[gmx-users] interrupting mdrun

[David]

On Tue, 2004-03-23 at 20:10, Martina Bertsch, PhD wrote:
> I am running gmx 3.1.4. Can I stil kill mdrun with -USR1?
> 
yes but your continuation run will not be identical to the one that will
be killed. This has been fixed in 3.2.1. The differences arev ery small
though, and (in my opinion) only relevant in special cases where you run
without Temp and Pres coupling.

> Martina
> 
> David van der Spoel wrote:
> > On Mon, 2004-03-22 at 23:38, Martina Bertsch, PhD wrote:
> > 
> > > Dear gmx developers and users,
> > > 
> > > Our administrator is planning to bring down our Linux cluster for 
> > > upgrades later this week. I have an mdrun job that is running on the 
> > > cluster for about a month and a half, and will not be complete for at 
> > > least another month. Is there a special command to terminate an mdrun 
> > > job nicely? Is there a recommended kill command? I know how to restart 
> > > jobs that crashed, but I do not want to destabilize a perfectly running 
> > > job by intentionally crashing it.
> > > 
> > > 
> > If this is gmx 3.2 or higher you can continue with binary precision
> > using tpbconv. You can kill the mdrun with -USR1 signal and it will
> > gracefully stop, even in parallel.
> > 
> > 
> > >  I was also wondering if anybody could share any experience using 
> > > GROMACS on a cluster with the Condor queuing system?
> > > 
> > > 
> > 
> > 
> > 
> > > Best regards,
> > > Martina Bertsch, Ph.D.
> > > 
> > > _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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