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Stop automatically creating jupyter notebooks when using interactive window #8984

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rob-mccutcheon opened this issue Feb 10, 2022 · 11 comments
Closed

Stop automatically creating jupyter notebooks when using interactive window #8984

rob-mccutcheon opened this issue Feb 10, 2022 · 11 comments
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@DonJayamanne
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bug Issue identified by VS Code Team member as probable bug info-needed Issue requires more information from poster interactive-window Impacts interactive window

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@rob-mccutcheon
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I typically use the python interactive window to explore scripts. Since one of the updates, however, this now automatically generate a .ipynb notebook in whichever directory I am in, cluttering the file system.

Is there a way to use the interactive window without it automatically creating a .ipynb file?
@rebornix rebornix transferred this issue from microsoft/vscode Feb 10, 2022
@greazer greazer assigned IanMatthewHuff and unassigned rebornix Feb 10, 2022
@greazer greazer added interactive-window Impacts interactive window bug Issue identified by VS Code Team member as probable bug and removed needs-triage labels Feb 10, 2022
@IanMatthewHuff
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@rob-mccutcheon Thanks for the report here, this isn't something that should be happening. Could you please in this scenario where the files are being created pull the logs from the Jupyter section of the VS Code output window? That would have our diagnostic logging that we can use to investigate this. Also the version of VS Code and the Jupyter extension that you are using would be helpful.

@IanMatthewHuff IanMatthewHuff added the info-needed Issue requires more information from poster label Feb 10, 2022
@rob-mccutcheon
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Thanks @IanMatthewHuff

It is VS Code 1.64.2 and Jupyter v2022.1.1001821375

On further exploration this seems to be only occurring on remote hosts, I am using Remote -SSH v0.70.0

The contents of the output window is

[05:43:24.423] Log Level: 2
[05:43:24.424] remote-ssh@0.70.0
[05:43:24.424] darwin arm64
[05:43:24.430] SSH Resolver called for "ssh-remote+login2.ucl.ac.uk", attempt 1
[05:43:24.431] "remote.SSH.useLocalServer": false
[05:43:24.431] "remote.SSH.showLoginTerminal": true
[05:43:24.431] "remote.SSH.remotePlatform": {"login2.ucl.ac.uk":"linux","login.rosalind.kcl.ac.uk":"linux"}
[05:43:24.431] "remote.SSH.path": undefined
[05:43:24.431] "remote.SSH.configFile": undefined
[05:43:24.431] "remote.SSH.useFlock": true
[05:43:24.431] "remote.SSH.lockfilesInTmp": false
[05:43:24.431] "remote.SSH.localServerDownload": auto
[05:43:24.431] "remote.SSH.remoteServerListenOnSocket": false
[05:43:24.431] "remote.SSH.showLoginTerminal": true
[05:43:24.432] "remote.SSH.defaultExtensions": []
[05:43:24.432] "remote.SSH.loglevel": 2
[05:43:24.432] "remote.SSH.serverPickPortsFromRange": {}
[05:43:24.432] "remote.SSH.enableDynamicForwarding": true
[05:43:24.432] "remote.SSH.serverInstallPath": {}
[05:43:24.432] SSH Resolver called for host: login2.ucl.ac.uk
[05:43:24.432] Setting up SSH remote "login2.ucl.ac.uk"
[05:43:24.434] Using commit id "f80445acd5a3dadef24aa209168452a3d97cc32" and quality "stable" for server
[05:43:24.436] Install and start server if needed
[05:43:24.437] PATH: /opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/Postgres.app/Contents/Versions/latest/bin
[05:43:24.437] Checking ssh with "ssh -V"
[05:43:24.441] > OpenSSH_8.6p1, LibreSSL 2.8.3

[05:43:24.442] Running script with connection command: ssh -T -D 52721 -o ConnectTimeout=15 'login2.ucl.ac.uk' bash
[05:43:26.295] > 
>  #  Server  : cana.ucl.ac.uk
> 
[05:43:26.295] Got some output, clearing connection timeout
[05:43:26.317] > dmz@cana.ucl.ac.uk's password: 
[05:43:30.432] > 
[05:43:30.953] > 
>  #  Neuroimaging Analysis Network (NaN)
>  #  Server  : login2.ucl.ac.uk

