error in process filter: zmq--subprocess-filter: Error in ZMQ subprocess: error,

[JonatanSahar]

Hi!
when trying to run a jupyter-REPL for the first time, emacs hung for a bit, and then I got the following error.
I have no idea how to proceed, and would appreciate any help!

Launching python3 kernel...
Starting python3 kernel process...done
Launching python3 kernel...done
Requesting kernel info...
Loading /home/yonatan/.config/emacs-local-build/.local/straight/build-29.2.50/zmq/emacs-zmq (module)...done
error in process filter: zmq--subprocess-filter: Error in ZMQ subprocess: error, ("Invalid signature (695dfb0b2c0cfae2dce5d56397e84630b9d36264fb99c70690fcf0dfbe92630a) for parts ("{\"msg_id\": \"4f8b8ba3-ad46c5da5a4f97cf7aeb76c0_738179_1\", \"msg_type\": \"stream\", \"username\": \"yonatan\", \"session\": \"4f8b8ba3-ad46c5da5a4f97cf7aeb76c0\", \"date\": \"2024-02-27T10:55:19.129527Z\", \"version\": \"5.3\"}" "{}" "{}" "{\"name\": \"stderr\", \"text\": \"--- Logging error ---\\nTraceback (most recent call last):\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelbase.py\\\", line 395, in dispatch_shell\\n msg = self.session.deserialize(msg, content=True, copy=False)\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/jupyter_client/session.py\\\", line 1074, in deserialize\\n raise ValueError(msg)\\nValueError: Invalid Signature: b'faa4bed25f4be28411a7a4761fbf705bb2bf5ecdd73d0f9799f81acc0d40c289'\\n\\nDuring handling of the above exception, another exception occurred:\\n\\nTraceback (most recent call last):\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/logging/init.py\\\", line 1104, in emit\\n self.flush()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/logging/init.py\\\", line 1084, in flush\\n self.stream.flush()\\nOSError: [Errno 5] Input/output error\\nCall stack:\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/runpy.py\\\", line 196, in _run_module_as_main\\n return _run_code(code, main_globals, None,\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/runpy.py\\\", line 86, in _run_code\\n exec(code, run_globals)\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel_launcher.py\\\", line 18, in \\n app.launch_new_instance()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/traitlets/config/application.py\\\", line 1075, in launch_instance\\n app.start()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelapp.py\\\", line 739, in start\\n self.io_loop.start()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/tornado/platform/asyncio.py\\\", line 205, in start\\n self.asyncio_loop.run_forever()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/asyncio/base_events.py\\\", line 603, in run_forever\\n self._run_once()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/asyncio/base_events.py\\\", line 1909, in _run_once\\n handle._run()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/asyncio/events.py\\\", line 80, in _run\\n self._context.run(self._callback, self._args)\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelbase.py\\\", line 542, in dispatch_queue\\n await self.process_one()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelbase.py\\\", line 531, in process_one\\n await dispatch(args)\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelbase.py\\\", line 397, in dispatch_shell\\n self.log.error(\\\"Invalid Message\\\", exc_info=True) # noqa: G201\\nMessage: 'Invalid Message'\\nArguments: ()\\n\"}")")
