VMD-L Mailing List

From: James MacDonald (j.macdonald_at_mail.cryst.bbk.ac.uk)
Date: Fri Mar 04 2005 - 06:33:28 CST

Hi John,

Yes, VMD works normally when I do that. What do you miss out on with
VMDSIMPLEGRAPHICS? I must say the ATI drivers are a pain to install.

Thanks,
  
James.

On Thu, 2005-03-03 at 15:17 -0600, John Stone wrote:
> James,
> I'm wondering if your ATI video driver may be killing VMD on you.
> What happens if you do this:
> setenv VMDSIMPLEGRAPHICS 1
> vmd
>
> Does it run normally then?
> Others have recently started having problems with the ATI drivers on Linux,
> which makes me wonder if this is what's causing your problem.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Tue, Mar 01, 2005 at 11:46:09PM +0000, James MacDonald wrote:
> > 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
> > > > >
> > >
>