[gmx-users] errors on restart

gianluca santarossa gianluca_santarossa at fastmail.fm
Thu May 18 16:18:27 CEST 2006

Mark Abraham wrote:
> You can
> a) prevent your simulations from crashing,
I can't. I run simulations on a cluster through a queue, and sometimes 
the jobs are longer than the max time of the queue.
> b) restart from the last frame common to both files, here 8, or
Ok, I want to do it automatically... Moreover, in this way it would be 
tricky to rebuild the trajectories and the energies.
> c) if they simulations are crashing in response to a signal, use a 
> less vigorous one and gromacs will catch it and exit gracefully, 
> writing output.
This is how my job works now. If you have better ideas, I would be happy 
to try them...
I submit to the queue a script running mdrun . The script just traps the 
signals SIGUSR2 (or, eventually, SIGINT) and copies the trajectories and 
the energies back to $SOMEWHERE.
The script looks like this:

cp ener.edr traj.trr $SOMEWHERE
other stuff
trap backup SIGUSR2 SIGINT
mdrun > mdrun.log

At the end, if I try to restart the simulation with tpbconv, I sometimes 
find that, as you said, ener.edr was interrupted while writing. How can 
I modify the script to let mdrun exit normally?
As you can see, I catch SIGUSR2, not SIGKILL...

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