From: Aric Newton (
Date: Thu May 02 2013 - 06:17:49 CDT

VMD users,
I am experiencing a variant of the problem documented last weekend with
Xubuntu/ Kubuntu (and perhaps related to this week's unanswered post re:
Ubuntu 12.04). I've followed the recommended diagnostic and workaround
procedures, but have not had any luck in remedying the problem.
I am running Ubuntu 12.04.03 LTS (64-bit), with an NVidia GeForce GTX
550 Ti GPU. The proprietary NVidia driver v. 310.44 is installed as
well as the CUDA 5.0 Toolkit. I have purged the nvidia drivers from the
Ubuntu distro (sudo apt-get purge nvidia*). I have also blacklisted a
number of modules int he /etc/modprobe.d file that were suggested for
the proper running CUDA 5.0. These modules were leftover/ legacy
modules from my 10.04 LTS.

        blacklist vga16fb
        blacklist nouveau
        blacklist rivafb
        blacklist nvidiafb
        blacklist rivatv

I've followed the advice of Denilson and created a symlink to avoid
having Xorg overwrite the link (content
of /usr/lib/xorg/modules/extensions below).

        newton_at_newton-desktop:/usr/lib/xorg/modules/extensions$ ls -l
        total 9664
        -rw-r--r-- 1 root root 22840 Apr 11 22:08
        -rw-r--r-- 1 root root 22776 Apr 11 22:08
        -rw-r--r-- 1 root root 43704 Apr 11 22:08
        -rw-r--r-- 1 root root 106032 Apr 11 22:08
        lrwxrwxrwx 1 root root 16 Apr 27 22:31 ->
        -rwxr-xr-x 1 root root 9661320 Apr 27 22:31
        -rw-r--r-- 1 root root 31200 Apr 11 22:08

Per the diagnostic check recommended by John, the output from the
glxinfo | grep commands are:

        newton_at_newton-desktop:~$ glxinfo | grep server
        server glx vendor string: NVIDIA Corporation
        server glx version string: 1.4
        server glx extensions:

        newton_at_newton-desktop:~$ glxinfo | grep client
        client glx vendor string: NVIDIA Corporation
        client glx version string: 1.4
        client glx extensions:

What other diagnostic test should I consider to repair my installation
of VMD? I the 310.44 driver still too "beta"? I can start VMD if it's
the first program launched on system startup. If I try to launch it
after other programs, then the system will "seize". I do get a Warning)
about the "Composite" extension when it does startup properly, but
disabling the "Composite" extension doesn't fix the problem (a sample
start-up is provided below). I suspect the answer is in a system log
file somewhere, but I am not sure which one to check. Your input is

                Info) Multithreading available, 12 CPUs detected.
                Info) Free system memory: 11262MB (93%)
                Info) Creating CUDA device pool and initializing
                Info) Detected 1 available CUDA accelerator:
                Info) [0] GeForce GTX 550 Ti 4 SM_2.1 @ 1.80 GHz, 1.0GB
                KTO, OIO,
                Warning) Detected X11 'Composite' extension: if
                display occurs
                Warning) try disabling this optional X server feature.
                Info) OpenGL renderer: GeForce GTX 550 Ti/PCIe/SSE2
                Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP
                Info) Full GLSL rendering mode is available.
                Info) Textures: 2-D (16384x16384), 3-D
                Info) Dynamically loaded 2 plugins in directory:
                Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile

# These blacklist modules have been added for the sake of the CUDA 5.0
# installation. These modules were identified/ specified from the
blacklist vga16fb
blacklist nouveau
blacklist rivafb
blacklist nvidiafb
blacklist rivatv