[gmx-users] System blowing up at restart
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 (-:
Data prefix: /opt/software/applications/gromacs/5.1/bullxmpi
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
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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