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

[Justin Lemkul]

On 1/19/18 11:53 AM, ZHANG Cheng wrote:
> Thank you very much Justin! Sorry I did not realise that.
>
>
> I will need to include an "except md_0_1.edr" in the deletion.
>
>
> But does it correct that I can delete all the 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>
>

Those are output from your cluster and its queuing system. They are 
irrelevant to GROMACS.

-Justin

>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Sat, Jan 20, 2018 00:45 AM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  Which files does "-cpi -append" need?
>
>
>
> 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?
>
>
> Thank you.

-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================