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

[Justin Lemkul]

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

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

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