error in process filter: Error in ZMQ subprocess: error, ("Invalid signature (695dfb0b2c0cfae2dce5d56397e84630b9d36264fb99c70690fcf0dfbe92630a) for parts ("{\"msg_id\": \"4f8b8ba3-ad46c5da5a4f97cf7aeb76c0_738179_1\", \"msg_type\": \"stream\", \"username\": \"yonatan\", \"session\": \"4f8b8ba3-ad46c5da5a4f97cf7aeb76c0\", \"date\": \"2024-02-27T10:55:19.129527Z\", \"version\": \"5.3\"}" "{}" "{}" "{\"name\": \"stderr\", \"text\": \"--- Logging error ---\\nTraceback (most recent call last):\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelbase.py\\\", line 395, in dispatch_shell\\n msg = self.session.deserialize(msg, content=True, copy=False)\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/jupyter_client/session.py\\\", line 1074, in deserialize\\n raise ValueError(msg)\\nValueError: Invalid Signature: b'faa4bed25f4be28411a7a4761fbf705bb2bf5ecdd73d0f9799f81acc0d40c289'\\n\\nDuring handling of the above exception, another exception occurred:\\n\\nTraceback (most recent call last):\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/logging/init.py\\\", line 1104, in emit\\n self.flush()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/logging/init.py\\\", line 1084, in flush\\n self.stream.flush()\\nOSError: [Errno 5] Input/output error\\nCall stack:\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/runpy.py\\\", line 196, in _run_module_as_main\\n return _run_code(code, main_globals, None,\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/runpy.py\\\", line 86, in _run_code\\n exec(code, run_globals)\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel_launcher.py\\\", line 18, in \\n app.launch_new_instance()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/traitlets/config/application.py\\\", line 1075, in launch_instance\\n app.start()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelapp.py\\\", line 739, in start\\n self.io_loop.start()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/tornado/platform/asyncio.py\\\", line 205, in start\\n self.asyncio_loop.run_forever()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/asyncio/base_events.py\\\", line 603, in run_forever\\n self._run_once()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/asyncio/base_events.py\\\", line 1909, in _run_once\\n handle._run()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/asyncio/events.py\\\", line 80, in _run\\n self._context.run(self._callback, self._args)\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelbase.py\\\", line 542, in dispatch_queue\\n await self.process_one()\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelbase.py\\\", line 531, in process_one\\n await dispatch(args)\\n File \\\"/home/yonatan/miniforge3/lib/python3.10/site-packages/ipykernel/kernelbase.py\\\", line 397, in dispatch_shell\\n self.log.error(\\\"Invalid Message\\\", exc_info=True) # noqa: G201\\nMessage: 'Invalid Message'\\nArguments: ()\\n\"}")")
or: Timeout before idle: #s(jupyter-request "853aa1bc-9e6c-4d55-b3d8-45a4f5f3e55c" "kernel_info_request" nil #s(jupyter-repl-client jupyter--clients (#) "idle" 1 nil #s(hash-table size 65 test equal rehash-size 1.5 rehash-threshold 0.8125 data ()) ((closure ((pub-fn closure ((--cl-start-- closure ((--cl-ch-start-- closure ... ... ...) (--cl-ch-put-- closure ... ... ...) (ioloop . #s(jupyter-zmq-channel-ioloop ... # nil ... ... ...)) (kernel-io closure #4 ... ...) (session . #s(jupyter-session ... "e499f46e-ade9-46b3-a025-cf3b5c271750" "ab5dc0da-83a7-445d-aa51-e7f409cb8c3b")) (channels :shell :iopub :stdin :control)) nil (progn (if ioloop nil ... ... ...) (if ... nil ... ...) ioloop)) (--cl-set-session-- closure ((session . #s(jupyter-session ... "e499f46e-ade9-46b3-a025-cf3b5c271750" "ab5dc0da-83a7-445d-aa51-e7f409cb8c3b")) (kernel . #s(jupyter-kernel-process #s(jupyter-kernelspec "python3" ... "/home/yonatan/.local/share/jupyter/kernels/python3") #s(jupyter-session ... "e499f46e-ade9-46b3-a025-cf3b5c271750" "ab5dc0da-83a7-445d-aa51-e7f409cb8c3b") nil))) nil (or (setq session ...) (error "A session is needed to connect to a kernel's I/O"))) (shutdown) (hb) (session . #s(jupyter-session (:shell_port 40637 :iopub_port 33747 :stdin_port 56947 :control_port 45489 :hb_port 48285 ...) "e499f46e-ade9-46b3-a025-cf3b5c271750" "ab5dc0da-83a7-445d-aa51-e7f409cb8c3b"))) (content) (if shutdown (error "Kernel I/O no longer available: %s" (cl-prin1-to-string session)) (let ((val ...)) (cond (... ...) (... ...) (... ...) (t ...))))) (subs subscribers (closure ((pub-fn closure (... ...) (msg) (cond ... ...)) (subs subscribers (closure ... ... ...))) (pub-value) (let ((val ...)) (cond (... ...) (... ...) (t ...)))))) (pub-value) (let ((val (car-safe pub-value))) (cond ((eq val 'content) (let nil (jupyter-pseudo-bind-content pub-fn (car ...) subs))) ((eq val 'subscribe) (let nil (let (... ...) (setcdr v ...)))) (t (let nil (error "Unhandled publisher content: %s" pub-value)))))) (closure ((sub-fn closure ((--cl-stop-- closure ((ioloop . #s(jupyter-zmq-channel-ioloop ... # nil ... ... ...)) (hb)) nil (progn (if hb ...) (if ioloop ...))) (--cl-start-- closure ((--cl-ch-start-- closure ... ... ...) (--cl-ch-put-- closure ... ... ...) (ioloop . #s(jupyter-zmq-channel-ioloop ... # nil ... ... ...)) (kernel-io closure ... ... ...) (session . #s(jupyter-session ... "e499f46e-ade9-46b3-a025-cf3b5c271750" "ab5dc0da-83a7-445d-aa51-e7f409cb8c3b")) (channels :shell :iopub :stdin :control)) nil (progn (if ioloop nil ... ... ...) (if ... nil ... ...) ioloop)) (--cl-set-ch-group-- closure ((--cl-set-session-- closure ... nil ...) (ch-group :shell ... :iopub ... :stdin ... :control ...) (channels :shell :iopub :stdin :control)) nil (let (...) (setq ch-group ...))) (shutdown) (kernel . #s(jupyter-kernel-process #s(jupyter-kernelspec "python3" ... "/home/yonatan/.local/share/jupyter/kernels/python3") #s(jupyter-session ... "e499f46e-ade9-46b3-a025-cf3b5c271750" "ab5dc0da-83a7-445d-aa51-e7f409cb8c3b") nil))) (action) (cond ((eq action 'interrupt) (let nil (jupyter-interrupt kernel))) ((eq action 'shutdown) (let nil (jupyter-shutdown kernel) (funcall --cl-stop--) (setq shutdown t))) ((eq action 'restart) (let nil (setq shutdown nil) (jupyter-restart kernel) (funcall --cl-stop--) (funcall --cl-set-ch-group--) (funcall --cl-start--))) ((consp action) (let* (...) (if ... ...)))))) (sub-content) (if (consp sub-content) (let* ((x127 (car-safe sub-content))) (cond ((eq x127 'content) (let* (...) (if ... ... ...))) ((eq x127 'subscribe) (let* (...) (if ... ... ...))) (t (let nil (error "Unhandled subscriber content: %s" sub-content))))) (let nil (error "Unhandled subscriber content: %s" sub-content))))) #<buffer jupyter-kernel-client> nil ...) (26077 49046 316752 489000) nil nil nil (closure ((pub-fn closure ((id . "853aa1bc-9e6c-4d55-b3d8-45a4f5f3e55c") (req . #0)) (msg) (cond ((and (progn (or (progn ...) (signal ... ...)) (aref req 6)) (string= (jupyter-message-type msg) "status")) (jupyter-unsubscribe)) ((string= id (jupyter-message-parent-id msg)) (progn (or (progn (and ... t)) (signal 'wrong-type-argument (list ... req))) (let* ((v req)) (aset v 7 msg))) (progn (or (progn (and ... t)) (signal 'wrong-type-argument (list ... req))) (let* ((v req)) (aset v 8 (nconc ... ...)))) (if (or (jupyter-message-status-idle-p msg) (string= (jupyter-message-type msg) "kernel_info_reply") (string= (jupyter-message-type msg) "shutdown_reply")) (progn (progn (or ... ...) (let* ... ...)))) (jupyter-content (cons :parent-request (cons req msg)))))) (subs subscribers (closure ((sub-fn closure ((client . #s(jupyter-repl-client jupyter--clients ... "idle" 1 nil #s(hash-table size 65 test equal rehash-size 1.5 rehash-threshold 0.8125 data ()) ... #<buffer jupyter-kernel-client> nil ...))) (msg) (let ((channel ...)) (jupyter-handle-message client channel msg)))) (sub-content) (if (consp sub-content) (let* ((x127 (car-safe sub-content))) (cond ((eq x127 ...) (let* ... ...)) ((eq x127 ...) (let* ... ...)) (t (let nil ...)))) (let nil (error "Unhandled subscriber content: %s" sub-content)))))) (pub-value) (let* ((val (car-safe pub-value))) (cond ((eq val 'content) (let nil (jupyter-pseudo-bind-content pub-fn (car (cdr pub-value)) subs))) ((eq val 'subscribe) (let nil (let* ((a1 (car ...)) (v subs)) (setcdr v (let* (...) (if ... vlist ...)))))) (t (let nil (error "Unhandled publisher content: %s" pub-value)))))) ...)
Mark set

