[gmx-developers] Lost particles while sorting

[Berk Hess]

On 11/08/2013 01:44 PM, Mark Abraham wrote:
>
>
>
> On Fri, Nov 8, 2013 at 12:58 PM, Carsten Kutzner <ckutzne at gwdg.de 
> <mailto:ckutzne at gwdg.de>> wrote:
>
>     Hi Mark, hi Berk,
>
>     On Nov 7, 2013, at 6:48 PM, Berk Hess <hess at kth.se
>     <mailto: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.
This is 4.6.4-dev which seems to include my fix for the previous issue, 
so this issue is surely present in the current 4-6-release branch. It 
must be due to a somewhat exotic condition, since this code is widely 
used and we haven't had other reports.

I think it should be easy to track this down with all the debug checks 
in the code.
And if Carsten can send me his system and the conditions to reproduce 
it, I can also help with debugging.

Cheers,

Berk
>
> Mark
>
>
>     Carsten
>
>     >>
>     >> Mark
>     >>
>     >>
>     >> On Thu, Nov 7, 2013 at 5:18 PM, Carsten Kutzner
>     <ckutzne at gwdg.de <mailto: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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