Hello, <br><br>System Admin said that the J<font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">ob fails on 32 and 128 because memory <br>is insufficient for each task,
so upon increasing the nodes, data gets <br>distributed across more number of
nodes and each node gets less <br>memory occupancy and he also mentioned that he was able to run <br>on 512 nodes but it was giving error for not having sufficient data for <br>512 nodes.</font><br><br>I have run the same job on 8 nodes in i7 machine. <br>
<br>Thank you<br>With Regards<br>Kavya<br><br><div class="gmail_quote">On Mon, Oct 31, 2011 at 5:47 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Users,<br>
<br>
I was trying to run a simulation (gromacs4.5.3)<br>
on a Bluegene/L machine. But I was unable to run.<br>
System admin say that I need to change the input<br>
file. I am not sure what needs to be changed in the<br>
input file which specifies no. of nodes usage.<br>
<br>
</blockquote>
<br></div>
Sounds like your system admin should be offering you some more help, since they know the specifics of the hardware, queuing software, etc.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am not familiar with the bluegene machines. Kindly<br>
suggest the possible solutions.<br>
<br>
</blockquote>
<br></div>
Without seeing your input file(s), there's nothing anyone can do. Be mindful that this list pertains to Gromacs-specific problems, which do not seem to be present here.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></blockquote></div><br>