[gmx-users] System blowing up at restart

Marlon Sidore marlon.sidore at gmail.com
Wed Dec 2 11:21:41 CET 2015

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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