hello<br><br>Just to share information. My parallel MD run also crash (very rarely) but I can always bypass the crash point using cpt files.<br><br>dawei <br><br><div class="gmail_quote">On Fri, Aug 12, 2011 at 10:02 AM, Sebastian Breuers <span dir="ltr"><<a href="mailto:breuerss@uni-koeln.de">breuerss@uni-koeln.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hey,<br>
<br>
thank you both for the response. I at least could restart the system. And it is running beyond the crashing point. Keep the fingers crossed. :)<br>
<br>
Kind regards<br>
<br>
<br>
Sebastian<br>
<br>
Am 12.08.2011 15:41, schrieb lina:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers<br>
<<a href="mailto:breuerss@uni-koeln.de" target="_blank">breuerss@uni-koeln.de</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear all,<br>
<br>
searching for the mentioned error message I found a bug report for mdrun. It<br>
seemed to be fixed, but in my setup it appears again and I am not sure if I<br>
could do something about it.<br>
<br>
I did not attach the tpr file since it is bounced by the mailing list and<br>
I'd like to get at least a hint without waitng for approval of the rejected<br>
mail. :)<br>
The simulation crashes with 64 CPUs after step 11237000 with the following<br>
entry in the log file:<br>
<br>
------------------------------<u></u>-------------------------<br>
Program mdrun, VERSION 4.5.4<br>
Source code file:<br>
/home/breuerss/local/src/<u></u>gromacs-4.5.4/src/mdlib/<u></u>domdec_top.c, line: 352<br>
<br>
Software inconsistency error:<br>
One or more interactions were multiple assigned in the domain decompostion<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a><br>
------------------------------<u></u>-------------------------<br>
<br>
That means that the simulation already ran for some time. I could also<br>
finish some runs successfully with the very same topology but different<br>
simulation parameters.<br>
<br>
For any help or hints how I could fix it I would be grateful.<br>
</blockquote>
<br>
Have you tried to re-submit it, use the -cpi state.cpt -append<br>
<br>
and see whether it can continue or not?<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Best regards<br>
<br>
<br>
Sebastian<br>
<br>
--<br>
______________________________<u></u>______________________________<u></u>_________________<br>
<br>
Sebastian Breuers Tel: <a href="tel:%2B49-221-470-4108" value="+492214704108" target="_blank">+49-221-470-4108</a><br>
EMail: <a href="mailto:breuerss@uni-koeln.de" target="_blank">breuerss@uni-koeln.de</a><br>
<br>
Universität zu Köln University of Cologne<br>
Department für Chemie Department of Chemistry<br>
Organische Chemie Organic Chemistry<br>
<br>
Greinstraße 4 Greinstraße 4<br>
Raum 325 Room 325<br>
D-50939 Köln D-50939 Cologne, Federal Rep. of Germany<br>
______________________________<u></u>______________________________<u></u>_________________<br>
<br>
--<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<br>
<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<br>
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>
<br>
</blockquote>
<br>
<br>
<br>
</blockquote>
<br>
-- <br>
______________________________<u></u>______________________________<u></u>_________________<br>
<br>
Sebastian Breuers Tel: <a href="tel:%2B49-221-470-4108" value="+492214704108" target="_blank">+49-221-470-4108</a><br>
EMail: <a href="mailto:breuerss@uni-koeln.de" target="_blank">breuerss@uni-koeln.de</a><br>
<br>
Universität zu Köln University of Cologne<br>
Department für Chemie Department of Chemistry<br>
Organische Chemie Organic Chemistry<br>
<br>
Greinstraße 4 Greinstraße 4<br>
Raum 325 Room 325<br>
D-50939 Köln D-50939 Cologne, Federal Rep. of Germany<br>
______________________________<u></u>______________________________<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>