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Published 20 hours ago • verified publisher icon mwouts

jupyter lab crashes on startup since jupytext install

Open MaximilianHoffmann opened this issue 3 years ago • 4 comments

After I installed jupytext I cannot run jupyter lab anymore, because of the following error

[I 13:40:30.138 LabApp] [nb_conda_kernels] enabled, 3 kernels found
[I 13:40:31.215 LabApp] JupyterLab extension loaded from ,,, anaconda3\envs\labplot\lib\site-packages\jupyterlab
[I 13:40:31.216 LabApp] JupyterLab application directory is ,,, anaconda3\envs\labplot\share\jupyter\lab
[I 13:40:31.335 LabApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[I 13:40:31.336 LabApp] Serving notebooks from local directory: ,,,,
[I 13:40:31.337 LabApp] The Jupyter Notebook is running at:
[I 13:40:31.337 LabApp] http://localhost:8888/
[I 13:40:31.337 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 13:40:34.496 LabApp] Build is up to date
/[I 13:40:36.629 LabApp] Kernel started: e5dde3c3-dd03-4295-98e6-e4fcd96d6e3d
[I 13:40:36.654 LabApp] Kernel started: 387b94eb-8052-428d-b420-8f670962312a
-[I 13:40:36.714 LabApp] Kernel started: f94070bb-dafe-4de4-b6b1-7704e6ef92fb
[I 13:40:36.745 LabApp] Kernel started: 2fafa0c2-5092-49f3-89fa-5567564647a5
|Active code page: 850
Active code page: 850
/Active code page: 850
[IPKernelApp] WARNING | Parent appears to have exited, shutting down.

MaximilianHoffmann avatar Jul 13 '20 11:07 MaximilianHoffmann

Hi @MaximilianHoffmann , thank you for reporting this.

For troubleshooting it would be useful to know a bit more about your environment (which OS, are you using pip or conda, which version of Jupyter, etc). When exactly does the problem occur (when you create a new notebook, open an existing one?). Also, are you able to reproduce the issue in a conda environment with just jupyterlab and jupytext?

mwouts avatar Jul 13 '20 17:07 mwouts

Sorry, of course. It's Windows 10, and conda, this is the clean env before I installed jupytext/ i.e. the one that I had to re-install yesterday

