Your message dated Thu, 29 Jan 2026 16:26:15 +0100
with message-id <20260129162615.67ac1812@debian>
and subject line Re: Bug#1016549: python3-vtk9: disturbed access of
vtkGenericOpenGLRenderWindow
has caused the Debian Bug report #1016549,
regarding python3-vtk9: disturbed access of vtkGenericOpenGLRenderWindow
to be marked as done.
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If this is not the case it is now your responsibility to reopen the
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--
1016549: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016549
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: python3-vtk9
Version: 9.1.0+really9.1.0+dfsg2-4
Severity: normal
X-Debbugs-Cc: [email protected]
Dear Maintainer,
I whish to use an application[1] known to work with Python2.7.14 and libvtk6.3
(Xubuntu 18.04LTS) as well as Python3.6.7 libvtk7.1.1 (Windows) now with
Python3.10.5/vtk9.10 as provided by Debian 12/bookworm testing
(5.18.0-3-amd64). When running the Python application from the terminal, the
application should open a new window. Instead, the terminal reports
```
[ 3CBAD740]vtkOpenGLRenderWindow.c:499 ERR| vtkXOpenGLRenderWindow
(0x558a03b66170): Unable to find a valid OpenGL 3.2 or later implementation.
Please update your video card driver to the latest version. If you are using
Mesa please make sure you have version 11.2 or later and make sure your driver
in Mesa supports OpenGL 3.2 such as llvmpipe or openswr. If you are on windows
and using Microsoft remote desktop note that it only supports OpenGL 3.2 with
nvidia quadro cards. You can use other remoting software such as nomachine to
avoid this issue.
```
Searching for a solution, I identified a recent entry (Jul 18th) in the vtk
forum[2] which possibly could remove the cause for the problem by addition of
QSurfaceFormat::setDefaultFormat(QVTKOpenGLWindow::defaultFormat());
to file main.cpp of the underlying executable provided by Debian.
[1] https://github.com/nbehrnd/aRMSD
[1] https://discourse.vtk.org/t/unable-to-find-a-valid-opengl-3-2-or-later-
implementation/8857
-- System Information:
Debian Release: bookworm/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.18.0-3-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages python3-vtk9 depends on:
ii libc6 2.33-8
ii libgcc-s1 12.1.0-7
ii libopenmpi3 4.1.4-1
ii libpython3.10 3.10.5-1
ii libstdc++6 12.1.0-7
ii libtbb12 2021.5.0-12
ii libvtk9.1 9.1.0+really9.1.0+dfsg2-4
ii libvtk9.1-qt 9.1.0+really9.1.0+dfsg2-4
ii python3 3.10.5-3
ii python3-mpi4py 3.1.3-2+b1
python3-vtk9 recommends no packages.
Versions of packages python3-vtk9 suggests:
pn mayavi2 <none>
pn vtk9-doc <none>
pn vtk9-examples <none>
-- no debconf information
=============================================================================
aRMSD: Version 0.9.5
=============================================================================
A. Wagner, University of Heidelberg (2017)
forked by Norwid Behrnd (2018)
-------------------------------- Description --------------------------------
Key features:
* Parses data from various file formats
* Establishes consistency and matches coordinate sequences of two molecules
* Aligns two molecular structures based on the Kabsch algorithm
* Supports different weighting functions for the superposition
* Supports error propagation for experimental structures
* Generates different visualization types of the superposition results
* Writes outfiles that can be passed to other programs
* ... more features and changes can be found in the documentation
... this project is hosted on GitHub: https://github.com/armsd/aRMSD
... and https://github.com/nbehrnd/aRMSD
... documentation: http://armsd.rtfd.io
-----------------------------------------------------------------------------
*** Cite this program as:
A. Wagner, H.-J. Himmel, J. Chem. Inf. Model, 2017, 57, 428-438.
Release dates of the individual modules:
core module: '2017-01-03'
plot module: '2018-10-15'
log module: '2017-04-05'
Module check:
- numpy '1.21.5'
- VTK '9.1.0'
- matplotlib '3.5.2'
- uncertainties '3.1.6'
- openbabel '3.1.1'
> Starting program ...
-----------------------------------------------------------------------------
Enter the file name with extension for the first file (comp./model)
>> bzamid01.xyz
> 'bzamid01.xyz' has been loaded successfully! (#Atoms: 16)
Enter the file name with extension for the second file (exp./reference)
>> bzamid02.xyz
> 'bzamid02.xyz' has been loaded successfully! (#Atoms: 16)
-----------------------------------------------------------------------------
... Files have been loaded!
-----------------------------------------------------------------------------
> Checking for coordinate standard deviations...
... No standard deviations were found!
-----------------------------------------------------------------------------
Checking length unit of xyz coordinates ...
The coordinate unit is [Angstrom]
Checking length unit of xyz coordinates ...
The coordinate unit is [Angstrom]
> The current status was saved successfully!
-----------------------------------------------------------------------------
=============== Consistency Checks and Structural Modification ==============
-----------------------------------------------------------------------------
> Performing consistency checks ... (Number of atoms: 16, 16)
There are (7 & 7) H atoms in the molecules
> The structures of both molecules are consistent.
-----------------------------------------------------------------------------
What should happen to the remaining 7 H-atoms?
-----------------------------------------------------------------------------
Info: The exclusion of H-atoms in RMSD calculations is recommended if
they were not located and refined in the X-ray experiment
-----------------------------------------------------------------------------
0 ... remove all hydrogen atoms (7)
1 ... remove all hydrogen atoms bound to carbon (5)
3 ... keep all hydrogen atoms
-----------------------------------------------------------------------------
>> Enter your choice: 1
Removing all hydrogen atoms bound to carbon ...
All respective hydrogen atoms (5 & 5) have been removed!
