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VS Code Jupyter extension
https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter
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Jupyter kernel started crashing #11808

Closed janosh closed 1 year ago

janosh commented 1 year ago

Applies To

What happened?

The Kernel crashed while executing code in the the current cell or a previous cell. Please review the code in the cell(s) to identify a possible cause of the failure. Click here for more info. View Jupyter log for further details.

Canceled future for execute_request message before replies were done

I have a code cell I've run successfully in the past that started bringing the whole server down recently. I think it may have started after upgrading some packages in my venv. Tried downgrading those again which didn't help.

VS Code Version

1.72.2

Jupyter Extension Version

2022.9.1202862440

Jupyter logs

[I 16:40:12.337 NotebookApp] Creating new notebook in /data/wbm/2022-10-13
[I 16:40:12.339 NotebookApp] Saving Untitled.ipynb
info 16:40:12.347: installMissingDependencies /Users/janosh/.venv/py310/bin/python, ui.disabled=false for resource '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
info 16:40:12.349: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 1ms
info 16:40:12.349: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 1ms
info 16:40:12.349: Process Execution: > ~/.venv/py310/bin/python -c "import ipykernel"
> ~/.venv/py310/bin/python -c "import ipykernel"
info 16:40:12.487: Spec argv[0] updated from '/Users/janosh/.venv/py310/bin/python' to '/Users/janosh/.venv/py310/bin/python'
info 16:40:12.487: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 0ms
info 16:40:12.487: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 0ms
[I 16:40:12.510 NotebookApp] Kernel started: 310beb35-d16d-4ca5-a923-9abc44016165, name: python3106jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837
[W 16:40:12.518 NotebookApp] delete /data/wbm/2022-10-13/get-ppd-mp-stabilities.py-jvsc-4073c550-2bd7-4839-94d4-a0448b7b7109d13e587a-5aa9-4a9e-99a5-9ef9bb5c4713.ipynb
info 16:40:12.602: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 0ms
info 16:40:12.602: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 0ms
info 16:40:12.978: Started session for kernel startUsingPythonInterpreter:.jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837./Users/janosh/.venv/py310/python./Users/janosh/.venv/py310/python.-m#ipykernel_launcher
info 16:40:12.980: UpdateWorkingDirectoryAndPath in Kernel
info 16:40:13.084: Generated code for 1 = <ipython-input-1-686d59e8522a> with 20 lines
info 16:40:14.599: Generated code for 2 = <ipython-input-2-ed09f49fb273> with 19 lines
info 16:40:28.731: Interrupt requested /Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py
info 16:40:28.731: Interrupt requested & sent for Interactive-2.interactive in notebookEditor.
info 16:40:28.731: Interrupt kernel execution
info 16:40:28.731: Interrupt kernel execution
info 16:40:28.731: Interrupting kernel: python3106jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837
[I 16:40:28.734 NotebookApp] Kernel interrupted: 310beb35-d16d-4ca5-a923-9abc44016165
info 16:40:29.332: Cancel all remaining cells true || Error || undefined
info 16:40:32.286: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py
> ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py
info 16:40:32.349: Generated code for 3 = <ipython-input-3-6a472a48d249> with 1 lines
info 16:40:34.758: Generated code for 4 = <ipython-input-4-7d14fe430f41> with 6 lines
[I 16:40:39.500 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
error 16:40:39.508: Error in waiting for cell to complete Error: Canceled future for execute_request message before replies were done
    at a.KernelShellFutureHandler.dispose (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:32353)
    at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:26572
    at Map.forEach (<anonymous>)
    at y._clearKernelState (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:26557)
    at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:29000
    at processTicksAndRejections (node:internal/process/task_queues:96:5)
warn 16:40:39.508: Cell completed with errors {
  message: 'Canceled future for execute_request message before replies were done'
}
info 16:40:39.508: Cancel all remaining cells true || Error || undefined
