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:
bakup()
{
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...
Thanks,
Gianluca
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