VMD-L Mailing List

From: Haberl Florian (Florian.Haberl_at_chemie.uni-erlangen.de)
Date: Wed Mar 02 2005 - 03:44:07 CST

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

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 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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