[I 16:40:39.508 NotebookApp] Starting buffering for 310beb35-d16d-4ca5-a923-9abc44016165:fb7ba576-f786-4ef5-9bcd-646dd43f3772
[I 16:40:39.525 NotebookApp] Restoring connection for 310beb35-d16d-4ca5-a923-9abc44016165:fb7ba576-f786-4ef5-9bcd-646dd43f3772
info 16:43:16.079: Disposing kernel .jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837./Users/janosh/.venv/py310/python./Users/janosh/.venv/py310/python.-m#ipykernel_launcher for notebook Interactive-2.interactive due to selection of another kernel or closing of the notebook
info 16:43:16.079: Dispose Kernel 'Interactive-2.interactive' associated with '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
info 16:43:16.084: Dispose Kernel 'Interactive-2.interactive' associated with '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
[I 16:43:16.092 NotebookApp] Kernel shutdown: 310beb35-d16d-4ca5-a923-9abc44016165
info 16:43:18.378: Starting interactive window for resource '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
info 16:43:18.431: Attempting to start a server because of preload conditions ...
info 16:43:18.432: Preferred Remote kernel for Interactive-2.interactive is undefined
info 16:43:18.610: Starting Jupyter Session startUsingPythonInterpreter, .jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837./Users/janosh/.venv/py310/python./Users/janosh/.venv/py310/python.-m#ipykernel_launcher (Python Path: /Users/janosh/.venv/py310, EnvType: Venv, EnvName: 'py310', Version: 3.10.6) for 'Interactive-2.interactive' (disableUI=false)
[I 16:43:18.618 NotebookApp] Creating new notebook in /data/wbm/2022-10-13
[I 16:43:18.622 NotebookApp] Saving Untitled.ipynb
info 16:43:18.634: installMissingDependencies /Users/janosh/.venv/py310/bin/python, ui.disabled=false for resource '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
info 16:43:18.635: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 1ms
info 16:43:18.635: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 1ms
info 16:43:18.635: Process Execution: > ~/.venv/py310/bin/python -c "import ipykernel"
> ~/.venv/py310/bin/python -c "import ipykernel"
info 16:43:18.801: Spec argv[0] updated from '/Users/janosh/.venv/py310/bin/python' to '/Users/janosh/.venv/py310/bin/python'
info 16:43:18.802: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 1ms
info 16:43:18.802: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 1ms
[I 16:43:18.826 NotebookApp] Kernel started: 2f6284de-54ae-40a0-9c20-2c2654676244, name: python3106jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837
[W 16:43:18.834 NotebookApp] delete /data/wbm/2022-10-13/get-ppd-mp-stabilities.py-jvsc-c3f5fa42-5131-46d7-9fb3-5f0b4fd19cd38c4d3ab2-a8d6-49e0-b076-7d2e07429436.ipynb
info 16:43:18.933: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 1ms
info 16:43:18.933: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 1ms
info 16:43:19.390: Started session for kernel startUsingPythonInterpreter:.jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837./Users/janosh/.venv/py310/python./Users/janosh/.venv/py310/python.-m#ipykernel_launcher
info 16:43:19.391: UpdateWorkingDirectoryAndPath in Kernel
info 16:43:19.492: Generated code for 1 = <ipython-input-1-686d59e8522a> with 20 lines
info 16:43:20.680: Generated code for 2 = <ipython-input-2-be806d201031> with 20 lines
info 16:43:32.231: Generated code for 3 = <ipython-input-3-7d14fe430f41> with 6 lines
[I 16:43:36.820 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
error 16:43:36.825: Error in waiting for cell to complete Error: Canceled future for execute_request message before replies were done
    at a.KernelShellFutureHandler.dispose (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:32353)
    at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:26572
    at Map.forEach (<anonymous>)
    at y._clearKernelState (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:26557)
    at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:29000
    at processTicksAndRejections (node:internal/process/task_queues:96:5)
warn 16:43:36.825: Cell completed with errors {
  message: 'Canceled future for execute_request message before replies were done'
}
info 16:43:36.826: Cancel all remaining cells true || Error || undefined
[I 16:43:36.825 NotebookApp] Starting buffering for 2f6284de-54ae-40a0-9c20-2c2654676244:20006cc3-ff15-4b48-9faf-d024f0caab14
[I 16:43:36.834 NotebookApp] Restoring connection for 2f6284de-54ae-40a0-9c20-2c2654676244:20006cc3-ff15-4b48-9faf-d024f0caab14
