[gmx-users] mdrun error

Mark Abraham mark.j.abraham at gmail.com
Sat May 17 13:53:46 CEST 2014


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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