[gmx-users] Performance problems with more than one node

[Jochen Hub]

Tiago Marques wrote:
> I don't know how large the system is. I'm the cluster's system administrator
> and don't understand much of what's going on. The test was given to me by a
> person who works with it. I can ask him or look at it, if you can point me
> how to do it.

Hi,

you can count the nr of atoms in the structure:

grep -c ATOM protein.pdb

Jochen

> 
> Thanks, I will look at some of his posts.
> 
> Best regards,
> 
>                         Tiago Marques
> 
> 
> On Tue, Sep 23, 2008 at 4:03 PM, Jochen Hub <jhub at gwdg.de> wrote:
> Tiago Marques wrote:
>> Hi!
>>
>> I've been using Gromacs on dual-socket quad-core Xeons with 8GiB of RAM,
>> connected with Gigabit Ethernet and I always seem to have problems scaling
>> to more than a node.
>>
>> When I run a test on 16 cores, it does run but the result is often slower
>> than when running on only 8 cores on the same machine. The best result
> I've
>> managed is not being slower than 8 cores on 16.
>>
>> What am I missing here, or are the tests inappropriate to run over more
> than
>> one machine?
> 
> How large is your system? Which gromacs version are you using?
> 
> And have a look at the messages by Carsten Kutzner in this list, he
> wrote a lot on gromacs scaling.
> 
> Jochen
> 
>> Best regards,
>>
>> Tiago Marques
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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> 
> --
> ************************************************
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************