> 
[05:43:30.979] > k12034@login2.ucl.ac.uk's password: 
[05:43:34.807] > 
[05:43:36.147] > 712eb9e56d8c: running
[05:43:36.167] > Acquiring lock on /home/k12034/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/vscode-remote-lock.k12034.f80445acd5a3dadef24aa209168452a3d97cc326
> Found existing installation at /home/k12034/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326...
> Checking /home/k12034/.vscode-server/.f80445acd5a3dadef24aa209168452a3d97cc326.log and /home/k12034/.vscode-server/.f80445acd5a3dadef24aa209168452a3d97cc326.pid for a running server
> Looking for server with pid: 196944
[05:43:36.262] > Found running server...
[05:43:36.287] >  
> *
> * Reminder: You may only use this software with Visual Studio family products,
> * as described in the license (https://go.microsoft.com/fwlink/?linkid=2077057)
> *
>  
[05:43:36.319] > Checking server status on port 32976 with wget
[05:43:36.337] > 712eb9e56d8c: start
> SSH_AUTH_SOCK====
> DISPLAY====
> webUiAccessToken====
> listeningOn==32976==
> osReleaseId==scientific==
> arch==x86_64==
> tmpDir==/run/user/1599==
> platform==linux==
> unpackResult====
> didLocalDownload==0==
> downloadTime====
> installTime====
> extInstallTime====
> serverStartTime====
> connectionToken==1a11aaaa-1a11-111a-11aa-11a11a11==
> 712eb9e56d8c: end
[05:43:36.337] Received install output: 
SSH_AUTH_SOCK====
DISPLAY====
webUiAccessToken====
listeningOn==32976==
osReleaseId==scientific==
arch==x86_64==
tmpDir==/run/user/1599==
platform==linux==
unpackResult====
didLocalDownload==0==
downloadTime====
installTime====
extInstallTime====
serverStartTime====
connectionToken==1a11aaaa-1a11-111a-11aa-11a11a11==

[05:43:36.338] Remote server is listening on 32976
[05:43:36.338] Parsed server configuration: {"serverConfiguration":{"remoteListeningOn":{"port":32976},"osReleaseId":"scientific","arch":"x86_64","webUiAccessToken":"","sshAuthSock":"","display":"","tmpDir":"/run/user/1599","platform":"linux","connectionToken":"1a11aaaa-1a11-111a-11aa-11a11a11"},"installUnpackCode":""}
[05:43:36.339] Starting forwarding server. localPort 52764 -> socksPort 52721 -> remotePort 32976
[05:43:36.340] Forwarding server listening on 52764
[05:43:36.340] Waiting for ssh tunnel to be ready
[05:43:36.340] Tunneled 32976 to local port 52764
[05:43:36.341] Resolved "ssh-remote+login2.ucl.ac.uk" to "127.0.0.1:52764"
[05:43:36.341] [Forwarding server 52764] Got connection 0
[05:43:36.345] ------


[05:43:36.354] [Forwarding server 52764] Got connection 1
[05:43:36.461] [Forwarding server 52764] Got connection 2
[05:43:50.829] [Forwarding server 52764] Got connection 3
[05:43:50.830] [Forwarding server 52764] Got connection 4
[05:43:50.831] [Forwarding server 52764] Got connection 5

@IanMatthewHuff
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So sorry, but that seems to be a different log. This is the output area that I'm looking for (needs to be the Jupyter section).

image

@rob-mccutcheon
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Sorry! Here is the jupyter log:

