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

[Diego Enry]

Tiago you can try merging two network interfaces with "channel
bonding" it's native on all new (2.6.x) linux kernels. You only need
two network adapters (most dual socket boards come with then), two
network switches ( or two VPN on the same switch).

To tell you the truth, you will not much improvement even with the
latest gromacs version (4beta). However other software that may be
used by your group like NAMD, GAMESS, will benefit a lot from this
approach. (it almost doubles network bandwidth)

The best solution for gromacs is to migrate to infiniband. Go for it,
it is not super expensive anymore.


On Tue, Sep 23, 2008 at 1:48 PM, Jochen Hub <jhub at gwdg.de> wrote:
> 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
> ************************************************
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.