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.<br><br><div class="gmail_quote">
On Mon, Sep 14, 2009 at 11:09 AM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
If mdrun hangs -maxh won't help.<br>You can kill mdrun using the kill command.<br>But since mdrun catches signals, you might need kill -9 (the 'KILL' signal).<br><br>Berk<br><br>> Date: Mon, 14 Sep 2009 10:56:43 -0400<br>
> From: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>> To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>> Subject: Re: [gmx-users] Limit mdrun runtime<div>
<div></div><div class="h5"><br>> <br>> <br>> <br>> Jack Shultz wrote:<br>> > Hello,<br>> > <br>> > I have developed a workflow for prepping structures. One problem I have <br>> > is sometimes it gets hung up on mdrun. Are there any mdrun parameters we <br>
> > can use to kill this process if it runs too long? The parameters we are <br>> > using should not run over 5 minutes. I have not figured out how to do <br>> > this with my script, but I guess there may be a way using SIGALRM.<br>
> > <br>> <br>> mdrun -maxh<br>> <br>> -Justin<br>> <br>> > -- <br>> > Jack<br>> > <br>> > <a href="http://drugdiscoveryathome.com" target="_blank">http://drugdiscoveryathome.com</a><br>
> > <a href="http://hydrogenathome.org" target="_blank">http://hydrogenathome.org</a><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>
> > _______________________________________________<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
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Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Jack<br><br><a href="http://drugdiscoveryathome.com">http://drugdiscoveryathome.com</a><br>
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