VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 10 2009 - 10:15:06 CST

Rob,
  From the traceback, it looks like your crash is being caused by
an interaction between Tcl/Tk 8.5.x (compiled into VMD) and your
local X11 installation. The specific X11 call that's causing your
crash is a routine that checks for special input handling that would
likely be associated with internationalization functionality, perhaps
tied to your system's use of SCIM or your locale setting on your machine.
Since nobody else has experienced the problem you're running into thus
far, I am assuming that either you've got a buggy X11, or the Tcl/Tk 8.5.x
that's compiled into VMD has a bug that is (thus far) only triggered by
something that is specific to your system configuration. What locale is
your system using? Do you have SCIM enabled or disabled? Do you have any
special internationalized keyboard handling turned on?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 09, 2009 at 08:24:16PM -0800, Rob wrote:
> John Stone wrote on Tue Dec 08 2009:
> >
> > Rather than guess however, you can do a couple of simple
> > tests and see how far VMD got when the crash occured,
> > by running it like this:
> vmd -debug
>
> $ vmd -debug
> [...skip...]
> (gdb) run
> Starting program: /usr/local/lib/vmd/vmd_LINUXAMD64
> [Thread debugging using libthread_db enabled]
> Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
> 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, 8 CPUs detected.
> Info) Free system memory: 5249MB (87%)
> Info) No CUDA accelerator devices available.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: Software Rasterizer
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x0000003278c528b6 in XGetICValues () from /usr/lib64/libX11.so.6
> Missing separate debuginfos, use: debuginfo-install expat-2.0.1-8.fc12.x86_64 glibc-2.11-2.x86_64 libX11-1.3-1.fc12.x86_64 libXau-1.0.5-1.fc12.x86_64 libXcursor-1.1.10-1.fc12.x86_64 libXdamage-1.1.2-1.fc12.x86_64 libXext-1.1-1.fc12.x86_64 libXfixes-4.0.4-1.fc12.x86_64 libXi-1.3-1.fc12.x86_64 libXrender-0.9.5-1.fc12.x86_64 libXxf86vm-1.1.0-1.fc12.x86_64 libdrm-2.4.15-6.fc12.x86_64 libgcc-4.4.2-7.fc12.x86_64 libselinux-2.0.87-1.fc12.x86_64 libstdc++-4.4.2-7.fc12.x86_64 libxcb-1.4-2.fc12.x86_64 mesa-dri-drivers-7.6-0.13.fc12.x86_64 mesa-libGL-7.6-0.13.fc12.x86_64 mesa-libGLU-7.6-0.13.fc12.x86_64
>
> (gdb) where
> #0 0x0000003278c528b6 in XGetICValues () from /usr/lib64/libX11.so.6
> #1 0x00000000007e053b in Tk_HandleEvent ()
> #2 0x00000000007e0ed3 in ?? ()
> #3 0x0000000000874c4a in Tcl_ServiceEvent ()
> #4 0x0000000000874fc7 in Tcl_DoOneEvent ()
> #5 0x00000000005ee43e in TclTextInterp::doTkUpdate() ()
> #6 0x00000000005b11ec in UIText::check_event() ()
> #7 0x00000000004f7428 in CommandQueue::check_events() ()
> #8 0x00000000005b260c in VMDApp::VMDupdate(int) ()
> #9 0x00000000005daec2 in main ()
>
>
>
> Does this help?
>
> Rob.
>
>
> 

-- 
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