jupyter / docker-stacks

Ready-to-run Docker images containing Jupyter applications

Home Page:https://jupyter-docker-stacks.readthedocs.io

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jhyungjeon opened this issue · comments

What docker image(s) are you using?

tensorflow-notebook

Host OS system

k8s container

Host architecture

x86_64

What Docker command are you running?

docker run -p 8888:8888 [image]

How to Reproduce the problem?

Hello. I want to run eclipse-che using the scipy docker image. When I try to run it, I encounter an error: "[Errno 13] Permission denied: '/home/jovyan/.local'". I'm not sure what the cause is.

Command output

No response

Expected behavior

No response

Actual behavior

Entered start.sh with args: jupyter lab
There is no entry in /etc/passwd for our UID=1234. Attempting to fix...
Renaming old jovyan user to nayvoj (1000:100)
Added new jovyan user (1234:0). Fixed UID!
WARNING: no write access to /home/jovyan. Try starting the container with group 'users' (100), e.g. using "--group-add=users".
Executing the command: jupyter lab
[I 2023-09-18 04:59:38.922 ServerApp] Package jupyterlab took 0.0000s to import
[I 2023-09-18 04:59:38.928 ServerApp] Package jupyter_lsp took 0.0059s to import
[W 2023-09-18 04:59:38.928 ServerApp] A _jupyter_server_extension_points function was not found in jupyter_lsp. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
[I 2023-09-18 04:59:38.930 ServerApp] Package jupyter_server_mathjax took 0.0014s to import
[I 2023-09-18 04:59:38.934 ServerApp] Package jupyter_server_terminals took 0.0036s to import
[I 2023-09-18 04:59:38.951 ServerApp] Package jupyterlab_git took 0.0171s to import
[I 2023-09-18 04:59:38.953 ServerApp] Package nbclassic took 0.0011s to import
[W 2023-09-18 04:59:38.954 ServerApp] A _jupyter_server_extension_points function was not found in nbclassic. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
[I 2023-09-18 04:59:38.954 ServerApp] Package nbdime took 0.0000s to import
[I 2023-09-18 04:59:38.954 ServerApp] Package notebook took 0.0000s to import
[I 2023-09-18 04:59:38.955 ServerApp] Package notebook_shim took 0.0000s to import
[W 2023-09-18 04:59:38.955 ServerApp] A _jupyter_server_extension_points function was not found in notebook_shim. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
[I 2023-09-18 04:59:38.956 ServerApp] jupyter_lsp | extension was successfully linked.
[I 2023-09-18 04:59:38.958 ServerApp] jupyter_server_mathjax | extension was successfully linked.
[I 2023-09-18 04:59:38.960 ServerApp] jupyter_server_terminals | extension was successfully linked.
[I 2023-09-18 04:59:38.963 ServerApp] jupyterlab | extension was successfully linked.
[I 2023-09-18 04:59:38.963 ServerApp] jupyterlab_git | extension was successfully linked.
[I 2023-09-18 04:59:38.965 ServerApp] nbclassic | extension was successfully linked.
[I 2023-09-18 04:59:38.965 ServerApp] nbdime | extension was successfully linked.
[I 2023-09-18 04:59:38.967 ServerApp] notebook | extension was successfully linked.
[W 2023-09-18 04:59:38.968 ServerApp] notebook_shim | error linking extension: [Errno 13] Permission denied: '/home/jovyan/.local'
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 656, in get
value = obj._trait_values[self.name]
~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'browser_open_file'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 656, in get
    value = obj._trait_values[self.name]
            ~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'runtime_dir'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/site-packages/jupyter_server/extension/manager.py", line 342, in link_extension
    extension.link_all_points(self.serverapp)
  File "/opt/conda/lib/python3.11/site-packages/jupyter_server/extension/manager.py", line 224, in link_all_points
    self.link_point(point_name, serverapp)
  File "/opt/conda/lib/python3.11/site-packages/jupyter_server/extension/manager.py", line 214, in link_point
    point.link(serverapp)
  File "/opt/conda/lib/python3.11/site-packages/jupyter_server/extension/manager.py", line 136, in link
    linker(serverapp)
  File "/opt/conda/lib/python3.11/site-packages/notebook_shim/nbserver.py", line 109, in _link_jupyter_server_extension
    members = diff_members(serverapp, nbapp)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/notebook_shim/nbserver.py", line 62, in diff_members
    m1 = public_members(obj1)
         ^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/notebook_shim/nbserver.py", line 56, in public_members
    members = inspect.getmembers(obj)
              ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/inspect.py", line 595, in getmembers
    return _getmembers(object, predicate, getattr)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/inspect.py", line 573, in _getmembers
    value = getter(object, key)
            ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 703, in __get__
    return self.get(obj, cls)
           ^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 659, in get
    default = obj.trait_defaults(self.name)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 1872, in trait_defaults
    return self._get_trait_default_generator(names[0])(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 1233, in __call__
    return self.func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/jupyter_server/serverapp.py", line 1598, in _default_browser_open_file
    return os.path.join(self.runtime_dir, basename)
                        ^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 703, in __get__
    return self.get(obj, cls)
           ^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 659, in get
    default = obj.trait_defaults(self.name)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 1872, in trait_defaults
    return self._get_trait_default_generator(names[0])(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/jupyter_core/application.py", line 107, in _runtime_dir_default
    ensure_dir_exists(rd, mode=0o700)
  File "/opt/conda/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 25, in ensure_dir_exists
    os.makedirs(path, mode=mode)
  File "<frozen os>", line 215, in makedirs
  File "<frozen os>", line 215, in makedirs
  File "<frozen os>", line 215, in makedirs
  File "<frozen os>", line 225, in makedirs
PermissionError: [Errno 13] Permission denied: '/home/jovyan/.local'

Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 656, in get
value = obj._trait_values[self.name]
~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'runtime_dir'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/conda/bin/jupyter-lab", line 10, in
sys.exit(main())
^^^^^^
File "/opt/conda/lib/python3.11/site-packages/jupyter_server/extension/application.py", line 607, in launch_instance
serverapp = cls.initialize_server(argv=args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/jupyter_server/extension/application.py", line 577, in initialize_server
serverapp.initialize(
File "/opt/conda/lib/python3.11/site-packages/traitlets/config/application.py", line 113, in inner
return method(app, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/jupyter_server/serverapp.py", line 2548, in initialize
self.init_configurables()
File "/opt/conda/lib/python3.11/site-packages/jupyter_server/serverapp.py", line 1879, in init_configurables
connection_dir=self.runtime_dir,
^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 703, in get
return self.get(obj, cls)
^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 659, in get
default = obj.trait_defaults(self.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/traitlets/traitlets.py", line 1872, in trait_defaults
return self._get_trait_default_generator(names[0])(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/jupyter_core/application.py", line 107, in _runtime_dir_default
ensure_dir_exists(rd, mode=0o700)
File "/opt/conda/lib/python3.11/site-packages/jupyter_core/utils/init.py", line 25, in ensure_dir_exists
os.makedirs(path, mode=mode)
File "", line 215, in makedirs
File "", line 215, in makedirs
File "", line 215, in makedirs
File "", line 225, in makedirs
PermissionError: [Errno 13] Permission denied: '/home/jovyan/.local'

Anything else?

No response

Latest Docker version

  • I've updated my Docker version to the latest available, and the issue still persists

WARNING: no write access to /home/jovyan. Try starting the container with group 'users' (100), e.g. using "--group-add=users".

Do you mount /home/jovyan?
If yes, please, take a look in the troubleshooting guide.
You need to make sure, that your /home/jovyan is write-able.

I am closing this one, as no information has been received from the user, and the troubleshooting guide should help.