Cytoflow 1.2 fails to launch

[protist]

PLATFORM (Mac, PC, Linux, other)

Linux

OPERATING SYSTEM (eg OSX 10.7, Windows 8.1)

Arch Linux, up to date

SEVERITY (Critical? Major? Minor? Enhancement?)

Critical

DESCRIPTION:

• What were you trying to do? Launch Cytoflow 1.2
• What happened? A dialog box is shown with an error, and Cytoflow fails to launch.
• What did you expect to happen? Cytoflow to launch

Don't forget to attach the log file to this bug report!

The dialog box contains

An exception has occurred. Please report a problem from the Help menu!

Afterwards, may need to restart Cytoflow to continue working.

Qt message: Failed to create OpenGL context for format QSurfaceFormat(version 2.0, options QFlagsQSurfaceFormat::FormatOption(), depthBufferSize 24, redBufferSize -1, greenBufferSize -1, blueBufferSize -1, alphaBufferSize -1, stencilBufferSize 8, samples 0, swapBehavior QSurfaceFormat::SwapBehavior(DefaultSwapBehavior), swapInterval 1, profile QSurfaceFormat::OpenGLContextProfile(NoProfile))

And the command line has the following

libGL error: MESA-LOADER: failed to open iris: /tmp/cytoflow-1.2/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib/dri/iris_dri.so) (search paths /usr/lib/dri, suffix _dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open iris: /tmp/cytoflow-1.2/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib/dri/iris_dri.so) (search paths /usr/lib/dri, suffix _dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open swrast: /tmp/cytoflow-1.2/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib/dri/swrast_dri.so) (search paths /usr/lib/dri, suffix _dri)
libGL error: failed to load driver: swrast
2022-02-10 13:53:52,690 CRITICAL:root:Qt message: Failed to create OpenGL context for format QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize 24, redBufferSize -1, greenBufferSize -1, blueBufferSize -1, alphaBufferSize -1, stencilBufferSize 8, samples 0, swapBehavior QSurfaceFormat::SwapBehavior(DefaultSwapBehavior), swapInterval 1, profile  QSurfaceFormat::OpenGLContextProfile(NoProfile)) 
composeAndFlush: makeCurrent() failed
composeAndFlush: makeCurrent() failed
composeAndFlush: makeCurrent() failed
Fatal Python error: Aborted

Thread 0x00007fb763fff640 (most recent call first):
  File "threading.py", line 302 in wait
  File "threading.py", line 558 in wait
  File "matplotlib_backend_local.py", line 200 in send_to_remote
  File "threading.py", line 870 in run
  File "threading.py", line 932 in _bootstrap_inner
  File "threading.py", line 890 in _bootstrap

Thread 0x00007fb778b67640 (most recent call first):
  File "selectors.py", line 415 in select
  File "multiprocessing/connection.py", line 931 in wait
  File "multiprocessing/connection.py", line 424 in _poll
  File "multiprocessing/connection.py", line 257 in poll
  File "matplotlib_backend_local.py", line 165 in listen_for_remote
  File "threading.py", line 870 in run
  File "threading.py", line 932 in _bootstrap_inner
  File "threading.py", line 890 in _bootstrap

Thread 0x00007fb7793a8640 (most recent call first):
  File "threading.py", line 302 in wait
  File "queue.py", line 170 in get
  File "workflow/workflow.py", line 361 in send_main
  File "threading.py", line 870 in run
  File "threading.py", line 932 in _bootstrap_inner
  File "threading.py", line 890 in _bootstrap

Thread 0x00007fb779ba9640 (most recent call first):
  File "selectors.py", line 415 in select
  File "multiprocessing/connection.py", line 931 in wait
  File "multiprocessing/connection.py", line 424 in _poll
  File "multiprocessing/connection.py", line 257 in poll
  File "workflow/workflow.py", line 290 in recv_main
  File "threading.py", line 870 in run
  File "threading.py", line 932 in _bootstrap_inner
  File "threading.py", line 890 in _bootstrap

Thread 0x00007fb77c748640 (most recent call first):
  File "multiprocessing/popen_fork.py", line 27 in poll
  File "multiprocessing/popen_fork.py", line 47 in wait
  File "multiprocessing/process.py", line 149 in join
  File "run.py", line 303 in monitor_remote_process
  File "threading.py", line 870 in run
  File "threading.py", line 932 in _bootstrap_inner
  File "threading.py", line 890 in _bootstrap

