[gmx-users] soft "exit"
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
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users