[gmx-users] Restart

[Mark Abraham]

Hi,

On Tue, Jul 31, 2018, 19:56 Eric Smoll <ericsmoll at gmail.com> wrote:

> Hi Mark,
>
> Thanks for the reply.  I do use directories for project management but, up
> until now, I also had a preference for custom filenames.  Lesson learned.
> I need to use the default naming scheme if I want smooth restarts.


You don't have to, but it sure makes it easier.

I
> wrongfully assumed that the consistent use of output filename flags in
> GROMACS tools meant that custom output filenames were supported and
> encouraged.  I wrongfully assumed that GROMACS code snippets that suppress
> custom output filenames were just being concise for clarity and simplicity.
>

They are being concise and clear. You can totally have custom names and
restarts with and without appending, but you have to call mdrun the same
way, which is extra work for you.

When attempting to restart, it would be nice if mdrun listed the file names
> it is looking for.  Can I find this information anywhere or is it
> completely hidden from the user?
>

Did you look in the log file to see what it said when mdrun considered the
restart? IIRC even these older versions will tell you what expected file
was not found, or vice versa.

Mark

Thanks again,
> Eric
>
> On Tue, Jul 31, 2018 at 11:33 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > As you can probably see in the log file, mdrun is refusing to do the
> > default restart with appending from the checkpoint because the output
> > filenames when you wrote the files are different to the ones supplied by
> > the mdrun defaults now. I'm sure the behavior of mdrun has been improved
> > since then, but in choosing to rename all the files you have created for
> > yourself the problem of making sure the restart also has all the names
> > matching. Perhaps -noappend will let you get something done, but I
> strongly
> > suggest using directories for your project organization using the default
> > file names, rather than manually managing file names.
> >
> > Mark
> >
> >
> > On Tue, Jul 31, 2018, 04:14 Eric Smoll <ericsmoll at gmail.com> wrote:
> >
> > > Hello GROMACS users,
> > >
> > > I had a simulation terminate unexpectedly very close to completion and
> I
> > > would like to resume the simulation from a checkpoint file.
> > >
> > > my mdrun flags are -cpi, -s, -o, -x, -c, -e, -g, and -cpo.
> > > All of the associated files are present (except the -c file since there
> > was
> > > a crash).  Looking at the last saved checkpoint in the log file and
> > running
> > > "gmx check -f state.cpt" on the cpo file "state.cpt" confirms that the
> > > proper time has been saved.  An important point is that the files
> names I
> > > provided are not used because gromacs has added the infix ".part0001"
> > >
> > > The GROMACS 2016 page on "Managing Long Simulations" claims I can
> restart
> > > with the command "gmx mdrun -cpi state.cpt."  However, this starts the
> > > simulation at step 0 and does not append to the current file (instead
> > > adding to a file without the ".part0001" infix).  It is unclear if this
> > > will only execute the remaining number of steps or not.
> > >
> > > How can I get mdrun to launch this restart correctly?
> > >
> > > Best,
> > > Eric
> > > --
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