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<div class="moz-cite-prefix">On 11/08/2013 01:44 PM, Mark Abraham
wrote:<br>
</div>
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<div class="gmail_quote">On Fri, Nov 8, 2013 at 12:58 PM,
Carsten Kutzner <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:ckutzne@gwdg.de"
target="_blank">ckutzne@gwdg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Mark,
hi Berk,<br>
<div class="im"><br>
On Nov 7, 2013, at 6:48 PM, Berk Hess <<a
moz-do-not-send="true" href="mailto:hess@kth.se">hess@kth.se</a>>
wrote:<br>
<br>
> Hi Carsten,<br>
><br>
> After how many steps does this happen?<br>
</div>
this happens immedeately at startup.<br>
<div class="im"><br>
> Could you run with a debug build (or without NDEBUG
defined)?<br>
> I added a lot of checks, not done with NDEBUG, in
the fix for the issue you linked.<br>
</div>
Will do that now.<br>
<div class="im"><br>
> On 11/07/2013 06:27 PM, Mark Abraham wrote:<br>
>> 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?<br>
</div>
This is basically mainstream 4-6, since in my commit I
only changed the default behavior of<br>
appending to no.<br>
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<div>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.</div>
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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.<br>
<br>
I think it should be easy to track this down with all the debug
checks in the code.<br>
And if Carsten can send me his system and the conditions to
reproduce it, I can also help with debugging.<br>
<br>
Cheers,<br>
<br>
Berk<br>
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<div>Mark</div>
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<span class="HOEnZb"><font color="#888888"><br>
Carsten<br>
</font></span>
<div class="HOEnZb">
<div class="h5"><br>
>><br>
>> Mark<br>
>><br>
>><br>
>> On Thu, Nov 7, 2013 at 5:18 PM, Carsten
Kutzner <<a moz-do-not-send="true"
href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a>>
wrote:<br>
>> Hi,<br>
>><br>
>> we have a 120k atom system that crashes with<br>
>><br>
>>
------------------------------------------------------<br>
>> Program mdrun_mpi, VERSION
4.6.4-dev-20131015-6583c94<br>
>> Source code file:
/home/c/gromacs/src/mdlib/nbnxn_search.c, line: 685<br>
>><br>
>> Software inconsistency error:<br>
>> Lost particles while sorting<br>
>> For more information and tips for
troubleshooting, please check the GROMACS<br>
>> website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
>>
-------------------------------------------------------<br>
>><br>
>> if run with >= 2 MPI processes on a GPU
and small values for nstlist. On my workstation,<br>
>> nstlist = 34 and larger works, whereas
nstlist <= 33 lead to the above problem.<br>
>><br>
>> Another system (60k atoms) does not produce
this problem, so system size seems<br>
>> to matter as well.<br>
>><br>
>> Looks like an old ghost:<br>
>><br>
>> <a moz-do-not-send="true"
href="http://redmine.gromacs.org/issues/1153"
target="_blank">http://redmine.gromacs.org/issues/1153</a><br>
>><br>
>><br>
>> Should I file a redmine issue?<br>
>><br>
>> Carsten<br>
>><br>
>><br>
>> --<br>
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>><br>
>><br>
><br>
> --<br>
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