#
# Name                    Version                   Build  Channel
attrs                     19.3.0                     py_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
bleach                    3.1.5              pyh9f0ad1d_0    conda-forge
brotlipy                  0.7.0           py38h1e8a9f7_1000    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
certifi                   2020.6.20        py38h32f6830_0    conda-forge
cffi                      1.14.0           py38ha419a9e_0    conda-forge
chardet                   3.0.4           py38h32f6830_1006    conda-forge
colorama                  0.4.3                      py_0    conda-forge
cryptography              2.9.2            py38hba49e27_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
entrypoints               0.3             py38h32f6830_1001    conda-forge
freetype                  2.10.2               hd328e21_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
importlib-metadata        1.7.0            py38h32f6830_0    conda-forge
importlib_metadata        1.7.0                         0    conda-forge
intel-openmp              2020.1                      216
ipykernel                 5.3.2            py38h5ca1d4c_0    conda-forge
ipympl                    0.5.6              pyh9f0ad1d_1    conda-forge
ipython                   7.16.1           py38h23f93f0_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge
jedi                      0.17.1           py38h32f6830_0    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
json5                     0.9.4              pyh9f0ad1d_0    conda-forge
jsonschema                3.2.0            py38h32f6830_1    conda-forge
jupyter_client            6.1.5                      py_0    conda-forge
jupyter_core              4.6.3            py38h32f6830_1    conda-forge
jupyterlab                2.1.5                      py_0    conda-forge
jupyterlab_server         1.2.0                      py_0    conda-forge
kiwisolver                1.2.0            py38heaebd3c_0    conda-forge
libblas                   3.8.0                    16_mkl    conda-forge
libcblas                  3.8.0                    16_mkl    conda-forge
liblapack                 3.8.0                    16_mkl    conda-forge
libpng                    1.6.37               hfe6a214_1    conda-forge
libsodium                 1.0.17               h2fa13f4_0    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gmp                 6.1.0                         2
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
markupsafe                1.1.1            py38h9de7a3e_1    conda-forge
matplotlib-base           3.2.2            py38hbe5506b_1    conda-forge
mistune                   0.8.4           py38h9de7a3e_1001    conda-forge
mkl                       2020.1                      216
msys2-conda-epoch         20160418                      1
nb_conda_kernels          2.2.3                    py38_0    conda-forge
nbconvert                 5.6.1            py38h32f6830_1    conda-forge
nbformat                  5.0.7                      py_0    conda-forge
nodejs                    13.13.0                       0    conda-forge
notebook                  6.0.3            py38h32f6830_1    conda-forge
numpy                     1.18.5           py38h72c728b_0    conda-forge
openssl                   1.1.1g               he774522_0    conda-forge
packaging                 20.4               pyh9f0ad1d_0    conda-forge
pandoc                    2.10                          0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.7.0              pyh9f0ad1d_0    conda-forge
pickleshare               0.7.5           py38h32f6830_1001    conda-forge
pip                       20.1.1                     py_1    conda-forge
prometheus_client         0.8.0              pyh9f0ad1d_0    conda-forge
prompt-toolkit            3.0.5                      py_1    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pygments                  2.6.1                      py_0    conda-forge
pyopenssl                 19.1.0                     py_1    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyrsistent                0.16.0           py38h9de7a3e_0    conda-forge
pysocks                   1.7.1            py38h32f6830_1    conda-forge
python                    3.8.3           cpython_h5fd99cc_0    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.8                      1_cp38    conda-forge
pywin32                   227              py38hfa6e2cd_0    conda-forge
pywinpty                  0.5.7                    py38_0    conda-forge
pyzmq                     19.0.1           py38h77b9d75_0    conda-forge
requests                  2.24.0             pyh9f0ad1d_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                49.2.0           py38h32f6830_0    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlite                    3.32.3               he774522_1    conda-forge
terminado                 0.8.3            py38h32f6830_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tornado                   6.0.4            py38hfa6e2cd_0    conda-forge
traitlets                 4.3.3            py38h32f6830_1    conda-forge
urllib3                   1.25.9                     py_0    conda-forge
vc                        14.1                 h869be7e_1    conda-forge
vs2015_runtime            14.16.27012          h30e32a0_2    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.34.2                     py_1    conda-forge
widgetsnbextension        3.5.1            py38h32f6830_1    conda-forge
win_inet_pton             1.1.0                    py38_0    conda-forge
wincertstore              0.2                   py38_1003    conda-forge
winpty                    0.4.3                         4    conda-forge
zeromq                    4.3.2                ha925a31_3    conda-forge
zipp                      3.1.0                      py_0    conda-forge
zlib                      1.2.11            h2fa13f4_1006    conda-forge

The crash directly occurse when I start jupyter lab, allthough it was my existing one, so I guess it would have launched some notebooks on startup. The environment is my plot/lab environment, which pretty much only contains jupyter lab and matplotlib.

MaximilianHoffmann avatar Jul 14 '20 05:07 MaximilianHoffmann

Interesting. I just gave it a try with

conda create -n jupytext_566 python=3.8.3 jupyterlab=2.1.5 matplotlib-base=3.2.2 jupytext=1.5.1 nodejs=13.13.0 -c conda-forge
conda activate jupytext_566
jupyter lab

on Windows 10 (Miniconda under powershell), and I didn't get any crash. The logs are

