[gmx-users] soft "exit"

[Daskalakis Vangelis]

Thank you Mark.
That's very helpful
Vangelis


On Thu, May 11, 2017 at 10:00 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Thu, May 11, 2017 at 8:54 AM Daskalakis Vangelis <vdas.pilot at gmail.com>
> wrote:
>
> > Dear all,
> > I am running Gromacs 5.1.4 on a cluster with SLURM workload manager. How
> > can I terminate the running gromacs jobs (i.e. send the TERM/ INT
> signals)
> > but also allow time for each job to "soft exit" on the next step ? By
> "soft
> > exit" I mean that the job should be like it is finished (all the usual
> > output will be written to file), but before its end simulation time
> defined
> > in the tpr. There is of course the "scancel" command within slurm, but
> this
> > does not guarantee that the job will have the adequate time to "soft
> exit".
> >
>
> scancel -s SIGINT
>
> directs slurm to give the processes in the batch job that signal. When
> GROMACS gets it, it writes a checkpoint and does an orderly exit at the
> next neighbour-search step.
>
> Using mdrun -maxh 24 is a useful way to have mdrun know in advance that it
> should stop before 24 hours, which might be when a job scheduler starts
> sending signals.
>
> Mark
>
> Thanks,
> > Vangelis.
> > <http://www.cut.ac.cy/>
> >
> > <http://www.cut.ac.cy/>
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