RE: How to let NAMD terminate automatically at a given time

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Mar 03 2015 - 02:35:36 CST

Just want to add that using "exec date" to measure time caused a random segfault for CUDA enabled build while running REMD. I wasn't able to find out why, CPU version was running fine with the same system. So it might be nice if the TCLs native "clock" command would be made available in NAMD.

Thanks

Norman Geist

> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of Jeff Comer
> Sent: Monday, March 02, 2015 8:58 PM
> To: NAMD list; hannes.loeffler_at_stfc.ac.uk
> Subject: Re: namd-l: How to let NAMD terminate automatically at a given
> time
>
> NAMD has a Tcl interface, so you can find a way to do many things.
> Let's say I want my job to finish after 50 minutes and I don't want to
> write restart files for some reason:
>
> set timeLimit 3000
> set steps 5000
> set t0 [exec date +%s]
> while {1} {
> run $steps
> if {[exec date +%s]-$t0 > $timeLimit} {
> break
> }
> }
>
> NAMD will run until 50 minutes have passed and then quit, writing the
> final output. If you want it to finish just before a certain amount of
> time has passed, you could even have the script keep track of the
> maximum time required to run 5000 steps and quit when [exec date +%s]
> - $t0 + $max_time_for_5000_steps > $timeLimit.
>
> Jeff
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
>
>
> On Mon, Mar 2, 2015 at 1:19 PM, <hannes.loeffler_at_stfc.ac.uk> wrote:
> > I believe what the OP is really asking for is a graceful termination
> after a specified time a la Gromacs. Gromacs will terminate at, say,
> 99% of the allocated runtime and write out a checkpoint file which can
> then be used for a smooth restart. This is basically a convenience
> function to max out the runtime limit. As far as I am aware of there
> is no equivalence in NAMD and the user would have to find sensible
> frequency for writing out the restart information for themselves.
> >
> > ________________________________________
> > From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf
> of Jérôme Hénin [jerome.henin_at_ibpc.fr]
> > Sent: 02 March 2015 17:12
> > To: Namd Mailing List; Dong Luo
> > Cc: 吕晴
> > Subject: Re: namd-l: How to let NAMD terminate automatically at a
> given time
> >
> > If you use Unix, the "at" command will let you kill the namd job when
> its time is up. Just write restart files somewhat frequently.
> >
> > Jerome
> >
> > On 2 March 2015 at 16:27, Dong Luo
> <us917_at_remove_yahoo.com<mailto:us917_at_remove_yahoo.com>> wrote:
> > Hi Qing,
> > If you are running NAMD locally, there is no meaning to restrict the
> running time since you must own the computer resource. If it's run on
> cluster, there should be some kind of queue system for you to submit
> your job. That system will allow you to specify the max time each job
> that is allowed to run
> >
> >

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