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

Thu Sep 25 15:52:30 CEST 2008

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>

> 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
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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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>
>
>
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