VMD-L Mailing List

From: Rob (spamrefuse_at_yahoo.com)
Date: Thu May 20 2010 - 02:16:43 CDT

On Tue May 18 John Stone wrote:
> Rob,
> This does not cause any crash when I try it locally.
> Try running VMD with "vmd -debug" with your normal LANG
> setting and do a stack traceback in gdb. If you can get
> a traceback, we can figure out what is going wrong there.
> My guess is that this is most likely an issue with Tcl,
> or a difference in the behavior of your C runtime library's
> internationalization functionality vs. RHEL4. What distribution
> are you running?

In the past I had a Linux Fedora 12 64 bits; it's traceback is here:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14944.html

Now I'm running the 32bits version of the same distro on the same
computer....and I get this:

$ vmd -debug
/usr/bin/which: no rlwrap in (<snip...>)
***
*** Running VMD in debugger, type 'run' at debugger prompt
***
GNU gdb (GDB) Fedora (7.0.1-45.fc12)
<...snip...>
(gdb) run
Starting program: /opt/vmd/lib/vmd/vmd_LINUX
warning: .dynamic section for "/usr/lib/libstdc++.so.6" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/usr/lib/libfontconfig.so.1" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
warning: .dynamic section for "/lib/libexpat.so.1" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
[Thread debugging using libthread_db enabled]
Info) VMD for LINUX, 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: 5138MB (85%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
warning: .dynamic section for "/usr/lib/libXcursor.so.1" is not at the expected address
warning: difference appears to be caused by prelink, adjusting expectations
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)
Found 1 plugins or data handlers in directory
    '/opt/vmd/lib/vmd/plugins/LINUX/molfile'.

Program received signal SIGSEGV, Segmentation fault.
0x00cb9db0 in XGetICValues () from /usr/lib/libX11.so.6
Missing separate debuginfos, use: debuginfo-install expat-2.0.1-8.fc12.i686 fontconfig-2.8.0-1.fc12.i686 freetype-2.3.11-3.fc12.i686 glibc-2.11.1-6.i686 libX11-1.3-1.fc12.i686 libXau-1.0.5-1.fc12.i686 libXcursor-1.1.10-1.fc12.i686 libXdamage-1.1.2-1.fc12.i686 libXext-1.1-2.fc12.i686 libXfixes-4.0.4-1.fc12.i686 libXft-2.1.13-4.fc12.i686 libXi-1.3-2.fc12.i686 libXrender-0.9.5-1.fc12.i686 libXxf86vm-1.1.0-1.fc12.i686 libdrm-2.4.18-2.fc12.i686 libgcc-4.4.3-4.fc12.i686 libselinux-2.0.90-5.fc12.i686 libstdc++-4.4.3-4.fc12.i686 libxcb-1.5-1.fc12.i686 mesa-dri-drivers-7.7-4.fc12.i686 mesa-libGL-7.7-4.fc12.i686 mesa-libGLU-7.7-4.fc12.i686
(gdb) where
#0 0x00cb9db0 in XGetICValues () from /usr/lib/libX11.so.6
#1 0x08340636 in Tk_HandleEvent ()
#2 0x0834112f in ?? ()
#3 0x08e65988 in ?? ()
#4 0x00000028 in ?? ()
#5 0xbfffee48 in ?? ()
#6 0x085bd848 in ?? ()
#7 0x083410e0 in ?? ()
#8 0x08e65980 in ?? ()
#9 0xbfffee48 in ?? ()
#10 0x083e7e80 in Tcl_ServiceEvent ()
Backtrace stopped: frame did not save the PC

I indeed also use an input method, IBus, for allowing me to input Korean.
Is there some bad interference with the input method?
Then how come other software is not affected by the input method?

Regards,
Rob.