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

[Tiago Marques]

Hmmm...

I don't have any .pdb file, what can I look for then?

Best regards,

                         Tiago Marques

On Tue, Sep 23, 2008 at 5:48 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
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> Please search the archive at http://www.gromacs.org/search before posting!
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