VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 03 2005 - 15:17:44 CST

Hi,
  What video chipset and drivers are you using on your machine?

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 02, 2005 at 10:44:07AM +0100, Haberl Florian wrote:
> hi,
>
> i ve also the problem that vmd 1.8.3 won^t run on my laptop with gentoo
> (unstable branch).
> I see the same errors popping up like beyond, same system running with
> suse 9.1 works fine.
> Other system i got (also suse 9.1) also without probs.
> So i fear it^s perhaps a lib problem, too new.
>
>
>
> > Hi John,
> >
> > I've only recently did a clean install of FC3 on this machine so I don't
> > have a great deal on it. I don't have a .cshrc file at all because i'm
> > using bash as the default shell. If i run 'vmd -dispdev text' i get
> >
> > Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
> > Info) http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > Info) Please include this reference in published work using VMD:
> > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > Info) -------------------------------------------------------------
> > Info) Multithreading available, 2 CPUs detected.
> > vmd >
> >
> > so it looks fine.
> >
> > I can also run the /usr/local/lib/vmd/vmd_LINUX binary directly and get
> > the OpenGL window and load in and display trajectories but obviously the
> > environmental variables are missing so I get these messages:
> >
> > Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
> > Info) http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > Info) Please include this reference in published work using VMD:
> > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > Info) -------------------------------------------------------------
> > Info) Multithreading available, 2 CPUs detected.
> > Info) OpenGL renderer: RADEON X300 Generic
> > Info) Features: STENCIL RN MDE CVA MTX PP PS GLSL(OVF)
> > ERROR) Unable to locate VMD vertex and fragment shader path, VMDDIR
> > environment variable not set
> > Info) GLSL rendering mode is NOT available.
> > Info) Textures: 2-D (2048x2048), 3-D (2048x2048x2048), Multitexture
> > (8)
> > ERROR) Tcl startup error: Can't find a usable init.tcl in the following
> > directories:
> > ERROR) /usr/local/lib/tcl8.4 /usr/local/lib/lib/tcl8.4
> > /usr/local/lib/tcl8.4 /usr/local/lib/library /usr/local/library
> > /usr/local/tcl8.4.1/library /usr/tcl8.4.1/library /usr/local/lib/tcl8.4
> > ERROR)
> > ERROR)
> > ERROR)
> > ERROR) This probably means that Tcl wasn't installed properly.
> > ERROR) Tk startup error: invalid command name "tcl_findLibrary"
> > ERROR) VMDDIR undefined, startup failure likely.
> > ERROR) Could not read the vmd initialization file -
> > ERROR) source {/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl}
> > ERROR) can't find package http 2.4
> > ERROR) The VMDDIR environment variable is set by the startup
> > ERROR) script and should point to the top of the VMD hierarchy.
> > ERROR) VMD will continue with limited functionality.
> > ERROR) invalid command name "vmd_load_extension_packages"
> >
> >
> > thanks,
> >
> > James.
> >
> >
> >
> > PS I hope you are well!
> >
> >
> >
> > On Tue, 2005-03-01 at 17:29 -0600, John Stone wrote:
> >> James,
> >> Have you tried renaming your .cshrc file to see if your login scripts
> >> are the source of the problem? If that didn't cure the problem, then
> >> you
> >> may in fact have a different problem than Daniel did. There are various
> >> things that can potentially cause this behavior. I assume you're
> >> running
> >> the 32-bit version of VMD right? What happens if you run 'vmd -dispdev
> >> text'?
> >> Does that work? If so, then you have a graphics problem of some sort.
> >> If not, then it's probably an environment or shared library issue.
> >>
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >>
> >> On Tue, Mar 01, 2005 at 11:17:15PM +0000, James MacDonald wrote:
> >> >
> >> > Hi all,
> >> >
> >> > Has the problem with installing VMD 1.8.3 on Fedora Core 3 been solved
> >> > because I'm suffering exactly the same problem as Daniel (main window
> >> > flashing up and disappearing on startup...) but I don't have InsightII
> >> > installed? I had a previous installation of VMD 1.8.2 which I deleted
> >> > and which did work fine.
> >> >
> >> > I had a look through the mailing list for a solution to his problem
> >> but
> >> > couldn't find one, so apologies if any one has to repeat themselves!
> >> >
> >> >
> >> > James.
> >> >
> >> >
> >> >
> >> > On Wed, 2005-01-12 at 09:33 +0200, Dr. Daniel James White PhD wrote:
> >> > > Hi,
> >> > >
> >> > > There seems to be a conflict between InsightII from acellrys,
> >> > > and VMD
> >> > >