[pati-ni]

I have been affected from a similar error:

error in process filter: zmq--subprocess-filter: Error in ZMQ subprocess: error, ("Invalid signature (5871e47b524943ce283666c67e790c8021c672b146a5d73f667db13cea64e7ef) for parts ("{\"msg_id\": \"3d41ede7-4778abad688ac883c92f7987_7237_5\", \"msg_type\": \"stream\", \"username\": \"main\", \"session\": \"3d41ede7-4778abad688ac883c92f7987\", \"date\": \"2024-04-01T15:24:51.429056Z\", \"version\": \"5.3\"}" "{}" "{}" "{\"name\": \"stderr\", \"text\": \"--- Logging error ---\\nTraceback (most recent call last):\\n File \\\"/usr/lib/python3.11/site-packages/ipykernel/kernelbase.py\\\", line 395, in dispatch_shell\\n msg = self.session.deserialize(msg, content=True, copy=False)\\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\\n File \\\"/usr/lib/python3.11/site-packages/jupyter_client/session.py\\\", line 1074, in deserialize\\n raise ValueError(msg)\\nValueError: Invalid Signature: b'ff2d99912628331910ff0eed61c7cf092b2bf56c54ec61890c1511a8e3aee0db'\\n\\nDuring handling of the above exception, another exception occurred:\\n\\nTraceback (most recent call last):\\n File \\\"/usr/lib/python3.11/logging/init.py\\\", line 1114, in emit\\n self.flush()\\n File \\\"/usr/lib/python3.11/logging/init.py\\\", line 1094, in flush\\n self.stream.flush()\\nOSError: [Errno 5] Input/output error\\nCall stack:\\n File \\\"\\\", line 198, in _run_module_as_main\\n File \\\"\\\", line 88, in _run_code\\n File \\\"/usr/lib/python3.11/site-packages/ipykernel_launcher.py\\\", line 18, in \\n app.launch_new_instance()\\n File \\\"/usr/lib/python3.11/site-packages/traitlets/config/application.py\\\", line 1075, in launch_instance\\n app.start()\\n File \\\"/usr/lib/python3.11/site-packages/ipykernel/kernelapp.py\\\", line 739, in start\\n self.io_loop.start()\\n File \\\"/usr/lib/python3.11/site-packages/tornado/platform/asyncio.py\\\", line 195, in start\\n self.asyncio_loop.run_forever()\\n File \\\"/usr/lib/python3.11/asyncio/base_events.py\\\", line 608, in run_forever\\n self._run_once()\\n File \\\"/usr/lib/python3.11/asyncio/base_events.py\\\", line 1936, in _run_once\\n handle._run()\\n File \\\"/usr/lib/python3.11/asyncio/events.py\\\", line 84, in _run\\n self._context.run(self._callback, *self._args)\\n File \\\"/usr/lib/python3.11/site-packages/ipykernel/kernelbase.py\\\", line 545, in dispatch_queue\\n await self.process_one()\\n File \\\"/usr/lib/python3.11/site-packages/ipykernel/kernelbase.py\\\", line 534, in process_one\\n await dispatch(*args)\\n File \\\"/usr/lib/python3.11/site-packages/ipykernel/kernelbase.py\\\", line 397, in dispatch_shell\\n self.log.error(\\\"Invalid Message\\\", exc_info=True) # noqa: G201\\nMessage: 'Invalid Message'\\nArguments: ()\\n\"}")")

[pati-ni]

In my case, the error is related to a systemd update. It happens when I invoke emacs as a daemon using systemd

[JonatanSahar]

In my case I had to build emacs from source, since the snap emacs didn't have enough permissions to alter the libraries zmq was linking to, or some such nonsense. I don't recall exactly

…

On Wed, 3 Apr 2024 at 21:26, Monish Singhal ***@***.***> wrote: Any way around other than manually reopening Emacs? — Reply to this email directly, view it on GitHub <#527 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEL3S3EZC4C5BCTIWAM3EUTY3RCVTAVCNFSM6AAAAABD34EUWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZVGMYDINZZGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[dalanicolai]

I had a similar issue. On another laptop with exactly the same Emacs setup things were working fine, so I figured it must be an issue on the 'python/jupyter' side (well, combined with the emacs-jupyter library of course, because jupyter-notebook itself was working just fine). Anyway, I looked up the jupyter version on my other laptop using jupyter --version
and it returned the following:

IPython          : 8.17.2
ipykernel        : 6.26.0
ipywidgets       : 8.1.1
jupyter_client   : 8.6.0
jupyter_core     : 5.5.0
jupyter_server   : 2.10.1
jupyterlab       : 4.0.8
nbclient         : 0.10.0
nbconvert        : 7.16.3
nbformat         : 5.10.4
notebook         : 7.0.6
qtconsole        : 5.5.1
traitlets        : 5.14.2

So after downgrading the python packages to these versions, things have been fixed on my 'new' laptop also.

