[gmx-users] soft "exit"

Mark Abraham mark.j.abraham at gmail.com
Thu May 11 09:00:16 CEST 2017


On Thu, May 11, 2017 at 8:54 AM Daskalakis Vangelis <vdas.pilot at gmail.com>

> 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.


> Vangelis.
> <http://www.cut.ac.cy/>
> <http://www.cut.ac.cy/>
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