[gmx-users] domain decomposition error

[nikhil damle]

Hi,

It is a vacuum simulation. That's why a molecule can be considered in isolation and i do not need to use periodic box. Secondly, even when i try to run the process on 2 nodes it gives same error. So number of processors might not be the actual reason.

Regards,
Nikhil




________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sun, 11 October, 2009 4:20:58 PM
Subject: Re: [gmx-users] domain decomposition error



nikhil damle wrote:
> Hi,
> 
> I am trying to run a vacuum simulation of a system associated with ATP and peptide. Being vacuum MD i removed pressure coupling and included plain electrostatic cut-offs while calculating potential. Energy minimisation converged to machine precesion even though not upto the specified cut-off limits.
> 
> Now when i am running production MD on multiple processors it gives following error.
> 
> There were 96 inconsistent shifts. Check your topology
> There were 96 inconsistent shifts. Check your topology
> There were 4 inconsistent shifts. Check your topology
> There were 4 inconsistent shifts. Check your topology
> There were 6 inconsistent shifts. Check your topology
> There were 6 inconsistent shifts. Check your topology
> 

These are related to periodic boundary conditions.  Search the list archive.

> -------------------------------------------------------
> Program mdrun, VERSION 4.0.5
> Source code file: domdec.c, line: 5873
> 
> Fatal error:
> There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 1.025 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
> Look in the log file for details on the domain decomposition
> 
> Why in the very first place, it is considering box and cell size for a vacuum MD when no related parameters are input ? This error is not given 

If you are running MD, then you most certainly have a box.  How could you have periodicity if your unit cell was not defined?

The simple fact is that DD cannot split such a small system over 8 processors. Either try fewer processors, or switch to particle decomposition with mdrun -pd.

-Justin

> if i run on single processor. What could be the possible reason ? I have checked my topology and it is proper. How should i proceed. Fast reply will be appreciated.
> 
> Regards,
> Nikhil
> 
> ------------------------------------------------------------------------
> Keep up with people you care about with Yahoo! India Mail. Learn how <http://in.rd.yahoo.com/tagline_galaxy_1/*http://in.overview.mail.yahoo.com/connectmore>.
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



      Now, send attachments up to 25MB with Yahoo! India Mail. Learn how. http://in.overview.mail.yahoo.com/photos
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091011/e8410217/attachment.html>