VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Mar 11 2019 - 18:15:16 CDT

I can vouch for Brian's approach. It is what I myself have used for the past several Ubuntu iterations I've had. One comment for those of you working in 18.04 land, is that lightdm was replaced by gdm, and that dropping to a terminal now requires ctrl+alt+f2 or ctrl+alt+f3 (f1 gets you back your current X-windows session).

-Josh

On 2019-03-11 16:56:27-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

I might be able to help, although I have not wrestled with this issue since Ubuntu 14.04 or so and with a totally different Quadro model (a 4400 I think?). I should also add that this is not expert advice since I myself cobbled it together from various "Googled" sources. My issue was also a bit more severe in that I actually wanted to compile Cuda code (i.e. install the Cuda toolkit) and not just update the driver.
1) Download the shell script installer for the correct cuda driver from Nvidia
2) if you have FOSS nouveau (as in most new installs)
$ sudo vim /etc/modprobe.d/blacklist.conf
and edit its contents to contain
"""
blacklist nouveau
blacklist lbm-nouveau
options nouveau modeset=0
alias nouveau off
alias lbm-nouveau off
"""
$ echo options nouveau modeset=0 | sudo tee -a /etc/modprobe.d/nouveau-kms.conf
$ sudo update-initramfs -u
3) reboot and drop to terminal (ctrl+alt+F1)
if you do not blacklist nouveau, it is possible that the screen will hang when you drop to terminal, you'll just have to reboot and fix this
4) # turn off the xserver, the nvidia installers will take their time and then
# error telling you do to this anyway
$ sudo service lightdm stop

5) This is probably fixed in modern Ubuntu, but I have a note for it anyway:
# The following were missing and/or broken on my system, it would appear that
# the drivers will work w/o this, but cuda toolkit may not
#
$ sudo apt-get install libglu1-mesa libxi-dev libxmu-dev
$ sudo find / -name 'libGLU*'
# the above cmd led me to do this -->
$ sudo ln -s /usr/lib/x86_64-linux-gnu/libGLU.so.1 /usr/lib/x86_64-linux-gnu/libGLU.so
6) Now you can actually run the installer NB: cuda toolkit comes with a driver also, although it may not be the super new one that the website recommends. Back in the day I ran something like:
$ chmod u+x cuda_6.5.14_linux_64.run
$ sudo ./cuda_6.5.14_linux_64.run
Restart the xserver
$ sudo service lightdm start

A MAJOR CAVEAT ON THE ABOVE. Installing your own driver generally leads to a mismatch between your graphics driver and the Linux kernel headers, which do in fact update from time to time. I had to routinely perform this whole process all over again each and every time the kernel headers were updated, otherwise my graphics would go totally wonky and not match my monitor settings. There was talk of this being fixed in Ubuntu for over 10 years, but obviously some cases still fall through. If you are going through this process you can probably bet that your hardware doesn't support the auto-update procedure correctly.
HTH,
BKR

On Mon, Mar 11, 2019 at 5:07 PM John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:
Hi Shivam,
  I'm not personally an Ubuntu expert (we run RHEL derivatives here), however
there is usually a documented method you can follow to replace the
distribution-provided graphics driver with the latest NVIDIA-provided drivers.
This can be complicated in some cases, but it would resolve the
specific problem you're having where Ubuntu are far far behind where the
latest NVIDIA drivers are.

The situation you have described having run into sounds like
a version of the problems caused by conflicts between the open source
"nouveau" driver and the proprietary NVIDIA drivers (which are what
you need to use for VMD). I've pasted in some potentially useful links
below.

Perhaps an Ubuntu wizard can give more specific or better guidance here.

I don't know if the "PPA" upstream repo for Ubuntu is still active,
but this web site has some instructions that might be worth trying:
  https://websiteforstudents.com/install-proprietary-nvidia-gpu-drivers-on-ubuntu-16-04-17-10-18-04/
  https://itsfoss.com/install-additional-drivers-ubuntu/

Here is another page that similarly provides some guidance, albeit much
more hard-core (a fresh OS install) aimed at using the proprietary
NVIDIA drivers exclusively:
  https://www.pugetsystems.com/labs/hpc/The-Best-Way-To-Install-Ubuntu-16-04-with-NVIDIA-Drivers-and-CUDA-1097/

Best,
  John Stone
  vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>

On Mon, Mar 11, 2019 at 05:27:59AM +0000, SHIVAM TIWARI wrote:
> Hi, John
> Although my issue is not about vmd but it is related to vmd. I have Nvidia
> Quadro K620 and I am using Ubuntu 16.04 LTS, some time back I have
> installed the latest drivers available for my graphics card from Nvidia's
> website, but after that my OS started having issues with boot (whenever I
> try logging in my system, it will go in an endless loop but it will not
> log in, and I have to restart my system), so I searched for the solution,
> and I found that the issue is due to the proprietary graphics driver which
> are somehow not compatible with Ubuntu, and you have to use the drivers
> available in the ubuntu's repository(which is pretty outdated). So I
> uninstalled the driver and installed the driver available on Ubuntu's
> repository and then I didn't have that issue, but then I have to use an
> outdated driver version (384.130). so is there any workaround you can
> suggest for this.
> regards
> shivam
>
> --------------------------------------------------------------------------
>
> From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of John
> Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>>
> Sent: Tuesday, February 26, 2019 8:10 AM
> To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
> Subject: vmd-l: RTX-accelerated VMD 1.9.4 test build for 64-bit Linux
> posted...
>
> Hi,
> Now that the NVIDIA drivers with RTX support are generally
> available, I have made a current 64-bit Linux test build of VMD 1.9.4
> (a29)
> that includes RTX hardware-accelerated ray tracing, and it is
> posted on the web site. To use this version you will need the latest
> NVIDIA 418.xx (where xx >= 30) driver version from the NVIDIA web site.
>
> VMD users should expect TachyonLOPtiX ray tracing performance gains
> that range as high as 8x faster when comparing the new RTX GPUs with
> the new VMD with prior versions of VMD running on so-called
> Pascal and Volta class NVIDIA GPUs.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [1]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [2]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/~johns/
> 2. http://www.ks.uiuc.edu/Research/vmd/ 

--
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/