Add data fails in linux (wayland).

umgpy · January 31, 2023, 7:23pm

The data loading module fails after the first time and results in a blank window. Only way to fix it is to restart Slicer.

My platform is Fedora 36 (linux) with wayland.
Slicer version - Slicer-5.3.0-2023-01-28
I’m attaching the terminal output along with the slicer log to help solve this issue.

[usr@usr ~]$ ~/Software/Slicer-5.3.0-2023-01-28-linux-amd64/Slicer 
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/lib/Python/lib/python3.9/imp.py", line 169, in load_source
    module = _exec(spec, sys.modules[name])
  File "<frozen importlib._bootstrap>", line 613, in _exec
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewer.py", line 23, in <module>
    from MONAILabelReviewerLib.ImageData import ImageData
  File "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewerLib/__init__.py", line 14, in <module>
    from .ImageDataController import ImageDataController
  File "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewerLib/ImageDataController.py", line 19, in <module>
    from MONAILabelReviewerLib.ImageDataStatistics import ImageDataStatistics
ModuleNotFoundError: No module named 'MONAILabelReviewerLib.ImageDataStatistics'
loadSourceAsModule - Failed to load file "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewer.py"  as module "MONAILabelReviewer" !
Fail to instantiate module  "MONAILabelReviewer"
The following modules failed to be instantiated:
   MONAILabelReviewer
Switch to module:  "Welcome"
QXcbConnection: XCB error: 8 (BadMatch), sequence: 2117, resource id: 20971620, major code: 130 (Unknown), minor code: 3
QXcbConnection: XCB error: 8 (BadMatch), sequence: 2120, resource id: 20971620, major code: 130 (Unknown), minor code: 3
QXcbConnection: XCB error: 8 (BadMatch), sequence: 2136, resource id: 20971620, major code: 130 (Unknown), minor code: 3
QXcbConnection: XCB error: 8 (BadMatch), sequence: 2137, resource id: 20971620, major code: 130 (Unknown), minor code: 3
QXcbConnection: XCB error: 8 (BadMatch), sequence: 2166, resource id: 20971620, major code: 130 (Unknown), minor code: 3
QXcbConnection: XCB error: 8 (BadMatch), sequence: 2174, resource id: 20971620, major code: 130 (Unknown), minor code: 3

Slicer log

[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Session start time .......: 2023-01-31 09:34:49
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Slicer version ...........: 5.3.0-2023-01-28 (revision 31553 / 0f25e18) linux-amd64 - installed release
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Operating system .........: Linux / 5.17.13-300.fc36.x86_64 / #1 SMP PREEMPT Mon Jun 6 14:29:43 UTC 2022 / UTF-8 - 64-bit
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Memory ...................: 15365 MB physical, 8191 MB virtual
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - CPU ......................: AuthenticAMD AMD Ryzen 7 4800HS with Radeon Graphics, 8 cores, 16 logical processors
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - VTK configuration ........: OpenGL2 rendering, Sequential threading
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Qt configuration .........: version 5.15.2, with SSL, requested OpenGL 3.2 (core profile)
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Internationalization .....: disabled, language=
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Developer mode ...........: disabled
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Application path .........: /home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/bin
[DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Additional module paths ..: NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -   File "<string>", line 1, in <module>
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -   File "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/lib/Python/lib/python3.9/imp.py", line 169, in load_source
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -     module = _exec(spec, sys.modules[name])
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -   File "<frozen importlib._bootstrap>", line 613, in _exec
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -   File "<frozen importlib._bootstrap_external>", line 850, in exec_module
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -   File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -   File "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewer.py", line 23, in <module>
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -     from MONAILabelReviewerLib.ImageData import ImageData
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -   File "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewerLib/__init__.py", line 14, in <module>
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -     from .ImageDataController import ImageDataController
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -   File "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewerLib/ImageDataController.py", line 19, in <module>
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) -     from MONAILabelReviewerLib.ImageDataStatistics import ImageDataStatistics
[CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - ModuleNotFoundError: No module named 'MONAILabelReviewerLib.ImageDataStatistics'
[CRITICAL][Qt] 31.01.2023 09:34:54 [] (unknown:0) - loadSourceAsModule - Failed to load file "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewer.py"  as module "MONAILabelReviewer" !
[CRITICAL][Qt] 31.01.2023 09:34:54 [] (unknown:0) - Fail to instantiate module  "MONAILabelReviewer"
[CRITICAL][Qt] 31.01.2023 09:34:54 [] (unknown:0) - The following modules failed to be instantiated:
[CRITICAL][Qt] 31.01.2023 09:34:54 [] (unknown:0) -    MONAILabelReviewer
[DEBUG][Python] 31.01.2023 09:34:57 [Python] (/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/lib/Slicer-5.3/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 31.01.2023 09:34:57 [Python] (/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/lib/Slicer-5.3/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 31.01.2023 09:34:57 [] (unknown:0) - Switch to module:  "Welcome"
[WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2117, resource id: 20971620, major code: 130 (Unknown), minor code: 3
[WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2120, resource id: 20971620, major code: 130 (Unknown), minor code: 3
[WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2136, resource id: 20971620, major code: 130 (Unknown), minor code: 3
[WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2137, resource id: 20971620, major code: 130 (Unknown), minor code: 3
[WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2166, resource id: 20971620, major code: 130 (Unknown), minor code: 3
[WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2174, resource id: 20971620, major code: 130 (Unknown), minor code: 3

