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SageMath WSL2 kernel timed out #3977

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darkl opened this issue Nov 19, 2020 · 6 comments
Closed

SageMath WSL2 kernel timed out #3977

darkl opened this issue Nov 19, 2020 · 6 comments
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bug Issue identified by VS Code Team member as probable bug language-any Area covering general issues geared to supporting any language (not just Python) notebook-execution Kernels issues (start/restart/switch/execution, install ipykernel)

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@darkl
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darkl commented Nov 19, 2020 •
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Environment data

Version: 1.52.0-insider (user setup)
Commit: a36c68b9ec3d6a0aca9799d7a10be741a6658a51
Date: 2020-11-19T05:37:52.577Z
Electron: 9.3.3
Chrome: 83.0.4103.122
Node.js: 12.14.1
V8: 8.3.110.13-electron.0
OS: Windows_NT x64 10.0.19042

I use WSL2 with an Ubuntu-20.04 image.

Expected behaviour

Installed using sudo apt-get install sagemath. I am trying to use VSCode with the remote development extension and make the Jupyter extension use SageMath.

Actual behaviour

I get a Timed out waiting to get a heartbeat from process message.

Steps to reproduce:

  1. Choose Remote-WSL: New Window
  2. Choose Jupyter: Create New Blank Jupyter Notebook
  3. Insert x=3 in the first cell
  4. Execute cell
  5. When prompted "Select a notebook kernel to run this notebook" select SageMath 9.0.

Logs

Note: I set the logs to debug mode by adding this line to settings.json:

"jupyter.logging.level": "debug"

Additional information:

~$ /usr/bin/sage --python --version
Python 3.8.5
~$ /usr/bin/sage --python -m ipykernel --version
7.13.0
~$ /usr/bin/sage --python -m jupyter notebook --version
6.0.3

Output for Jupyter in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Jupyter) 

User belongs to experiment group 'NativeNotebookEditor'
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/sage --python -m sage.repl.ipython_kernel -f /tmp/tmp-1175bneWkEsS7Qdu.json
cwd: /mnt/c/Users/Elad Zelingher/.vscode-insiders/extensions/ms-vscode-remote.remote-wsl-0.51.3
Error 2020-11-19 14:33:07: Timed out waiting to get a heartbeat from kernel process.
Error 2020-11-19 14:33:07: Failed to connect raw kernel session: Error: Timed out waiting to get a heartbeat from kernel process.
Error 2020-11-19 14:33:07: failed to create INotebook in kernel [Error: Timed out waiting to get a heartbeat from kernel process.
	at m.waitForHeartbeat (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/out/client/extension.js:49:646443)]
Error 2020-11-19 14:33:07: DataScience Error [Error: Timed out waiting to get a heartbeat from kernel process.
	at m.waitForHeartbeat (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.358541065/out/client/extension.js:49:646443)]

@darkl darkl added the bug Issue identified by VS Code Team member as probable bug label Nov 19, 2020
@greazer
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greazer commented Nov 19, 2020

@darkl , looks like the output you supplied isn't actually debug output. Can you please restart VS Code and generate it again? Thanks!

@greazer greazer added the info-needed Issue requires more information from poster label Nov 19, 2020
@darkl
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darkl commented Nov 20, 2020

@greazer maybe you can help me, as I'm not able to make it output the debug log. I restarted my VSCode Insiders and still get the same result.

User belongs to experiment group 'NativeNotebookEditor'
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
Started kernel Python 3
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/sage --python -m sage.repl.ipython_kernel -f /tmp/tmp-431cKYfsdNGhA9B.json
cwd: /mnt/c/Users/Elad Zelingher/.vscode-insiders/extensions/ms-vscode-remote.remote-wsl-0.51.3
Error 2020-11-19 21:02:53: Timed out waiting to get a heartbeat from kernel process.
Error 2020-11-19 21:02:53: Failed to connect raw kernel session: Error: Timed out waiting to get a heartbeat from kernel process.
Error 2020-11-19 21:02:53: failed to create INotebook in kernel [Error: Timed out waiting to get a heartbeat from kernel process.
	at m.waitForHeartbeat (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:49:646441)]
Error 2020-11-19 21:02:53: DataScience Error [Error: Timed out waiting to get a heartbeat from kernel process.
	at m.waitForHeartbeat (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:49:646441)]
Error 2020-11-19 21:02:53: Failed to determine if a notebook is active for the current editor [Error: Timed out waiting to get a heartbeat from kernel process.
	at m.waitForHeartbeat (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:49:646441)]

My settings.json:
image

Thanks!

