[gmx-users] Re: I want to stop my run
mark.j.abraham at gmail.com
Wed Dec 12 17:04:34 CET 2012
Unix signals SIGTERM and SIGUSR1 can be sent to mdrun that will cause it to
stop next step or next neighbour search step. That ensures an orderly
termination, inasmuch as the file system buffering then has time to flush
before the power goes off :-) Various shell or queue system commands can
send these signals, but you should do your own homework there. These do not
help a restart, as they do not trigger checkpointing.
On Wed, Dec 12, 2012 at 2:38 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:
> > On Wed, Dec 12, 2012 at 10:26 AM, Ali Alizadeh <
> > ali.alizadehmojarad at gmail.com> wrote:
> >> Dear All users
> >> How can i stop my mdrun before it reaches to final step?
> >> My mdrun will finish tomorrow but my system is turned off today,
> >> How can i get completely output files( .gro , .xtc , .trr )?
> >> Can i analyze my simulation when my run is killed?
> >> --
> >> Sincerely
> >> Ali Alizadeh
> Dear Ali Alizadeh -
> Yes, you can analyze your system. Even you can do this, if your system
> is running.
> But if you just terminate the mdrun process immediately, you may get
> an incomplete last coordinates/energy frame.
> There are many scientific software, which have a parameter key, which
> is read at each time-step. If certain value is found for this key,
> than the run stops correctly at the very next iteration. I am not
> aware if gromacs has such a mechanism, as well as I do not think it
> would be widely used.
> Dr. Vitaly V. Chaban
> MEMPHYS - Center for Biomembrane Physics
> Department of Physics, Chemistry and Pharmacy
> University of Southern Denmark
> Campusvej 55, 5230 Odense M, Denmark
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