Fwd: [gmx-users] Performance problems with more than one node
vivek sharma
viveksharma.iitb at gmail.com
Fri Sep 26 09:22:47 CEST 2008
Hi Carsten and Justin,
I am interrupting here as I tried with the option u suggested..
I tried cut-off instead of PME as coulombtype option it is running well for
24 processor, then I tried with 60 processor , following is the result I am
getting
Result1: When tried for 50 ps of run on 24 processors, with PME took 12:29
in comparison to 7:54 with cut-off
Result2: When tried for 500 ps of run on 60 processors, with PME it is
giving same segmentation fault again and with cut-off it is giving LINCS
warning and exiting with writing the intermediate step.pdb
Can you suggest some more option that I can try for scaling experiment...
Also I tried with shuffle and sort option it didn't worked for me as my
system is simply one protein molecule in a ater box (around 45000 no. of
atoms)
connected Gromacs version I am using is 3.3.3 and the hardware is like all
nodes contain quad-core 3.0 GHz Intel Xeon processors connected via
infiniband.
With Thanks,
Vivek
2008/9/26 Carsten Kutzner <ckutzne at gwdg.de>
> Hi Tiago,
>
> if you swith off PME and suddenly your system scales, then the
> problems are likely to result from bad MPI_Alltoall performance. Maybe
> this is worth a check. If this is the case, there's a lot more information
> about this in the paper "Speeding up parallel GROMACS on high-
> latency networks" from 2007 to which you will also find link on the
> gromacs webpage.
>
> What you can also do to track down the problem is to compile gromacs with
> MPE logging, for which you have to enable the #define USE_MPE macro at the
> begin of mpelogging.h (you will have to use gmx version 4, though). You
> will get a logfile which you can view with jumpshot then. The MPE tools
> come with the MPICH MPI distribution.
>
> Carsten
>
>
> Tiago Marques wrote:
>
>> 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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>> >>
>> >>
>>
>> ------------------------------------------------------------------------
>> >>
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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
>> > ************************************************
>> > _______________________________________________
>> > gmx-users mailing list gmx-users at gromacs.org
>> <mailto: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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>>
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>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics Department
> Am Fassberg 11
> 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> www.mpibpc.mpg.de/home/grubmueller/
> www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/
>
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