Thank you Mark. That's very helpful Vangelis
On Thu, May 11, 2017 at 10:00 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Thu, May 11, 2017 at 8:54 AM Daskalakis Vangelis <vdas.pi...@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/> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * 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-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * 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-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * 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-requ...@gromacs.org.