[gmx-developers] Lost particles while sorting

[Mark Abraham]

On Fri, Nov 8, 2013 at 12:58 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:

> Hi Mark, hi Berk,
>
> On Nov 7, 2013, at 6:48 PM, Berk Hess <hess at kth.se> wrote:
>
> > Hi Carsten,
> >
> > After how many steps does this happen?
> this happens immedeately at startup.
>
> > Could you run with a debug build (or without NDEBUG defined)?
> > I added a lot of checks, not done with NDEBUG, in the fix for the issue
> you linked.
> Will do that now.
>
> > On 11/07/2013 06:27 PM, Mark Abraham wrote:
> >> Unclear. 6583c94 is one of your commits. Some very recent stuff has
> been playing with nstlist and rlist (safely, or so we thought.) Can you
> reproduce with mainstream release-4-6?
> This is basically mainstream 4-6, since in my commit I only changed the
> default behavior of
> appending to no.
>

Right. What's the mainstream parent commit? I was going to release 4.6.4
today - if you're based off the current tip then maybe we shouldn't. If
you're based off code a month back then we know the problem, if any, is of
longer standing.

Mark


> Carsten
>
> >>
> >> Mark
> >>
> >>
> >> On Thu, Nov 7, 2013 at 5:18 PM, Carsten Kutzner <ckutzne at gwdg.de>
> wrote:
> >> Hi,
> >>
> >> we have a 120k atom system that crashes with
> >>
> >> ------------------------------------------------------
> >> Program mdrun_mpi, VERSION 4.6.4-dev-20131015-6583c94
> >> Source code file: /home/c/gromacs/src/mdlib/nbnxn_search.c, line: 685
> >>
> >> Software inconsistency error:
> >> Lost particles while sorting
> >> For more information and tips for troubleshooting, please check the
> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >> -------------------------------------------------------
> >>
> >> if run with >= 2 MPI processes on a GPU and small values for nstlist.
> On my workstation,
> >> nstlist = 34 and larger works, whereas nstlist <= 33 lead to the above
> problem.
> >>
> >> Another system (60k atoms) does not produce this problem, so system
> size seems
> >> to matter as well.
> >>
> >> Looks like an old ghost:
> >>
> >> http://redmine.gromacs.org/issues/1153
> >>
> >>
> >> Should I file a redmine issue?
> >>
> >> Carsten
> >>
> >>
> >> --
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> >>
> >>
> >>
> >
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