@darkl
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darkl commented Nov 20, 2020

Ok, I just edited the default value of logging.level in the minified JavaScript...
Here's the debug output:

User belongs to experiment group 'NativeNotebookEditor'
Info 2020-11-19 21:14:21: Attempting to start a server because of preload conditions ...
Info 2020-11-19 21:14:21: ZMQ install verified.
Info 2020-11-19 21:14:23: Attempting to start a server because of preload conditions ...
Info 2020-11-19 21:14:23: Searching for kernel based on {} for Untitled-1.ipynb
Info 2020-11-19 21:14:29: Cached data exists getEnvironmentVariables, <No Resource>
Info 2020-11-19 21:14:29: Cached data exists getEnvironmentVariables, <No Resource>
Info 2020-11-19 21:14:29: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
Info 2020-11-19 21:14:29: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
Info 2020-11-19 21:14:29: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
Info 2020-11-19 21:14:29: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
Info 2020-11-19 21:14:29: Cached data exists getEnvironmentVariables, <No Resource>
Info 2020-11-19 21:14:29: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
Info 2020-11-19 21:14:29: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py -c "import ipykernel"
Info 2020-11-19 21:14:29: Wrote trust for untitled:Untitled-1.ipynb to /home/elad/.vscode-server-insiders/data/User/globalStorage/ms-toolsai.jupyter/nbsignatures/996297221cd94a1c2edc08996bb59311061afaff107f9247029d1382ef163f4a
Info 2020-11-19 21:14:29: Cached data exists getEnvironmentVariables, <No Resource>
Info 2020-11-19 21:14:29: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
Info 2020-11-19 21:14:29: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
Info 2020-11-19 21:14:30: Cached data exists getEnvironmentVariables, <No Resource>
Info 2020-11-19 21:14:30: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
Info 2020-11-19 21:14:30: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.kernel_launcher_daemon -v
Info 2020-11-19 21:14:31: Cached data exists getEnvironmentVariables, <No Resource>
Info 2020-11-19 21:14:31: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
Info 2020-11-19 21:14:31: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
Info 2020-11-19 21:14:31: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
Info 2020-11-19 21:14:31: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
Info 2020-11-19 21:14:31: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
Info 2020-11-19 21:14:31: > /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> /usr/bin/python3 ~/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
Info 2020-11-19 21:14:38: Python Daemon (pid: 1066): Execute rpc method prewarm_kernel in DS Daemon
Info 2020-11-19 21:14:38: Python Daemon (pid: 1066): Execute rpc method prewarm_kernel from /usr/bin/python3
Info 2020-11-19 21:14:39: Python Daemon (pid: 1066): Pre-Warm DS Kernel in DS Kernel Launcher Daemon
Info 2020-11-19 21:14:39: Python Daemon (pid: 1066): Exec in DS Kernel Launcher Daemon (observable) ['/usr/bin/python3', '/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/vscode_datascience_helpers/../pyvsc-run-isolated.py', '/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/pythonFiles/vscode_datascience_helpers/kernel_prewarm_starter.py']
Info 2020-11-19 21:14:39: Python Daemon (pid: 1066): Exec in DS Kernel Launcher Daemon (observable)
Info 2020-11-19 21:14:39: Python Daemon (pid: 1066): Kernel launched, with PID 1074
Warn 2020-11-19 21:14:39: Python Daemon (pid: 1066): Waiting for Kernel to die 1074
Info 2020-11-19 21:14:39: Python Daemon (pid: 1066): Kernel launched, with PID as a daemon 1074
Info 2020-11-19 21:14:39: Find kernel spec, Class name = C, completed in 15940ms, has a truthy return value, Arg 1: <Uri:Untitled-1.ipynb>, Arg 2: {"language_info":{"name":"python","nbconvert_exporter":"python"},"orig_nbformat":2}, Arg 3: {"_isCancelled":false,"_emitter":null}, Return Value: {"name":"python3","argv":["/usr/bin/python3","-m","ipykernel_launcher","-f","{connection_file}"],"language":"python","path":"/usr/bin/python3","specFile":"/usr/share/jupyter/kernels/python3/kernel.json","display_name":"Python 3"}
