VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 25 2006 - 23:54:27 CDT

Brian,
  I'm glad that helped you solve the problem. I'm going to spend some
time and add this info to the Linux release notes as these are pretty
common issues, and I seem to have come up with a good sequence of
mechanistic steps for helping people solve these problems.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 25, 2006 at 09:02:17PM -0700, Brian Kidd wrote:
> John,
>
> I was able to install the correct video driver and now both OpenGL and
> VMD are working.
>
> Thank you for helping me debug this problem by offering excellent
> suggestions.
> -Brian
>
> On Apr 25, 2006, at 8:51 PM, John Stone wrote:
>
> >
> >Brian,
> > The error from 'glxinfo' says it all. There's something VERY
> >broken with OpenGL on this machine. What video card/chipset and
> >driver are you using on this machine? Chances are that the OpenGL
> >driver or library install is corrupt, or possibly the kernel drivers
> >for your graphics chipset aren't working correctly.
> >The general rule of thumb is that if you get errors running
> >'glxinfo' then there's no way VMD (or any other OpenGL program)
> >is going to run correctly. I'd start by re-checking everything in
> >the OpenGL and X11 configuration on this machine and looking for
> >problems. You may have errors in the X server logs which would help
> >narrow down the problem...
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Apr 25, 2006 at 06:06:50PM -0700, Brian Kidd wrote:
> >>John,
> >>
> >>Thanks for the quick reply.
> >>
> >>I followed the installation from the README.
> >>
> >>It does seem to be a problem with the OpenGL setup. Now I need to
> >>track
> >>down the proper package to install or configuration change to make.
> >>Any
> >>suggestions?
> >>
> >>Below are the outputs from your various suggestions.
> >>
> >>Thanks,
> >>-Brian
> >>
> >>glxinfo
> >>
> >>name of display: :0.0
> >>X Error of failed request: GLXBadContext
> >> Major opcode of failed request: 143 (GLX)
> >> Minor opcode of failed request: 5 (X_GLXMakeCurrent)
> >> Serial number of failed request: 17
> >> Current serial number in output stream: 17
> >>
> >>vmd -dispdev text
> >>
> >>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.
> >>vmd >
> >>
> >>vmd -debug
> >>
> >>***
> >>*** Running VMD in debugger, type 'run' at debugger prompt
> >>***
> >>GNU gdb Red Hat Linux (6.3.0.0-1.122rh)
> >>Copyright 2004 Free Software Foundation, Inc.
> >>GDB is free software, covered by the GNU General Public License, and
> >>you are
> >>welcome to change it and/or distribute copies of it under certain
> >>conditions.
> >>Type "show copying" to see the conditions.
> >>There is absolutely no warranty for GDB. Type "show warranty" for
> >>details.
> >>This GDB was configured as "x86_64-redhat-linux-gnu"...(no debugging
> >>symbols found)
> >>Using host libthread_db library "/lib64/libthread_db.so.1".
> >>
> >>(gdb) run
> >>
> >>Starting program: /usr/local/lib/vmd/vmd_LINUXAMD64
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>[Thread debugging using libthread_db enabled]
> >>[New Thread 47492242014784 (LWP 9847)]
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found) (no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>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.
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>(no debugging symbols found)
> >>XRequest.143: GLXBadContext 0x3600045
> >>
> >>Program received signal SIGSEGV, Segmentation fault.
> >>[Switching to Thread 47492242014784 (LWP 9847)]
> >>0x0000003c9a64f1c7 in glGetString () from /usr/lib64/libGL.so.1
> >>
> >>(gdb) where
> >>
> >>#0 0x0000003c9a64f1c7 in glGetString () from /usr/lib64/libGL.so.1
> >>#1 0x00000000004973ab in OpenGLExtensions::find_renderer ()
> >>#2 0x000000000049cd3b in OpenGLRenderer::setup_initial_opengl_state
> >>()
> >>#3 0x000000000049670b in OpenGLDisplayDevice::open_window ()
> >>#4 0x000000000049685c in OpenGLDisplayDevice::init ()
> >>#5 0x000000000055ad92 in VMDApp::VMDinit ()
> >>#6 0x00000000005692f2 in main ()
> >>
> >>On Apr 25, 2006, at 5:20 PM, John Stone wrote:
> >>
> >>>
> >>>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
> >>>
> >
> >--
> >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
> > 

-- 
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