[gmx-users] no error on missing cpt file

[Mark Abraham]

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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