Info 2020-11-19 21:14:39: Found matching interpreter based on metadata, for the kernel python3, Python 3
Info 2020-11-19 21:14:39: Find kernel spec, Class name = T, completed in 16021ms, has a truthy return value, Arg 1: <Uri:Untitled-1.ipynb>, Arg 2: {"language_info":{"name":"python","nbconvert_exporter":"python"},"orig_nbformat":2}, Arg 3: {"_isCancelled":false,"_emitter":null}, Arg 4: true, Return Value: {"kind":"startUsingKernelSpec","kernelSpec":{"name":"python3","argv":["/usr/bin/python3","-m","ipykernel_launcher","-f","{connection_file}"],"language":"python","path":"/usr/bin/python3","specFile":"/usr/share/jupyter/kernels/python3/kernel.json","display_name":"Python 3"},"interpreter":{"architecture":3,"path":"/usr/bin/python3","version":{"options":{"loose":false,"includePrerelease":false},"loose":false,"raw":"3.8.5-final","major":3,"minor":8,"patch":5,"prerelease":["final"],"build":[],"version":"3.8.5-final"},"sysVersion":"3.8.5 (default, Jul 28 2020, 12:59:40) \n[GCC 9.3.0]","sysPrefix":"/usr","fileHash":"8464b0be1e80a9f5648d98be82323dbf525c1354f3056eb948ba039ffe8dfc62b1387fa59ccae4033db6d32be8499dfb81a9e9a0908bd9231ae1372cbd2ac109","envType":"Unknown","displayName":"Python 3.8.5 64-bit"}}
Info 2020-11-19 21:14:57: Execute Cell in KernelProvider.ts
Info 2020-11-19 21:14:57: Creating raw notebook for untitled:Untitled-1.ipynb
Info 2020-11-19 21:14:57: Getting preferred kernel for untitled:Untitled-1.ipynb
Info 2020-11-19 21:14:57: Searching for kernel based on {"name":"sagemath","display_name":"SageMath 9.0"} for Untitled-1.ipynb
Info 2020-11-19 21:14:57: Find kernel spec, Class name = C, completed in 5ms, has a truthy return value, Arg 1: <Uri:Untitled-1.ipynb>, Arg 2: {"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":3},"orig_nbformat":2,"kernelspec":{"name":"sagemath","display_name":"SageMath 9.0"}}, Arg 3: {"_isCancelled":false,"_emitter":null}, Return Value: {"name":"sagemath","argv":["/usr/bin/sage","--python","-m","sage.repl.ipython_kernel","-f","{connection_file}"],"language":"sage","path":"/usr/bin/sage","specFile":"/usr/share/jupyter/kernels/sagemath/kernel.json","display_name":"SageMath 9.0","env":{"SAGE_ROOT":"/usr/share/sagemath","SAGE_LOCAL":"/usr"}}
Info 2020-11-19 21:14:57: Find kernel spec, Class name = T, completed in 58ms, has a truthy return value, Arg 1: <Uri:Untitled-1.ipynb>, Arg 2: {"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":3},"orig_nbformat":2,"kernelspec":{"name":"sagemath","display_name":"SageMath 9.0"}}, Arg 3: {"_isCancelled":false,"_emitter":null}, Arg 4: undefined, Return Value: {"kind":"startUsingKernelSpec","kernelSpec":{"name":"sagemath","argv":["/usr/bin/sage","--python","-m","sage.repl.ipython_kernel","-f","{connection_file}"],"language":"sage","path":"/usr/bin/sage","specFile":"/usr/share/jupyter/kernels/sagemath/kernel.json","display_name":"SageMath 9.0","env":{"SAGE_ROOT":"/usr/share/sagemath","SAGE_LOCAL":"/usr"}}}
Info 2020-11-19 21:14:57: Computing working directory untitled:Untitled-1.ipynb
Info 2020-11-19 21:14:57: Connecting to raw session for untitled:Untitled-1.ipynb
Info 2020-11-19 21:14:57: Cached data exists getEnvironmentVariables, Untitled-1.ipynb
Info 2020-11-19 21:14:57: > /usr/bin/sage --python -m sage.repl.ipython_kernel -f /tmp/tmp-1031owxPNhkIuACZ.json
> /usr/bin/sage --python -m sage.repl.ipython_kernel -f /tmp/tmp-1031owxPNhkIuACZ.json
Info 2020-11-19 21:14:57: cwd: /mnt/c/Users/Elad Zelingher/.vscode-insiders/extensions/ms-vscode-remote.remote-wsl-0.51.3
cwd: /mnt/c/Users/Elad Zelingher/.vscode-insiders/extensions/ms-vscode-remote.remote-wsl-0.51.3
Info 2020-11-19 21:14:58: KernelProcess output: NOTE: When using the `ipython kernel` entry point, Ctrl-C will not work.

