All atom labels are displayed as rectangles (AMD Mesa[radeonsi] driver)

[dryndyk]

Hi all. I have been using PyMol for many years, usually compiling from source.
After the last compilation, I no longer see atom labels; instead, all are shown as rectangles.
Please help, or at least provide some guidance on what is wrong.

Thank you,
Dmitry

[JarrettSJohnson]

Are you compiling 3.1 or the latest commit on master? I don't see this observation on either. If you have more information regarding your hardware, that may help too.

[dryndyk]

Today I compiled the last commit, but the problem appeared earlier.
Notebooks Lenovo T14 and X13. I'm not sure about the big workstation; I'll check.
Ubuntu 24.04.4 -- not sure if it appeared with the Ubuntu update.

$ git clone https://github.com/schrodinger/pymol-open-source.git
$ git clone https://github.com/rcsb/mmtf-cpp.git
$ mv mmtf-cpp/include/mmtf* pymol-open-source/include/
$ cd pymol-open-source
$ sudo apt-get install git build-essential python3-dev libglew-dev libpng-dev libfreetype6-dev libxml2-dev libmsgpack-dev python3-pyqt5.qtopengl libglm-dev libnetcdf-dev
$python3 setup.py build install

I tried other methods with pip, but nothing works.

[JarrettSJohnson]

This may be related to the Ubuntu update since 24.04 defaults to the Wayland. Can you try xwayland?

[dryndyk]

I use MATE 1.26.2, it works on X11

$ loginctl show-session c2 -p Type
Type=x11

[dryndyk]

But they could remove some libraries.
It would be nice to understand what could cause all labels to be displayed incorrectly?
Some font problem?

[JarrettSJohnson]

Unsure. I'll have to get back to you perhaps next week--I don't have Ubuntu 24.04 on hand at the moment.

[dryndyk]

I will try to get something new. Check at my workstation with Ubuntu 24.04.3 (previous minor version) and it works OK! Very strange.
Actually, 24.04.4 is also OK. The other difference of large comp is NVIDIA card.

[dryndyk]

Problem detected.
OpenGL shaders do not work and should be switched off.

[JarrettSJohnson]

I'd be curious to know your Nvidia driver versions are (comparing the driver versions for those that work versus those that don't). Of course on our end, our primary rendering is with OpenGL shaders, so we cannot remove them nor have them off by default. If you need to: set use_shaders, 0 for now is your best bet if it is a driver issue while we can get this sorted.

Knowing this, are you able to use mesa drivers (as opposed to nvidia's) and see if that makes a difference for you?

[dryndyk]

NVIDIA works OK!
The problem with OpenGL shaders is with notebooks.

[JarrettSJohnson]

Ah, I see. It's not out of the realm of possibilities this is an intel or mesa driver bug. Can you post the driver information that PyMOL reports when it opens?

Should say something like

 Detected OpenGL version 2.1. Shaders available.
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   XXX
  GL_RENDERER: YYY
  GL_VERSION:  ZZZ

[dryndyk]

Detected OpenGL version 4.6. Shaders available.
Detected GLSL version 4.60.
OpenGL graphics engine:
GL_VENDOR: AMD
GL_RENDERER: AMD Radeon Graphics (radeonsi, rembrandt, LLVM 20.1.8, DRM 3.64, 6.17.0-14-generic)
GL_VERSION: 4.6 (Compatibility Profile) Mesa 25.2.8-0ubuntu0.25.10.1
Detected 16 CPU cores. Enabled multithreaded rendering.

[JarrettSJohnson]

Thanks! That's helpful (it's actually AMD!). I don't have a suitable card on hand that I can test this driver with, but I will try and ask around.