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

[Tsjerk Wassenaar]

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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