Visual Studio Code (1.64.2, ssh-remote, desktop)
Jupyter Extension Version: 2022.1.1001821375.
Python Extension Version: 2022.0.1814523869.
User belongs to experiment group 'jupyterTest'
User belongs to experiment group 'jupyterEnhancedDataViewer'
Error 08:00:55: Exception while attempting zmq : [Error: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/node_modules/zeromq/prebuilds/linux-x64/node.napi.glibc.node)
	at Object.Module._extensions..node (internal/modules/cjs/loader.js:1122:18)
	at Module.load (internal/modules/cjs/loader.js:928:32)
	at Function.Module._load (internal/modules/cjs/loader.js:769:14)
	at Function.i._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:112:32271)
	at Function.p._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:112:28855)
	at Function.v._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:107:60382)
	at Module.require (internal/modules/cjs/loader.js:952:19)
	at require (internal/modules/cjs/helpers.js:88:18)
	at load (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/node_modules/node-gyp-build/index.js:21:10)
	at Object.<anonymous> (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/node_modules/zeromq/lib/native.js:6:43)
	at Module._compile (internal/modules/cjs/loader.js:1063:30)
	at Object.Module._extensions..js (internal/modules/cjs/loader.js:1092:10)
	at Module.load (internal/modules/cjs/loader.js:928:32)
	at Function.Module._load (internal/modules/cjs/loader.js:769:14)
	at Function.i._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:112:32271)
	at Function.p._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:112:28855)
	at Function.v._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:107:60382)
	at Module.require (internal/modules/cjs/loader.js:952:19)
	at require (internal/modules/cjs/helpers.js:88:18)
	at Object.<anonymous> (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/node_modules/zeromq/lib/index.js:3:16)
	at Module._compile (internal/modules/cjs/loader.js:1063:30)
	at Object.Module._extensions..js (internal/modules/cjs/loader.js:1092:10)
	at Module.load (internal/modules/cjs/loader.js:928:32)
	at Function.Module._load (internal/modules/cjs/loader.js:769:14)
	at Function.i._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:112:32271)
	at Function.p._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:112:28855)
	at Function.v._load (/home/k1201869/.vscode-server/bin/f80445acd5a3dadef24aa209168452a3d97cc326/out/vs/workbench/services/extensions/node/extensionHostProcess.js:107:60382)
	at Module.require (internal/modules/cjs/loader.js:952:19)
	at require (internal/modules/cjs/helpers.js:88:18)
	at Object.<anonymous> (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:195125)
	at n (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:1:124)
	at d.zmqSupported (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:113:223967)
	at d.isSupportedForLocalLaunch (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:113:223758)
	at d.get isSupported [as isSupported] (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:113:223668)
	at t.registerTypes (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:66:1057519)
	at /home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:66:275217
	at async /home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:785306
	at async t.activate (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:784985)
	at async Promise.all (index 1)]
Info 08:00:57: Experiment status for python is {"enabled":true,"optInto":[],"optOutFrom":[]}
Info 08:02:09: Process Execution: > ~/.conda/envs/kong/bin/python -m pip list
> ~/.conda/envs/kong/bin/python -m pip list
Info 08:02:09: Process Execution: > ~/.conda/envs/kong/bin/python -c "import jupyter"
> ~/.conda/envs/kong/bin/python -c "import jupyter"
Info 08:02:09: Process Execution: > ~/.conda/envs/kong/bin/python -c "import notebook"
> ~/.conda/envs/kong/bin/python -c "import notebook"
Info 08:02:18: Process Execution: > ~/.conda/envs/kong/bin/python -m jupyter kernelspec --version
> ~/.conda/envs/kong/bin/python -m jupyter kernelspec --version
Info 08:03:05: Creating controller for interactive with interpreter ~/.conda/envs/kong/bin/python
Info 08:03:05: Starting interactive window with controller ID ms-toolsai.jupyter/.jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1./home/k1201869/.conda/envs/kong/python./home/k1201869/.conda/envs/kong/python.-m#ipykernel_launcher (Interactive)
Info 08:03:05: Setting setActiveController for vscode-interactive:Interactive-1.interactive
Info 08:03:05: Starting Notebook in kernel.ts id = .jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1./home/k1201869/.conda/envs/kong/python./home/k1201869/.conda/envs/kong/python.-m#ipykernel_launcher
Info 08:03:05: Checking for server existence.
Info 08:03:05: Checking for server usability.
Info 08:03:05: Starting notebook server.
Info 08:03:05: Connecting to server
Info 08:03:05: Launching server
Info 08:03:05: Starting Notebook
Info 08:03:05: Creating daemon pool for ~/.conda/envs/kong/bin/python with env variables count 95
Info 08:03:05: Process Execution: > ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
> ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
Info 08:03:05: Process Execution: > ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
> ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
Info 08:03:05: Process Execution: > ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
> ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
Info 08:03:05: Registering dummy command feature
Info 08:03:06: Creating controller for interactive with interpreter ~/.conda/envs/kong/bin/python
Info 08:03:06: TargetController found ID: .jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1./home/k1201869/.conda/envs/kong/python./home/k1201869/.conda/envs/kong/python.-m#ipykernel_launcher (Interactive) for document vscode-interactive:Interactive-1.interactive
Info 08:03:06: Setting controller affinity for vscode-interactive:Interactive-1.interactive .jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1./home/k1201869/.conda/envs/kong/python./home/k1201869/.conda/envs/kong/python.-m#ipykernel_launcher (Interactive)
Info 08:03:07: Generating custom default config at /tmp/977009f1-b8af-4559-8825-17e1b8f5677d/jupyter_notebook_config.py
Info 08:03:07: Starting Jupyter Notebook
Starting Jupyter from ~/.conda/envs/kong/bin/python with command line --no-browser --notebook-dir="/data/project/petProject/PHNO_AMPH_Rob/code" --config=/tmp/977009f1-b8af-4559-8825-17e1b8f5677d/jupyter_notebook_config.py --NotebookApp.iopub_data_rate_limit=10000000000.0
Error 08:03:10: Failed to start the Daemon, StdErr:  Traceback (most recent call last):
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 130, in main
    daemon_cls.start_daemon(queue_handler, args.ppid)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/daemon_python.py", line 221, in start_daemon
    server = cls(stdin, stdout, ppid)
TypeError: __init__() takes 3 positional arguments but 4 were given

