[gmx-developers] Lost particles while sorting

[Carsten Kutzner]

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.

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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