[gmx-users] surprising: what's the reason?

[Chetan Mahajan]

Hi Tsjerk,

Thanks. It is on the same machine Stampede, same number of nodes and
processors. It does go through minimization part (5000 steps) well and
gives this error near the start of equilibration run, which comes after
minimization.

Thank you.

regards
Chetan


On Wed, Mar 12, 2014 at 12:50 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> Hi Chetan,
>
> Was it on the same machine/node(s)? Same number of processors? How many
> steps until the error? Any difference may cause a different outcome.
>
> Cheers,
>
> Tsjerk
> On Mar 12, 2014 5:42 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
>
> > Hi
> >
> > I am testing one MD run using gromacs. 2 days back it ran fine. Today
> when
> > I ran the "exactly same" code again, it gave following error:
> >
> >
> > Increasing the number of cell to communicate in dimension X to 3 for the
> > first time
> >
> > -------------------------------------------------------
> > Program mdrun_mpi, VERSION 4.6.3
> > Source code file:
> > /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.3/src/mdlib/ns.c,
> line:
> > 2730
> >
> > Fatal error:
> > One of the box vectors has become shorter than twice the cut-off length
> or
> > box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> >
> > I am confused as to why same run should give different answers on
> different
> > occasions. Is it pointing to something wrong with the gromacs executable
> I
> > have or something else?
> >
> > Thank you.
> >
> > regards
> > Chetan
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