Jupyter Notebook ‘zmq message arrived on closed channel’ Error

caferistretto commented 1 year ago

Describe the bug Hello!

I’ve recently begun to experience near constant zmq/tornado errors when running Jupyter notebook from my conda environment (Jupyter, conda env, and traceback details below). When the error occurs, code cells in the Jupyter Notebook fail to either run entirely and/or the cells run but the output does not get printed to the Notebook.

The same error also occurs while using JupyterLab but seemingly less frequently. On occasion, Jupyter will run for several hours without exhibiting the issue while in other instances the error starts occurring immediately after a Notebook is started.

I would really appreciate any suggestions for resolving the issue. Thanks so much!

To Reproduce

Activate conda env
Start jupyter notebook by calling jupyter-notebook in bash
Open an .ipynb notebook and (preferably) run multiple cells at once using either 'Run All' or 'Run All Above'
If the error traceback (copied below) does not appear immediately, it will arise after the Notebook is used for a few minutes.

Expected behavior Connection to the notebook is maintained and output of stdout is printed/redirected to the notebook

Desktop (please complete the following information):

macOS v12.6.3 Firefox v109.0.1

Additional context

Output of jupyer --version

IPython : 8.9.0
ipykernel : 6.21.1
ipywidgets : 8.0.4 jupyter_client : 8.0.2 jupyter_core : 5.2.0 jupyter_server : 2.2.1 jupyterlab : 3.5.3 nbclient : 0.7.2 nbconvert : 7.2.9 nbformat : 5.7.3 notebook : 6.5.2 qtconsole : 5.4.0 traitlets : 5.9.0

Output of conda --list

anyio 3.6.2 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge appnope 0.1.3 pyhd8ed1ab_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py311h5547dcb_3 conda-forge arrow-cpp 11.0.0 h694c41f_2_cpu conda-forge asttokens 2.2.1 pyhd8ed1ab_0 conda-forge attrs 22.2.0 pyh71513ae_0 conda-forge aws-c-auth 0.6.23 hb2f45f0_1 conda-forge aws-c-cal 0.5.20 h3aaaed9_4 conda-forge aws-c-common 0.8.9 hb7f2c08_0 conda-forge aws-c-compression 0.2.16 h980c674_1 conda-forge aws-c-event-stream 0.2.18 h947c3fe_2 conda-forge aws-c-http 0.7.3 h9091ec1_1 conda-forge aws-c-io 0.13.14 h666a9c8_3 conda-forge aws-c-mqtt 0.8.6 h2814666_1 conda-forge aws-c-s3 0.2.3 h24f324c_3 conda-forge aws-c-sdkutils 0.1.7 h980c674_1 conda-forge aws-checksums 0.1.14 h980c674_1 conda-forge aws-crt-cpp 0.18.16 ha2465d3_13 conda-forge aws-sdk-cpp 1.10.57 hcf18aa8_2 conda-forge babel 2.11.0 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 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Error printed to Jupyter’s console:

[W TIMESTAMP NotebookApp] zmq message arrived on closed channel

Python traceback:

