[gmx-users] Limit mdrun runtime

[Jack Shultz]

So if I do this within a perl script, I will need to capture the pid and
kill that process if it runs over 5 minutes? I'll try the -maxh first.
Otherwise I'll spend some time trying to debug it.

On Mon, Sep 14, 2009 at 11:09 AM, Berk Hess <gmx3 at hotmail.com> wrote:

>  If mdrun hangs -maxh won't help.
> You can kill mdrun using the kill command.
> But since mdrun catches signals, you might need kill -9 (the 'KILL'
> signal).
>
> Berk
>
> > Date: Mon, 14 Sep 2009 10:56:43 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Limit mdrun runtime
>
> >
> >
> >
> > Jack Shultz wrote:
> > > Hello,
> > >
> > > I have developed a workflow for prepping structures. One problem I have
>
> > > is sometimes it gets hung up on mdrun. Are there any mdrun parameters
> we
> > > can use to kill this process if it runs too long? The parameters we are
>
> > > using should not run over 5 minutes. I have not figured out how to do
> > > this with my script, but I guess there may be a way using SIGALRM.
> > >
> >
> > mdrun -maxh
> >
> > -Justin
> >
> > > --
> > > Jack
> > >
> > > http://drugdiscoveryathome.com
> > > http://hydrogenathome.org
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> ------------------------------
> Express yourself instantly with MSN Messenger! MSN Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090914/70bb638e/attachment.html>