Multi core problem
> Hi,
> I am running namd on SUSE LINUX Enterprise Server 11 SP1 (x86_64)
> kernel 64bits, at 12 cores parallel in a single node of a SGI
> Altix ICE 8400 LX machine.
> The programs works fine, but when I submit another namd job to a
> different node, the velocity of processing decrease by half. If I
> submit a third job also in a different node, the velocity decrease by
> 1/3 at all nodes.
> Theoretically, the jobs running in different nodes do not suppose to
> interfere in eat other.
> Does someone experience a similar problem to give me some clue about
> what happen?
> Regards,
> Flavio

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