[gmx-users] Restarting a simulation: failed to lock the log file

[Kutzner, Carsten]

> On 7. Jan 2019, at 11:55, morpheus <morpheus.sommer2008 at gmail.com> wrote:
> 
> Hi,
> 
> I am running simulations on a cluster that terminates jobs after a hard
> wall clock time limit. Normally this is not a problem as I just restart the
> simulations using -cpi state.cpt but for the last batch of simulations I
> got (for most but not all of them) the error:
> 
> "Failed to lock: 1uao.md.log. Already running simulation?"
> 
> There is definitely nothing running. I have tried to move the log file to
> another directory and then moved it back (to get rid of any write locks)
> but the error stays the same. If I delete the logfile it also crashes
> because it cant find the file and if I replace the log file with an empty
> new file then I get "Can't read 1048576 bytes of '1uao.md.log' to compute
> checksum. The file has been replaced or its contents have been modified.
> Cannot do appending because of this condition.".
> Using "-noappend" and then concatenating is also not a great solution as
> this becomes quite cumbersome with many simulations.
> 
> Any ideas?
You can move the simulation output files to some temporary location and
then _copy_ them back into the original directory.

Carsten

> 
> Thanks!
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa