[gmx-users] Using a 4.6.5 cpt file in 5.0 to extend a run?

[Mark Abraham]

On Thu, Sep 25, 2014 at 3:59 PM, Nathan Scott <scottjn at gmail.com> wrote:

> Mark
>
> Thank you very much for your help. The one part of your reply that confuses
> me a bit is that I *did* actually pass the old cpt file to grompp to
> generate a new tpr file before beginning mdrun. I should have been clear
> about that in my original post. To be specific, below is the grompp command
> I used:
>
> grompp_mpi -f stn_wt_d_in_1.mdp -c stn_wt_c_1.gro -t stn_wt_c_1.cpt -p
> ../topol_exc.top -o stn_wt_d_1.tpr -po stn_wt_d_out_1.mdp -e stn_wt_c_1.edr
>
> So I pass to grompp my new mdp file, the old (from 4.6.5) gro, cpt, edr,
> and topology files, and generate a tpr file based on that information.
> Grompp doesn't complain in any way, and yet mdrun does.
>

If you did that, then you don't need to pass the checkpoint later with
mdrun -cpi... actual copy-pasted command lines are always the most useful
thing to provide ;-)

Mark


> Your point about switching versions mid-project is very well taken, and
> that was my first thought as well. I've got an email in to XSEDE help to
> address the issue, but I'm not expecting much via that route.
>
> Best Wishes,
> Nathan
>
> On Thu, Sep 25, 2014 at 3:55 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > On Thu, Sep 25, 2014 at 5:03 AM, Nathan Scott <scottjn at gmail.com> wrote:
> >
> > > Hi all,
> > >
> > > I am trying to extend some simulations done on the XSEDE Trestles
> system
> > > over the summer, and they have upgraded to 5.0 since then from 4.6.5.
> > >
> >
> > That's not normal practice at compute centers - older versions should
> > generally continue to be made available, so that a scientific project can
> > have a consistent methodology. In principle, a trajectory could be
> > continued with newer software if it implements the same method, but
> proving
> > that this principle holds is more trouble than you should normally want
> to
> > buy...
> >
> > Can anyone give any tips for navigating around the below error?
> > >
> > > Program mdrun_mpi, VERSION 5.0
> > > Source code file:
> > >
> > >
> >
> /state/partition1/git/chemistry-roll/BUILD/gromacs_intel_mvapich2_ib-5.0/gromacs-5.0/src/gromacs/gmxlib/checkpoint.c,
> > > line: 2037
> > >
> > > Fatal error:
> > > You seem to have switched ensemble, integrator, T and/or P-coupling
> > > algorithm between the cpt and tpr file. The recommended way of doing
> this
> > > is passing the cpt file to grompp (with option -t) instead of to mdrun.
> > If
> > > you know what you are doing, you can override this error by setting the
> > > env.var. GMX_ALLOW_CPT_MISMATCH
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > > In fact, I haven't switched any of the mdp options that were used for
> the
> > > original simulation, except nsteps, and doing a diff of the mdp file
> the
> > > original cpt file is based off of and the new one that I am trying to
> use
> > > to extend the simulation confirms this fact.
> > >
> >
> > OK, but sometimes the internal representation has to change, as it did
> for
> > (say) the new implementation of the default sd integrator, or the default
> > for cutoff-scheme. Depending what the actual issue is here, maybe the
> error
> > message could use improvement.
> >
> > Is there a workaround for this?
> >
> >
> > Like the message says, you can do
> >  grompp -f new -c whatever -p topol -t the-4.6.5.cpt
> >
> >  in order that your intentions are explicit. mdrun should have logic to
> > stop you doing things that likely are mistakes, such as
> >
> >  mdrun -s nvt -cpi npt
> >
> > but we can't write code that anticipates all possible scenarios and
> reacts
> > the way every user would expect...
> >
> > Or might I just be making some kind of
> > > simple mistake? Any advice would be greatly appreciated!
> > >
> > > Best Wishes,
> > > Nathan
> > > --
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