> The molecules were rotated into 'Standard Orientation' ...
> The current status was saved successfully!
-----------------------------------------------------------------------------
================ Symmetry Adjustments & Sequence Matching ===================
-----------------------------------------------------------------------------
-6 Set number of deviations which are highlighted in the plot (current = 5)
-5 Load the saved status (save point available: 'True')
-4 Change plot settings
-3 Manually swap atoms in Model structure
-2 Change matching algorithm or solver
-1 Match molecular sequences based on current alignment
-----------------------------------------------------------------------------
Current matching algorithm : 'distance'
Current matching solver : 'hungarian'
Structures were matched : 'False'
-----------------------------------------------------------------------------
0 ... exit the menu (no return)
1 ... inversion at the origin
2 ... reflection at the xy plane
3 ... reflection at the xz plane
4 ... reflection at the yz plane
5 ... rotation around the x axis
6 ... rotation around the y axis
7 ... rotation around the z axis
8 ... show the molecules again
-----------------------------------------------------------------------------
10 ... save current changes (status was saved: 'True')
20 ... export structures
-----------------------------------------------------------------------------
> Results are now shown ... close the pop-up window to continue!
> Press the 's' button to save the scene as .png file or 'h' for help.
2022-08-02 15:55:29.951 ( 22.541s) [
3CBAD740]vtkOpenGLRenderWindow.c:499 ERR| vtkXOpenGLRenderWindow
(0x558a03b66170): Unable to find a valid OpenGL 3.2 or later implementation.
Please update your video card driver to the latest version. If you are using
Mesa please make sure you have version 11.2 or later and make sure your driver
in Mesa supports OpenGL 3.2 such as llvmpipe or openswr. If you are on windows
and using Microsoft remote desktop note that it only supports OpenGL 3.2 with
nvidia quadro cards. You can use other remoting software such as nomachine to
avoid this issue.
2022-08-02 15:55:29.951 ( 22.541s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.951 ( 22.541s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.953 ( 22.542s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.953 ( 22.543s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.953 ( 22.543s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.955 ( 22.544s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.955 ( 22.544s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.962 ( 22.551s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.962 ( 22.551s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.965 ( 22.555s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.965 ( 22.555s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:29.965 ( 22.555s) [ 3CBAD740]
vtkOpenGLState.cxx:1795 WARN| Hardware does not support the number of textures
defined.
2022-08-02 15:55:30.015 ( 22.605s) [ 3CBAD740]
vtkShaderProgram.cxx:437 ERR| vtkShaderProgram (0x558a046fa800): 1: #version
150
2: #ifndef GL_ES
3: #define highp
4: #define mediump
5: #define lowp
6: #endif // GL_ES
7: #define attribute in
8: #define varying out
9:
10:
11: /*=========================================================================
12:
13: Program: Visualization Toolkit
14: Module: vtkPolyDataVS.glsl
15:
16: Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
17: All rights reserved.
18: See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
19:
20: This software is distributed WITHOUT ANY WARRANTY; without even
21: the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
22: PURPOSE. See the above copyright notice for more information.
23:
24: =========================================================================*/
25:
26: in vec4 vertexMC;
27:
28:
29:
30: // frag position in VC
31: out vec4 vertexVCVSOutput;
32:
33: // optional normal declaration
34: //VTK::Normal::Dec
35: in vec3 normalMC;
36: uniform mat3 normalMatrix;
37: out vec3 normalVCVSOutput;
38:
39: // extra lighting parameters
40: //VTK::Light::Dec
41:
42: // Texture coordinates
43: //VTK::TCoord::Dec
44:
45: // material property values
46: //VTK::Color::Dec
47:
48: // clipping plane vars
49: //VTK::Clip::Dec
50:
51: // camera and actor matrix values
52: uniform mat4 MCDCMatrix;
53: uniform mat4 MCVCMatrix;
54:
55: // Apple Bug
56: //VTK::PrimID::Dec
57:
58: // Value raster
59: //VTK::ValuePass::Dec
60:
61: // picking support
62: //VTK::Picking::Dec
63:
64: void main()
65: {
66: //VTK::CustomBegin::Impl
67:
68: //VTK::Color::Impl
69:
70: normalVCVSOutput = normalMatrix * normalMC;
71: //VTK::Normal::Impl
72:
73: //VTK::TCoord::Impl
74:
75: //VTK::Clip::Impl
76:
77: //VTK::PrimID::Impl
78:
79: vertexVCVSOutput = MCVCMatrix * vertexMC;
80: gl_Position = MCDCMatrix * vertexMC;
81:
82:
83: //VTK::ValuePass::Impl
84:
85: //VTK::Light::Impl
86:
87: //VTK::Picking::Impl
88:
89: //VTK::CustomEnd::Impl
90: }
2022-08-02 15:55:30.015 ( 22.605s) [ 3CBAD740]
vtkShaderProgram.cxx:438 ERR| vtkShaderProgram (0x558a046fa800): 0:1(10):
error: GLSL 1.50 is not supported. Supported versions are: 1.10, 1.20, and 1.00
ES
--- End Message ---
--- Begin Message ---
Dear Drew
thank you for your follow up. Hereby I close this bug.
At present, aRMSD is used within a "time capsule" of an old instance of
Xubuntu, or dedicated copy of WinPython and corresponding dependencies
preserved elsewhere[1] -- both to work with Python 3.6 set up and called
separately from the interpreter used by default. Meanwhile, the interaction
between Python and vtk evolved to a somewhat different syntax to the one the
original author of aRMSD[2] used. Today, AI might assist in a more general
modernization of the project, though this is a different story.
[1] https://github.com/nbehrnd/aRMSD-minimalWindowsSupport
[2] https://github.com/armsd/aRMSD
--- End Message ---
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