> >> > > InsightII requires that the following cshrc file is sourced before
> >> > > insightII is launched
> >> > > so I was instructed to put a line in my .cshrc to source this file
> >> > >
> >> > > this is what causes vmd to fail
> >> > > I wouldn't be surprised is there is a problem here as the linux
> >> support
> >> > > for InsightII from accelrys is very new ? it's not even working at
> >> the
> >> > > moment for some odd reason ( although before Xmas it was......
> >> fedora
> >> > > core 3 self updates likely to be the problem there, but I
> >> digress....)
> >> > >
> >> > > any clues ?
> >> > >
> >> > > Dan
> >> > >
> >> > >
> >> > > # cshrc
> >> > > # Environment definition script for Accelrys software.
> >> > > #
> >> > > # Place the following line in the ~/.cshrc file of any user
> >> > > # desiring to use Accelrys software products:
> >> > > #
> >> > > # source /usr/msi/cshrc
> >> > > #
> >> > > # Accelrys Inc. 2001
> >> > > #---------------------------------------------------------------
> >> > >
> >> > > source /home/dan/Desktop/insightII/cdrom/License_Pack/msi_lic_cshrc
> >> > >
> >> > > # Set the BIOSYM_ROOT environment variable to point to the root
> >> > > # of the Installation tree and set BIOSYM_CONTEXT to the default
> >> > > context.
> >> > > setenv BIOSYM_ROOT /usr/local/accelrys
> >> > > if ($?BIOSYM_CONTEXT == 0) setenv BIOSYM_CONTEXT I2000.3
> >> > >
> >> > > # Set up additional interactive environment variables.
> >> > > setenv BIOSYM ${BIOSYM_ROOT}/${BIOSYM_CONTEXT}
> >> > > setenv BIOSYM `echo $BIOSYM | sed 's%//%/%g' `
> >> > > #source $BIOSYM/config/special/cshrc_platform # Set
> >> BIOSYM_PLATFORM
> >> > >
> >> > > # Create set_biosym_context alias
> >> > > alias set_biosym_context \
> >> > > 'setenv setcontext_arg "\!:*"; source $BIOSYM_ROOT/biosym_setcon'
> >> > >
> >> > > # Create set_context alias
> >> > > alias set_context \
> >> > > 'setenv setcontext_arg "\!:*"; source $BIOSYM_ROOT/biosym_setcon'
> >> > >
> >> > > alias reset_env \
> >> > > 'setenv setcontext_arg $BIOSYM_CONTEXT; unsetenv BIOSYM_CONTEXT;
> >> > > source $BIOSYM_ROOT/biosym_setcon'
> >> > >
> >> > > # Use biosym_setcon to define context
> >> > > setenv setcontext_arg $BIOSYM_CONTEXT
> >> > > setenv BIOSYM_CONTEXT Undefined
> >> > > source $BIOSYM_ROOT/biosym_setcon
> >> > >
> >> > >
> >> > > On 11 Jan 2005, at 18:50, Axel Kohlmeyer wrote:
> >> > >
> >> > > >
> >> > > >>>> "DW" == Daniel James White PhD <Dr.> writes:
> >> > > >
> >> > > >
> >> > > > dan,
> >> > > >
> >> > > > this check is easy. just rename your .cshrc to .disabled.cshrc
> >> > > > or something else and try again. for some setups you have to
> >> > > > log out and back in to have this change take full effect.
> >> > > >
> >> > > > axel.
> >> > > >
> >> > > >
> >> > > > DW> Hi John,
> >> > > >
> >> > > > DW> I have stuff added to my .cshrc file for insightII
> >> > > >
> >> > > > DW> I can start csh and tcsh
> >> > > > DW> with no errors output to the terminal....
> >> > > >
> >> > > > DW> so how do I check if something really is bombing but the shell
> >> isnt
> >> > > > DW> telling me?
> >> > > >
> >> > > > DW> Dan
> >> > > >
> >> > > >
> >> > > > [...]
> >> > > >
> >> > > >
> >> > > >
> >> > > > --
> >> > > >
> >> > > > =======================================================================
> >> > > > Axel Kohlmeyer e-mail:
> >> axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> >> > > > Lehrstuhl fuer Theoretische Chemie Phone: ++49
> >> (0)234/32-26673
> >> > > > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49
> >> (0)234/32-14045
> >> > > > D-44780 Bochum
> >> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> >> > > > =======================================================================
> >> > > > If you make something idiot-proof, the universe creates a better
> >> idiot.
> >> > > >
> >> > > >
> >> > > Dr. Daniel James White BSc. (Hons.) PhD
> >> > > Bioimaging Coordinator
> >> > > Nanoscience Centre and
> >> > > Department of Biological and Environmental science
> >> > > Division of Molecular Recognition
> >> > > Ambiotica C242
> >> > > PO Box 35
> >> > > University of Jyväskylä
> >> > > Jyväskylä FIN 40014
> >> > > Finland
> >> > > +358 14 260 4183 (work)
> >> > > +358 468102840 (mobile)
> >> > >
> >> > > http://www.chalkie.org.uk
> >> > > dan_at_chalkie.org.uk
> >> > > white_at_cc.jyu.fi
> >> > >
> >>
> >
>
> Greetings,
>
> Florian
>
>
> ------------------------------------------------------------------------
> Florian Haberl Universitaet Erlangen/Nuernberg
> Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen
>
> Mailto: florian.haberl AT chemie.uni-erlangen.de
>
> ------------------------------------------------------------------------ 

-- 
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