Thread 0x00007fb77cf89640 (most recent call first):
  File "multiprocessing/connection.py", line 379 in _recv
  File "multiprocessing/connection.py", line 414 in _recv_bytes
  File "multiprocessing/connection.py", line 216 in recv_bytes
  File "multiprocessing/queues.py", line 97 in get
  File "logging/handlers.py", line 1431 in dequeue
  File "logging/handlers.py", line 1482 in _monitor
  File "threading.py", line 870 in run
  File "threading.py", line 932 in _bootstrap_inner
  File "threading.py", line 890 in _bootstrap

Current thread 0x00007fb7d8077b80 (most recent call first):
  File "pyface/ui/qt4/tasks/main_window_layout.py", line 217 in set_layout_for_area
  File "pyface/ui/qt4/tasks/main_window_layout.py", line 153 in set_layout
  File "pyface/ui/qt4/tasks/task_window_backend.py", line 169 in set_layout
  File "pyface/ui/qt4/tasks/task_window_backend.py", line 123 in _layout_state
  File "pyface/ui/qt4/tasks/task_window_backend.py", line 82 in show_task
  File "pyface/tasks/task_window.py", line 158 in activate_task
  File "pyface/tasks/task_window.py", line 348 in set_window_layout
  File "envisage/ui/tasks/tasks_application.py", line 269 in create_window
  File "envisage/ui/tasks/tasks_application.py", line 353 in _create_windows
  File "envisage/ui/tasks/tasks_application.py", line 175 in run
  File "cytoflow_application.py", line 163 in run
  File "run.py", line 293 in run_gui
  File "run.py", line 399 in <module>
[1]    21315 abort (core dumped)  ./cytoflow

I was trying to test the fix to #320. I firstly retested the older version 1.1.1, which launched fine (and I could indeed replicate the problem reported in that issue). I then downloaded the current version 1.2, which failed to launch as above.

[protist]

I needed to do more flow analysis lately, so I tried this again. I'm still getting the same error. I did some more troubleshooting.

On my system, libstdc++.so.6 is located in /usr/lib/. From the logs above, it seemed like Cytoflow was looking in /usr/lib/dri/, so I tried creating a symlink.

cd /usr/lib/dri
sudo ln -s ../libstdc++.so.6 .

but this still failed. However, if I manually preload it, it seems to launch fine.

export LD_PRELOAD=/usr/lib/libstdc++.so.6
./cytoflow

[SamSeven777]

Hi, I had a similar issue and I fixed it.

PLATFORM (Mac, PC, Linux, other)

Linux

OPERATING SYSTEM (eg OSX 10.7, Windows 8.1)

Fedora 39

Command line output

MESA-LOADER: failed to open radeonsi: /tmp/cytoflow-gui-1.2.linux_x86-64/cytoflow-1.2/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib64/dri/radeonsi_dri.so) (search paths /usr/lib64/dri, suffix _dri)
failed to load driver: radeonsi
MESA-LOADER: failed to open swrast: /tmp/cytoflow-gui-1.2.linux_x86-64/cytoflow-1.2/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib64/dri/swrast_dri.so) (search paths /usr/lib64/dri, suffix _dri)
failed to load driver: swrast
Qt message: Failed to create OpenGL context for format QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize 24, redBufferSize -1, greenBufferSize -1, blueBufferSize -1, alphaBufferSize -1, stencilBufferSize 8, samples 0, swapBehavior QSurfaceFormat::SwapBehavior(DefaultSwapBehavior), swapInterval 1, profile  QSurfaceFormat::OpenGLContextProfile(NoProfile))

Testing

strings /tmp/cytoflow-gui-1.2.linux_x86-64/cytoflow-1.2/libstdc++.so.6 | grep GLIBCXX
The output has no GLIBCXX_3.4.29

strings /usr/lib64/libstdc++.so.6 | grep GLIBCXX
This output has GLIBCXX_3.4.29

Solution

I replaced the /tmp/cytoflow-gui-1.2.linux_x86-64/cytoflow-1.2/libstdc++.so.6 with /usr/lib64/libstdc++.so.6

So I suppose that the libstdc++.so.6 should be updated.

[bpteague]

Yup, @protist found the right workaround. The DRI drivers need the system version of libstdc++ -- you can either the one that comes with cytoflow or replace it with the one in /usr/lib64. I think there's an underlying issue in conda's QT package -- I'm leaving this bug open so I will remember to fix the packaging.