VMD-L Mailing List

From: Brian Kidd (bkidd_at_u.washington.edu)
Date: Tue Apr 25 2006 - 23:02:17 CDT

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
>