[gmx-users] mdrun_mpi error Signal: Segmentation fault

[Justin A. Lemkul]

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

========================================