Some boilerplate I have for similar issues:
Running Mathematica with the following options will work around the
problem in many instances:
mathematica -mesa -defaultvisual
If this works, then the problem is with 3D hardware acceleration.
If your computer uses a NVIDIA graphics card, try running Mathematica
with the following command:
$ env MATHEMATICA_GL_FBO=1 mathematica
Or similar for your shell.
If this works, you can try adding this environment variable to the
bashrc/cshrc/whatever. You may also wish to try upgrading the video
driver(s) or changing video driver from a closed-source version to the
open-source version, or vice versa.
If you are running multiple monitors, check /etc/X11/xorg.conf.
There is a known driver issue when "xinerama" is enabled. If you are
using an NVIDIA graphic card, press Ctrl+Alt+F1 (which switches to the
terminal), kill X (usually by running /etc/init.d/gdm stop, where "gdm"
could be "xdm", "slim", or "xdm", depending on the distribution),
then run the following:
# mv /etc/X11/xorg.conf /etc/X11/xorg.conf.backup
- restart the display manager (something like /etc/init.d/gdm start).
This will have only one screen configured.
- run the nvidia-settings command as root and
- set up the second screen using "TwinView",
- then save the changes to the Xorg configuration file.
The -mesa option causes the Mathematica graphics system to use a
software version of OpenGL, instead of a hardware-accelerated version
of OpenGL. This will significantly slow down both complex 2D graphics
and most 3D graphics.