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

[Tiago Marques]

Hi.

I've checked with the person who did the test and the system is 36000 atoms
large, it seems small, doesn't it? Maybe that's the problem, coupled with
the high latency of GbE connection.

What I find strange though, is that for many computers in the Top 500, this
is sufficient.

Best regards,

                          Tiago Marques


On Tue, Sep 23, 2008 at 5:04 PM, Tiago Marques <a28427 at ua.pt> 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.
>
> 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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