[gmx-users] Performance problems with more than one node
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 25 17:02:16 CEST 2008
vivek sharma wrote:
> Sorry for the incomplete mail...i sent it by mistake
>
> what i want to add is I am not able to run it with any of the
> option.....any help and suggestion will be highly appreciated.
> FYI size of my system is around 45000 atoms.
>
The performance will depend upon a lot of factors, the first of which is the
version of Gromacs you're using. The new release (4.0rc1) is substantially
faster than any previous release. Other factors are mostly related to hardware
and connectivity between nodes.
If you try to run on a huge number of processors, you wind up with a lot of
latency, which counteracts the perceived speed increase.
As a general rule (when using, e.g. GMX-3.3.x) a reasonable starting place for
determining the number of CPU's is (total atoms) / (# of atoms in largest
molecule) to get good balance across the nodes. The -shuffle and -sort options
of grompp often improve scaling for heterogeneous systems like membranes.
-Justin
> Thanks in advance,
> Vivek
>
> 2008/9/25 vivek sharma <viveksharma.iitb at gmail.com
> <mailto:viveksharma.iitb at gmail.com>>
>
> Hi friends,
> I am also facing the similar problem when tried to scale gromacs for
> more number of processors ,
> I have tried one job using gromacs on EKA, in an attempt to scale it
> for more number of processor I am able to get the reduction in
> simulation time upto 20 processors, it is taking more time for 40
> processor for same simulation, and when tried with 60 processor, it
> crashed with segmentation fault.
> i HAVE TRIED OTHER OPTION LIKE CONSTRAINT_ALGO, COULOMBTYPE AND
> SHUFFLE OPTION
>
> 2008/9/25 Tiago Marques <a28427 at ua.pt <mailto:a28427 at ua.pt>>
>
> 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 <mailto: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
> <mailto: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 <mailto: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 <http://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 <http://gwdg.de>
> > Tel.: +49 (0)551 201-2312
> > ************************************************
> > _______________________________________________
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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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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