<div dir="ltr">Hmmm...<div dir="ltr"><p>I don't have any .pdb file, what can I look for then?<br></p><p>Best regards, </p><p> Tiago Marques</p><div><div class="Wj3C7c"><br><div class="gmail_quote">
On Tue, Sep 23, 2008 at 5:48 PM, Jochen Hub <span dir="ltr"><<a href="mailto:jhub@gwdg.de" target="_blank">jhub@gwdg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>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>
</div>Hi,<br>
<br>
you can count the nr of atoms in the structure:<br>
<br>
grep -c ATOM protein.pdb<br>
<font color="#888888"><br>
Jochen<br>
</font><div><div><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>
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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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</div></div></blockquote></div><br></div></div></div>
<br></div>