<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Nov 8, 2013 at 12:58 PM, Carsten Kutzner <span dir="ltr"><<a 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 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></blockquote><div><br></div><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>
<div><br></div><div>Mark</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<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 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 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 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>
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>><br>
>><br>
>><br>
><br>
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</div></div></blockquote></div><br></div></div>