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 139, in <module>
    main()
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 135, in main
    raise Exception("Failed to start daemon")
Exception: Failed to start daemon

Error 08:03:10: Failed to start the Daemon, ProcEndEx [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed  to start the Daemon, Ex [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Pinging Daemon Failed, Class name = d, completed in 5008ms, has a falsy return value, Arg 1: {}, Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed to create daemon, Class name = d, completed in 5036ms, has a falsy return value, , Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed to create the daemon service, defaulting to activated environment [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed to create the daemon service, defaulting to activated environment [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Info 08:03:10: Process Execution: > ~/.conda/envs/kong/bin/python -m jupyter notebook --no-browser --notebook-dir="/data/project/petProject/PHNO_AMPH_Rob/code" --config=/tmp/977009f1-b8af-4559-8825-17e1b8f5677d/jupyter_notebook_config.py --NotebookApp.iopub_data_rate_limit=10000000000.0
> ~/.conda/envs/kong/bin/python -m jupyter notebook --no-browser --notebook-dir="/data/project/petProject/PHNO_AMPH_Rob/code" --config=/tmp/977009f1-b8af-4559-8825-17e1b8f5677d/jupyter_notebook_config.py --NotebookApp.iopub_data_rate_limit=10000000000.0
Info 08:03:10: Waiting for Jupyter Notebook
Error 08:03:10: Failed to start the Daemon, StdErr:  Traceback (most recent call last):
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 130, in main
    daemon_cls.start_daemon(queue_handler, args.ppid)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/daemon_python.py", line 221, in start_daemon
    server = cls(stdin, stdout, ppid)
TypeError: __init__() takes 3 positional arguments but 4 were given

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 139, in <module>
    main()
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 135, in main
    raise Exception("Failed to start daemon")
Exception: Failed to start daemon

Error 08:03:10: Failed to start the Daemon, ProcEndEx [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed  to start the Daemon, Ex [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Pinging Daemon Failed, Class name = d, completed in 5024ms, has a falsy return value, Arg 1: {}, Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed to create daemon, Class name = d, completed in 5043ms, has a falsy return value, , Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed to start the Daemon, StdErr:  Traceback (most recent call last):
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 130, in main
    daemon_cls.start_daemon(queue_handler, args.ppid)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/daemon_python.py", line 221, in start_daemon
    server = cls(stdin, stdout, ppid)
TypeError: __init__() takes 3 positional arguments but 4 were given

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 139, in <module>
    main()
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 135, in main
    raise Exception("Failed to start daemon")
Exception: Failed to start daemon

Error 08:03:10: Failed to start the Daemon, ProcEndEx [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed  to start the Daemon, Ex [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Pinging Daemon Failed, Class name = d, completed in 5012ms, has a falsy return value, Arg 1: {}, Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:10: Failed to create daemon, Class name = d, completed in 5034ms, has a falsy return value, , Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
[I 08:03:47.830 NotebookApp] Serving notebooks from local directory: /data/project/petProject/PHNO_AMPH_Rob/code
Info 08:03:47: [I 08:03:47.830 NotebookApp] Serving notebooks from local directory: /data/project/petProject/PHNO_AMPH_Rob/code

[I 08:03:47.831 NotebookApp] Jupyter Notebook 6.4.8 is running at:
[I 08:03:47.831 NotebookApp] http://localhost:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
[I 08:03:47.831 NotebookApp]  or http://127.0.0.1:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
[I 08:03:47.831 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
Info 08:03:47: [I 08:03:47.830 NotebookApp] Serving notebooks from local directory: /data/project/petProject/PHNO_AMPH_Rob/code
[I 08:03:47.831 NotebookApp] Jupyter Notebook 6.4.8 is running at:
[I 08:03:47.831 NotebookApp] http://localhost:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
[I 08:03:47.831 NotebookApp]  or http://127.0.0.1:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
[I 08:03:47.831 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

