<div dir="ltr">OK, thanks Berk. Szilard and I each have thought of some minor documentation things that would be nice to fix also.<div><br></div><div>I suggest we try to get all that in so we can shift focus away from release-4-6, with the 5.0 beta only weeks away now!!<div>
<br></div><div>Mark</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Nov 8, 2013 at 3:30 PM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
I think I found the source of the problem, now I have to come up
with a solution.<br>
It seems you have a harmonic potential between two atoms at a
distance of 2.9 nm. This is much longer than the pair-list range.
So one (non-local) atom ends up beyond the non-local search grid.
I thought I had accounted for such cases, but apparently not.<br>
We can probaly simply round down the index to the maximum, but
that means we can't check for other cases, such as without DD,
where atoms can't be beyond the grid.<br>
The fix will be very simple and quick, but I need to think a over
a bit deeper.<br>
<br>
Cheers,<br>
<br>
Berk<div><div class="h5"><br>
<br>
On 11/08/2013 02:58 PM, Carsten Kutzner wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div>Hi Berk,<br>
<br>
On 11/08/2013 02:48 PM, Berk Hess wrote:<br>
</div>
<blockquote type="cite">
<div>Hi,<br>
<br>
I assume this is with GPUs.<br>
If you run in a debugger, break on exit, can you tell me which
sort_atoms call this comes from?<br>
<br>
</div>
</blockquote>
It comes from sort_columns_supersub:<br>
<br>
<br>
Breakpoint 1, 0x00007ffff5d17920 in exit () from /lib64/libc.so.6<br>
(gdb) where<br>
#0 0x00007ffff5d17920 in exit () from /lib64/libc.so.6<br>
#1 0x0000000000a60558 in quit_gmx (msg=0x7fffee092290 "\n", '-'
<repeats 55 times>, "\nProgram mdrun, VERSION
4.6.4-dev-20131107-ba8232e\nSource code file:
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/mdlib/nbnxn_search.c,
l"...) at
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/gmxlib/gmx_fatal.c:284<br>
#2 0x0000000000a61609 in _gmx_error (key=0x185ecde "fatal",
msg=0x7fffee094af0 "(int)((x[74522][x]=11.764535 -
10.229600)*58.394176) = 89, not in 0 - 16*4\n", file=0x1836ad8
"/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/mdlib/nbnxn_search.c",
line=609) at
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/gmxlib/gmx_fatal.c:774<br>
#3 0x0000000000a61054 in gmx_fatal (f_errno=0, file=0x1836ad8
"/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/mdlib/nbnxn_search.c",
line=609, fmt=0x1836c80 "(int)((x[%d][%c]=%f - %f)*%f) = %d, not
in 0 - %d*%d\n") at
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/gmxlib/gmx_fatal.c:509<br>
#4 0x00000000004e91db in sort_atoms (dim=0, Backwards=0,
a=0x7ffff212e920, n=2, x=0x7ffff148a650, h0=10.2296,
invh=58.3941765, n_per_h=16, sort=0x7ffff10bb2b0) at
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/mdlib/nbnxn_search.c:609<br>
#5 0x00000000004ebcee in sort_columns_supersub
(nbs=0x7ffff057f2a0, dd_zone=1, grid=0x7ffff06d6f60, a0=61048,
a1=74523, atinfo=0x7ffff0c51840, x=0x7ffff148a650,
nbat=0x7ffff05d3bb0, cxy_start=10, cxy_end=15,
sort_work=0x7ffff10bb2b0) at
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/mdlib/nbnxn_search.c:1394<br>
#6 0x00000000004ecf09 in calc_cell_indices.omp_fn.1
(.omp_data_i=0x7ffff516f670) at
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/mdlib/nbnxn_search.c:1651<br>
#7 0x00007ffff62a50ba in ?? () from /usr/lib64/libgomp.so.1<br>
#8 0x00007ffff796de0e in start_thread () from
/lib64/libpthread.so.0<br>
#9 0x00007ffff5dc42cd in clone () from /lib64/libc.so.6<br>
<br>
<blockquote type="cite">
<div> On how many MPI ranks is this?<br>
If I can easily run this, could you mail me the tpr and the
run settings?<br>
</div>
</blockquote>
mdrun_threads -ntmpi 2 -s in.tpr -v -gpu_id 00<br>
<br>
Best,<br>
Carsten<br>
<br>
<blockquote type="cite">
<div> <br>
Cheers,<br>
<br>
Berk<br>
<br>
On 11/08/2013 02:30 PM, Carsten Kutzner wrote:<br>
</div>
<blockquote type="cite">
<div>Hi,<br>
<br>
using a just checked-out 4.6 branch compiled with debug
checks I get<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.6.4-dev-20131107-ba8232e<br>
Source code file:
/home/ckutzne/junoworkspace/git-gromacs-vanilla/src/mdlib/nbnxn_search.c,
line: 609<br>
<br>
Fatal error:<br>
(int)((x[74522][x]=11.764535 - 10.229600)*58.394176) = 89,
not in 0 - 16*4<br>
<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>
Carsten<br>
<br>
<br>
On 11/08/2013 02:00 PM, Berk Hess wrote:<br>
</div>
<blockquote type="cite">
<div>On 11/08/2013 01:44 PM, Mark
Abraham wrote:<br>
</div>
<blockquote type="cite">
<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><br>
On Nov 7, 2013, at 6:48 PM, Berk Hess <<a href="mailto:hess@kth.se" target="_blank">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><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><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>
</div>
</div>
</blockquote>
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>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<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><font color="#888888"><br>
Carsten<br>
</font></span>
<div>
<div><br>
>><br>
>> Mark<br>
>><br>
>><br>
>> On Thu, Nov 7, 2013 at 5:18 PM,
Carsten Kutzner <<a href="mailto:ckutzne@gwdg.de" target="_blank">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>
>> --<br>
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>><br>
><br>
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</blockquote>
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