[gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm

[Mark Abraham]

4.5 can only handle about 500-1000 atoms per processor. Details vary.

Mark
On Oct 17, 2013 5:39 AM, "Nilesh Dhumal" <ndhumal at andrew.cmu.edu> wrote:

> Thanks for you reply.
>
> I am doing simulation for ionic liquids BMIM + CL. Total number of atoms
> are 3328.
>
> Nilesh
>
> > Assuming you're using LINCS, from the manual:
> > "With domain decomposition, the cell size is limited by the distance
> > spanned by *lincs-order*+1 constraints."
> > Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance
> > for
> > 5 bonds.
> >
> > Which means that you're probably using too many nodes for the size of
> your
> > system.
> >
> > Hope that helps. If it doesn't you'll need to provide some information
> > about your system.
> >
> > -Trayder
> >
> >
> >
> > On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal
> > <ndhumal at andrew.cmu.edu>wrote:
> >
> >> Hello,
> >>
> >> I am getting the following error for simulation. I am using Gromacs
> >> VERSION 4.5.5 and running on 24 processors.
> >>
> >> Should I reduce the number of processor or the problem is in bonded
> >> parameters. If I use -nt 1 option. I could run the simulation.
> >>
> >> Fatal error:
> >> There is no domain decomposition for 16 nodes that is compatible with
> >> the
> >> given box and a minimum cell size of 0.826223 nm
> >> Change the number of nodes or mdrun option -rdd or -dds
> >> Look in the log file for details on the domain decomposition
> >>
> >>
> >> Nilesh
> >>
> >> --
> >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >>
> > --
> > 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
>
>
> --
> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>