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

[Mark Abraham]

Hi,

One could just avoid using -deffnm and avoid creating problems ;-) Or if
the md_0_1 name reveals that what you want is each piece on its own, and to
have to append manually later, use just -noappend and let mdrun generate
md.part0001.log, energy.part0001.log etc for you.

Mark

On Fri, Jan 19, 2018, 17:56 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
>
> --
> 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.
>