jupyter lab 的全新 conda 安装无法连接到 kernel

Question

I'm trying to run jupyter lab with miniconda, but Jupyter is having trouble connecting with the kernel. Below is some background info, the steps I've done, and the code that results.

Background Info

• I have been successfully using jupyter lab for months.
• It was only today that this problem started occurring.
  • I suspected that this is related to the fact that I installed XCode Command Line Tools 13 this morning, which was only released yesterday, but the same problem occurred after a downgrade to 12.5.1.
• I am using miniconda.

Steps

• Create a fresh conda environment
• Activate it with conda activate test
• I then run conda install jupyterlab
• After installation, I run jupyter lab to open the browser and navigate to my .ipynb

Now, the bottom left corner of the browser reads "Python 3 (ipykernel) | Connecting", which doesn't say much. Here's a summary of the logs:

Regular log output

There's the initial info (which I don't think contains anything novel, but may help to answer some questions you might have that I haven't thought of):

[I 2021-09-21 09:36:33.353 ServerApp] jupyterlab | extension was successfully linked.
[I 2021-09-21 09:36:34.278 ServerApp] nbclassic | extension was successfully linked.
[I 2021-09-21 09:36:34.509 LabApp] JupyterLab extension loaded from /opt/miniconda3/envs/test/lib/python3.9/site-packages/jupyterlab
[I 2021-09-21 09:36:34.509 LabApp] JupyterLab application directory is /opt/miniconda3/envs/test/share/jupyter/lab
[I 2021-09-21 09:36:34.515 ServerApp] jupyterlab | extension was successfully loaded.
[I 2021-09-21 09:36:34.526 ServerApp] nbclassic | extension was successfully loaded.
[I 2021-09-21 09:36:34.527 ServerApp] Serving notebooks from local directory: /Users/connorpancoast/Code/grassmaNN
[I 2021-09-21 09:36:34.527 ServerApp] Jupyter Server 1.4.1 is running at:
[I 2021-09-21 09:36:34.527 ServerApp] http://localhost:8888/lab?token=fa21e773398a0c8bbeccdb7a67ffb20950bac831209b9373
[I 2021-09-21 09:36:34.527 ServerApp]  or http://127.0.0.1:8888/lab?token=fa21e773398a0c8bbeccdb7a67ffb20950bac831209b9373
[I 2021-09-21 09:36:34.527 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2021-09-21 09:36:34.535 ServerApp]

    To access the server, open this file in a browser:
        file:///Users/connorpancoast/Library/Jupyter/runtime/jpserver-24903-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/lab?token=fa21e773398a0c8bbeccdb7a67ffb20950bac831209b9373
     or http://127.0.0.1:8888/lab?token=fa21e773398a0c8bbeccdb7a67ffb20950bac831209b9373

After this is when things get strange.

Strange log output

First is this warning about nodejs , which may or may not be important.

[W 2021-09-21 09:36:39.621 LabApp] Could not determine jupyterlab build status without nodejs
/opt/miniconda3/envs/test/lib/python3.9/json/encoder.py:257: UserWarning: date_default is deprecated since jupyter_client 7.0.0. Use jupyter_client.jsonutil.json_default.
  return _iterencode(o, 0)

Next, the kernel starts, but there's a connection timeout.

[I 2021-09-21 09:36:51.114 ServerApp] Kernel started: b38270f5-9a72-42cf-86e5-0e8e4b3b9514
[W 2021-09-21 09:37:51.549 ServerApp] Timeout waiting for kernel_info reply from b38270f5-9a72-42cf-86e5-0e8e4b3b9514
[W 2021-09-21 09:37:56.092 ServerApp] Nudge: attempt 10 on kernel b38270f5-9a72-42cf-86e5-0e8e4b3b9514
[W 2021-09-21 09:37:56.093 ServerApp] Nudge: attempt 10 on kernel b38270f5-9a72-42cf-86e5-0e8e4b3b9514
[W 2021-09-21 09:37:56.109 ServerApp] Nudge: attempt 10 on kernel b38270f5-9a72-42cf-86e5-0e8e4b3b9514

I'm unsure why three separate "nudge processes" are occurring, but after 120 nudge attempts (shown), this error message also appears three times, not shown for space:

[W 2021-09-21 09:38:51.474 ServerApp] Nudge: attempt 120 on kernel b38270f5-9a72-42cf-86e5-0e8e4b3b9514
[W 2021-09-21 09:38:51.475 ServerApp] Nudge: attempt 120 on kernel b38270f5-9a72-42cf-86e5-0e8e4b3b9514
[W 2021-09-21 09:38:51.476 ServerApp] Nudge: attempt 120 on kernel b38270f5-9a72-42cf-86e5-0e8e4b3b9514
[E 2021-09-21 09:38:51.558 ServerApp] Uncaught exception GET /api/kernels/b38270f5-9a72-42cf-86e5-0e8e4b3b9514/channels?session_id=f834b0b3-b8ed-4b2d-bfc9-7a535593a24f (::1)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/api/kernels/b38270f5-9a72-42cf-86e5-0e8e4b3b9514/channels?session_id=f834b0b3-b8ed-4b2d-bfc9-7a535593a24f', version='HTTP/1.1', remote_ip='::1')
    Traceback (most recent call last):
      File "/opt/miniconda3/envs/test/lib/python3.9/site-packages/tornado/websocket.py", line 956, in _accept_connection
        await open_result
    tornado.util.TimeoutError: Timeout

After those, these appear:

[W 2021-09-21 09:39:21.571 ServerApp] WebSocket ping timeout after 90003 ms.
[W 2021-09-21 09:39:21.585 ServerApp] WebSocket ping timeout after 90003 ms.
[W 2021-09-21 09:42:51.594 ServerApp] Replacing stale connection: b38270f5-9a72-42cf-86e5-0e8e4b3b9514:ee46fa70-0af0-489d-8993-acf4f55bf3aa
[W 2021-09-21 09:42:52.123 ServerApp] Replacing stale connection: b38270f5-9a72-42cf-86e5-0e8e4b3b9514:ee46fa70-0af0-489d-8993-acf4f55bf3aa
/opt/miniconda3/envs/test/lib/python3.9/json/encoder.py:257: UserWarning: date_default is deprecated since jupyter_client 7.0.0. Use jupyter_client.jsonutil.json_default.
  return _iterencode(o, 0)
[I 2021-09-21 09:46:52.126 ServerApp] Starting buffering for b38270f5-9a72-42cf-86e5-0e8e4b3b9514:ee46fa70-0af0-489d-8993-acf4f55bf3aa
[W 2021-09-21 09:46:52.146 ServerApp] Replacing stale connection: b38270f5-9a72-42cf-86e5-0e8e4b3b9514:f834b0b3-b8ed-4b2d-bfc9-7a535593a24f
[W 2021-09-21 09:46:55.306 ServerApp] Replacing stale connection: b38270f5-9a72-42cf-86e5-0e8e4b3b9514:1db7c82b-2627-4c43-b9d3-da7bef15ca32

Answer 1

I also use Jupyter Lab with Miniconda, and this is what I did a few days ago.

It seems that you need the install node.js and ipykernel with:

conda install nodej ipykernel

Also, I read somewhere that you need to "tell" Jupyter Lab to use your environment as follow:

python -m ipykernel install --user --name test --display-name “enviroment_test”

Note that test is your environment name, and “enviroment_test” is the name that it will show in Jupyter.

Finally, I would suggest installing Jupyter from conda-forge with:

conda install jupyterlab -c conda-forge

Obs.: all this need to be done with your desired environment activated