info 16:44:02.465: Disposing kernel .jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837./Users/janosh/.venv/py310/python./Users/janosh/.venv/py310/python.-m#ipykernel_launcher for notebook Interactive-2.interactive due to selection of another kernel or closing of the notebook
info 16:44:02.465: Dispose Kernel 'Interactive-2.interactive' associated with '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
info 16:44:02.470: Dispose Kernel 'Interactive-2.interactive' associated with '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
[I 16:44:02.484 NotebookApp] Kernel shutdown: 2f6284de-54ae-40a0-9c20-2c2654676244
info 16:44:03.974: Starting interactive window for resource '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
info 16:44:04.026: Attempting to start a server because of preload conditions ...
info 16:44:04.027: Preferred Remote kernel for Interactive-2.interactive is undefined
info 16:44:04.201: Starting Jupyter Session startUsingPythonInterpreter, .jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837./Users/janosh/.venv/py310/python./Users/janosh/.venv/py310/python.-m#ipykernel_launcher (Python Path: /Users/janosh/.venv/py310, EnvType: Venv, EnvName: 'py310', Version: 3.10.6) for 'Interactive-2.interactive' (disableUI=false)
[I 16:44:04.208 NotebookApp] Creating new notebook in /data/wbm/2022-10-13
[I 16:44:04.210 NotebookApp] Saving Untitled.ipynb
info 16:44:04.222: installMissingDependencies /Users/janosh/.venv/py310/bin/python, ui.disabled=false for resource '/Users/janosh/dev/matbench-discovery/data/wbm/2022-10-13/get-ppd-mp-stabilities.py'
info 16:44:04.223: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 0ms
info 16:44:04.224: Process Execution: > ~/.venv/py310/bin/python -c "import ipykernel"
> ~/.venv/py310/bin/python -c "import ipykernel"
info 16:44:04.329: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 106ms
info 16:44:04.371: Spec argv[0] updated from '/Users/janosh/.venv/py310/bin/python' to '/Users/janosh/.venv/py310/bin/python'
info 16:44:04.372: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 1ms
[I 16:44:04.397 NotebookApp] Kernel started: 1c0ab3ac-e385-4877-8122-af130a8bbb9f, name: python3106jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837
[W 16:44:04.407 NotebookApp] delete /data/wbm/2022-10-13/get-ppd-mp-stabilities.py-jvsc-2ab4bf8c-b9a0-450d-ae61-f21f9a2ea24173a59c11-1598-49ba-86f3-f07b5c0d6c31.ipynb
info 16:44:04.413: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 42ms
info 16:44:04.526: Got env vars with python /Users/janosh/.venv/py310/bin/python, with env var count 47 and custom env var count 0 in 0ms
info 16:44:04.526: Got env vars ourselves faster /Users/janosh/.venv/py310/bin/python with env var count 46 in 0ms
info 16:44:05.020: Started session for kernel startUsingPythonInterpreter:.jvsc74a57bd08022b3e932e045c760cb4633b91dd1cb8bc60d104ca9808334cbd1645adbe837./Users/janosh/.venv/py310/python./Users/janosh/.venv/py310/python.-m#ipykernel_launcher
info 16:44:05.021: UpdateWorkingDirectoryAndPath in Kernel
info 16:44:05.134: Generated code for 1 = <ipython-input-1-686d59e8522a> with 20 lines
info 16:44:06.259: Generated code for 2 = <ipython-input-2-be806d201031> with 20 lines
info 16:44:18.356: Generated code for 3 = <ipython-input-3-7d14fe430f41> with 6 lines
error 16:44:22.398: Error in waiting for cell to complete Error: Canceled future for execute_request message before replies were done
    at a.KernelShellFutureHandler.dispose (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:32353)
    at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:26572
    at Map.forEach (<anonymous>)
    at y._clearKernelState (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:26557)
    at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:29000
    at processTicksAndRejections (node:internal/process/task_queues:96:5)
warn 16:44:22.399: Cell completed with errors {
  message: 'Canceled future for execute_request message before replies were done'
}
info 16:44:22.400: Cancel all remaining cells true || Error || undefined
[I 16:44:22.385 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
[I 16:44:22.401 NotebookApp] Starting buffering for 1c0ab3ac-e385-4877-8122-af130a8bbb9f:75f86d89-4574-4565-ab7c-5cb949edbe79
[I 16:44:22.415 NotebookApp] Restoring connection for 1c0ab3ac-e385-4877-8122-af130a8bbb9f:75f86d89-4574-4565-ab7c-5cb949edbe79

