jupyter failing while trying to modify /gnu/store

jupyter failing while trying to modify /gnu/store

[Alexander Asteroth]

Dear all,

yesterday I added jupyter to my profile and it worked perfectly
fine. Overnight I shut down the computer and rebooted today.
Now jupyter refuses to start with the messages below.  It seems that
jupyter-notebook tries to create directories (or modifiy them) in the location it
is installed wich is mounted ro. I have no idea why this didn't happen
yesterday but it seems that there is some misconfiguration somewhere...

Cheers,
Alex

PS: same effect with jupyterlab from the guix-science channel.

-------------------------------
~$  jupyter-notebook 
Traceback (most recent call last):
  File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/bin/.jupyter-notebook-real", line 11, in <module>
    load_entry_point('notebook==6.3.0', 'console_scripts', 'jupyter-notebook')()
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 254, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 663, in launch_instance
    app.initialize(argv)
  File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun
    return caller(func, *(extras + args), **kw)
  File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/lib/python3.8/site-packages/notebook/notebookapp.py", line 2122, in initialize
    super().initialize(argv)
  File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun
    return caller(func, *(extras + args), **kw)
  File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 229, in initialize
    self.migrate_config()
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 155, in migrate_config
    migrate()
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/migrate.py", line 244, in migrate
    ensure_dir_exists(env['jupyter_config'])
  File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 11, in ensure_dir_exists
    os.makedirs(path, mode=mode)
  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  [Previous line repeated 7 more times]
  File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/home/[user]/.guix-profile/etc/jupyter:'

Re: jupyter failing while trying to modify /gnu/store

[Alexander Asteroth]

I now tried to run it using

> guix shell --pure jupyter -- jupyter-notebook

works perfectly fine.

... wait ...

I found the cause:

in ~/.guix-profile/etc/profile environment variables are set:

> export JUPYTER_PATH="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/share/jupyter${JUPYTER_PATH:+:}$JUPYTER_PATH"
> export JUPYTER_CONFIG_DIR="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/etc/jupyter${JUPYTER_CONFIG_DIR:+:}$JUPYTER_CONFIG_DIR"

The jupyter config path causes the problem, since jupyter tries to write
into it (and it is located in a read only filesystem). Unsetting the
environment variable solves the issue.

Cheers,

        Alex


On Sat, Nov 27 2021, 12:40:59, Alexander Asteroth <alexander.asteroth@h-brs.de> wrote:

> Dear all,
>
> yesterday I added jupyter to my profile and it worked perfectly
> fine. Overnight I shut down the computer and rebooted today.
> Now jupyter refuses to start with the messages below.  It seems that
> jupyter-notebook tries to create directories (or modifiy them) in the location it
> is installed wich is mounted ro. I have no idea why this didn't happen
> yesterday but it seems that there is some misconfiguration somewhere...
>
> Cheers,
> Alex
>
> PS: same effect with jupyterlab from the guix-science channel.
>
> -------------------------------
> ~$  jupyter-notebook 
> Traceback (most recent call last):
>   File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/bin/.jupyter-notebook-real", line 11, in <module>
>     load_entry_point('notebook==6.3.0', 'console_scripts', 'jupyter-notebook')()
>   File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 254, in launch_instance
>     return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
>   File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 663, in launch_instance
>     app.initialize(argv)
>   File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun
>     return caller(func, *(extras + args), **kw)
>   File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error
>     return method(app, *args, **kwargs)
>   File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/lib/python3.8/site-packages/notebook/notebookapp.py", line 2122, in initialize
>     super().initialize(argv)
>   File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun
>     return caller(func, *(extras + args), **kw)
>   File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error
>     return method(app, *args, **kwargs)
>   File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 229, in initialize
>     self.migrate_config()
>   File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 155, in migrate_config
>     migrate()
>   File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/migrate.py", line 244, in migrate
>     ensure_dir_exists(env['jupyter_config'])
>   File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 11, in ensure_dir_exists
>     os.makedirs(path, mode=mode)
>   File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
>     makedirs(head, exist_ok=exist_ok)
>   File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
>     makedirs(head, exist_ok=exist_ok)
>   File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs
>     makedirs(head, exist_ok=exist_ok)
>   [Previous line repeated 7 more times]
>   File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 223, in makedirs
>     mkdir(name, mode)
> OSError: [Errno 30] Read-only file system: '/home/[user]/.guix-profile/etc/jupyter:'