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

[morpheus]

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?

Thanks!