Info 08:03:47: Creating daemon pool for ~/.conda/envs/kong/bin/python with env variables count 95
Info 08:03:47: Process Execution: > ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
> ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
Info 08:03:47: Process Execution: > ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
> ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
Info 08:03:47: Process Execution: > ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
> ~/.conda/envs/kong/bin/python -m vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v --ppid 236572
[C 08:03:47.911 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///home/k1201869/.local/share/jupyter/runtime/nbserver-236878-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
     or http://127.0.0.1:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
Info 08:03:47: [I 08:03:47.830 NotebookApp] Serving notebooks from local directory: /data/project/petProject/PHNO_AMPH_Rob/code
[I 08:03:47.831 NotebookApp] Jupyter Notebook 6.4.8 is running at:
[I 08:03:47.831 NotebookApp] http://localhost:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
[I 08:03:47.831 NotebookApp]  or http://127.0.0.1:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
[I 08:03:47.831 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 08:03:47.911 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///home/k1201869/.local/share/jupyter/runtime/nbserver-236878-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906
     or http://127.0.0.1:8888/?token=648e3ddd8f367952e267982427db9af81491c5e112fb1906

Error 08:03:52: Failed to start the Daemon, StdErr:  Traceback (most recent call last):
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 130, in main
    daemon_cls.start_daemon(queue_handler, args.ppid)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/daemon_python.py", line 221, in start_daemon
    server = cls(stdin, stdout, ppid)
TypeError: __init__() takes 3 positional arguments but 4 were given

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 139, in <module>
    main()
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 135, in main
    raise Exception("Failed to start daemon")
Exception: Failed to start daemon

Error 08:03:52: Failed to start the Daemon, ProcEndEx [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed  to start the Daemon, Ex [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Pinging Daemon Failed, Class name = d, completed in 5002ms, has a falsy return value, Arg 1: {}, Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed to create daemon, Class name = d, completed in 5028ms, has a falsy return value, , Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed to create the daemon service, defaulting to activated environment [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed to create the daemon service, defaulting to activated environment [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Info 08:03:52: Process Execution: > ~/.conda/envs/kong/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/getServerInfo.py
> ~/.conda/envs/kong/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/getServerInfo.py
Info 08:03:52: Process Execution: > ~/.conda/envs/kong/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/getServerInfo.py
> ~/.conda/envs/kong/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/getServerInfo.py
Error 08:03:52: Failed to start the Daemon, StdErr:  Traceback (most recent call last):
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 130, in main
    daemon_cls.start_daemon(queue_handler, args.ppid)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/daemon_python.py", line 221, in start_daemon
    server = cls(stdin, stdout, ppid)
TypeError: __init__() takes 3 positional arguments but 4 were given

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 139, in <module>
    main()
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 135, in main
    raise Exception("Failed to start daemon")
Exception: Failed to start daemon

Error 08:03:52: Failed to start the Daemon, ProcEndEx [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed  to start the Daemon, Ex [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Pinging Daemon Failed, Class name = d, completed in 5030ms, has a falsy return value, Arg 1: {}, Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed to create daemon, Class name = d, completed in 5049ms, has a falsy return value, , Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed to start the Daemon, StdErr:  Traceback (most recent call last):
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 130, in main
    daemon_cls.start_daemon(queue_handler, args.ppid)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/daemon_python.py", line 221, in start_daemon
    server = cls(stdin, stdout, ppid)
TypeError: __init__() takes 3 positional arguments but 4 were given

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/k1201869/.conda/envs/kong/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 139, in <module>
    main()
  File "/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/vscode_datascience_helpers/daemon/__main__.py", line 135, in main
    raise Exception("Failed to start daemon")
Exception: Failed to start daemon

