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 <g...@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: jalem...@vt.edu > > To: gmx-users@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@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-requ...@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@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-requ...@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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org
_______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php