<div dir="ltr">Sorry for the incomplete mail...i sent it by mistake<br><br>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.<br>FYI size of my system is around 45000 atoms.<br>
<br>Thanks in advance,<br>Vivek<br><br><div class="gmail_quote">2008/9/25 vivek sharma <span dir="ltr"><<a href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div dir="ltr">Hi friends,<br>I am also facing the similar problem when tried to scale gromacs for more number of processors ,<br><font size="2">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.<br>i HAVE TRIED OTHER OPTION LIKE CONSTRAINT_ALGO, COULOMBTYPE AND SHUFFLE OPTION<br></font><br><div class="gmail_quote">2008/9/25 Tiago Marques <span dir="ltr"><<a href="mailto:a28427@ua.pt" target="_blank">a28427@ua.pt</a>></span><div>
<div></div><div class="Wj3C7c"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr">We currently have no funds available to migrate to infiniband but we will in the future.<div class="gmail_quote">
<div dir="ltr"><p>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.<br>
</p><p>Best regards, </p><p> Tiago Marques</p><div><div></div><div><div><div></div><div><p></p><br><div class="gmail_quote">On Tue, Sep 23, 2008 at 6:30 PM, Diego Enry <span dir="ltr"><<a href="mailto:diego.enry@gmail.com" target="_blank">diego.enry@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Tiago you can try merging two network interfaces with "channel<br>
bonding" it's native on all new (2.6.x) linux kernels. You only need<br>
two network adapters (most dual socket boards come with then), two<br>
network switches ( or two VPN on the same switch).<br>
<br>
To tell you the truth, you will not much improvement even with the<br>
latest gromacs version (4beta). However other software that may be<br>
used by your group like NAMD, GAMESS, will benefit a lot from this<br>
approach. (it almost doubles network bandwidth)<br>
<br>
The best solution for gromacs is to migrate to infiniband. Go for it,<br>
it is not super expensive anymore.<br>
<div><div><br>
<br>
On Tue, Sep 23, 2008 at 1:48 PM, Jochen Hub <<a href="mailto:jhub@gwdg.de" target="_blank">jhub@gwdg.de</a>> wrote:<br>
> Tiago Marques wrote:<br>
>> I don't know how large the system is. I'm the cluster's system administrator<br>
>> and don't understand much of what's going on. The test was given to me by a<br>
>> person who works with it. I can ask him or look at it, if you can point me<br>
>> how to do it.<br>
><br>
> Hi,<br>
><br>
> you can count the nr of atoms in the structure:<br>
><br>
> grep -c ATOM protein.pdb<br>
><br>
> Jochen<br>
><br>
>><br>
>> Thanks, I will look at some of his posts.<br>
>><br>
>> Best regards,<br>
>><br>
>> Tiago Marques<br>
>><br>
>><br>
>> On Tue, Sep 23, 2008 at 4:03 PM, Jochen Hub <<a href="mailto:jhub@gwdg.de" target="_blank">jhub@gwdg.de</a>> wrote:<br>
>> Tiago Marques wrote:<br>
>>> Hi!<br>
>>><br>
>>> I've been using Gromacs on dual-socket quad-core Xeons with 8GiB of RAM,<br>
>>> connected with Gigabit Ethernet and I always seem to have problems scaling<br>
>>> to more than a node.<br>
>>><br>
>>> When I run a test on 16 cores, it does run but the result is often slower<br>
>>> than when running on only 8 cores on the same machine. The best result<br>
>> I've<br>
>>> managed is not being slower than 8 cores on 16.<br>
>>><br>
>>> What am I missing here, or are the tests inappropriate to run over more<br>
>> than<br>
>>> one machine?<br>
>><br>
>> How large is your system? Which gromacs version are you using?<br>
>><br>
>> And have a look at the messages by Carsten Kutzner in this list, he<br>
>> wrote a lot on gromacs scaling.<br>
>><br>
>> Jochen<br>
>><br>
>>> Best regards,<br>
>>><br>
>>> Tiago Marques<br>
>>><br>
>>><br>
>>><br>
>>> ------------------------------------------------------------------------<br>
>>><br>
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>><br>
>> --<br>
>> ************************************************<br>
>> Dr. Jochen Hub<br>
>> Max Planck Institute for Biophysical Chemistry<br>
>> Computational biomolecular dynamics group<br>
>> Am Fassberg 11<br>
>> D-37077 Goettingen, Germany<br>
>> Email: jhub[at]<a href="http://gwdg.de" target="_blank">gwdg.de</a><br>
>> Tel.: +49 (0)551 201-2312<br>
>> ************************************************<br>
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>><br>
>> ------------------------------------------------------------------------<br>
>><br>
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><br>
><br>
> --<br>
> ************************************************<br>
> Dr. Jochen Hub<br>
> Max Planck Institute for Biophysical Chemistry<br>
> Computational biomolecular dynamics group<br>
> Am Fassberg 11<br>
> D-37077 Goettingen, Germany<br>
> Email: jhub[at]<a href="http://gwdg.de" target="_blank">gwdg.de</a><br>
> Tel.: +49 (0)551 201-2312<br>
> ************************************************<br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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><br>
<br>
<br>
<br>
</div></div><font color="#888888">--<br>
Diego Enry B. Gomes<br>
Laboratório de Modelagem e Dinamica Molecular<br>
Universidade Federal do Rio de Janeiro - Brasil.<br>
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