[gmx-users] mdrun segmentation fault

[Mark Abraham]

On 12/04/2012 3:30 PM, priya thiyagarajan wrote:
> hello sir,
>
> Thanks for your kind reply..
>
> i am performing final md run for 60molecules ..
>
> after i submitted my job for 5ns, when i analyse the result my run is 
> completed only for 314ps initially..

At this point, you should have looked at your .log file and your stdout 
and stderr files to see why the simulation stopped, rather than blindly 
continuing.

> then i extende my simulation.. but again it completed only for 500ps.. 
> initially i thought because of queue limit its getting stopped.. but 
> 3rd time i extended my simulation it came for 538ps..
>
> when i analysed my log file it just showing like this
>
>
> DD  step 268999 load imb.: force  1.5%
>
>            Step           Time         Lambda
>          269000      538.00000        0.00000
>
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     
> Coulomb-14
>     9.84673e+03    5.10424e+03    1.80376e+03    2.90591e+03   
> -2.97052e+03
>         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      
> Potential
>     9.69125e+04   -1.59583e+03   -7.80231e+05   -3.04364e+04   
> -6.98661e+05
>     Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure 
> (bar)
>     1.17775e+05   -5.80886e+05    2.97568e+02   -1.04033e+02    
> 2.31825e+01
>    Constr. rmsd
>     2.24598e-05
>
>
>
> when i checked my errorfile i got this is because of segmentation fault..
>
> my errorfile showed like this
>
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> /var/spool/PBS/mom_priv/jobs/244266.vega.SC <http://244266.vega.SC>: 
> line 11: 26308 Segmentation fault      mdrun -s md.tpr -o md3.trr -c 
> md3.pdb -e md3.edr -g md3.log -cpi state2.cpt -cpo state3.cpt -x 
> traj3.xtc -noappend

There should be more descriptive error output somewhere. In any case, 
you are probably 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and need to 
follow the diagnostic advice there.

Mark

<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
>
>
> i searched in archieves but i didnt get the point clearly...
>
> can anyone please help me by explaining that reason for my problem and 
> solve it.
>
> i am waiting for your reply..
>
> pls help me with your valuable answer..
>
> i am using gromacs 4.5.5 version.
>
> thanking you,
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120412/dbf1c611/attachment.html>