[MasonProtter]

I'm also getting this :(

[rvf0068]

I'm also getting this :(

Me too. I did as @dalanicolai mentioned, I have those python libraries exactly as that, and I am getting this when trying to run an org block.

Launching python3 kernel...
Starting python3 kernel process...done
Launching python3 kernel...done
Requesting kernel info...
error in process filter: zmq--subprocess-filter: Error in ZMQ subprocess: error, ("Invalid signature (88020047b89dd2a740c715a128501aa9bcaab4e62ed8205a4611d87b81725c0a) for parts (\"{\\\"msg_id\\\": \\\"cd75312d-cca5d6ce24da80d084b617a6_74620_1\\\", \\\"msg_type\\\": \\\"stream\\\", \\\"username\\\": \\\"rafael\\\", \\\"session\\\": \\\"cd75312d-cca5d6ce24da80d084b617a6\\\", \\\"date\\\": \\\"2024-05-16T22:10:53.449880Z\\\", \\\"version\\\": \\\"5.3\\\"}\" \"{}\" \"{}\" \"{\\\"name\\\": \\\"stderr\\\", \\\"text\\\": \\\"--- Logging error ---\\\\nTraceback (most recent call last):\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelbase.py\\\\\\\", line 376, in dispatch_shell\\\\n    msg = self.session.deserialize(msg, content=True, copy=False)\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/jupyter_client/session.py\\\\\\\", line 1074, in deserialize\\\\n    raise ValueError(msg)\\\\nValueError: Invalid Signature: b'9c7d3e48c02405a8e688828c7cd4a2aaf879126eb09c30d1797a17726f312f46'\\\\n\\\\nDuring handling of the above exception, another exception occurred:\\\\n\\\\nTraceback (most recent call last):\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/logging/__init__.py\\\\\\\", line 1083, in emit\\\\n    self.flush()\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/logging/__init__.py\\\\\\\", line 1063, in flush\\\\n    self.stream.flush()\\\\nOSError: [Errno 5] Input/output error\\\\nCall stack:\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/runpy.py\\\\\\\", line 197, in _run_module_as_main\\\\n    return _run_code(code, main_globals, None,\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/runpy.py\\\\\\\", line 87, in _run_code\\\\n    exec(code, run_globals)\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel_launcher.py\\\\\\\", line 17, in <module>\\\\n    app.launch_new_instance()\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/traitlets/config/application.py\\\\\\\", line 1075, in launch_instance\\\\n    app.start()\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelapp.py\\\\\\\", line 737, in start\\\\n    self.io_loop.start()\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/tornado/platform/asyncio.py\\\\\\\", line 205, in start\\\\n    self.asyncio_loop.run_forever()\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/asyncio/base_events.py\\\\\\\", line 596, in run_forever\\\\n    self._run_once()\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/asyncio/base_events.py\\\\\\\", line 1890, in _run_once\\\\n    handle._run()\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/asyncio/events.py\\\\\\\", line 80, in _run\\\\n    self._context.run(self._callback, *self._args)\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelbase.py\\\\\\\", line 524, in dispatch_queue\\\\n    await self.process_one()\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelbase.py\\\\\\\", line 513, in process_one\\\\n    await dispatch(*args)\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelbase.py\\\\\\\", line 378, in dispatch_shell\\\\n    self.log.error(\\\\\\\"Invalid Message\\\\\\\", exc_info=True)\\\\nMessage: 'Invalid Message'\\\\nArguments: ()\\\\n\\\"}\")")
error in process filter: Error in ZMQ subprocess: error, ("Invalid signature (88020047b89dd2a740c715a128501aa9bcaab4e62ed8205a4611d87b81725c0a) for parts (\"{\\\"msg_id\\\": \\\"cd75312d-cca5d6ce24da80d084b617a6_74620_1\\\", \\\"msg_type\\\": \\\"stream\\\", \\\"username\\\": \\\"rafael\\\", \\\"session\\\": \\\"cd75312d-cca5d6ce24da80d084b617a6\\\", \\\"date\\\": \\\"2024-05-16T22:10:53.449880Z\\\", \\\"version\\\": \\\"5.3\\\"}\" \"{}\" \"{}\" \"{\\\"name\\\": \\\"stderr\\\", \\\"text\\\": \\\"--- Logging error ---\\\\nTraceback (most recent call last):\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelbase.py\\\\\\\", line 376, in dispatch_shell\\\\n    msg = self.session.deserialize(msg, content=True, copy=False)\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/jupyter_client/session.py\\\\\\\", line 1074, in deserialize\\\\n    raise ValueError(msg)\\\\nValueError: Invalid Signature: b'9c7d3e48c02405a8e688828c7cd4a2aaf879126eb09c30d1797a17726f312f46'\\\\n\\\\nDuring handling of the above exception, another exception occurred:\\\\n\\\\nTraceback (most recent call last):\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/logging/__init__.py\\\\\\\", line 1083, in emit\\\\n    self.flush()\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/logging/__init__.py\\\\\\\", line 1063, in flush\\\\n    self.stream.flush()\\\\nOSError: [Errno 5] Input/output error\\\\nCall stack:\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/runpy.py\\\\\\\", line 197, in _run_module_as_main\\\\n    return _run_code(code, main_globals, None,\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/runpy.py\\\\\\\", line 87, in _run_code\\\\n    exec(code, run_globals)\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel_launcher.py\\\\\\\", line 17, in <module>\\\\n    app.launch_new_instance()\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/traitlets/config/application.py\\\\\\\", line 1075, in launch_instance\\\\n    app.start()\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelapp.py\\\\\\\", line 737, in start\\\\n    self.io_loop.start()\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/tornado/platform/asyncio.py\\\\\\\", line 205, in start\\\\n    self.asyncio_loop.run_forever()\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/asyncio/base_events.py\\\\\\\", line 596, in run_forever\\\\n    self._run_once()\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/asyncio/base_events.py\\\\\\\", line 1890, in _run_once\\\\n    handle._run()\\\\n  File \\\\\\\"/home/rafael/.pyenv/versions/3.9.2/lib/python3.9/asyncio/events.py\\\\\\\", line 80, in _run\\\\n    self._context.run(self._callback, *self._args)\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelbase.py\\\\\\\", line 524, in dispatch_queue\\\\n    await self.process_one()\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelbase.py\\\\\\\", line 513, in process_one\\\\n    await dispatch(*args)\\\\n  File \\\\\\\"/home/rafael/Python/pycliques-dev/lib/python3.9/site-packages/ipykernel/kernelbase.py\\\\\\\", line 378, in dispatch_shell\\\\n    self.log.error(\\\\\\\"Invalid Message\\\\\\\", exc_info=True)\\\\nMessage: 'Invalid Message'\\\\nArguments: ()\\\\n\\\"}\")")