Coding Language and Runtime Version

Python 3.10

Language Extension Version (if applicable)

No response

Anaconda Version (if applicable)

No response

Running Jupyter locally or remotely?

Local

DonJayamanne commented 1 year ago

@janosh Sorry yo'ure runing into this issue.

info 16:40:28.731: Interrupt requested

Based on the logs it seems that somehow the kernel is getting interrupted. Can you do me a faviour:

  1. Please could you enable logging as follows:

    • Open settings & go into Jupyter->Logging
    • Change the value to verbose
    • Reload VS Code,
    • Attempt to repro the issue & then copy the output from the Jupyter output panel.

  2. Can you try the same thing in VS Code insiders with the pre-release version of Jupyter extension & ensure you have the same verbose logging. Do provide the logs for that too.

janosh commented 1 year ago

@DonJayamanne Thanks for the quick reply! 👍

Here are the logs for the pre-release Jupyter extension ```log info 08:46:30.435: Generated code for 6 = with 1 lines debug 08:46:30.438: Start Jupyter Session in kernel.ts with disableUI = false info 08:46:31.809: Cancel all remaining cells true || Error || undefined debug 08:46:31.809: Cancel pending cells debug 08:46:31.809: Cell 6 executed with state Error debug 08:46:37.725: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:46:37.772: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:46:38.173: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:46:38.220: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:46:52.069: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:46:52.116: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:46:54.554: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:46:54.600: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:46:55.236: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:46:55.280: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) info 08:47:01.920: Generated code for 7 = with 30 lines debug 08:47:01.926: Start Jupyter Session in kernel.ts with disableUI = false debug 08:47:06.005: Cell 7 executed with state Success debug 08:47:06.027: CodeLensFactory: Generating new code lenses for version 52 of document file:///Users/janosh/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py for commands jupyter.runcell, jupyter.runallcellsabove, jupyter.runcellandallbelow, jupyter.debugcell, jupyter.debugcontinue, jupyter.debugstop, jupyter.debugstepover debug 08:47:11.518: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:11.566: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:47:12.868: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:12.913: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:47:21.146: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:21.195: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:47:21.841: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:21.888: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:47:22.103: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:22.145: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:47:23.228: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:23.274: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:47:41.942: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:41.989: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:47:45.111: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:45.148: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:47:47.579: Get Active Interpreter, Class name = j (started execution), Arg 1: undefined debug 08:47:47.581: Get Active Interpreter, Class name = j, completed in 2ms, has a truthy return value, Arg 1: undefined, Return Value: {"id":"/Users/janosh/.venv/py310/bin/python","sysPrefix":"/Users/janosh/.venv/py310","envPath":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"envName":"py310","uri":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"displayName":"py310","envType":"Venv","version":{"major":3,"minor":10,"patch":8,"raw":"3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)]"}} debug 08:47:47.581: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 08:47:47.581: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:47:47.581: Cached data exists getEnvironmentVariables, debug 08:47:47.581: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:47:47.581: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 08:47:47.582: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py info 08:47:47.637: Generated code for 8 = with 1 lines debug 08:47:47.640: Start Jupyter Session in kernel.ts with disableUI = false debug 08:47:47.689: Cell 8 executed with state Success debug 08:47:47.695: CodeLensFactory: Generating new code lenses for version 69 of document file:///Users/janosh/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py for commands jupyter.runcell, jupyter.runallcellsabove, jupyter.runcellandallbelow, jupyter.debugcell, jupyter.debugcontinue, jupyter.debugstop, jupyter.debugstepover debug 08:47:51.728: Get Active Interpreter, Class name = j (started execution), Arg 1: undefined debug 08:47:51.730: Get Active Interpreter, Class name = j, completed in 2ms, has a truthy return value, Arg 1: undefined, Return Value: {"id":"/Users/janosh/.venv/py310/bin/python","sysPrefix":"/Users/janosh/.venv/py310","envPath":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"envName":"py310","uri":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"displayName":"py310","envType":"Venv","version":{"major":3,"minor":10,"patch":8,"raw":"3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)]"}} debug 08:47:51.730: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 08:47:51.730: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:47:51.730: Cached data exists getEnvironmentVariables, debug 08:47:51.730: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:47:51.730: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 08:47:51.731: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py info 08:47:51.789: Generated code for 9 = with 6 lines debug 08:47:51.792: Start Jupyter Session in kernel.ts with disableUI = false debug 08:47:51.880: Cell 9 executed with state Success debug 08:47:53.066: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:47:53.113: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:05.480: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:48:05.527: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:05.694: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:48:05.734: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:07.885: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:48:07.931: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:09.716: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:48:09.764: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:09.768: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:48:09.795: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:14.293: Get Active Interpreter, Class name = j (started execution), Arg 1: undefined debug 08:48:14.296: Get Active Interpreter, Class name = j, completed in 3ms, has a truthy return value, Arg 1: undefined, Return Value: {"id":"/Users/janosh/.venv/py310/bin/python","sysPrefix":"/Users/janosh/.venv/py310","envPath":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"envName":"py310","uri":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"displayName":"py310","envType":"Venv","version":{"major":3,"minor":10,"patch":8,"raw":"3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)]"}} debug 