[gmx-developers] Always an error output and "usage" text even without error

[Mark Abraham]

Hi,

There is also -nocopyright. See
http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx.html

Mark

On Mon, 18 Apr 2016 18:15 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/18/16 4:23 AM, Andreas Delleske wrote:
> > Dear Gromacs developers,
> >
> > I am maintaining a test system that encloses test runs of GROMACS in our
> > environment - I hope it's not a FAQ.
> >
> > I don't know anything about what exactly GROMACs does but what I see is:
> >
> > When issueing these commands
> >
> > grompp -f /some/folder/vacuum.mdp -c molecule_0.gro -p molecule_0.top &>
> > out1.txt ; sync ; mdrun -s  topol.tpr -rerun molecule_0.gro &> out2.txt
> > ; sync
> >
> > although there is no error, my error file fills up with output like the
> > centered header and stuff like this (I cite only parts)
> >
> >
> > Option     Filename  Type         Description
> > ------------------------------------------------------------
> >    -f /some/folder/vacuum.mdp  Input        grompp input file with MD
> > parameters
> >   -po      mdout.mdp  Output       grompp input file with MD parameters
> >    -c molecule_0.gro  Input        Structure file: gro g96 pdb tpr etc.
> >    -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
> >   -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
> >    -n      index.ndx  Input, Opt.  Index file
> >    -p molecule_0.top  Input        Topology file
> >   -pp  processed.top  Output, Opt. Topology file
> >    -o      topol.tpr  Output       Run input file: tpr tpb tpa
> >    -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
> >    -e       ener.edr  Input, Opt.  Energy file
> > -ref     rotref.trr  In/Out, Opt. Full precision trajectory: trr trj cpt
> >
> >
> > Why does this have to go in the error output? Can I turn it off?
> >
>
> Users often find such logged information useful for verifying settings, as
> the
> defaults are displayed in the case of options that are not explicitly
> set.  This
> can be meaningful when diagnosing issues.
>
> The output can be turned off (or at least, greatly reduced) by using the
> -quiet
> argument.
>
> > And then, an even bigger issue for me:
> >
> > -maxwarn     int    0       Number of allowed warnings during input
> >                              processing. Not for normal use and may
> generate
> >                              unstable systems
> > -[no]zero    bool   no      Set parameters for bonded interactions
> without
> >                              defaults to zero instead of generating an
> error
> >
> > .. and the I get two notes.
> >
> > I understand that it is desired behaviour to print the notes into the
> > error output, my problem is that in the abovementioned text both words
> > "error" and "warning" occur - so when I grep the text for those
> > keywords, I get false positives.
> >
>
> Meaningful errors and warnings are indicated by ERROR and WARNING,
> respectively,
> so grep for case-sensitive matches.  For grompp, any number of errors or
> warnings will be fatal, so you can grep for "fatal" as well.
>
> -Justin
>
> > My question: Can this output be less verbose? Without the header? Can I
> > do something about it?
> >
> > Many thanks -
> >
> > Andreas
> >
> >
> >
> >
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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