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

[Tiago Marques]

We currently have no funds available to migrate to infiniband but we will in
the future.

I thought on doing interface bonding but I really think that isn't really
the problem here, there must be something I'm missing, since most
applications scale well to 32 cores on GbE. I can't scale any application to
more than 8 though.

Best regards,

                           Tiago Marques


On Tue, Sep 23, 2008 at 6:30 PM, Diego Enry <diego.enry at gmail.com> wrote:

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