[gmx-users] no error on missing cpt file

[gromacs query]

Thanks Carsten and Mark


As of now I think Carsten's suggestion is good but this intelligent option
seems harmful which I can see in the link provided by Mark is under
consideration. Otherwise in code it will be good if somehow '-force' option
is implemented which bounds to use file names as such without any
compromise.

regards,
Jiom


On Wed, Apr 29, 2015 at 12:36 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Wed, Apr 29, 2015 at 1:20 PM Kutzner, Carsten <ckutzne at gwdg.de> wrote:
>
> > Hi JIom,
> >
> > > On 29 Apr 2015, at 11:50, gromacs query <gromacsquery at gmail.com>
> wrote:
> > >
> > > Dear All,
> > >
> > > mdrun is not giving any error about missing cpt file. It runs using tpr
> > > from initial time zero. Sometimes my job get killed and I need to use
> cpt
> > > file in some script but if cpt is not found my job starts running from
> > zero
> > > time in tpr file which is harmful as it consumes my processors to run
> job
> > > again from time zero. I would expect it should get killed with error if
> > > some cpt file is not found. My command line in script goes like this:
> > This is not a bug but a feature :)
> >
>
> Debatable - if the other output files actually *are* present, then mdrun
> ignores it, which is not necessarily a good thing.
> https://gerrit.gromacs.org/#/c/4439/1 proposed to fix this and related
> issues (though as you point out, I'd need to change the doc string below,
> also).
>
> Mark
>
>
> > From mdrun -h:
> > "A simulation can be continued by
> > reading the full state from file with option -cpi. This option is
> > intelligent
> > in the way that if no checkpoint file is found, Gromacs just assumes a
> > normal
> > run and starts from the first step of the .tpr file.”
> >
> > >
> > > mdrun_mpi -s dyn.tpr -x dyn.xtc -e dyn.edr -c dyn.gro -g dyn.log -cpi
> > > previous.cpt -cpo dyn.cpt
> > >
> > > In this case if provious.cpt is not found mdrun still runs my job but
> > > starting from zero time. Why it should not get killed complaining about
> > > missing previous.cpt file?
> > >
> > > Do I need to force something?
> > If you specifically only want to run an MD if a .cpt file is found,
> > you could do that, e.g. in bash with:
> >
> > if [ -f previous.cpt ] ; then
> >     mdrun …
> > else
> >     printf “No checkpoint file found.”
> > fi
> >
> > Carsten
> >
> >
> >
> > >
> > > Thanks,
> > > JIom
> > > --
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> >
> > --
> > Dr. Carsten Kutzner
> > Max Planck Institute for Biophysical Chemistry
> > Theoretical and Computational Biophysics
> > Am Fassberg 11, 37077 Goettingen, Germany
> > Tel. +49-551-2012313, Fax: +49-551-2012302
> > http://www.mpibpc.mpg.de/grubmueller/kutzner
> > http://www.mpibpc.mpg.de/grubmueller/sppexa
> >
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