Thanks in advance!

jamesobutler · January 31, 2023, 8:18pm

@umgpy Did the observed behavior change after building Slicer from source? I saw that you mentioned this over on the GitHub issue.

github.com/Slicer/Slicer

Add data menu fails in wayland linux

opened 10:06AM - 31 Jan 23 UTC

umgpy

type:bug

## Summary The add data menu fails after loading the first time. Upon opening… the menu the second time it results in a blank window. Only way to fix this is to restart slicer. My system is using fedora with wayland. ## Steps to reproduce Open slicer -> open the add data menu -> close the menu and reopen again. ## Expected behavior Add data menu should not fail. ## Environment - Slicer version: 5.3.0-2023-01-28 (revision 31553 / 0f25e18) linux-amd64 - Operating system: Linux / 5.17.13-300.fc36.x86_64 I am attaching the terminal output and slicer log to help solve this is issue. ``` [usr@usr ~]$ ~/Software/Slicer-5.3.0-2023-01-28-linux-amd64/Slicer Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway. Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/lib/Python/lib/python3.9/imp.py", line 169, in load_source module = _exec(spec, sys.modules[name]) File "<frozen importlib._bootstrap>", line 613, in _exec File "<frozen importlib._bootstrap_external>", line 850, in exec_module File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed File "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewer.py", line 23, in <module> from MONAILabelReviewerLib.ImageData import ImageData File "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewerLib/__init__.py", line 14, in <module> from .ImageDataController import ImageDataController File "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewerLib/ImageDataController.py", line 19, in <module> from MONAILabelReviewerLib.ImageDataStatistics import ImageDataStatistics ModuleNotFoundError: No module named 'MONAILabelReviewerLib.ImageDataStatistics' loadSourceAsModule - Failed to load file "/home/usr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewer.py" as module "MONAILabelReviewer" ! Fail to instantiate module "MONAILabelReviewer" The following modules failed to be instantiated: MONAILabelReviewer Switch to module: "Welcome" QXcbConnection: XCB error: 8 (BadMatch), sequence: 2117, resource id: 20971620, major code: 130 (Unknown), minor code: 3 QXcbConnection: XCB error: 8 (BadMatch), sequence: 2120, resource id: 20971620, major code: 130 (Unknown), minor code: 3 QXcbConnection: XCB error: 8 (BadMatch), sequence: 2136, resource id: 20971620, major code: 130 (Unknown), minor code: 3 QXcbConnection: XCB error: 8 (BadMatch), sequence: 2137, resource id: 20971620, major code: 130 (Unknown), minor code: 3 QXcbConnection: XCB error: 8 (BadMatch), sequence: 2166, resource id: 20971620, major code: 130 (Unknown), minor code: 3 QXcbConnection: XCB error: 8 (BadMatch), sequence: 2174, resource id: 20971620, major code: 130 (Unknown), minor code: 3 ``` Slicer log ``` [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Session start time .......: 2023-01-31 09:34:49 [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Slicer version ...........: 5.3.0-2023-01-28 (revision 31553 / 0f25e18) linux-amd64 - installed release [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Operating system .........: Linux / 5.17.13-300.fc36.x86_64 / #1 SMP PREEMPT Mon Jun 6 14:29:43 UTC 2022 / UTF-8 - 64-bit [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Memory ...................: 15365 MB physical, 8191 MB virtual [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - CPU ......................: AuthenticAMD AMD Ryzen 7 4800HS with Radeon Graphics, 8 cores, 16 logical processors [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - VTK configuration ........: OpenGL2 rendering, Sequential threading [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Qt configuration .........: version 5.15.2, with SSL, requested OpenGL 3.2 (core profile) [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Internationalization .....: disabled, language= [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Developer mode ...........: disabled [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Application path .........: /home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/bin [DEBUG][Qt] 31.01.2023 09:34:49 [] (unknown:0) - Additional