[gmx-users] MPI segmentation Fault

[Xu Dong Huang]

Dear Justin,

I will try your suggestion to rerun it on Berendsen coupling and see if there is any further problems. The system indeed contain the star shaped structure I showed you earlier (running multiple versions, containing from 1, 5, 10, 15 and 20 stars in a solvent box), the solvent is just martini defined water system. The first 50 beads of all 4 arms has hydrophobic interaction with the Water solvent. and the last 5 remaining beads on all 4 arms are set to have extreme similar hydrophilic interaction with martini water bead. 


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu 

On Jan 2, 2013, at 3:43 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:

> @Justin,
> 
> forgot to mention, yes the NVT was ran using MPI as well. (You're right, the MPI is not the issue, because I took the file off my cluster and attempted to run NPT on my personal computer, it reported same segmentation error, fault 11)
> 
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering 
> xudongh at eden.rutgers.edu 
> 
> On Jan 2, 2013, at 3:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
>> 
>> 
>> On 1/2/13 3:20 PM, Xu Dong Huang wrote:
>>> Dear gromac users,
>>> 
>>> after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial
>>> Xu Dong Huangnvt nstep=10000, should I increase it to resolve the problem? if that resolves the problem at all that is)
>>> 
>> 
>> There is no "outside" of a periodic cell, so this is a non-problem.  Was the NVT run done in parallel?  If it was, it eliminates a faulty MPI installation.  If not, then that's an easily testable variable to determine the problem with NPT.  You haven't posted any .mdp files, which is another variable in determining the viability of any simulation.
>> 
>> -Justin
>> 
>>> Thanks for any input,
>>> 
>>> Chemical & Biochemical Engineering
>>> Rutgers School of Engineering
>>> xudongh at eden.rutgers.edu
>>> 
>>> On Jan 2, 2013, at 3:08 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
>>> 
>>>> Dear gromac users,
>>>> 
>>>> after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error:
>>>> 
>>>> Getting Loaded...
>>>> Reading file npt.tpr, VERSION 4.5.3 (single precision)
>>>> Loaded with Money
>>>> 
>>>> 
>>>> WARNING: This run will generate roughly 3890 Mb of data
>>>> 
>>>> starting mdrun 'star'
>>>> 1000000 steps,  20000.0 ps.
>>>> 
>>>> step 0[Ultranode02:26884] *** Process received signal ***
>>>> [Ultranode02:26884] Signal: Segmentation fault (11)
>>>> [Ultranode02:26884] Signal code: Address not mapped (1)
>>>> [Ultranode02:26884] Failing at address: 0x1f5acf020
>>>> [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0]
>>>> [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509]
>>>> [Ultranode02:26884] *** End of error message ***
>>>> /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault      mdrun_mpi -v -deffnm npt
>>>> 
>>>> 
>>>> -----Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors)
>>>> 
>>>> Xu Dong Huang
>>>> Chemical & Biochemical Engineering
>>>> Rutgers School of Engineering
>>>> xudongh at eden.rutgers.edu
>>>> 
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>>> 
>> 
>> -- 
>> ========================================
>> 
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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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