[I 22:39:06.767 LabApp] JupyterLab extension loaded from C:\Users\Marc\Miniconda3\envs\jupytext_566\lib\site-packages\jupyterlab
[I 22:39:06.774 LabApp] JupyterLab application directory is C:\Users\Marc\Miniconda3\envs\jupytext_566\share\jupyter\lab
[I 22:39:07.303 LabApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[I 22:39:07.306 LabApp] Serving notebooks from local directory: C:\Users\Marc
[I 22:39:07.307 LabApp] The Jupyter Notebook is running at:
[I 22:39:07.307 LabApp] http://localhost:8888/?token=...
[I 22:39:07.308 LabApp]  or http://127.0.0.1:8888/?token=...
[I 22:39:07.309 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 22:39:07.503 LabApp]

    To access the notebook, open this file in a browser:
        file:///C:/Users/Marc/AppData/Roaming/jupyter/runtime/nbserver-13972-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/?token=...
     or http://127.0.0.1:8888/?token=...
[W 22:39:11.842 LabApp] Build recommended
[W 22:39:11.843 LabApp] jupyterlab-jupytext needs to be included in build
|[I 22:39:13.326 LabApp] Kernel started: b30ec30f-f349-4955-9cdb-da7100592d8c
/[I 22:39:15.639 LabApp] Building jupyterlab assets (build:dev)
\[I 22:39:43.643 LabApp] Saving file at /Untitled.ipynb
[I 22:39:43.652 LabApp] Saving Untitled.ipynb
[I 22:43:20.811 LabApp] Starting buffering for b30ec30f-f349-4955-9cdb-da7100592d8c:df21de97-6183-447c-bf8e-8bed1f0167df
[I 22:43:20.848 LabApp] Restoring connection for b30ec30f-f349-4955-9cdb-da7100592d8c:df21de97-6183-447c-bf8e-8bed1f0167df
[I 22:43:20.858 LabApp] Starting buffering for b30ec30f-f349-4955-9cdb-da7100592d8c:df21de97-6183-447c-bf8e-8bed1f0167df
[I 22:43:23.857 LabApp] Build is up to date

Compared to your logs, I see that I don't have Active code page: 850 like you. Do you have any idea where this comes from?

Also, if you'd like to compare our environments, here is my conda list. Do you see any difference with yours? Please let me know if you can share the specifications for your env in the form of a single command, or in the form of an environment.yml file.

