The kernel base 'Python 3.9.7' died

Applies To

• Notebooks (.ipynb files)
• Interactive Window and/or Cell Scripts (.py files with #%% markers)

What happened?

Expected: Implementing .pivot Actually: Getting a message saying “The kernel base ‘Python 3.9.7’ died”

I tried 2 ways; first using Python 3.8.9 64-bit, and second using base (Python 3.9.7). Both are giving similar issues and stops kernel.

VS Code Version

1.65.2 (Universal)

Jupyter Extension Version

2022.2.103 (7 March 2022)

Jupyter logs

Warn 14:23:05: StdErr from Kernel Process /Users/lucy/Library/Python/3.8/lib/python/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '7af8a52c-54c5-46a5-8090-47083d33bc35' instead of 'b"7af8a52c-54c5-46a5-8090-47083d33bc35"'.
  warn(

Info 14:23:05: 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 /var/folders/bv/ll6j7g452_15zbvc974c7y7w0000gn/T/tmp-4138eLQjtKVIMba3.json

Info 14:23:06: Got new session ecd38373-69f2-4605-9d42-81cea567aa98
Info 14:23:06: Started new restart session
Info 14:23:06: Executing silently Code (idle) = import sys\nprint(sys.executable)
Info 14:23:06: Executing silently Code (completed) = import sys\nprint(sys.executable)
Info 14:23:06: Process Execution: > /usr/bin/python3 -c "import sys;print(sys.executable)"
> /usr/bin/python3 -c "import sys;print(sys.executable)"
Info 14:23:06: UpdateWorkingDirectoryAndPath in Kernel
Info 14:23:06: Executing silently Code (idle) = import site\nsite.addsitedir(site.getusersitepackages())\nimport os\nimport sys\n%cd "/Users/lucy/Deskto
Info 14:23:06: Executing silently Code (completed) = import site\nsite.addsitedir(site.getusersitepackages())\nimport os\nimport sys\n%cd "/Users/lucy/Deskto
Info 14:23:06: Waiting for idle on (kernel): ecd38373-69f2-4605-9d42-81cea567aa98 -> idle
Info 14:23:06: Finished waiting for idle on (kernel): ecd38373-69f2-4605-9d42-81cea567aa98 -> idle
Info 14:23:07: Cancel all remaining cells true || Error
Info 14:23:07: Cancel pending cells
Info 14:23:07: Cell 5 executed with state Error
Info 14:23:13: Execute Cells request 0
Info 14:23:13: Execute Cell 0 ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Info 14:23:18: Cell 0 executed with state Success
Info 14:23:21: Execute Cells request 1
Info 14:23:21: Execute Cell 1 ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Info 14:23:43: Cell 1 executed with state Success
Info 14:24:03: Execute Cells request 5
Info 14:24:03: Execute Cell 5 ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Error 14:25:50: Disposing session as kernel process died ExitCode: undefined, Reason: /Users/lucy/Library/Python/3.8/lib/python/site-packages/traitlets/traitlets.py:2202: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5.
  warn(
/Users/lucy/Library/Python/3.8/lib/python/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use '7af8a52c-54c5-46a5-8090-47083d33bc35' instead of 'b"7af8a52c-54c5-46a5-8090-47083d33bc35"'.
  warn(

Info 14:25:50: Dispose Kernel process
Error 14:25:50: Raw kernel process exited code: undefined
Info 14:25:50: Cancel all remaining cells due to dead kernel
Info 14:25:50: Cancel pending cells
Info 14:25:50: Cell 5 executed with state Success
Info 14:38:53: Disposing kernel .jvsc74a57bd031f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6./usr/bin/python3./usr/bin/python3.-m#ipykernel_launcher for notebook ~/Desktop/Projects/MovieLens/recommendatiion.ipynb due to selection of another kernel or closing of the notebook
Info 14:38:53: Dispose kernel file:///Users/lucy/Desktop/Projects/MovieLens/recommendatiion.ipynb
Info 14:38:53: Setting setActiveController for ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Info 14:38:53: Interrupt requested & no kernel.
Info 14:38:53: KernelProvider switched kernel to id = .jvsc74a57bd01945a49d8267038c199a72e8f61b6bfcbb9f4626ddb3ddff4ec56a3f45e14a7a./Users/lucy/opt/anaconda3/python./Users/lucy/opt/anaconda3/python.-m#ipykernel_launcher
Info 14:38:53: Starting Notebook in kernel.ts id = .jvsc74a57bd01945a49d8267038c199a72e8f61b6bfcbb9f4626ddb3ddff4ec56a3f45e14a7a./Users/lucy/opt/anaconda3/python./Users/lucy/opt/anaconda3/python.-m#ipykernel_launcher
Info 14:38:53: Creating raw notebook for ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Info 14:38:53: Getting preferred kernel for ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Info 14:38:53: Computing working directory ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Info 14:38:53: Starting raw kernel base (Python 3.9.7) for interpreter ~/opt/anaconda3/bin/python
Info 14:38:53: installMissingDependencies ~/opt/anaconda3/bin/python
Info 14:38:53: IPyKernel found previously in this environment ~/opt/anaconda3/bin/python
Info 14:38:53: Kernel launching with ports 9000,9001,9002,9003,9004. Start port is 9000
Info 14:38:53: Process Execution: > ~/opt/anaconda3/bin/python -m pip list
> ~/opt/anaconda3/bin/python -m pip list
Info 14:38:53: Process Execution: > ~/opt/anaconda3/bin/python -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)"
> ~/opt/anaconda3/bin/python -c "import ipykernel; print(ipykernel.__version__); print("5dc3a68c-e34e-4080-9c3e-2a532b2ccb4d"); print(ipykernel.__file__)"
Info 14:38:53: Adding env Variable PYTHONNOUSERSITE to ~/opt/anaconda3/bin/python
Info 14:38:53: Process Execution: > ~/opt/anaconda3/bin/python -m ipykernel_launcher --ip=127.0.0.1 --stdin=9003 --control=9001 --hb=9000 --Session.signature_scheme="hmac-sha256" --Session.key=b"a9f0b4e1-5572-4d3b-a689-821b871a174f" --shell=9002 --transport="tcp" --iopub=9004 --f=/var/folders/bv/ll6j7g452_15zbvc974c7y7w0000gn/T/tmp-4138Nf5pqr22khJW.json
> ~/opt/anaconda3/bin/python -m ipykernel_launcher --ip=127.0.0.1 --stdin=9003 --control=9001 --hb=9000 --Session.signature_scheme="hmac-sha256" --Session.key=b"a9f0b4e1-5572-4d3b-a689-821b871a174f" --shell=9002 --transport="tcp" --iopub=9004 --f=/var/folders/bv/ll6j7g452_15zbvc974c7y7w0000gn/T/tmp-4138Nf5pqr22khJW.json
Info 14:38:53: Process Execution: cwd: ~/Desktop/Projects/MovieLens
cwd: ~/Desktop/Projects/MovieLens
Info 14:38:55: ipykernel version 6.4.1 for ~/opt/anaconda3/bin/python
Info 14:38:55: ipykernel location ~/opt/anaconda3/lib/python3.9/site-packages/ipykernel/__init__.py for ~/opt/anaconda3/bin/python
Info 14:38:56: Execute Cells request 0
Info 14:38:56: Execute Cell 0 ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Warn 14:38:58: StdErr from Kernel Process /Users/lucy/opt/anaconda3/lib/python3.9/site-packages/traitlets/traitlets.py:2202: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5.
  warn(

