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

[Tiago Marques]

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.

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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