08:48:14.296: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 08:48:14.296: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:14.296: Cached data exists getEnvironmentVariables, debug 08:48:14.296: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:14.296: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 08:48:14.297: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py info 08:48:14.365: Generated code for 10 = with 1 lines debug 08:48:14.369: Start Jupyter Session in kernel.ts with disableUI = false debug 08:48:14.412: Cell 10 executed with state Success debug 08:48:18.145: Get Active Interpreter, Class name = j (started execution), Arg 1: undefined debug 08:48:18.147: Get Active Interpreter, Class name = j, completed in 2ms, has a truthy return value, Arg 1: undefined, Return Value: {"id":"/Users/janosh/.venv/py310/bin/python","sysPrefix":"/Users/janosh/.venv/py310","envPath":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"envName":"py310","uri":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"displayName":"py310","envType":"Venv","version":{"major":3,"minor":10,"patch":8,"raw":"3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)]"}} debug 08:48:18.147: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 08:48:18.147: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:18.147: Cached data exists getEnvironmentVariables, debug 08:48:18.148: Get Custom Env Variables, Class name = w, completed in 1ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:18.148: Create ProcessService, Class name = h, completed in 1ms, has a truthy return value, Arg 1: undefined info 08:48:18.149: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py info 08:48:18.211: Generated code for 11 = with 1 lines debug 08:48:18.215: Start Jupyter Session in kernel.ts with disableUI = false debug 08:48:18.253: Cell 11 executed with state Success debug 08:48:19.522: Get Active Interpreter, Class name = j (started execution), Arg 1: undefined debug 08:48:19.523: Get Active Interpreter, Class name = j, completed in 1ms, has a truthy return value, Arg 1: undefined, Return Value: {"id":"/Users/janosh/.venv/py310/bin/python","sysPrefix":"/Users/janosh/.venv/py310","envPath":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"envName":"py310","uri":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"displayName":"py310","envType":"Venv","version":{"major":3,"minor":10,"patch":8,"raw":"3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)]"}} debug 08:48:19.523: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 08:48:19.523: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:19.523: Cached data exists getEnvironmentVariables, debug 08:48:19.524: Get Custom Env Variables, Class name = w, completed in 1ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:19.524: Create ProcessService, Class name = h, completed in 1ms, has a truthy return value, Arg 1: undefined info 08:48:19.524: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py info 08:48:19.581: Generated code for 12 = with 1 lines debug 08:48:19.584: Start Jupyter Session in kernel.ts with disableUI = false debug 08:48:19.622: Cell 12 executed with state Success debug 08:48:26.987: Get Active Interpreter, Class name = j (started execution), Arg 1: undefined debug 08:48:26.990: Get Active Interpreter, Class name = j, completed in 3ms, has a truthy return value, Arg 1: undefined, Return Value: {"id":"/Users/janosh/.venv/py310/bin/python","sysPrefix":"/Users/janosh/.venv/py310","envPath":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"envName":"py310","uri":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"displayName":"py310","envType":"Venv","version":{"major":3,"minor":10,"patch":8,"raw":"3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)]"}} debug 08:48:26.990: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 08:48:26.990: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:26.990: Cached data exists getEnvironmentVariables, debug 08:48:26.990: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:26.990: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 08:48:26.991: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py info 08:48:27.050: Generated code for 13 = with 1 lines debug 08:48:27.054: Start Jupyter Session in kernel.ts with disableUI = false info 08:48:27.101: Cancel all remaining cells true || Error || undefined debug 08:48:27.101: Cancel pending cells debug 08:48:27.101: Cell 13 executed with state Error debug 08:48:29.664: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:48:29.711: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:31.248: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:48:31.293: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:32.084: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 08:48:32.124: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 08:48:33.283: Get Active Interpreter, Class name = j (started execution), Arg 1: undefined debug 08:48:33.285: Get Active Interpreter, Class name = j, completed in 2ms, has a truthy return value, Arg 1: undefined, Return Value: {"id":"/Users/janosh/.venv/py310/bin/python","sysPrefix":"/Users/janosh/.venv/py310","envPath":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"envName":"py310","uri":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"displayName":"py310","envType":"Venv","version":{"major":3,"minor":10,"patch":8,"raw":"3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)]"}} debug 08:48:33.285: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 08:48:33.285: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:33.285: Cached data exists getEnvironmentVariables, debug 08:48:33.285: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:33.285: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 08:48:33.286: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py info 08:48:33.341: Generated code for 14 = with 1 lines debug 08:48:33.345: Start Jupyter Session in kernel.ts with disableUI = false debug 08:48:33.401: Cell 14 executed with state Success debug 08:48:36.560: Get Active Interpreter, Class name = j (started execution), Arg 1: undefined debug 08:48:36.562: Get Active Interpreter, Class name = j, completed in 2ms, has a truthy return value, Arg 1: undefined, Return Value: {"id":"/Users/janosh/.venv/py310/bin/python","sysPrefix":"/Users/janosh/.venv/py310","envPath":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"envName":"py310","uri":{"$mid":1,"path":"/Users/janosh/.venv/py310/bin/python","scheme":"file"},"displayName":"py310","envType":"Venv","version":{"major":3,"minor":10,"patch":8,"raw":"3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)]"}} debug 08:48:36.562: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 08:48:36.562: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:36.562: Cached data exists getEnvironmentVariables, debug 08:48:36.562: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 08:48:36.562: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 08:48:36.563: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/pythonFiles/normalizeSelection.py info 08:48:36.623: Generated code for 15 = with 1 lines debug 08:48:36.627: Start Jupyter Session in kernel.ts with disableUI = false debug 08:48:37.320: Python Daemon (pid: 6562): write to stderr: [I 08:48:37.319 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports error 08:48:37.326: Error in waiting for cell to complete Error: Canceled future for execute_request message before replies were done at a.KernelShellFutureHandler.dispose (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/out/node_modules/@jupyterlab/services.js:2:32353) at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/out/node_modules/@jupyterlab/services.js:2:26572 at Map.forEach () at y._clearKernelState (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/out/node_modules/@jupyterlab/services.js:2:26557) at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.10.1103011060/out/node_modules/@jupyterlab/services.js:2:29000 at processTicksAndRejections (node:internal/process/task_queues:96:5) warn 08:48:37.328: Cell completed with errors { message: 'Canceled future for execute_request message before replies were done' } info 08:48:37.329: Cancel all remaining cells true || Error || undefined debug 08:48:37.329: Cancel pending cells debug 08:48:37.330: Cell 15 executed with state Error [I 08:48:37.319 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports debug 08:48:37.333: Python Daemon (pid: 6562): kernel 8662166f-3c06-43e9-8438-876180c56184 restarted debug 08:48:37.334: Python Daemon (pid: 6562): write to stderr: [I 08:48:37.327 NotebookApp] Starting buffering for 8662166f-3c06-43e9-8438-876180c56184:cf5d72dd-f703-40cd-a154-c140cdfcf0ea [I 08:48:37.327 NotebookApp] Starting buffering for 8662166f-3c06-43e9-8438-876180c56184:cf5d72dd-f703-40cd-a154-c140cdfcf0ea debug 08:48:37.344: Python Daemon (pid: 6562): write to stderr: [I 08:48:37.343 NotebookApp] Restoring connection for 8662166f-3c06-43e9-8438-876180c56184:cf5d72dd-f703-40cd-a154-c140cdfcf0ea [I 08:48:37.343 NotebookApp] Restoring connection for 8662166f-3c06-43e9-8438-876180c56184:cf5d72dd-f703-40cd-a154-c140cdfcf0ea ```
janosh commented 1 year ago
logs for the release version ```log info 09:02:40.358: Generated code for 5 = with 32 lines debug 09:02:40.363: Start Jupyter Session in kernel.ts with disableUI = false debug 09:02:44.913: Cell 5 executed with state Success debug 09:02:46.707: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:02:46.752: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:02:47.936: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:02:47.984: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:02:48.582: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:02:48.634: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:02:48.942: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:02:48.983: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:03:09.277: Get Active Interpreter, Class name = I (started execution), Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:03:09.277: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" info 09:03:09.326: Generated code for 6 = with 51 lines debug 09:03:09.331: Start Jupyter Session in kernel.ts with disableUI = false debug 09:03:16.219: Get Active Interpreter, Class name = I (started execution), Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:03:16.220: Get Active Interpreter, Class name = I, completed in 1ms, has a truthy return value, Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:03:16.221: Get Active Interpreter, Class name = I (started execution), Arg 1: undefined debug 09:03:16.221: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: undefined debug 09:03:16.221: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 09:03:16.221: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:03:16.221: Cached data exists getEnvironmentVariables, debug 09:03:16.221: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:03:16.221: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 09:03:16.222: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py debug 09:03:17.982: Executing silently Code (busy) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info info 09:03:21.922: Cancel all remaining cells true || Error || undefined debug 09:03:21.922: Cancel pending cells debug 09:03:21.922: Cell 6 executed with state Error debug 09:03:21.949: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:03:41.707: Get Active Interpreter, Class name = I (started execution), Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:03:41.707: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:03:41.708: Get Active Interpreter, Class name = I (started execution), Arg 1: undefined debug 09:03:41.708: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: undefined debug 09:03:41.708: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 09:03:41.708: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:03:41.708: Cached data exists getEnvironmentVariables, debug 09:03:41.708: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:03:41.708: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 09:03:41.709: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py info 09:03:41.761: Generated code for 7 = with 1 lines debug 09:03:41.773: Start Jupyter Session in kernel.ts with disableUI = false debug 09:03:41.822: Cell 8 executed with state Success debug 09:03:42.876: Get Active Interpreter, Class name = I (started execution), Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:03:42.876: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:03:42.877: Get Active Interpreter, Class name = I (started execution), Arg 1: undefined debug 09:03:42.877: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: undefined debug 09:03:42.877: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 09:03:42.877: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:03:42.877: Cached data exists getEnvironmentVariables, debug 09:03:42.877: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:03:42.877: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 09:03:42.878: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py info 09:03:42.932: Generated code for 8 = with 1 lines debug 09:03:42.941: Start Jupyter Session in kernel.ts with disableUI = false debug 09:03:43.000: Cell 9 executed with state Success debug 09:03:55.180: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:03:55.227: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:03:57.432: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:03:57.479: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:03:57.999: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:03:58.046: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:01.705: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:01.754: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:01.937: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:01.981: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:02.921: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:02.967: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:03.189: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:03.233: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:03.658: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:03.706: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:04.268: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:04.309: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:04.938: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:04.984: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:08.120: