[gmx-users] System blowing up at restart

[Mark Abraham]

Hi,

That's indeed curious. Please open an issue at http://redmine.gromacs.org and
attach your .tpr and .cpt files so we can see if we can reproduce it.

Mark

On Wed, Dec 2, 2015 at 9:22 PM Marlon Sidore <marlon.sidore at gmail.com>
wrote:

> It actually went on a few steps before blowing up, it didn't blow up
> directly at restart.
> Does that mean it simply blew up because of the system ? It always blows up
> a little time after restarting though, and that's strange given the time it
> ran the first time.
>
> gmx dump doesn't say anything special, should I include its output in a
> file here ?
>
> The restarted log file says:
> "Restarting from checkpoint, appending to previous log file.
>
> Log file opened on Tue Dec  1 14:26:27 2015
> Host: occigen1318  pid: 36303  rank ID: 0  number of ranks:  96
>                     :-) GROMACS - mdrun_mpi, VERSION 5.1 (-:
>
> Executable:   /opt/software/applications/gromacs/5.1/bullxmpi/bin/mdrun_mpi
> Data prefix:  /opt/software/applications/gromacs/5.1/bullxmpi
> Command line:
>   mdrun_mpi -deffnm vict -cpi vict.cpt -maxh 22 -append
> "
> ...
> "Started mdrun on rank 0 Tue Dec  1 14:26:27 2015
>            Step           Time         Lambda
>       155718960   3114379.20000        0.00000
>
>    Energies (kJ/mol)
>            Bond  Harmonic Pot.       G96Angle    Proper Dih.  Improper Dih.
>     2.66021e+04    2.78094e+03    1.40622e+04    7.50553e+02    1.72141e+02
>         LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
>    -8.26979e+05   -1.38652e+04   -7.96476e+05    1.43116e+05   -6.53360e+05
>     Temperature Pressure (bar)   Constr. rmsd
>     3.22749e+02   -1.62340e+01    0.00000e+00
>
> DD  step 155718979 load imb.: force 79.6%
>
> At step 155718980 the performance loss due to force load imbalance is 6.2 %
>
> NOTE: Turning on dynamic load balancing
>
> DD  step 155719999  vol min/aver 0.516  load imb.: force  3.2%
> "
> it then continued for a few steps before blowing up. It's basically the
> same as the beginning of the log file (for the first run).
> --
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