VMD-L Mailing List

From: Aric Newton (agnewton_at_berkeley.edu)
Date: Sun May 05 2013 - 10:32:15 CDT

Denilson,

Thank you for the detailed instructions. Following your instructions,
my VMD installation is whole again. The restart in Step 6 never did
restart "clean"; but if I held the <SHIFT> key to enter the GRUB menu
during startup, I could complete the remaining steps as root. The
problem with step 6 probably indicates something else that was incorrect
in my system setup; I mention it only for someone else who may share the
problem I was having.

My thanks again.

Aric

On Fri, 2013-05-03 at 15:36 -0300, DENILSON FERREIRA DE OLIVEIRA wrote:
> 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