Error 08:03:52: Failed to start the Daemon, ProcEndEx [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed  to start the Daemon, Ex [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Pinging Daemon Failed, Class name = d, completed in 5019ms, has a falsy return value, Arg 1: {}, Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Error 08:03:52: Failed to create daemon, Class name = d, completed in 5037ms, has a falsy return value, , Return Value: undefined [Error: Timeout waiting for daemon to start
	at Timeout._onTimeout (/home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/out/client/extension.js:51:490231)
	at listOnTimeout (internal/timers.js:554:17)
	at processTimers (internal/timers.js:497:7)]
Info 08:03:53: Connecting to process server
Info 08:03:53: Connecting server kernel http://localhost:8888/
Info 08:03:53: Creating server with settings : {"baseUrl":"http://localhost:8888/","appUrl":"","wsUrl":"ws://localhost:8888/","token":"648e3ddd8f367952e267982427db9af81491c5e112fb1906","appendToken":true,"init":{"cache":"no-store","credentials":"same-origin"}}
Info 08:03:53: Connection complete server
Info 08:03:53: Server started.
[I 08:03:54.995 NotebookApp] Creating new notebook in /mfm_kong_paper/fit_model
Info 08:03:55: installMissingDependencies ~/.conda/envs/kong/bin/python
Info 08:03:55: IPykernel found previously in this environment ~/.conda/envs/kong/bin/python
Info 08:03:56: Spec argv[0] updated from '/home/k1201869/.conda/envs/kong/bin/python' to '~/.conda/envs/kong/bin/python'
Info 08:03:56: Starting a new session for kernel id = .jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1./home/k1201869/.conda/envs/kong/python./home/k1201869/.conda/envs/kong/python.-m#ipykernel_launcher, name = python3613jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1
[I 08:03:57.196 NotebookApp] Kernel started: abdef45b-21cf-4096-a536-f98aa316f47a, name: python3613jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1
Info 08:03:57: Waiting for idle on (kernel): abdef45b-21cf-4096-a536-f98aa316f47a -> unknown
[W 08:03:57.229 NotebookApp] delete /mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb
[E 08:03:57.322 NotebookApp] Uncaught exception DELETE /api/contents/mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb?1644825837218 (127.0.0.1)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='DELETE', uri='/api/contents/mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb?1644825837218', version='HTTP/1.1', remote_ip='127.0.0.1')
    Traceback (most recent call last):
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/tornado/web.py", line 1704, in _execute
        result = await result
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/tornado/gen.py", line 234, in wrapper
        yielded = ctx_run(next, result)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/tornado/gen.py", line 162, in _fake_ctx_run
        return f(*args, **kw)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/notebook/services/contents/handlers.py", line 242, in delete
        yield maybe_future(cm.delete(path))
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/notebook/services/contents/manager.py", line 279, in delete
        self.delete_file(path)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/notebook/services/contents/filemanager.py", line 533, in delete_file
        send2trash(os_path)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/send2trash/plat_other.py", line 211, in send2trash
        trash_move(path_b, dest_trash, topdir)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/send2trash/plat_other.py", line 117, in trash_move
        os.rename(src, op.join(filespath, destname))
    OSError: [Errno 18] Invalid cross-device link: b'/data/project/petProject/PHNO_AMPH_Rob/code/mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb' -> b'/home/k1201869/.local/share/Trash/files/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb'
[W 08:03:57.788 NotebookApp] Unhandled error
[E 08:03:57.789 NotebookApp] {
      "Authorization": "token 648e3ddd8f367952e267982427db9af81491c5e112fb1906",
      "Content-Type": "application/json",
      "Accept": "*/*",
      "User-Agent": "node-fetch/1.0 (+https://github.com/bitinn/node-fetch)",
      "Accept-Encoding": "gzip,deflate",
      "Connection": "close",
      "Host": "localhost:8888"
    }
[E 08:03:57.790 NotebookApp] 500 DELETE /api/contents/mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb?1644825837218 (127.0.0.1) 562.850000ms referer=None
