[gmx-users] strange but true : How to explain and avoid?

[Chetan Mahajan]

Hi Tsjerk,

Thanks. I get it. So in verision 4.6.5, adding 2>/dev/null at the end of
the command seems the only way out, since, as I said, I am also getting
greeting messages in addition to gcq quotes. However, adding  2>/dev/null  will
also suppress unusual errors, if any at all. There does not seem a way out
of this.

Thanks
Chetan


On Tue, Jul 8, 2014 at 1:14 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Chetan,
>
> A file has two terminal output streams: stdout, which is buffered, and
> stderr, which is unbuffered. The messages are written to stderr and printed
> as soon as they are received. The coordinates and such are collected until
> the buffer is full and then printed, or printed upon exit of the program.
> the latter accounts for the quote appearing in the middle of your output.
>
> Cheers,
>
> Tsjerk
> On Jul 8, 2014 5:06 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
>
> > Thanks, Justin. GMX_NO_QUOTES is working and there is no such quote, but
> a
> > different message at the same place:
> >
> > Thanx for Using GROMACS - Have a Nice Day
> >
> > Why are such messages ( even previous ones) appearing in the middle of
> > coordinates, although from last timeframe?
> >
> > Thanks
> > Chetan
> >
> >
> >
> >
> > On Mon, Jul 7, 2014 at 8:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 7/7/14, 9:06 PM, Chetan Mahajan wrote:
> > >
> > >> Thanks, Justin and Roland. While 2>/dev/null/ at the end of gmxdump
> > >> command
> > >> removes that quote nicely, adding either of following commands fails.
> I
> > am
> > >> using gromacs 4.6.5.:
> > >>
> > >> Following did not work ( why? curious since above 2>/dev/null/ will
> > >> suppress all errors getting displayed)
> > >>
> > >> 1. GMX_NO_QUOTES = 1
> > >> gmxdump -f lnanop.xtc
> > >>
> > >>
> > > Incorrect syntax.
> > >
> > > export GMX_NO_QUOTES=1
> > >
> > >
> > >  2. gmxdump -f lnanop.xtc -quiet
> > >>
> > >>
> > > The -quiet option will suppress quotes in 5.0, not 4.6.5, as Roland
> said.
> > >
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > 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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