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

[Chetan Mahajan]

Thanks, Tsjerk. Got to focus on unix sometime :-)


On Tue, Jul 8, 2014 at 11:58 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Chetan,
>
> You can write the error stream to file: 2>stderr.log
> That way, you can check afterwards.
>
> Cheers,
>
> Tsjerk
> On Jul 8, 2014 6:45 PM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
>
> > 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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