module paths ..: NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - Traceback (most recent call last): [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - File "<string>", line 1, in <module> [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - File "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/lib/Python/lib/python3.9/imp.py", line 169, in load_source [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - module = _exec(spec, sys.modules[name]) [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - File "<frozen importlib._bootstrap>", line 613, in _exec [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - File "<frozen importlib._bootstrap_external>", line 850, in exec_module [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - File "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewer.py", line 23, in <module> [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - from MONAILabelReviewerLib.ImageData import ImageData [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - File "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewerLib/__init__.py", line 14, in <module> [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - from .ImageDataController import ImageDataController [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - File "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewerLib/ImageDataController.py", line 19, in <module> [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - from MONAILabelReviewerLib.ImageDataStatistics import ImageDataStatistics [CRITICAL][Stream] 31.01.2023 09:34:54 [] (unknown:0) - ModuleNotFoundError: No module named 'MONAILabelReviewerLib.ImageDataStatistics' [CRITICAL][Qt] 31.01.2023 09:34:54 [] (unknown:0) - loadSourceAsModule - Failed to load file "/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/NA-MIC/Extensions-31553/MONAILabel/lib/Slicer-5.3/qt-scripted-modules/MONAILabelReviewer.py" as module "MONAILabelReviewer" ! [CRITICAL][Qt] 31.01.2023 09:34:54 [] (unknown:0) - Fail to instantiate module "MONAILabelReviewer" [CRITICAL][Qt] 31.01.2023 09:34:54 [] (unknown:0) - The following modules failed to be instantiated: [CRITICAL][Qt] 31.01.2023 09:34:54 [] (unknown:0) - MONAILabelReviewer [DEBUG][Python] 31.01.2023 09:34:57 [Python] (/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/lib/Slicer-5.3/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentEditor [DEBUG][Python] 31.01.2023 09:34:57 [Python] (/home/uusr/Software/Slicer-5.3.0-2023-01-28-linux-amd64/lib/Slicer-5.3/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentStatistics [DEBUG][Qt] 31.01.2023 09:34:57 [] (unknown:0) - Switch to module: "Welcome" [WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2117, resource id: 20971620, major code: 130 (Unknown), minor code: 3 [WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2120, resource id: 20971620, major code: 130 (Unknown), minor code: 3 [WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2136, resource id: 20971620, major code: 130 (Unknown), minor code: 3 [WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2137, resource id: 20971620, major code: 130 (Unknown), minor code: 3 [WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2166, resource id: 20971620, major code: 130 (Unknown), minor code: 3 [WARNING][Qt] 31.01.2023 09:35:07 [] (unknown:0) - QXcbConnection: XCB error: 8 (BadMatch), sequence: 2174, resource id: 20971620, major code: 130 (Unknown), minor code: 3 ```

umgpy · February 6, 2023, 2:34pm

Hello @jamesobutler not yet, I’ll try to build it this week. Shall report back soon!

Jens_Munk_Hansen · November 10, 2023, 6:56pm

I can build slicer on Debian 12 using wayland.

I use the following startup script

#!/bin/bash

__NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia QT_XCB_GL_INTEGRATION=xcb_egl QT_WAYLAND_SHELL_INTEGRATION=ivi-shell QT_WAYLAND_CLIENT_BUFFER_INTEGRATION=wayland-egl $@ -platform wayland

The first entries I use because I work on a laptop using hybrid graphics. Sometimes my entire computer freezes. I needed to install a different version for SSL to make it work.

pieper · November 10, 2023, 7:29pm

Interesting - maybe that should go in slicer’s readthedocs somewhere.

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Add data fails in linux (wayland).

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