Re: feature request: external initiated clean exit

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 21 2015 - 17:03:32 CDT

On Fri, Aug 21, 2015 at 5:44 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> Dear Daniel,
> Have you looked into namd’s use of restart files? With appropriate
> configuration they regularly produce files that can be used for clean
> restarts.
> Why would you have an ‘exit’ file and not just send a termination signal
> to the namd process?
>

​hi peter,

FYI, restart files in plane-wave DFT calculations can be huge compared to
classical MD, and thus writing them frequently has much more impact on
performance. also, due to the high algorithmic load of such calculations,
you usually run with many more CPU cores. thus the loss of computer time
when a job crashes without a usable last restart can be significant. for
very large calculations across a some 1000s of CPU cores, it can quickly
take of the order of 30 minutes to write a restart. that leads to a
different "restart culture"... ;-)

axel.

> Best,
> Peter
>
> > On Aug 21, 2015, at 8:37 AM, Daniel Möller <
> daniel.moeller3_at_uni-greifswald.de> wrote:
> >
> > Hi,
> >
> > Is it possible to integrate a feature into NAMD to stop with an external
> signal, like with a new file in the working directory?
> > I know this from CPMD and think it’s quite useful to stop a simulation
> and don’t lose any progress:
> > You just put a file named “EXIT” in the current working directory and
> the next time the programme looks into this folder (for example to write in
> the dcd) it will write a restart and exit in a clean way (and will not
> remove this file). A script, who build the NAMD-scripts and start them,
> could see this file and stops too (that’s why don’t remove it with the
> restart writing).
> > If a simulation wants to start and see this file, it could remove this
> (cause if you start a simulation, you don’t want it to end at the same
> time).
> >
> > I’m just asking, because i’m not firm enough in programming to implant
> this on my own.
> >
> > Sincerely
> >
> > Daniel Möller
> >
> > --
> > ------------------------
> > Dipl. Biochem. Daniel Möller
> >
> > Biophysical Chemistry
> > Institut of Biochemistry
> > Unversity of Greifswald
> > Felix-Hausdorff-Strasse 4
> > 17489 Greifswald - Germany
> >
> > Tel +49 3834 86 4406
> >
> >
> http://www.mnf.uni-greifswald.de/institute/institut-fuer-biochemie/biophysikalische-chemie.html
>
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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