Info 08:03:59: Finished waiting for idle on (kernel): abdef45b-21cf-4096-a536-f98aa316f47a -> idle
Info 08:03:59: Started session for kernel .jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1./home/k1201869/.conda/envs/kong/python./home/k1201869/.conda/envs/kong/python.-m#ipykernel_launcher
Info 08:03:59: Waiting for idle (session) kernel .jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1./home/k1201869/.conda/envs/kong/python./home/k1201869/.conda/envs/kong/python.-m#ipykernel_launcher
Info 08:03:59: Waiting for idle on (kernel): abdef45b-21cf-4096-a536-f98aa316f47a -> idle
Info 08:03:59: Finished waiting for idle on (kernel): abdef45b-21cf-4096-a536-f98aa316f47a -> idle
Info 08:03:59: Finished connecting kernel .jvsc74a57bd007098b3d8367bed01e896ed0c14a93ac98adf90408f7fa2b9973c0852a3373e1./home/k1201869/.conda/envs/kong/python./home/k1201869/.conda/envs/kong/python.-m#ipykernel_launcher
Info 08:04:03: Executing silently Code (idle) = import sys\nprint(sys.executable)
Info 08:04:03: Executing silently Code (completed) = import sys\nprint(sys.executable)
Info 08:04:03: UpdateWorkingDirectoryAndPath in Kernel
Info 08:04:03: Executing silently Code (idle) = import site\nsite.addsitedir(site.getusersitepackages())\nimport os\nimport sys\n%cd "/data/project/petP
Info 08:04:03: Executing silently Code (completed) = import site\nsite.addsitedir(site.getusersitepackages())\nimport os\nimport sys\n%cd "/data/project/petP
Info 08:04:03: Waiting for idle on (kernel): abdef45b-21cf-4096-a536-f98aa316f47a -> idle
Info 08:04:03: Finished waiting for idle on (kernel): abdef45b-21cf-4096-a536-f98aa316f47a -> idle
Info 08:04:03: Executing silently Code (idle) = __file__ = '/data/project/petProject/PHNO_AMPH_Rob/code/mfm_kong_paper/fit_model/analysis.py'
Info 08:04:03: Executing silently Code (idle) = __file__ = '/data/project/petProject/PHNO_AMPH_Rob/code/mfm_kong_paper/fit_model/analysis.py'
Info 08:04:03: Executing silently Code (completed) = __file__ = '/data/project/petProject/PHNO_AMPH_Rob/code/mfm_kong_paper/fit_model/analysis.py'
Info 08:04:03: Process Execution: > ~/.conda/envs/kong/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/normalizeSelection.py
> ~/.conda/envs/kong/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/normalizeSelection.py
Info 08:04:04: Executing silently Code (completed) = __file__ = '/data/project/petProject/PHNO_AMPH_Rob/code/mfm_kong_paper/fit_model/analysis.py'
Info 08:04:04: Adding hash for 1 = d84cd08c79c4 with 1 lines
Info 08:04:20: Executing silently Code (busy) = # Query Jupyter server for the info about a dataframe\nimport json as _VSCODE_json\nimport builtins as
Info 08:04:21: Executing silently Code (busy) = # Query Jupyter server for the info about a dataframe\nimport json as _VSCODE_json\nimport builtins as
Info 08:04:23: Process Execution: > ~/.conda/envs/kong/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/normalizeSelection.py
> ~/.conda/envs/kong/bin/python ~/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1001821375/pythonFiles/normalizeSelection.py
Info 08:04:34: Execute Cells request 3
Info 08:04:34: Execute Cell 3 vscode-interactive:Interactive-1.interactive
Info 08:04:35: Execute Cells request 4
Info 08:04:35: Execute Cell 4 vscode-interactive:Interactive-1.interactive
Info 08:04:39: Cell 1 executed with state Success
Info 08:04:39: Executing silently Code (completed) = # Query Jupyter server for the info about a dataframe\nimport json as _VSCODE_json\nimport builtins as
Info 08:04:39: Executing silently Code (idle) = import builtins\n_rwho_ls = %who_ls\nbuiltins.print(_VSCODE_getVariableTypes(_rwho_ls))
Info 08:04:39: Executing silently Code (completed) = # Query Jupyter server for the info about a dataframe\nimport json as _VSCODE_json\nimport builtins as
Info 08:04:39: Executing silently Code (idle) = import builtins\n_rwho_ls = %who_ls\nbuiltins.print(_VSCODE_getVariableTypes(_rwho_ls))
Info 08:04:39: Executing silently Code (completed) = import builtins\n_rwho_ls = %who_ls\nbuiltins.print(_VSCODE_getVariableTypes(_rwho_ls))
Info 08:04:39: Cell 3 executed with state Success
Info 08:04:39: Executing silently Code (completed) = import builtins\n_rwho_ls = %who_ls\nbuiltins.print(_VSCODE_getVariableTypes(_rwho_ls))
Info 08:04:39: Cell 4 executed with state Success
Info 08:04:39: Adding hash for 4 = d3e4e19e1e01 with 1 lines
Info 08:04:39: Cell 2 executed with state Success

