[gmx-users] Which files does "-cpi -append" need?

Justin Lemkul jalemkul at vt.edu
Fri Jan 19 17:47:51 CET 2018

On 1/19/18 11:45 AM, ZHANG Cheng wrote:
> Dear Gromacs,
> I run Gromacs on our cluster, and use this command to continue my run from last checkpoint.
> gmx mdrun -deffnm md_0_1 -cpi -append
> Each new run will generate four log files:
> md_0_1.e<job_ID>
> md_0_1.o<job_ID>
> md_0_1.pe<job_ID>
> md_0_1.po<job_ID>
> Gradually, I have thousands of log files. So I used these commands to delete all of them in one go, :
> rm md_0_1.e*
> rm md_0_1.o*
> rm md_0_1.pe*
> rm md_0_1.po*
> I thought the checkpoint information is only stored in md_0_1.cpt, md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not delete.
> However, after deleting all the log files, and then started a new run, I was told:
> Fatal error:
> File appending requested, but 1 of the 4 output files are not present or are named differently
> So it seems that the checkpoint information is also in one of those md_0_1.e<job_ID>, md_0_1.o<job_ID>, md_0_1.pe<job_ID>, md_0_1.po<job_ID> files?

The checkpoint file specifies all the names of the mdrun output files 
that you're trying to append to. By removing md_0_1.e* you have deleted 
md_0_1.edr, which stores your energy data. mdrun can't append to a file 
that isn't there. I suggest you be more judicious in your shell globbing 
to avoid removing important output.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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