[gmx-users] mdrun_mpi error Signal: Segmentation fault

[annalisa bordogna]

Hi,
I received a similar error during an equilibration by steepest descent in
which I had posed constraints on water, leaving the protein free to move.
I suggest to control your mdp file... maybe you did the same thing and the
system collapsed or exploded (you can see that reading the log file: if this
is the cause, you should see problems regarding water).

Cheers,
Annalisa

2009/4/13 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> nam kim wrote:
>
>> process crashes around 100 steps out of 1000 requested.
>>
>>
> Fine, but you still haven't answered my question.  Do you receive any other
> messages?
>
> Do other systems run on the specific hardware you're using?  You may just
> have some instability in this particular system that is causing a crash.
>  Examine the  trajectory, see what's going wrong, and post any other
> relevant error messages, if you receive any.  Often times there is some
> output before a seg fault.
>
> -Justin
>
>
>  On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu>
>> wrote:
>>
>>>
>>> nam kim wrote:
>>>
>>>> I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4).
>>>> I have installed gromacs 4.0.4 two month ago and been working fine.
>>>> Today, I just got Segment errors. Rebooting does not much help.
>>>>
>>>> Here is log:
>>>>
>>>> [rd:06790] *** Process received signal ***
>>>> [d:06790] Signal: Segmentation fault (11)
>>>> [rd:06790] Signal code:  (128)
>>>> [rd:06790] Failing at address: (nil)
>>>> [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430]
>>>> [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496]
>>>> [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e]
>>>> [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a]
>>>> [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552]
>>>> [rd:06790] [ 5]
>>>> /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0]
>>>> [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32]
>>>> [rd:06790] *** End of error message ***
>>>>
>>>>  Are there any other messages from mdrun?  Anything printed to the
>>> screen
>>> (LINCS warnings, etc)?
>>>
>>> -Justin
>>>
>>>  Thanks
>>>> _______________________________________________
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>>>>  --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> ICTAS Doctoral Scholar
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> _______________________________________________
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>>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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