@IanMatthewHuff
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Thanks for the more detailed log. At the start there are some issues with starting up the jupyter server, but I don't think that's the root issue here. To me it looks like this bit here is the core issue:

[W 08:03:57.229 NotebookApp] delete /mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb
[E 08:03:57.322 NotebookApp] Uncaught exception DELETE /api/contents/mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb?1644825837218 (127.0.0.1)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='DELETE', uri='/api/contents/mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb?1644825837218', version='HTTP/1.1', remote_ip='127.0.0.1')
    Traceback (most recent call last):
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/tornado/web.py", line 1704, in _execute
        result = await result
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/tornado/gen.py", line 234, in wrapper
        yielded = ctx_run(next, result)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/tornado/gen.py", line 162, in _fake_ctx_run
        return f(*args, **kw)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/notebook/services/contents/handlers.py", line 242, in delete
        yield maybe_future(cm.delete(path))
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/notebook/services/contents/manager.py", line 279, in delete
        self.delete_file(path)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/notebook/services/contents/filemanager.py", line 533, in delete_file
        send2trash(os_path)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/send2trash/plat_other.py", line 211, in send2trash
        trash_move(path_b, dest_trash, topdir)
      File "/home/k1201869/.conda/envs/kong/lib/python3.6/site-packages/send2trash/plat_other.py", line 117, in trash_move
        os.rename(src, op.join(filespath, destname))
    OSError: [Errno 18] Invalid cross-device link: b'/data/project/petProject/PHNO_AMPH_Rob/code/mfm_kong_paper/fit_model/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb' -> b'/home/k1201869/.local/share/Trash/files/analysis.py-jvsc-72a1e624-4f0c-487d-b3d8-c20089b13188.ipynb'
[W 08:03:57.788 NotebookApp] Unhandled error
[E 08:03:57.789 NotebookApp] {
      "Authorization": "token 648e3ddd8f367952e267982427db9af81491c5e112fb1906",
      "Content-Type": "application/json",
      "Accept": "*/*",
      "User-Agent": "node-fetch/1.0 (+https://github.com/bitinn/node-fetch)",
      "Accept-Encoding": "gzip,deflate",
      "Connection": "close",
      "Host": "localhost:8888"
    }

This is our call to the Jupyter notebook API to clean up the notebook file that we created. Is there maybe some type of symlink situation here that is happening? This error is happening in the Jupyter server itself, we are just calling the Jupyter API to delete the temp file. Sounds possibly related to home and root being on different directories?

https://unix.stackexchange.com/questions/79132/invalid-cross-device-link-while-hardlinking-in-the-same-file-system/79161

One thing to note, at the start we first attempt to start up ipython directly with ZMQ, this fails and we fallback to using the Jupyter server. The error that you have there GLIBCXX is due to having a very old gcc version on the machine. If you update that ZMQ might be able to start up directly and you won't have to start a Jupyter server which would sidestep the delete issue.

@rob-mccutcheon
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Thanks @IanMatthewHuff I think the home and root being on different directories may be tricky to fix as issue persists whether accessing the code directly or via a symlink on the home directory

I have tried with ensuring that .cshrc loads more recent gcc versions (have tried 10.2.0 and 7.5.0) but getting the same error:

Exception while attempting zmq : [Error: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/k1201869/.vscode-server/extensions/ms-toolsai.jupyter-2022.1.1301854968/out/client/node_modules/zeromq/prebuilds/linux-x64/node.napi.glibc.node)

@IanMatthewHuff IanMatthewHuff removed the info-needed Issue requires more information from poster label Mar 31, 2022
@IanMatthewHuff
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@rob-mccutcheon I've looked into this a bit more, and for now I'm going to mark this as an upstream issue. For a Jupyter connection we rely on the jupyterlab services to perform file deletion. Right now this same issue is an open issue on Jupyter. We might still be able to help with this from our side, but the fix would probably have to happen in the Jupyter source base and I don't believe that would be in the near future.

jupyterlab/jupyterlab#5781
jupyterlab/jupyterlab_server#80

@IanMatthewHuff IanMatthewHuff removed their assignment Apr 1, 2022
@DonJayamanne
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DonJayamanne commented Apr 5, 2022 •
edited

@rob-mccutcheon I believe this has been fixed in the latest pre-release version of the Jupyter extension.
Please could you install the pre-release version of the Jupyter extension from the extensions panel and let us know how this goes?

Possibly a duplicate of #6510

@DonJayamanne DonJayamanne added the info-needed Issue requires more information from poster label Apr 5, 2022
@DonJayamanne DonJayamanne self-assigned this Apr 5, 2022
@rob-mccutcheon
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Thanks @DonJayamanne - the ipynb notebooks don't appear to be created. There is still a pycache folder created, I dont know if that is also unwanted behaviour?

@DonJayamanne
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a pycache folder created, I dont know if that is also unwanted behaviour?

not sure about that, if you believe it's created by this extension, please file an issue. its most likely created by the python runtime for your modules.

closing as a duplicate of #6510

@astro-YYH
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I encountered the same problem when I use vs code in a Google drive directory, while running a code in a normal local path will not have this problem.

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