[E 09:29:38.352 NotebookApp] Uncaught exception in ZMQStream callback Traceback (most recent call last): File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 584, in _run_callback f = callback(*args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 308, in stream_callback return callback(self, msg) ^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/notebook/services/kernels/handlers.py", line 572, in _on_zmq_reply super()._on_zmq_reply(stream, msg) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/notebook/base/zmqhandlers.py", line 256, in _on_zmq_reply self.write_message(msg, binary=isinstance(msg, bytes)) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 339, in write_message return self.ws_connection.write_message(message, binary=binary) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 1086, in write_message fut = self._write_frame(True, opcode, message, flags=flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 1061, in _write_frame return self.stream.write(frame) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 546, in write self._handle_write() File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 976, in _handle_write self._write_buffer.advance(num_bytes) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 182, in advance assert 0 < size <= self._size AssertionError [E 09:29:38.357 NotebookApp] Uncaught exception in zmqstream callback Traceback (most recent call last): File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 621, in _handle_events self._handle_recv() File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 650, in _handle_recv self._run_callback(callback, msg) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 584, in _run_callback f = callback(*args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 308, in stream_callback return callback(self, msg) ^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/notebook/services/kernels/handlers.py", line 572, in _on_zmq_reply super()._on_zmq_reply(stream, msg) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/notebook/base/zmqhandlers.py", line 256, in _on_zmq_reply self.write_message(msg, binary=isinstance(msg, bytes)) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 339, in write_message return self.ws_connection.write_message(message, binary=binary) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 1086, in write_message fut = self._write_frame(True, opcode, message, flags=flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 1061, in _write_frame return self.stream.write(frame) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 546, in write self._handle_write() File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 976, in _handle_write self._write_buffer.advance(num_bytes) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 182, in advance assert 0 < size <= self._size AssertionError [E 09:29:38.358 NotebookApp] Exception in callback functools.partial(<function ZMQStream._update_handler.. at 0x1086751c0>) Traceback (most recent call last): File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/ioloop.py", line 740, in _run_callback ret = callback() ^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 705, in self.io_loop.add_callback(lambda: self._handle_events(self.socket, 0)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 621, in _handle_events self._handle_recv() File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 650, in _handle_recv self._run_callback(callback, msg) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 584, in _run_callback f = callback(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/zmq/eventloop/zmqstream.py", line 308, in stream_callback return callback(self, msg) ^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/notebook/services/kernels/handlers.py", line 572, in _on_zmq_reply super()._on_zmq_reply(stream, msg) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/notebook/base/zmqhandlers.py", line 256, in _on_zmq_reply self.write_message(msg, binary=isinstance(msg, bytes)) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 339, in write_message return self.ws_connection.write_message(message, binary=binary) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 1086, in write_message fut = self._write_frame(True, opcode, message, flags=flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/websocket.py", line 1061, in _write_frame return self.stream.write(frame) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 546, in write self._handle_write() File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 976, in _handle_write self._write_buffer.advance(num_bytes) File "/Users/data/miniconda3/envs/da/lib/python3.11/site-packages/tornado/iostream.py", line 182, in advance assert 0 < size <= self._size AssertionError

RRosio commented 1 year ago

Thanks everyone for your patience and feedback on this issue. Notebook 6.5.5 has been released with a temporary fix pinning jupyter_client < 8 and pyzmq < 25. I'll leave this issue open as a different fix should likely be implemented.

blink1073 commented 11 months ago

The underlying issue appears to be fixed in https://github.com/jupyter/jupyter_core/releases/tag/v5.3.2, but keeping a pin in Notebook 6 still makes sense to me.

noushinquazi commented 3 months ago

Am I the only one experiencing this issue now? TAT

RRosio commented 3 months ago

@noushinquazi, would you be able to share the package versions you are experiencing this issue with?

noushinquazi commented 3 months ago

@noushinquazi, would you be able to share the package versions you are experiencing this issue with?

For the longest time conda wasn't letting me downgrade tornado to 6.1, so I just now created a fresh environment with tornado pinned to 6.1; now I am no longer getting the same errors that's been reported in this thread. I am still very keen on a solution that doesn't involve downgrading multiple packages.

Lubuntu-Man commented 1 month ago

Facing same issue jupyter --version Selected Jupyter core packages... IPython : 8.26.0 ipykernel : 6.29.5 ipywidgets : 8.1.3 jupyter_client : 8.6.2 jupyter_core : 5.7.2 jupyter_server : 2.14.2 jupyterlab : 4.2.4 nbclient : 0.10.0 nbconvert : 7.16.4 nbformat : 5.10.4 notebook : 7.2.1 qtconsole : 5.5.2 traitlets : 5.14.3

jupyter / notebook

Jupyter Notebook ‘zmq message arrived on closed channel’ Error #6721