Re: Multi core problem

From: Axel Kohlmeyer (
Date: Tue Jul 10 2012 - 05:18:28 CDT

if this is on an SGI Altix with a single system image,
don't you have to use something like the dplace or
omplace command to have your job migrated/locked
to the suitable partition. have you talked to the sysadmins?


On Tue, Jul 10, 2012 at 7:38 AM, Norman Geist
<> wrote:
> 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
> working.
> 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

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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