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

Justin Lemkul jalemkul at vt.edu
Mon Apr 18 18:14:53 CEST 2016

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 

> 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.


> 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


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