Milad4849
commented
6 months ago Hi @gemmawilson, It appears that the steinbock docker container is not able to run a GUI via X forwarding. Have you taken the steps stated in the documentation under 'Graphical user interfaces on Mac OS'?
I got the following error message when I run the steinbock apps ilastik command (see below). Would appreciate your help to troubleshoot! Thanks so much.
My docker alias is as below: alias steinbock="docker run -v /Users/gemmawilson/Dropbox/steinbock/data:/data --platform linux/amd64 -u $(id -u):$(id -g) -p 8888:8888 -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/home/steinbock/.Xauthority:ro -e DISPLAY=host.docker.internal:0 ghcr.io/bodenmillergroup/steinbock:0.16.1" export PATH=$PATH:/Library/Frameworks/Python.framework/Versions/3.12/bin/python3 alias python=/usr/bin/python3
Error message: gemmawilson@Gemmas-MacBook-Pro ~ % steinbock apps ilastik /opt/ilastik/ilastik-meta/lazyflow/lazyflow/classifiers/init.py:20: UserWarning: init: Could not import tiktorch classifier warnings.warn("init: Could not import tiktorch classifier") Starting ilastik from "/opt/ilastik". QXcbConnection: Could not connect to display host.docker.internal:0 Fatal Python error: Aborted
Thread 0x00002aab0dc24700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 300 in wait File "/opt/ilastik/lib/python3.7/threading.py", line 552 in wait File "/opt/ilastik/lib/python3.7/threading.py", line 1156 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aab03549700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaafad47700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaaf2545700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaae9d43700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaab45c3700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaab6dc5700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaab75c7700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaab7dc9700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Current thread 0x00002aaaab669400 (most recent call first): File "/opt/ilastik/ilastik-meta/ilastik/ilastik/shell/gui/startShellGui.py", line 61 in startShellGui File "/opt/ilastik/ilastik-meta/ilastik/ilastik_main.py", line 176 in main File "/opt/ilastik/ilastik-meta/ilastik/ilastik.py", line 128 in main File "/opt/ilastik/ilastik-meta/ilastik/ilastik.py", line 134 in
Fatal Python error: Segmentation fault
Thread 0x00002aab0dc24700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 300 in wait File "/opt/ilastik/lib/python3.7/threading.py", line 552 in wait File "/opt/ilastik/lib/python3.7/threading.py", line 1156 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aab03549700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaafad47700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaaf2545700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaae9d43700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaab45c3700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaab6dc5700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaab75c7700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00002aaab7dc9700 (most recent call first): File "/opt/ilastik/lib/python3.7/threading.py", line 296 in wait File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 154 in _get_next_job File "/opt/ilastik/ilastik-meta/lazyflow/lazyflow/request/threadPool.py", line 99 in run File "/opt/ilastik/lib/python3.7/threading.py", line 917 in _bootstrap_inner File "/opt/ilastik/lib/python3.7/threading.py", line 885 in _bootstrap
Current thread 0x00002aaaab669400 (most recent call first): File "/opt/ilastik/ilastik-meta/ilastik/ilastik/shell/gui/startShellGui.py", line 61 in startShellGui File "/opt/ilastik/ilastik-meta/ilastik/ilastik_main.py", line 176 in main File "/opt/ilastik/ilastik-meta/ilastik/ilastik.py", line 128 in main File "/opt/ilastik/ilastik-meta/ilastik/ilastik.py", line 134 in
qemu: uncaught target signal 11 (Segmentation fault) - core dumped
/opt/ilastik/run_ilastik.sh: line 77: 68 Segmentation fault "${PREFIX}/bin/python" "${PREFIX}/ilastik-meta/ilastik/ilastik.py" "$@"