Warn 14:38:58: StdErr from Kernel Process /Users/lucy/opt/anaconda3/lib/python3.9/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use 'a9f0b4e1-5572-4d3b-a689-821b871a174f' instead of 'b"a9f0b4e1-5572-4d3b-a689-821b871a174f"'.
  warn(

Info 14:38:58: 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



Info 14:38:58: 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 /var/folders/bv/ll6j7g452_15zbvc974c7y7w0000gn/T/tmp-4138Nf5pqr22khJW.json

Info 14:38:58: Raw session started and connected
Started kernel base (Python 3.9.7)
Info 14:38:58: Finished connecting acd3fbdf-245e-4e63-a192-82d4c2f16392
Info 14:38:58: Executing silently Code (idle) = import sys\nprint(sys.executable)
Info 14:38:59: Executing silently Code (completed) = import sys\nprint(sys.executable)
Info 14:38:59: UpdateWorkingDirectoryAndPath in Kernel
Info 14:38:59: Executing silently Code (idle) = import site\nsite.addsitedir(site.getusersitepackages())\nimport os\nimport sys\n%cd "/Users/lucy/Deskto
Info 14:38:59: Executing silently Code (completed) = import site\nsite.addsitedir(site.getusersitepackages())\nimport os\nimport sys\n%cd "/Users/lucy/Deskto
Info 14:38:59: Waiting for idle on (kernel): 37e4eb8a-4d4b-458f-bc31-fd703b990ed0 -> idle
Info 14:38:59: Finished waiting for idle on (kernel): 37e4eb8a-4d4b-458f-bc31-fd703b990ed0 -> idle
Info 14:39:06: Cell 0 executed with state Success
Info 14:39:08: Execute Cells request 1
Info 14:39:08: Execute Cell 1 ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Info 14:39:31: Cell 1 executed with state Success
Info 14:39:38: Execute Cells request 5
Info 14:39:38: Execute Cell 5 ~/Desktop/Projects/MovieLens/recommendatiion.ipynb
Error 14:41:46: Disposing session as kernel process died ExitCode: undefined, Reason: /Users/lucy/opt/anaconda3/lib/python3.9/site-packages/traitlets/traitlets.py:2202: FutureWarning: Supporting extra quotes around strings is deprecated in traitlets 5.0. You can use 'hmac-sha256' instead of '"hmac-sha256"' if you require traitlets >=5.
  warn(
/Users/lucy/opt/anaconda3/lib/python3.9/site-packages/traitlets/traitlets.py:2157: FutureWarning: Supporting extra quotes around Bytes is deprecated in traitlets 5.0. Use 'a9f0b4e1-5572-4d3b-a689-821b871a174f' instead of 'b"a9f0b4e1-5572-4d3b-a689-821b871a174f"'.
  warn(

Info 14:41:46: Dispose Kernel process
Error 14:41:46: Raw kernel process exited code: undefined
Info 14:41:46: Cancel all remaining cells due to dead kernel
Info 14:41:46: Cancel pending cells
Info 14:41:46: Cell 5 executed with state Success

Coding Language and Runtime Version

No response

Language Extension Version (if applicable)

No response

Anaconda Version (if applicable)

conda version : 4.11.0, conda-build version : 3.21.5

Running Jupyter locally or remotely?

No response

[rchiodo]

Thanks. I get this on the pivot call.

IndexError: index 1007624404 is out of bounds for axis 0 with size 1007623835

Meaning I don’t think you can perform a pivot on that dataset. It’s too big. I may not have gotten a crash because I’m using 64 bit.

Sounds like this bug here: https://github.com/pandas-dev/pandas/issues/10582

I’d recommend running on a 64 bit machine if you’re not already, and installing 64 bit python. Or trimming the CSV down before trying to pivot.

[lucylee418]

By public I mean can you give us the ‘ratings.csv’ file so we can try your same code on our own machines.

Oh sure. Yes, it’s public, and I got the file from [ml-25m.zip] on https://grouplens.org/datasets/movielens/