[hpgisler]

In my case, the error is related to a systemd update. It happens when I invoke emacs as a daemon using systemd

@pati-ni I seem to have the exact same problem:
When starting the daemon via systemd, jupyter fails; when starting from command line, it works.
Did you find a solution for the systemd use-case?

[hpgisler]

Ok, have given up on this, after hours of trial and error (even setting the entire bash env in the emacs.service did not help).
How I do this now:

1. disabled emacs.service
2. starting emacs in .xinitrc like so (before my wm): emacs --daemon &

[MasonProtter]

Just an update on this, I was finally able to get things working again after I found this thread: #500

The fix for me was to add

(setq jupyter-use-zmq nil)

to stop jupyter from using the ZMQ connections because they seem to just be straight up broken, and then put in

(defun my-jupyter-api-http-request--ignore-login-error-a
    (func url endpoint method &rest data)
  (cond
   ((member endpoint '("login"))
    (ignore-error (jupyter-api-http-error)
      (apply func url endpoint method data)))
   (:else
    (apply func url endpoint method data))))
(advice-add
 #'jupyter-api-http-request
 :around #'my-jupyter-api-http-request--ignore-login-error-a)

to avoid the authentication screen.

Unfortunately, this package seems to be suffering from quite a bit of bitrot though, and I am getting pretty worried about its future...