Get Active Interpreter, Class name = I (started execution), Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:04:08.121: Get Active Interpreter, Class name = I, completed in 1ms, has a truthy return value, Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:04:08.121: Get Active Interpreter, Class name = I (started execution), Arg 1: undefined debug 09:04:08.121: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: undefined debug 09:04:08.121: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 09:04:08.121: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:04:08.122: Cached data exists getEnvironmentVariables, debug 09:04:08.122: Get Custom Env Variables, Class name = w, completed in 1ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:04:08.122: Create ProcessService, Class name = h, completed in 1ms, has a truthy return value, Arg 1: undefined info 09:04:08.123: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py info 09:04:08.185: Generated code for 9 = with 1 lines debug 09:04:08.193: Start Jupyter Session in kernel.ts with disableUI = false debug 09:04:08.252: Cell 10 executed with state Success debug 09:04:11.613: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:11.658: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:12.161: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:12.208: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:12.578: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:12.622: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:13.494: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:13.539: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:14.897: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:14.945: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:22.563: Get Active Interpreter, Class name = I (started execution), Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:04:22.564: Get Active Interpreter, Class name = I, completed in 1ms, has a truthy return value, Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:04:22.564: Get Active Interpreter, Class name = I (started execution), Arg 1: undefined debug 09:04:22.564: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: undefined debug 09:04:22.564: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 09:04:22.564: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:04:22.564: Cached data exists getEnvironmentVariables, debug 09:04:22.564: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:04:22.564: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 09:04:22.565: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py info 09:04:22.627: Generated code for 10 = with 13 lines debug 09:04:22.630: Start Jupyter Session in kernel.ts with disableUI = false debug 09:04:42.390: Get Active Interpreter, Class name = I (started execution), Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:04:42.390: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:04:42.390: Get Active Interpreter, Class name = I (started execution), Arg 1: undefined debug 09:04:42.390: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: undefined debug 09:04:42.390: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 09:04:42.390: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:04:42.390: Cached data exists getEnvironmentVariables, debug 09:04:42.390: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:04:42.390: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 09:04:42.391: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py debug 09:04:43.977: Cell 11 executed with state Success info 09:04:43.978: Generated code for 11 = with 4 lines debug 09:04:43.982: Start Jupyter Session in kernel.ts with disableUI = false info 09:04:44.027: Cancel all remaining cells true || Error || undefined debug 09:04:44.027: Cancel pending cells debug 09:04:44.027: Cell 12 executed with state Error debug 09:04:46.974: Executing silently Code (idle) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info debug 09:04:47.013: Executing silently Code (completed) = def _VSCODE_getVariable(what_to_get, is_debugging, *args):\n# Query Jupyter server for the info with 1 output(s) debug 09:04:53.853: Get Active Interpreter, Class name = I (started execution), Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:04:53.853: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: "~/dev/matbench-discovery/data/wbm/fetch_process_wbm_dataset.py" debug 09:04:53.854: Get Active Interpreter, Class name = I (started execution), Arg 1: undefined debug 09:04:53.854: Get Active Interpreter, Class name = I, completed in 0ms, has a truthy return value, Arg 1: undefined debug 09:04:53.854: Create ProcessService, Class name = h (started execution), Arg 1: undefined debug 09:04:53.854: Get Custom Env Variables, Class name = w (started execution), Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:04:53.854: Cached data exists getEnvironmentVariables, debug 09:04:53.854: Get Custom Env Variables, Class name = w, completed in 0ms, has a truthy return value, Arg 1: undefined, Arg 2: "RunNonPythonCode" debug 09:04:53.854: Create ProcessService, Class name = h, completed in 0ms, has a truthy return value, Arg 1: undefined info 09:04:53.857: Process Execution: > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py > ~/.venv/py310/bin/python ~/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/pythonFiles/normalizeSelection.py info 09:04:53.919: Generated code for 12 = with 5 lines debug 09:04:53.921: Start Jupyter Session in kernel.ts with disableUI = false debug 09:05:09.706: Python Daemon (pid: 7269): write to stderr: [I 09:05:09.706 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports error 09:05:09.709: Error in waiting for cell to complete Error: Canceled future for execute_request message before replies were done at a.KernelShellFutureHandler.dispose (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:32353) at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:26572 at Map.forEach () at y._clearKernelState (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:26557) at /Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2022.9.1202862440/out/node_modules/@jupyterlab/services.js:2:29000 at processTicksAndRejections (node:internal/process/task_queues:96:5) warn 09:05:09.710: Cell completed with errors { message: 'Canceled future for execute_request message before replies were done' } info 09:05:09.710: Cancel all remaining cells true || Error || undefined debug 09:05:09.710: Cancel pending cells debug 09:05:09.711: Cell 13 executed with state Error [I 09:05:09.706 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports debug 09:05:09.713: Python Daemon (pid: 7269): kernel c29cb5ea-c1cb-4804-81d7-2f5d4fd1abb3 restarted debug 09:05:09.713: Python Daemon (pid: 7269): write to stderr: [I 09:05:09.709 NotebookApp] Starting buffering for c29cb5ea-c1cb-4804-81d7-2f5d4fd1abb3:4415a2b2-b86a-4ddd-bc5d-bef14f64930b [I 09:05:09.709 NotebookApp] Starting buffering for c29cb5ea-c1cb-4804-81d7-2f5d4fd1abb3:4415a2b2-b86a-4ddd-bc5d-bef14f64930b debug 09:05:09.715: Python Daemon (pid: 7269): write to stderr: [I 09:05:09.715 NotebookApp] Restoring connection for c29cb5ea-c1cb-4804-81d7-2f5d4fd1abb3:4415a2b2-b86a-4ddd-bc5d-bef14f64930b [I 09:05:09.715 NotebookApp] Restoring connection for c29cb5ea-c1cb-4804-81d7-2f5d4fd1abb3:4415a2b2-b86a-4ddd-bc5d-bef14f64930b ```
janosh commented 1 year ago

