[gmx-users] The right way of killing Gromacs
lindahl at cbr.su.se
Fri Sep 15 12:05:59 CEST 2006
mdrun finishes on the next step when receiving TERM, and on the next
multiple of nstxout when receiving USR1.
On some systems, the USR1/SIGHUP is only sent to the parent MPI
program, not the actual mdrun process, and then there isn't much we
In your case, try altering the signals in src/kernel/md.c and see if
you get it working if you change both signals to cause an exit on the
On Sep 15, 2006, at 11:33 AM, kobi wrote:
> the runtime of our cluster is unfortunately limited. Before mdrun
> is terminated a USR1 signal is
> send, but this doesn't cause mdrun to writeout the current frame.
> Therefore most of the trajectory
> is lost. I'd like to write a skrip which converts the USR1 sinal to
> some other signal. The question
> is, which signal would cause mdrun to write out all data and
> terminate it afterwards?
> best regards
> Jan Neumann
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