[gmx-users] mdrun error

[Lovika Moudgil]

Mark thanks for your reply and support . [?]

Regards
Lovika


On Sat, May 17, 2014 at 5:23 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> No, the .mdp file mostly describes your model physics (but there are some
> implementation details that affect parallelization in there).
>
> Your GROMACS CMake configuration, mdrun command line and the attributes of
> your hardware are the biggest factors that determine how mdrun will try to
> parallelise. There's a lot of diagnostic reporting in the log file, but you
> are initially looking for the number of cells in the domain decomposition
> (DD). And you need to know how big your simulation system is. For example,
> a 900-molecule water system won't parallelise over a whole 32-core compute
> server with a domain per core. Background info here
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>
> Mark
>
>
> On Sat, May 17, 2014 at 9:02 AM, Lovika Moudgil <lovikamoudgil at gmail.com
> >wrote:
>
> > Thanks for quick reply Mark...what information you are asking for?Should
> I
> > search for this my .mdp file??
> >
> > Thanks
> >  Lovika
> >
> >
> > On Sat, May 17, 2014 at 11:35 AM, Mark Abraham <mark.j.abraham at gmail.com
> > >wrote:
> >
> > > Your simulation seems too small to parallelize in the way you/mdrun
> > tried.
> > > But we need more information to be sure.
> > >
> > > Mark
> > > On May 17, 2014 7:33 AM, "Lovika Moudgil" <lovikamoudgil at gmail.com>
> > wrote:
> > >
> > > > Hi Everyone ....
> > > > I need some help. With my mdrun command I am getting this following
> > error
> > > >  .
> > > >
> > > > Program mdrun, VERSION 4.6.5
> > > > Source code file:
> > > > /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c,
> > line:
> > > > 722
> > > >
> > > > Fatal error:
> > > > DD cell 0 0 1 could only obtain 1 of the 2 atoms that are connected
> via
> > > > constraints from the neighboring cells. This probably means your
> > > constraint
> > > > lengths are too long compared to the domain decomposition cell size.
> > > > Decrease the number of domain decomposition grid cells or
> lincs-order.
> > > > For more information and tips for troubleshooting, please check the
> > > GROMACS
> > > > website at http://www.gromacs.org/Documentation/Errors
> > > > -------------------------------------------------------
> > > >
> > > > Please help me to understand this error.What this error is all about
> ?
> > > > Where should I search to resolve this error ?
> > > >
> > > > Thanks
> > > > Lovika
> > > > --
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