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plasmabio / plasma

Plasma is an e-learning Jupyter-based platform for data analysis
https://docs.plasmabio.org
BSD 3-Clause "New" or "Revised" License
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Bash kernel died upon restart #214

Open pierrepo opened 2 years ago

pierrepo commented 2 years ago

In the Bash environment, the Bask kernel dies when we ask Jupyter Lab to "Rerun Kernel and Run All Cells":

image

The Docker container log is:

[I 2022-09-12 18:14:42.433 SingleUserNotebookApp log:189] 200 GET /user/ppoulain/api/sessions?1663006482417 (ppoulain@78.198.29.234) 2.61ms
[I 2022-09-12 18:14:42.437 SingleUserNotebookApp log:189] 200 GET /user/ppoulain/api/kernels?1663006482421 (ppoulain@78.198.29.234) 2.28ms
Exception in callback Task.task_wakeup(<Future finis...3565\r\n\r\n'>)
handle: <Handle Task.task_wakeup(<Future finis...3565\r\n\r\n'>)>
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.10/asyncio/events.py", line 80, in _run
    self._context.run(self._callback, *self._args)
RuntimeError: Cannot enter into task <Task pending name='Task-17' coro=<HTTP1ServerConnection._server_request_loop() running at /srv/conda/envs/notebook/lib/python3.10/site-packages/tornado/http1connection.py:823> wait_for=<Future finished result=b'GET /user/p...53565\r\n\r\n'> cb=[IOLoop.add_future.<locals>.<lambda>() at /srv/conda/envs/notebook/lib/python3.10/site-packages/tornado/ioloop.py:688]> while another task <Task pending name='Task-191' coro=<KernelManager._async_shutdown_kernel() running at /srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_client/manager.py:71>> is being executed.
Exception in callback Task.task_wakeup(<Future finis...3565\r\n\r\n'>)
handle: <Handle Task.task_wakeup(<Future finis...3565\r\n\r\n'>)>
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.10/asyncio/events.py", line 80, in _run
    self._context.run(self._callback, *self._args)
RuntimeError: Cannot enter into task <Task pending name='Task-67' coro=<HTTP1ServerConnection._server_request_loop() running at /srv/conda/envs/notebook/lib/python3.10/site-packages/tornado/http1connection.py:823> wait_for=<Future finished result=b'GET /user/p...53565\r\n\r\n'> cb=[IOLoop.add_future.<locals>.<lambda>() at /srv/conda/envs/notebook/lib/python3.10/site-packages/tornado/ioloop.py:688]> while another task <Task pending name='Task-191' coro=<KernelManager._async_shutdown_kernel() running at /srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_client/manager.py:71>> is being executed.
Exception in callback Task.task_wakeup(<Future finis...3565\r\n\r\n'>)
handle: <Handle Task.task_wakeup(<Future finis...3565\r\n\r\n'>)>
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.10/asyncio/events.py", line 80, in _run
    self._context.run(self._callback, *self._args)
RuntimeError: Cannot enter into task <Task pending name='Task-66' coro=<HTTP1ServerConnection._server_request_loop() running at /srv/conda/envs/notebook/lib/python3.10/site-packages/tornado/http1connection.py:823> wait_for=<Future finished result=b'GET /user/p...53565\r\n\r\n'> cb=[IOLoop.add_future.<locals>.<lambda>() at /srv/conda/envs/notebook/lib/python3.10/site-packages/tornado/ioloop.py:688]> while another task <Task pending name='Task-191' coro=<KernelManager._async_shutdown_kernel() running at /srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_client/manager.py:71>> is being executed.

Any idea @jtpio ?

This Bash environment works fine when built locally with mamba or built locally with repo2docker.