VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 09 2005 - 13:22:59 CST

Hi,
  Yes, VMD 1.8.3 now uses OpenGL Programmable Shading, but the rest of
the code is essentially the same. The issue really seems to be that ATI
has done something recently to break their drivers, as the beta versions
of VMD 1.8.3 worked fine previously. I'm still working to determine what
is causing this problem. The problem only affects the Linux ATI drivers,
they work fine on Windows and Mac machines.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 09, 2005 at 01:12:33PM -0600, Sabuj Pattanayek wrote:
> John Stone wrote:
>
> >Sabuj,
> > Ok, what happens if you do this:
> >setenv VMDSIMPLEGRAPHICS 1
> >vmd
> >
> >
> ok that seems to work. One more thing I realized is that this problem is
> happening only on machines with ATI radeon >=9600 (don't have firegl to
> test) hardware running xorg >=6.8 and fglrx >= 8.8.25. One machine
> running the same gentoo distribution but with nvidia quadro4 doesn't
> have this problem. Was there some drastic change with the opengl
> initialization between 1.8.2 and 1.8.3?
>
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Mar 09, 2005 at 12:53:36PM -0600, Sabuj Pattanayek wrote:
> >
> >
> >>John Stone wrote:
> >>
> >>
> >>
> >>>Sabuj,
> >>>If running the script opens and closes an xterm immediately, we need
> >>>to figure out why. VMD will not run correctly if you start the binary
> >>>manually. What happens when you run VMD like this:
> >>>vmd -dispdev text
> >>>
> >>>
> >>>
> >>>
> >>vmd -dispdev text
> >>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 > quit
> >>Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
> >>Info) Exiting normally.
> >>
> >>..no error messages there
> >>
> >>ls -l /bin/csh
> >>lrwxrwxrwx 1 root root 9 Jun 23 2004 /bin/csh -> /bin/tcsh
> >>tcsh --version
> >>tcsh 6.12.00 (Astron) 2002-07-23 (i386-intel-linux) options
> >>8b,nls,dl,al,rh,color,filec
> >>
> >>
> >>
> >>>Do you have /bin/csh installed on your machine?
> >>>
> >>>John Stone
> >>>vmd_at_ks.uiuc.edu
> >>>
> >>>On Wed, Mar 09, 2005 at 12:41:13PM -0600, Sabuj Pattanayek wrote:
> >>>
> >>>
> >>>
> >>>
> >>>>Hi,
> >>>>
> >>>>I get this error when I start vmd 1.8.3 (you have to run
> >>>>/path/to/vmd/vmd_LINUX since just running the vmd script opens a window
> >>>>and it closes immediately):
> >>>>
> >>>>ERROR) Tcl startup error: Can't find a usable init.tcl in the following
> >>>>directories:
> >>>>ERROR) /usr/local/lib/tcl8.4 /usr/local/sbin/lib/tcl8.4
> >>>>/usr/local/lib/tcl8.4 /usr/local/sbin/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) couldn't read file "/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl":
> >>>>no such file or directory
> >>>>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"
> >>>>
> >>>>I installed it according to the instructions (remove old vmd
> >>>>installtion; modify configure, run ./configure, and cd src; make
> >>>>install). Just to make sure there isn't anything wrong with the system
> >>>>I did a fresh install of vmd 1.8.2 and it works. The vmd 1.8.3 script
> >>>>has:
> >>>>
> >>>>set defaultvmddir=/usr/local/sbin/vmd
> >>>>set vmdbasename=vmd
> >>>>
> >>>>slocate init.tcl
> >>>>
> >>>>/usr/lib/tcl8.4/init.tcl
> >>>>/usr/local/sbin/vmd/scripts/vmd/vmdinit.tcl
> >>>>/usr/local/sbin/vmd/scripts/tcl8.4/init.tcl
> >>>>/usr/local/sbin/pymol/ext/lib/tcl8.4/init.tcl
> >>>>/usr/local/sbin/chimera1.2065/lib/tcl8.4/init.tcl
> >>>>/usr/local/sbin/ac3dlx/lib/tcl8.4/init.tcl
> >>>>/root/vmd-1.8.2/lib/scripts/tcl8.4/init.tcl
> >>>>/root/vmd-1.8.2/scripts/vmd/vmdinit.tcl
> >>>>/root/vmd-1.8.3/lib/scripts/tcl8.4/init.tcl
> >>>>/root/vmd-1.8.3/scripts/vmd/vmdinit.tcl
> >>>>
> >>>>Thanks,
> >>>>Sabuj Pattanayek
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >
> >
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078