(jupytext_566) PS C:\Users\Marc> conda list
# packages in environment at C:\Users\Marc\Miniconda3\envs\jupytext_566:
#
# Name                    Version                   Build  Channel
attrs                     19.3.0                     py_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
bleach                    3.1.5              pyh9f0ad1d_0    conda-forge
brotlipy                  0.7.0           py38h1e8a9f7_1000    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
certifi                   2020.6.20        py38h32f6830_0    conda-forge
cffi                      1.14.0           py38ha419a9e_0    conda-forge
chardet                   3.0.4           py38h32f6830_1006    conda-forge
colorama                  0.4.3                      py_0    conda-forge
cryptography              2.9.2            py38hba49e27_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
entrypoints               0.3             py38h32f6830_1001    conda-forge
freetype                  2.10.2               hd328e21_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
importlib-metadata        1.7.0            py38h32f6830_0    conda-forge
importlib_metadata        1.7.0                         0    conda-forge
intel-openmp              2020.1                      216
ipykernel                 5.3.2            py38h5ca1d4c_0    conda-forge
ipython                   7.16.1           py38h23f93f0_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.17.1           py38h32f6830_0    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
json5                     0.9.4              pyh9f0ad1d_0    conda-forge
jsonschema                3.2.0            py38h32f6830_1    conda-forge
jupyter_client            6.1.6                      py_0    conda-forge
jupyter_core              4.6.3            py38h32f6830_1    conda-forge
jupyterlab                2.1.5                      py_0    conda-forge
jupyterlab_server         1.2.0                      py_0    conda-forge
jupytext                  1.5.1              pyh9f0ad1d_0    conda-forge
kiwisolver                1.2.0            py38heaebd3c_0    conda-forge
libblas                   3.8.0                    16_mkl    conda-forge
libcblas                  3.8.0                    16_mkl    conda-forge
liblapack                 3.8.0                    16_mkl    conda-forge
libpng                    1.6.37               hfe6a214_1    conda-forge
libsodium                 1.0.17               h2fa13f4_0    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gmp                 6.1.0                         2
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
markupsafe                1.1.1            py38h9de7a3e_1    conda-forge
matplotlib-base           3.2.2            py38hbe5506b_1    conda-forge
mistune                   0.8.4           py38h9de7a3e_1001    conda-forge
mkl                       2020.1                      216
msys2-conda-epoch         20160418                      1
nbconvert                 5.6.1            py38h32f6830_1    conda-forge
nbformat                  5.0.7                      py_0    conda-forge
nodejs                    13.13.0                       0    conda-forge
notebook                  6.0.3            py38h32f6830_1    conda-forge
numpy                     1.18.5           py38h72c728b_0    conda-forge
openssl                   1.1.1g               he774522_0    conda-forge
packaging                 20.4               pyh9f0ad1d_0    conda-forge
pandoc                    2.10                          0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.7.0              pyh9f0ad1d_0    conda-forge
pickleshare               0.7.5           py38h32f6830_1001    conda-forge
pip                       20.1.1                     py_1    conda-forge
prometheus_client         0.8.0              pyh9f0ad1d_0    conda-forge
prompt-toolkit            3.0.5                      py_1    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pygments                  2.6.1                      py_0    conda-forge
pyopenssl                 19.1.0                     py_1    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyrsistent                0.16.0           py38h9de7a3e_0    conda-forge
pysocks                   1.7.1            py38h32f6830_1    conda-forge
python                    3.8.3           cpython_h5fd99cc_0    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.8                      1_cp38    conda-forge
pywin32                   227              py38hfa6e2cd_0    conda-forge
pywinpty                  0.5.7                    py38_0    conda-forge
pyyaml                    5.3.1            py38h9de7a3e_0    conda-forge
pyzmq                     19.0.1           py38h77b9d75_0    conda-forge
requests                  2.24.0             pyh9f0ad1d_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                49.2.0           py38h32f6830_0    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlite                    3.32.3               he774522_1    conda-forge
terminado                 0.8.3            py38h32f6830_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
toml                      0.10.1             pyh9f0ad1d_0    conda-forge
tornado                   6.0.4            py38hfa6e2cd_0    conda-forge
traitlets                 4.3.3            py38h32f6830_1    conda-forge
urllib3                   1.25.9                     py_0    conda-forge
vc                        14.1                 h869be7e_1    conda-forge
vs2015_runtime            14.16.27012          h30e32a0_2    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.34.2                     py_1    conda-forge
win_inet_pton             1.1.0                    py38_0    conda-forge
wincertstore              0.2                   py38_1003    conda-forge
winpty                    0.4.3                         4    conda-forge
yaml                      0.2.5                he774522_0    conda-forge
zeromq                    4.3.2                ha925a31_3    conda-forge
zipp                      3.1.0                      py_0    conda-forge
zlib                      1.2.11            h2fa13f4_1006    conda-forge
(jupytext_566) PS C:\Users\Marc>

mwouts avatar Jul 14 '20 20:07 mwouts

I am getting closer to your env with

conda create -n jupytext_566 python=3.8.3 jupyterlab=2.1.5 matplotlib-base=3.2.2 jupytext=1.5.1 nodejs=13.13.0 jupyter_client=6.1.5 ipympl=0.5.6 ipywidgets=7.5.1 nb_conda_kernels=2.2.3 widgetsnbextension=3.5.1 -c conda-forge

Now the only differences are that

  • I have jupytext and its dependencies (toml, pyyaml, yaml)
  • I have jupyter_client=6.1.5 from default while you have it from conda-forge.

Still no crash, and still no Active code page: 850 message, which makes me think that the message/crash may be specific to something you have in your notebook? Also, it is a bit strange that I can't get the same jupyter_client as you, maybe that is because a new version was published yesterday?

mwouts avatar Jul 15 '20 07:07 mwouts