To exit, you will have to explicitly quit this process, by either sending
"quit" from a client, or using Ctrl-\ in UNIX-like environments.

To read more about this, see https://github.com/ipython/ipython/issues/2049


To connect another client to this kernel, use:
    --existing /tmp/tmp-1031owxPNhkIuACZ.json

Info 2020-11-19 21:14:58: Kernel Output: NOTE: When using the `ipython kernel` entry point, Ctrl-C will not work.

To exit, you will have to explicitly quit this process, by either sending
"quit" from a client, or using Ctrl-\ in UNIX-like environments.

To read more about this, see https://github.com/ipython/ipython/issues/2049


To connect another client to this kernel, use:
    --existing /tmp/tmp-1031owxPNhkIuACZ.json

Info 2020-11-19 21:14:58: KernelProcess error: Traceback (most recent call last):
  File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/usr/lib/python3/dist-packages/sage/repl/ipython_kernel/__main__.py", line 3, in <module>
    IPKernelApp.launch_instance(kernel_class=SageKernel)
  File "/usr/lib/python3/dist-packages/traitlets/config/application.py", line 663, in launch_instance
    app.initialize(argv)
  File "<decorator-gen-124>", line 2, in initialize
  File "/usr/lib/python3/dist-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/usr/lib/python3/dist-packages/ipykernel/kernelapp.py", line 562, in initialize
    self.init_kernel()
  File "/usr/lib/python3/dist-packages/ipykernel/kernelapp.py", line 439, in init_kernel
    kernel = kernel_factory(parent=self, session=self.session,
  File "/usr/lib/python3/dist-packages/traitlets/config/configurable.py", line 412, in instance
    inst = cls(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/sage/repl/ipython_kernel/kernel.py", line 51, in __init__
    super(SageKernel, self).__init__(**kwds)
  File "/usr/lib/python3/dist-packages/ipykernel/ipkernel.py", line 64, in __init__
    self.shell = self.shell_class.instance(parent=self,
  File "/usr/lib/python3/dist-packages/traitlets/config/configurable.py", line 412, in instance
    inst = cls(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/IPython/core/interactiveshell.py", line 683, in __init__
    self.init_display_formatter()
  File "/usr/lib/python3/dist-packages/sage/repl/interpreter.py", line 229, in init_display_formatter
    from sage.repl.rich_output.backend_ipython import BackendIPythonNotebook
  File "/usr/lib/python3/dist-packages/sage/repl/rich_output/__init__.py", line 3, in <module>
    from .display_manager import get_display_manager
  File "/usr/lib/python3/dist-packages/sage/repl/rich_output/display_manager.py", line 39, in <module>
    from sage.structure.sage_object import SageObject
  File "/usr/lib/python3/dist-packages/sage/structure/__init__.py", line 2, in <module>
    import sage.structure.element
  File "sage/structure/element.pyx", line 1, in init sage.structure.element (build/cythonized/sage/structure/element.c:33585)
    r"""
  File "sage/structure/sage_object.pyx", line 6, in init sage.structure.sage_object (build/cythonized/sage/structure/sage_object.c:11581)
    from sage.misc.persist import (_base_dumps, _base_save,
  File "sage/misc/persist.pyx", line 43, in init sage.misc.persist (build/cythonized/sage/misc/persist.c:11833)
    from .misc import SAGE_DB
  File "/usr/lib/python3/dist-packages/sage/misc/misc.py", line 104, in <module>
    sage_makedirs(DOT_SAGE)
  File "/usr/lib/python3/dist-packages/sage/misc/misc.py", line 86, in sage_makedirs
    os.makedirs(dirname)
  File "/usr/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/.sage'

