pyvista freeze #130

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1. jorgensd commented on May 27, 2023

   

   jorgensd

   on May 27, 2023

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   How are you starting the docker container? Are you forwarding the necessary ports for a graphical user interface? Are you using a Python script or a notebook?
2. fghoussen commented on May 27, 2023

   

   fghoussen

   on May 27, 2023

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   This does work: I have a GUI that pops up and I can navigate the into the colored mesh

   >> cd /tmp
   >> wget https://docs.fenicsproject.org/dolfinx/main/python/_downloads/b94ac7be61dc3726ca331afd20f195d2/demo_poisson.py
   >> xhost +
   >> sudo docker run --rm -it -e DISPLAY="$DISPLAY" -v /tmp/.X11-unix:/tmp/.X11-unix -v /tmp:/root --name fenics_tuto dolfinx/dolfinx:stable
   root@6ed4aea976a6:~# ls *.py                       
   demo_poisson.py
   root@6ed4aea976a6:~# apt update
   root@6ed4aea976a6:~# apt install libgl1-mesa-glx xvfb
   root@6ed4aea976a6:~# python3 -m pip install pyvista
   root@6ed4aea976a6:~# python3 demo_poisson.py 
   
   

   But this doesn't work: the visualization stalls

   >> cd /tmp
   >> git clone https://github.com/jorgensd/dolfinx-tutorial
   >> xhost +
   >> sudo docker run --rm -it -e DISPLAY="$DISPLAY" -v /tmp/.X11-unix:/tmp/.X11-unix -v /tmp:/root --name fenics_tuto dolfinx/dolfinx:stable
   root@3f7f2f14821f:~# ls dolfinx-tutorial/
   Changelog.md  README.md    _toc.yml    chapter1  chapter3  docker  fenics_logo.png  index.ipynb			 references.bib  tox.ini
   Dockerfile    _config.yml  binder.png  chapter2  chapter4  fem.md  git.png	    jupyter_book.code-workspace  save.png
   root@3f7f2f14821f:~# apt-get update
   root@3f7f2f14821f:~# apt install libgl1-mesa-glx xvfb
   root@3f7f2f14821f:~# python3 -m pip install pyvista
   root@3f7f2f14821f:~# cd dolfinx-tutorial/chapter2/
   root@3f7f2f14821f:~/dolfinx-tutorial/chapter2# python3 linearelasticity_code.py
   ^C
   Loguru caught a signal: SIGINT
   Stack trace:
   23      0x55592eb8c245 _start + 37
   22      0x7fce699bbe40 __libc_start_main + 128
   21      0x7fce699bbd90 /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7fce699bbd90]
   20      0x55592eb8c34d Py_BytesMain + 45
   19      0x55592ebb60ae Py_RunMain + 702
   18      0x55592ebc4e33 _PyRun_AnyFileObject + 67
   17      0x55592ebc5138 _PyRun_SimpleFileObject + 424
   16      0x55592ebc5c55 python3(+0x265c55) [0x55592ebc5c55]
   15      0x55592ebbed5b python3(+0x25ed5b) [0x55592ebbed5b]
   14      0x55592ebc5f08 python3(+0x265f08) [0x55592ebc5f08]
   13      0x55592eb99456 PyEval_EvalCode + 134
   12      0x55592eaa1766 python3(+0x141766) [0x55592eaa1766]
   11      0x55592eaa514a _PyEval_EvalFrameDefault + 2058
   10      0x55592eabc3ac _PyFunction_Vectorcall + 124
   9       0x55592eaa514a _PyEval_EvalFrameDefault + 2058
   8       0x55592eabc3ac _PyFunction_Vectorcall + 124
   7       0x55592eaab48e _PyEval_EvalFrameDefault + 27470
   6       0x55592eab27db _PyObject_MakeTpCall + 603
   5       0x55592eabbb88 python3(+0x15bb88) [0x55592eabbb88]
   4       0x7fce470e68ed /usr/local/lib/python3.10/dist-packages/vtkmodules/vtkRenderingCore.cpython-310-x86_64-linux-gnu.so(+0x15c8ed) [0x7fce470e68ed]
   3       0x7fce43ebc8a4 vtkXRenderWindowInteractor::StartEventLoop() + 68
   2       0x7fce43ec048f vtkXRenderWindowInteractor::ProcessEvents() + 1039
   1       0x7fce69aad7ed __select + 349
   0       0x7fce699d4520 /lib/x86_64-linux-gnu/libc.so.6(+0x42520) [0x7fce699d4520]
   2023-05-27 14:44:07.110 (  37.145s) [main            ]                       :0     FATL| Signal: SIGINT
   
   

   Did I miss something?

   How are you starting the docker container?

   Yes

   Are you forwarding the necessary ports for a graphical user interface?

   Yes

   Are you using a Python script or a notebook?

   python script
3. fghoussen commented on May 28, 2023

   

   fghoussen

   on May 28, 2023

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   Any clue so far?
4. jorgensd commented on May 28, 2023

   

   jorgensd

   on May 28, 2023

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   Any clue so far?

   Please note that is the weekend, and it doesn't help adding extra posts here.
   Try removing pyvista.start_xvfb().
5. fghoussen commented on May 28, 2023

   

   fghoussen

   on May 28, 2023

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   Sorry didn't meant to disturb. As I work, I can only deal with that topic by the week-end.

   Try removing pyvista.start_xvfb().

   Worked, thanks! Do you want me to PR this change?
6. jorgensd commented on May 28, 2023

   

   jorgensd

   on May 28, 2023

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   Sorry didn't meant to disturb. As I work, I can only deal with that topic by the week-end.

   Try removing pyvista.start_xvfb().

   Worked, thanks! Do you want me to PR this change?

   No, as it stands, most pyvista visualization needs xvfb (for instance in jupyter notebook or for screenshots). As the tutorial is based on the ipynb scripts (to render the webpage) I need start_xvfb() to run and render plots there.

   What you could do is to add a comment or separate section about plotting in chapter1, where one goes through what is needed for various plotting methods.
7. Repository owner locked and limited conversation to collaborators on May 28, 2023
8. jorgensd

   converted this issue into a discussion #132 on May 28, 2023