ChimeraX OpenGL startup issue after updating system to Ubuntu 20.04

[luca.jovine@…]

Hello,

This is Luca Jovine from Karolinska Institutet in Stockholm. I recently updated one of our main machines from ubuntu 16.04 LTS to 20.04 LTS, and after this I can no longer run either Chimera (1.14) or ChimeraX (1.1). Clearly, in both cases there is an issue with OpenGL:

> chimera
X Error of failed request:  GLXBadCurrentWindow
  Major opcode of failed request:  148 (GLX)
  Minor opcode of failed request:  5 (X_GLXMakeCurrent)
  Serial number of failed request:  1545
  Current serial number in output stream:  1545
>

>chimerax
NOTE: available bundle cache has not been initialized yet
ERROR: ChimeraX requires OpenGL graphics version 3.3.
Your computer graphics driver provided version 1.4
Try updating your graphics driver.
WARNING: No statusbar messages will be shown due to inadequate OpenGL
WARNING: QOpenGLShader::compile(Vertex): failed
WARNING: QOpenGLShader::compile(Fragment): failed
WARNING: Could not link shader program:
 ""
Fatal Python error: Segmentation fault

Current thread 0x00007fe188bf5740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 204 in build
  File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/ChimeraX_main.py", line 626 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/ChimeraX_main.py", line 919 in <module>
  File "/usr/lib/ucsf-chimerax/lib/python3.7/runpy.py", line 85 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.7/runpy.py", line 193 in _run_module_as_main
Segmentation fault (core dumped)
>

However, looking at the above, I do not understand why my graphics drivers should be outdated, because on this machine (which has 2 x NVIDIA GTX 1080 Ti GPUs, and CUDA 10.2) I have installed the last (long-lived) driver version:

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 450.80.02    Driver Version: 450.80.02    CUDA Version: 11.0     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  GeForce GTX 108...  Off  | 00000000:0A:00.0 Off |                  N/A |
| 21%   55C    P2    60W / 250W |    183MiB / 11178MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   1  GeForce GTX 108...  Off  | 00000000:42:00.0 Off |                  N/A |
| 20%   31C    P8     8W / 250W |    162MiB / 11175MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+

I must be doing something wrong, but what? Any help would be very appreciated!

Thanks and best regards,

Luca

----------------------------------------------------------------------
Luca Jovine, Ph.D.
Professor of Structural Biology, Member of EMBO and the Nobel Assembly
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jovine@ki.se<mailto:luca.jovine@ki.se>
W3: http://jovinelab.org
----------------------------------------------------------------------






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[Tom Goddard]

This is a problem with the graphics driver, not with Chimera or ChimeraX. It might be related to having two graphics cards. You might run glxinfo to see what it says about your graphics, maybe it will give a clue. There is a glxgears program for testing whether OpenGL is working at all. You may want to try with a single graphics card in the machine. Also you could search for OpenGL not working in ubuntu 20 with two graphics cards. Sometimes there can be a problem where there is more than one graphics driver installed, or when the old graphics driver was not completely removed before the new one was installed.

Our expert on OpenGL graphics driver on Linux, Greg Couch, is on vacation all this week.

[luca.jovine@…]

Thanks for the follow-up! I do not think this is related to having two GPUs, because I had them before the OS upgrade and they worked just fine with both Chimera and ChimeraX. In any case, glxgears show the 3 rotating gears but glmark2 reports:

** GLX does not support GLX_EXT_swap_control or GLX_MESA_swap_control!
** Failed to set swap interval. Results may be bounded above by refresh rate.
Error: Glmark2 needs OpenGL(ES) version >= 2.0 to run (but version string is: '1.4 (2.1 Mesa 13.0.2)')!
Error: main: Could not initialize canvas

Maybe something messed up my drivers during the update? Just in case, I will try wiping out the drivers (and CUDA) completely, then re-install them.
Best regards,
Luca




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[Tom Goddard]

The important part of the glmark2 output is the OpenGL version string 1.4 (2.1 Mesa 13.0.2) which indicates that your Nvidia driver is not being used. And OpenGL 1.4 is from 2002 so almost no modern OpenGL program will run with that. glxgears is ancient and can probably run with even older OpenGL.

The swap_control messages are not important -- those extensions didn't even exist in OpenGL 1.4 and they just allow OpenGL to not be locked to the display refresh rate.

Your approach sounds best, completely uninstall the Nvidia drivers and reinstall.

There has been a discussion on the ChimeraX mailing list this week about using two Nvidia graphics cards on Ubuntu 20.04. Shasha Feng has that working but is trying to choose which graphics card ChimeraX uses. His email indicates he uses Nvidia-SMI driver 450.66 while you are using a newer version 450.80.0

​https://plato.cgl.ucsf.edu/pipermail/chimerax-users/2020-November/001705.html

[luca.jovine@…]

Hello again,

Just wanted to let you know that, after wiping out all CUDA and NVIDIA driver files from the system and reinstalling both from scratch, both Chimera and ChimeraX started working again (with both GPUs in). So I guess there must’ve been some kind of conflict generated during the OS upgrade.

Thanks and have a good weekend,

Luca




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[Tom Goddard]

Thanks for the info. Glad it is working now.