[gmx-developers] Always an error output and "usage" text even without error
mark.j.abraham at gmail.com
Mon Apr 18 18:26:58 CEST 2016
There is also -nocopyright. See
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
> 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
> > And then, an even bigger issue for me:
> > -maxwarn int 0 Number of allowed warnings during input
> > processing. Not for normal use and may
> > unstable systems
> > -[no]zero bool no Set parameters for bonded interactions
> > defaults to zero instead of generating an
> > .. 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,
> 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
> Gromacs Developers mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> or send a mail to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-developers