[gmx-users] storage problem during a simulation

[Mark Abraham]

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
> --
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