VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 25 2006 - 19:20:27 CDT

Brian,
  Did you follow the installation direction in the README?
You may also want to check the Linux release notes which warn
about various fun stuff with the SELinux settings on FC5.
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/linuxrelnotes.html

Normally you wouldn't run the vmd_LINUXAMD64 binary directly, but
rather via the startup script. Still though, the segmentation fault
you're receiving when running graphically might indicate a problem with
your OpenGL setup. What do you get when you run 'glxinfo' on that system?

If you installed with the normal process, you should have a VMD startup
script '/usr/local/bin/vmd' installed on your machine. What happens when
you run /usr/local/bin/vmd -dispdev text, and with no parameters?
You might also do this:
  /usr/local/bin/vmd -debug
when the gdb prompt comes up, do:
  run
if/when it crashes, do:
  where

and send me the output...

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 25, 2006 at 04:37:32PM -0700, Brian Kidd wrote:
> Hello,
>
> I downloaded the latest release of VMD 1.8.4 and am using the
> LinuxAMD64 version with the default installation settings.
> Unfortunately, the start up scripts seem to be configured improperly
> because VMD won't start up.
>
> I've included the outputs from a few different checks to see what is
> going wrong. I haven't been able to figure out what file I need to
> install or what setting I should change. Any help would be appreciated.
>
> Thanks,
> Brian
>
> checking the links
>
> ldd vmd_LINUXAMD64
> libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003c9a600000)
> libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x0000003c9d400000)
> libX11.so.6 => /usr/lib64/libX11.so.6 (0x0000003c94500000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003c95300000)
> libdl.so.2 => /lib64/libdl.so.2 (0x0000003c93d00000)
> libutil.so.1 => /lib64/libutil.so.1 (0x0000003c98d00000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003c99700000)
> libm.so.6 => /lib64/libm.so.6 (0x0000003c93b00000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003c98f00000)
> libc.so.6 => /lib64/libc.so.6 (0x0000003c93800000)
> libXext.so.6 => /usr/lib64/libXext.so.6 (0x0000003c94900000)
> libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1
> (0x0000003c9a400000)
> libdrm.so.2 => /usr/lib64/libdrm.so.2 (0x0000003c9d600000)
> libXau.so.6 => /usr/lib64/libXau.so.6 (0x0000003c94100000)
> libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x0000003c93f00000)
> /lib64/ld-linux-x86-64.so.2 (0x0000003c93400000)
>
>
> ./vmd_LINUXAMD64 -dispdev none
>
> Info) VMD for LINUXAMD64, version 1.8.4 (April 17, 2006)
> 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.
> 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/tcl
> ERROR)
> ERROR)
> ERROR)
> ERROR) This probably means that Tcl wasn't installed properly.
> 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"
>
>
> ./vmd_LINUXAMD64 -dispdev win
>
> Info) VMD for LINUXAMD64, version 1.8.4 (April 17, 2006)
> 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.
> XRequest.143: GLXBadContext 0x2e00045
> Segmentation fault 

-- 
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