[gmx-users] Problems with continuing simulation after time limit

Mark Abraham mark.j.abraham at gmail.com
Thu Aug 3 22:30:11 CEST 2017


On Thu, Aug 3, 2017 at 8:34 PM Searle Duay <searle.duay at uconn.edu> wrote:

> Hi everyone,
> I am running a simulation of 500 ns using GROMACS 2016 through submitting
> jobs in our HPC. Due to limited time to run per job, I wrote a bash code to
> resubmit the job and resume the simulation from  a checkpoint.

It is much easier to just do

mpirun gmx_mpi mdrun -cpi

for the default appending behaviour, or

mpirun gmx_mpi mdrun -cpi -noappend

for getting each part written to a different numbered set of output files.
The latter gives you the job of pasting things together later on.

However, I
> am receiving an error when the following command is run:
> Command line:
>  gmx_mpi mdrun -s /scratch/sad16109/clavanin/copy/gromacs/part1/part1.tpr
> -deffnm /scratch/sad16109/clavanin/copy/gromacs/part2/neutral2 -cpi
> /scratch/sad16109/clavanin/copy/gromacs/part1/part1.cpt -cpt 100 -cpo
> /scratch/sad16109/clavanin/copy/gromacs/part2/part2.cpt -maxh 12

As it says, the file you passed to -cpi was written when the output files
had different names, yet you've asked mdrun to default to appending to the
old output files. mdrun doesn't know which error you've made.

> the error being issued is:
> Output file appending has been requested,
> but some output files listed in the checkpoint file
> /scratch/sad16109/clavanin/copy/gromacs/part1/part1.cpt
> are not present or not named as the output files by the current program:
> Expect output files present:
> Expected output files not present or named differently:
>  /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.log
>  /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.trr
>  /scratch/sad16109/clavanin/20pope_80popg/gromacs/part1/neutral1.edr
> -------------------------------------------------------
> Program:     gmx mdrun, version 2016
> Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)
> MPI rank:    0 (out of 24)
> Fatal error:
> File appending requested, but 3 of the 3 output files are not present or
> are
> named differently. For safety reasons, GROMACS-2016 and later only allows
> file
> appending to be used when all files have the same names as they had in the
> original run. Checkpointing is merely intended for plain continuation of
> runs.
> For safety reasons you must specify all file names (e.g. with -deffnm), and
> all these files must match the names used in the run prior to checkpointing
> since we will append to them by default. If the files are not available,
> you
> can add the -noappend flag to mdrun and write separate new parts. For mere
> concatenation of files, you should use the gmx trjcat tool instead.
> I receive that error even if the neutral1.log, neutral1.trr, and
> neutral1.edr files are present in the "part1" folder. I was using the
> similar code with Gromacs 5 and I am not having problems. I am not sure if
> this is something new in Gromacs 2016.

It's new, exactly as the message says it is, because the old behaviour made
it easy for people to over-write their trajectory files within meaning to.

> I am thinking that there might be something wrong with how I name my files
> but I am not sure where.

Very likely you're just doing more work than you need to be / should be


> Thanks!
> --
> Searle Aichelle S. Duay
> Ph.D. Student
> Chemistry Department, University of Connecticut
> searle.duay at uconn.edu
> --
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