[gmx-developers] Lost particles while sorting

[Carsten Kutzner]

Hi,

using a just checked-out 4.6 branch compiled with debug checks I get

-------------------------------------------------------
Program mdrun, VERSION 4.6.4-dev-20131107-ba8232e
Source code file: 
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/mdlib/nbnxn_search.c, line: 
609

Fatal error:
(int)((x[74522][x]=11.764535 - 10.229600)*58.394176) = 89, not in 0 - 16*4

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Carsten


On 11/08/2013 02:00 PM, Berk Hess wrote:
> 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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