VMD-L Mailing List

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_dqi.ufla.br)
Date: Fri May 03 2013 - 13:36:24 CDT

Hi Aric.

It seems to me that you did not use the correct procedure to install the proprietary NVidia driver v. 310.44. Therefore, I suggest:

1) uninstall cuda and undo all the modifications that you have done to configuration files, blacklists etc.
2) do the same to the proprietary NVidia driver v. 310.44
3) install nouveau (default driver from Xorg) from ubuntu repository. Although we need to blacklist nouveau, we must have it installed because there are some dependencies without which Ubuntu probably will not work correctly.
4) Supposing you have done everything correctly (restart the computer and check), you are now ready to install the proprietary NVidia driver v. 310.44
5) sudo apt-get install build-essential linux-source linux-headers-`uname -r`
6) sudo shutdown -r now
7) sudo apt-get install dkms #If you do not install dkms you will probably have to re-install nvidia driver after any update of the linux source/linux headers.
8) sudo cp /etc/default/grub /etc/default/grub-original
9) sudo cp /boot/grub/grub.cfg /boot/grub/grub.cfg-original
10) sudo cp /etc/init/rc-sysinit.conf /etc/init/rc-sysinit.conf-original
11) sudo gedit /etc/default/grub

a) change
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash”
to
GRUB_CMDLINE_LINUX_DEFAULT="text rdblacklist=nouveau nouveau.modeset=0”

b) change
GRUB_HIDDEN_TIMEOUT=0
GRUB_HIDDEN_TIMEOUT_QUIET=true
to
#GRUB_HIDDEN_TIMEOUT=0
#GRUB_HIDDEN_TIMEOUT_QUIET=true

c) change
#GRUB_TERMINAL=console
to
GRUB_TERMINAL=console

12) sudo update-grub
13) sudo gedit /etc/modprobe.d/disable-nouveau.conf

write the following commands and save the file:
blacklist nouveau
options nouveau modeset=0

14) sudo shutdown -r now # As you are using "text" instead of "quiet splash" in your grub file, your machine will restart in text mode
15) Go to the directory where you have downloaded the nvidia driver and:
sudo sh NVIDIA-Linux-x86_64-310.44.run
Three questions will appear during the installation:
a) Do you want to use dkms ? I suggest yes.
b) Do you want to install OpenGL 32 bits ? I suggest yes.
c) Do you want to make alterations to the configuration file of Xorg/Xserver ? I suggest yes.

16) sudo shutdown -r now
17) As you are using "text" instead of "quiet splash" in your grub file, your machine will restart in text mode. Thus, type:
sudo service lightdm start
18) If you do not like to start in text mode, just change the grub file and update it (sudo update-grub).

Good luck.

Best regards.

Denilson.

Denilson F. Oliveira
Laboratório de produtos Naturais
Departamento de Química
Universidade Federal de Lavras
Caixa Postal 3037
Lavras (A CIDADE DAS QUEIMADAS) - MG - BRASIL
Fone: 55-35-3829-1623
Fax: 55-35-3829-1271
e-mail: denilson_at_dqi.ufla.br

-------- Mensagem original -------- Assunto: vmd-l: VMD Crash with Ubuntu
12.04 LTS and NVidia 310.44 driver. Data: Thu, 02 May 2013 20:17:49 +0900 De:
Aric Newton <agnewton_at_berkeley.edu> <agnewton_at_berkeley.edu> Para:
vmd-l_at_ks.uiuc.edu

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 libdbe.so
        -rw-r--r-- 1 root root 22776 Apr 11 22:08 libdri2.so
        -rw-r--r-- 1 root root 43704 Apr 11 22:08 libdri.so
        -rw-r--r-- 1 root root 106032 Apr 11 22:08 libextmod.so
        lrwxrwxrwx 1 root root 16 Apr 27 22:31 libglx.so ->
        libglx.so.310.44
        -rwxr-xr-x 1 root root 9661320 Apr 27 22:31 libglx.so.310.44
        -rw-r--r-- 1 root root 31200 Apr 11 22:08 librecord.so

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:
        newton_at_newton-desktop:~$

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
appreciated.

Aric

                Info) Multithreading available, 12 CPUs detected.
                Info) Free system memory: 11262MB (93%)
                Info) Creating CUDA device pool and initializing
hardware...
                Info) Detected 1 available CUDA accelerator:
                Info) [0] GeForce GTX 550 Ti 4 SM_2.1 @ 1.80 GHz, 1.0GB
RAM,
                KTO, OIO,
                ZCP
                Warning) Detected X11 'Composite' extension: if
incorrect
                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
PS
                GLSL(OVFGS)
                Info) Full GLSL rendering mode is available.
                Info) Textures: 2-D (16384x16384), 3-D
(2048x2048x2048),
                Multitexture
                (4)
                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
website
#http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/.
blacklist vga16fb
blacklist nouveau
blacklist rivafb
blacklist nvidiafb
blacklist rivatv