Just installed py3.11, started from a fresh environment and tried in there. Same kernel crash.

DonJayamanne commented 1 year ago

@janosh

janosh commented 1 year ago

Minimal code to reproduce:


!pip install pymatgen

from pymatgen.entries.computed_entries import ComputedStructureEntry
from pymatgen.entries.compatibility import MaterialsProjectCompatibility

dct = {'@module': 'pymatgen.entries.computed_entries',
 '@class': 'ComputedStructureEntry',
 'energy': -32.50022431,
 'composition': {'S': 2.0, 'Bi': 1.0, 'Li': 6.0},
 'correction': 0.0,
 'parameters': {'potcar_symbols': ['PAW_PBE S 17Jan2003',
   'PAW_PBE Bi 08Apr2002',
   'PAW_PBE Li_sv 23Jan2001'],
  'is_hubbard': False,
  'hubbards': {},
  'run_type': 'GGA',
  'potcar_spec': [{'hash': None, 'titel': 'PAW_PBE S 17Jan2003'},
   {'hash': None, 'titel': 'PAW_PBE Bi 08Apr2002'},
   {'hash': None, 'titel': 'PAW_PBE Li_sv 23Jan2001'}]},
 'data': {},
 'entry_id': 'wbm-step-1-24459',
 'structure': {'@module': 'pymatgen.core.structure',
  '@class': 'Structure',
  'charge': None,
  'lattice': {'matrix': [[4.0332905, 0.00019654, 0.00033189],
    [0.00019791, 4.09449716, 0.00105079],
    [2.01755058, 2.04667974, 9.83595687]],
   'a': 4.0332905184,
   'b': 4.0944972996,
   'c': 10.2472169807,
   'alpha': 78.4638510747,
   'beta': 78.6397987424,
   'gamma': 89.9944373726,
   'volume': 162.4224924451},
  'sites': [{'species': [{'element': 'S', 'occu': 1}],
    'abc': [0.67847964, 0.67665944, 0.64561893],
    'xyz': [4.0392082508, 4.0920886875, 6.3512161575],
    'label': 'S',
    'properties': {}},
   {'species': [{'element': 'S', 'occu': 1}],
    'abc': [0.32476989, 0.32232743, 0.35455337000000003],
    'xyz': [2.0252844611, 2.0454897761, 3.4878181418],
    'label': 'S',
    'properties': {}},
   {'species': [{'element': 'Bi', 'occu': 1}],
    'abc': [0.00178017, 0.99953694, 8.554e-05],
    'xyz': [0.0075503424, 4.092776585, 0.001892262],
    'label': 'Bi',
    'properties': {}},
   {'species': [{'element': 'Li', 'occu': 1}],
    'abc': [0.60702988, 0.10487906, 0.78886588],
    'xyz': [4.0399254186, 2.0441021331, 7.7595624449],
    'label': 'Li',
    'properties': {}},
   {'species': [{'element': 'Li', 'occu': 1}],
    'abc': [0.10382818, 0.60266268, 0.79410993],
    'xyz': [2.0210454349, 4.0929097432, 7.811498753],
    'label': 'Li',
    'properties': {}},
   {'species': [{'element': 'Li', 'occu': 1}],
    'abc': [0.39640045, 0.89413866, 0.21137099],
    'xyz': [2.0254267916, 4.0937348354, 2.0801070545],
    'label': 'Li',
    'properties': {}},
   {'species': [{'element': 'Li', 'occu': 1}],
    'abc': [0.7519066999999999, 0.24963494, 0.49971919000000004],
    'xyz': [4.0409162969, 2.0450424745, 4.9157282642],
    'label': 'Li',
    'properties': {}},
   {'species': [{'element': 'Li', 'occu': 1}],
    'abc': [0.25116892, 0.74921193, 0.5004725999999999],
    'xyz': [2.0229142799, 4.0920026152, 4.9234975331],
    'label': 'Li',
    'properties': {}},
   {'species': [{'element': 'Li', 'occu': 1}],
    'abc': [0.89971318, 0.39648191, 0.20599457000000002],
    'xyz': [4.0444875535, 2.0451757971, 2.026868931],
    'label': 'Li',
    'properties': {}}]}}

cse = ComputedStructureEntry.from_dict(dct)
MaterialsProjectCompatibility().process_entry(cse)
>>> kernel crashes on this line
janosh commented 1 year ago

Does this only occur when you run the cell 11?

No, I've found many different ways to trigger this crash. No idea what's going on.

Can you replicate this same behaviour with other code, I suspect it has something to do with the code that's getting executed in the notebook.

What do you mean by other code? I'm pretty sure it's the code being executed since the kernel crash is very reproducible.

I'm running arm64 (M1 Pro chip).

DonJayamanne commented 1 year ago

Great thanks, I'm on a M1 as well and can repro this same issue, will look into this.

DonJayamanne commented 1 year ago

@janosh Thanks for providing all of the information and specially the sample code, that helped a lot.

I can repro the same kernel crash even outside VS Code, i.e. if you run the same code in Jupyter Notebooks the kernel crashes. I have no idea why its crashing, however since it crashes in Juptyer Notebook as well, I'm going to close this issue.

janosh commented 1 year ago

I can repro the same kernel crash even outside VS Code, i.e. if you run the same code in Jupyter Notebooks the kernel crashes.

Should have tried that myself. 🤦

Just to check, do you have any advice how to debug this? Is there some hidden stack trace somewhere?

DonJayamanne commented 1 year ago

Just to check, do you have any advice how to debug this? Is there some hidden stack trace somewhere?

I've found that this is very difficult to trace, basically the process just dies before anything can be written to disc. Sorry, but really no idea how to trace this issue.

janosh commented 1 year ago

@DonJayamanne Found the problem over at https://github.com/spglib/spglib/issues/194.

TIL: The crash becomes easy to debug if you enable faulthandler.

# prefix repro code from above with

import faulthandler
faulthandler.enable()

Running python -Xfaulthandler t.py now prints stack trace which pointed me at spglib:

Fatal Python error: Segmentation fault

Thread 0x00000001705db000 (most recent call first):
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/tqdm/_monitor.py", line 60 in run
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001eae06500 (most recent call first):
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/spglib-2.0.1-py3.11-macosx-10.9-universal2.egg/spglib/spglib.py", line 270 in get_magnetic_symmetry
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/spglib-2.0.1-py3.11-macosx-10.9-universal2.egg/spglib/spglib.py", line 153 in get_symmetry
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/symmetry/analyzer.py", line 219 in _get_symmetry
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/symmetry/analyzer.py", line 240 in get_symmetry_operations
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/symmetry/analyzer.py", line 285 in get_symmetrized_structure
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/analysis/structure_analyzer.py", line 544 in sulfide_type
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/entries/compatibility.py", line 283 in get_correction
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/entries/compatibility.py", line 748 in get_corrections_dict
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/entries/compatibility.py", line 714 in get_adjustments
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/entries/compatibility.py", line 632 in process_entries
  File "/Users/janosh/.venv/py311/lib/python3.11/site-packages/pymatgen/entries/compatibility.py", line 590 in process_entry
  File "/Users/janosh/dev/matbench-discovery/t.py", line 123 in <module>
DonJayamanne commented 1 year ago

oh wow that's a great top, thank a lot for sharing