1

Error message

Traceback (most recent call last):
      File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/web.py", line 1699, in _execute
        result = await result
      File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "/home/djan/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/handlers.py", line 72, in post
        type=mtype))
      File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
        value = future.result()
      File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "/home/djan/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/sessionmanager.py", line 88, in create_session
        kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
      File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
        value = future.result()
      File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "/home/djan/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/sessionmanager.py", line 101, in start_kernel_for_session
        self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
      File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
        value = future.result()
      File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
        yielded = next(result)
      File "/home/djan/anaconda3/lib/python3.7/site-packages/notebook/services/kernels/kernelmanager.py", line 168, in start_kernel
        super(MappingKernelManager, self).start_kernel(**kwargs)
      File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/multikernelmanager.py", line 110, in start_kernel
        km.start_kernel(**kwargs)
      File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/manager.py", line 240, in start_kernel
        self.write_connection_file()
      File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/connect.py", line 547, in write_connection_file
        kernel_name=self.kernel_name
      File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/connect.py", line 212, in write_connection_file
        with secure_write(fname) as f:
      File "/home/djan/anaconda3/lib/python3.7/contextlib.py", line 112, in __enter__
        return next(self.gen)
      File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/connect.py", line 105, in secure_write
        assert '0600' == oct(stat.S_IMODE(os.stat(fname).st_mode)).replace('0o', '0')
    AssertionError

System information

Running Jupyter (v. 1.0.0) on a Linux server, with anaconda3 (v. 2019.07) 64-bit.

Available Kernels

Available kernels:
   python3    /home/djan/.local/share/jupyter/kernels/python3
   nn      /home/djan/.local/share/jupyter/kernels/nn

Reproducing the issue

  1. Install the newest anaconda3 version.
  2. Run Jupyter notebook in the base version --> Kernel runs fine
  3. Create a new environment with python: conda create -n test python=3.7
  4. After activating the environment, Jupyter notebook is not available, thus I must install it via Conda: conda install -c anaconda jupyter
  5. Run Jupyter notebook in the test environment --> Kernel breaks down as explained above

What I tried so far

There seems to be an issue with file permissions when running Jupyter on a server inside a Conda environment. I tried to give all files inside my anaconda3 folder the requested permissions (0600), but this did not help.

2 Answers 2

1

Update

It turns out that the newest version of jupyter_client, available under anaconda as version 5.3.3, breaks the Jupyter environment on a server.

Installing the previous version of jupyter_client via following command fixes this issue:

conda install -c anaconda jupyter_client=5.3.1

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3 Comments

Just some extra info: That line was added in 5.3.2, so yeah 5.3.1 is the minimal change.
Thanks for the clarification and the link!
@JDDS I'm getting the same error even after installing [email protected]
0

nice Update

It turns out that the newest version of jupyter_client, available under anaconda as version 5.3.3, breaks the Jupyter environment on a server.

Installing the previous version of jupyter_client via following command fixes this issue:

conda install -c anaconda jupyter_client=5.3.1

Comments

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