[gmx-users] System blowing up at restart
mark.j.abraham at gmail.com
Wed Dec 2 11:55:36 CET 2015
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.
On Wed, Dec 2, 2015 at 9:22 PM Marlon Sidore <marlon.sidore at gmail.com>
> 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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