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