Warn 2020-11-19 21:14:58: StdErr from Kernel Process Traceback (most recent call last):
  File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/usr/lib/python3/dist-packages/sage/repl/ipython_kernel/__main__.py", line 3, in <module>
    IPKernelApp.launch_instance(kernel_class=SageKernel)
  File "/usr/lib/python3/dist-packages/traitlets/config/application.py", line 663, in launch_instance
    app.initialize(argv)
  File "<decorator-gen-124>", line 2, in initialize
  File "/usr/lib/python3/dist-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/usr/lib/python3/dist-packages/ipykernel/kernelapp.py", line 562, in initialize
    self.init_kernel()
  File "/usr/lib/python3/dist-packages/ipykernel/kernelapp.py", line 439, in init_kernel
    kernel = kernel_factory(parent=self, session=self.session,
  File "/usr/lib/python3/dist-packages/traitlets/config/configurable.py", line 412, in instance
    inst = cls(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/sage/repl/ipython_kernel/kernel.py", line 51, in __init__
    super(SageKernel, self).__init__(**kwds)
  File "/usr/lib/python3/dist-packages/ipykernel/ipkernel.py", line 64, in __init__
    self.shell = self.shell_class.instance(parent=self,
  File "/usr/lib/python3/dist-packages/traitlets/config/configurable.py", line 412, in instance
    inst = cls(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/IPython/core/interactiveshell.py", line 683, in __init__
    self.init_display_formatter()
  File "/usr/lib/python3/dist-packages/sage/repl/interpreter.py", line 229, in init_display_formatter
    from sage.repl.rich_output.backend_ipython import BackendIPythonNotebook
  File "/usr/lib/python3/dist-packages/sage/repl/rich_output/__init__.py", line 3, in <module>
    from .display_manager import get_display_manager
  File "/usr/lib/python3/dist-packages/sage/repl/rich_output/display_manager.py", line 39, in <module>
    from sage.structure.sage_object import SageObject
  File "/usr/lib/python3/dist-packages/sage/structure/__init__.py", line 2, in <module>
    import sage.structure.element
  File "sage/structure/element.pyx", line 1, in init sage.structure.element (build/cythonized/sage/structure/element.c:33585)
    r"""
  File "sage/structure/sage_object.pyx", line 6, in init sage.structure.sage_object (build/cythonized/sage/structure/sage_object.c:11581)
    from sage.misc.persist import (_base_dumps, _base_save,
  File "sage/misc/persist.pyx", line 43, in init sage.misc.persist (build/cythonized/sage/misc/persist.c:11833)
    from .misc import SAGE_DB
  File "/usr/lib/python3/dist-packages/sage/misc/misc.py", line 104, in <module>
    sage_makedirs(DOT_SAGE)
  File "/usr/lib/python3/dist-packages/sage/misc/misc.py", line 86, in sage_makedirs
    os.makedirs(dirname)
  File "/usr/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/.sage'

Info 2020-11-19 21:14:58: KernelProcess Exit Exit - 1
Error 2020-11-19 21:14:58: Disposing session as kernel process died ExitCode: 1, Reason: undefined
Error 2020-11-19 21:14:58: Failed to connect raw kernel session: Error: Canceled
Info 2020-11-19 21:14:58: Shutdown session -- complete
Error 2020-11-19 21:14:58: failed to create INotebook in kernel [Error: Canceled
	at t.KernelShellFutureHandler.dispose (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:32:482268)
	at /home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:47:791737
	at Map.forEach (<anonymous>)
	at g._clearState (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:47:791680)
	at g.dispose (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:47:785428)
	at /home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:32:264587
	at Object.t.swallowExceptions (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:1:132614)
	at l.dispose (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:32:264549)
	at t.RawSession.dispose (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:49:187286)
	at processTicksAndRejections (internal/process/task_queues.js:94:5)]
Error 2020-11-19 21:14:58: DataScience Error [Error: Canceled
	at t.KernelShellFutureHandler.dispose (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:32:482268)
	at /home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:47:791737
	at Map.forEach (<anonymous>)
	at g._clearState (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:47:791680)
	at g.dispose (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:47:785428)
	at /home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:32:264587
	at Object.t.swallowExceptions (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:1:132614)
	at l.dispose (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:32:264549)
	at t.RawSession.dispose (/home/elad/.vscode-server-insiders/extensions/ms-toolsai.jupyter-2020.11.372831992/out/client/extension.js:49:187286)
	at processTicksAndRejections (internal/process/task_queues.js:94:5)]

@darkl
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darkl commented Nov 20, 2020

The error seems to be related to this issue. I guess it has to do with the fact that we see the lines of the form Info 2020-11-19 21:14:57: cwd: /mnt/c/Users/Elad Zelingher/.vscode-insiders/extensions/ms-vscode-remote.remote-wsl-0.51.3. Is there any way to make the cwd be the home directory for instance?

@IanMatthewHuff
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Yeah that linked WSL issue does look related. Might have to change how we start up in the WSL situation.

@DonJayamanne DonJayamanne added the notebook-execution Kernels issues (start/restart/switch/execution, install ipykernel) label Jan 4, 2021
@rchiodo rchiodo removed the info-needed Issue requires more information from poster label Feb 18, 2021
@IanMatthewHuff IanMatthewHuff removed their assignment Apr 5, 2021
@greazer greazer added the language-any Area covering general issues geared to supporting any language (not just Python) label Aug 4, 2021
@DonJayamanne
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Should be fixed with #7063
Closing as a duplicate

@DonJayamanne DonJayamanne mentioned this issue Feb 21, 2022
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@IanMatthewHuff @darkl @DonJayamanne @greazer @rchiodo