[gmx-users] Problem restarting job 2016.4 with gromacs 2019-4

[Mark Abraham]

Hi,

A checkpoint restart is indeed not supported. But you can be creative with
the old version of gromacs e.g. gmx grompp -f -p -c -cpi old.cpt -s
new.tpr, and then that .tpr file has the content of the .cpt in a format
that the newer gmx will be able to run (unless we actually removed
necessary functionality)

Mark

On Wed, 4 Dec 2019 at 18:58, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/4/19 11:58 AM, CROUZY Serge 119222 wrote:
> > Dear Gromacs users
> >
> > We just installed Gromacs 2019.4
> > And I get an error restarting free energy jobs (pull) run with Gromacs
> 2016.4
> > I' m using one GPU
> >    gmx mdrun -nt 20 -s umbrella3_60ns.tpr -cpi umbrella3.cpt -deffnm
> umbrella3 -pf pullf-umbrella3.xvg -px pullx-umbrella3.xvg
> >
> > GROMACS version:    2019.4
> > Precision:          single
> > Memory model:       64 bit
> > MPI library:        thread_mpi
> > OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
> > GPU support:        CUDA
> > SIMD instructions:  AVX2_256
> >
> > Using 1 MPI thread
> > Using 20 OpenMP threads
> > 1 GPU selected for this run.
> >
> > Fatal error:
> > Mismatch between number of energies in run input (52) and checkpoint
> file (51
> > or 51).
> >
> > And of course the run restarts OK with Gromacs 2016.4 ??
> > Anybody got an idea or bug fix ?
>
> It is not possible to continue your simulations with these different
> versions because of changes in what is saved to the checkpoint files. In
> general, you should not change major versions mid-simulation/mid-project
> because file formats change (and potentially due to changes in how the
> code works entirely!).
>
> -Justin
>
> >
> > Regards
> > Serge Crouzy
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>