[gmx-users] storage problem during a simulation

[Francesco]

the simulations are still running, they should end tomorrow afternoon.

Fra

On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote:
> What does gmxcheck have to say about your output files?
> On Jul 23, 2013 12:17 PM, "Francesco" <fracarb at myopera.com> wrote:
> 
> > Hi all,
> > This morning the gpu cluster that I'm using had some troubles with the
> > network connection between nodes that deny access to the storage.
> > Now, the simulations are still running and it seems that during the
> > "shut down" mdrun wrote a lot of checkpoints and restarted the
> > simulation once the communication was restored.
> >
> > Do you think that I will have distortions or errors in the final
> > results?
> >
> > this is a portion of the log file:
> >
> > ---------------- BEGIN LOG ----------------
> >
> > ...
> > DD  step 46809999  vol min/aver 0.851  load imb.: force 18.2%
> >
> >            Step           Time         Lambda
> >        46810000    93620.00000        0.00000
> >
> >    Energies (kJ/mol)
> >           Angle    Proper Dih.  Improper Dih.          LJ-14
> >           Coulomb-14
> >     3.29220e+04    3.94888e+04    2.06055e+03    1.69577e+04
> >     1.50705e+05
> >         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >         Potential
> >     3.28228e+05   -2.51293e+04   -3.04153e+06    8.44070e+03
> >     -2.48786e+06
> >     Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure
> >     (bar)
> >     4.98840e+05   -1.98902e+06    3.10237e+02   -2.13738e+02
> >     -4.80807e+01
> >    Constr. rmsd
> >     2.76295e-05
> >
> > Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013
> > Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013
> > Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013
> > Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013
> > Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013
> > ...
> > Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013
> >
> >
> > DD  step 46814999  vol min/aver 0.865  load imb.: force 26.2%
> >
> >            Step           Time         Lambda
> >        46815000    93630.00000        0.00000
> >
> > Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013
> >
> >
> >    Energies (kJ/mol)
> >           Angle    Proper Dih.  Improper Dih.          LJ-14
> >           Coulomb-14
> >     3.28615e+04    3.93530e+04    1.99727e+03    1.70754e+04
> >     1.51152e+05
> >         LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >         Potential
> >     3.30108e+05   -2.51173e+04   -3.04119e+06    8.48412e+03
> >     -2.48528e+06
> >     Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure
> >     (bar)
> >     4.97562e+05   -1.98772e+06    3.09443e+02   -2.13533e+02
> >     3.68992e+01
> >    Constr. rmsd
> >     2.70999e-05
> >
> > Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013
> >
> > ---------------- END LOG ----------------
> >
> > thank you for your help
> >
> > cheers,
> >
> > Fra
> > --
> > Francesco Carbone
> > PhD student
> > Institute of Structural and Molecular Biology
> > UCL, London
> > fra.carbone.12 at ucl.ac.uk
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
Francesco Carbone
PhD student
Institute of Structural and Molecular Biology
UCL, London
fra.carbone.12 at ucl.ac.uk