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

[Tsjerk Wassenaar]

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
> > > >
> > > > ==================================================
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>