[gmx-users] mdrun_mpi error Signal: Segmentation fault

nam kim namkkim at gmail.com
Fri Apr 17 21:53:32 CEST 2009


User reported it's problem with input file.

2009/4/15 annalisa bordogna <annalisa.bordogna at gmail.com>:
> 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
>>
>> ========================================
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>
>
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