Spyder: ERROR:tornado.general:Uncaught exception in ZMQStream callback

[adityamagarde]

Description

What steps will reproduce the problem?

1. Open spyder.
2. Tries to connect to the kernel.
3. Shows the error.

What is the expected output? What do you see instead?

An error ocurred while starting the kernel
ERROR:tornado.general:Uncaught exception in ZMQStream callback
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist‑packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(args, *kwargs)
File "/usr/local/lib/python3.5/dist‑packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(args, *kwargs)
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
self.pre_handler_hook()
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 248, in pre_handler_hook
self.saved_sigint_handler = signal(SIGINT, default_int_handler)
File "/usr/lib/python3.5/signal.py", line 47, in signal
handler = _signal.signal(_enum_to_int(signalnum), _enum_to_int(handler))
ValueError: signal only works in main thread
ERROR:tornado.general:Uncaught exception in zmqstream callback
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist‑packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/usr/local/lib/python3.5/dist‑packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/usr/local/lib/python3.5/dist‑packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(args, *kwargs)
File "/usr/local/lib/python3.5/dist‑packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(args, *kwargs)
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
self.pre_handler_hook()
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 248, in pre_handler_hook
self.saved_sigint_handler = signal(SIGINT, default_int_handler)
File "/usr/lib/python3.5/signal.py", line 47, in signal
handler = _signal.signal(_enum_to_int(signalnum), _enum_to_int(handler))
ValueError: signal only works in main thread
ERROR:tornado.application:Exception in callback functools.partial(.null_wrapper at 0x7f95db138f28>)
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist‑packages/tornado/ioloop.py", line 760, in _run_callback
ret = callback()
File "/usr/local/lib/python3.5/dist‑packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(args, *kwargs)
File "/usr/local/lib/python3.5/dist‑packages/zmq/eventloop/zmqstream.py", line 536, in
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/usr/local/lib/python3.5/dist‑packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/usr/local/lib/python3.5/dist‑packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/usr/local/lib/python3.5/dist‑packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(args, *kwargs)
File "/usr/local/lib/python3.5/dist‑packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(args, *kwargs)
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
self.pre_handler_hook()
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelbase.py", line 248, in pre_handler_hook
self.saved_sigint_handler = signal(SIGINT, default_int_handler)
File "/usr/lib/python3.5/signal.py", line 47, in signal
handler = _signal.signal(_enum_to_int(signalnum), _enum_to_int(handler))
ValueError: signal only works in main thread
Traceback (most recent call last):
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/spyder/utils/ipython/start_kernel.py", line 241, in
main()
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/spyder/utils/ipython/start_kernel.py", line 237, in main
kernel.start()
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelapp.py", line 477, in start
ioloop.IOLoop.instance().start()
File "/usr/local/lib/python3.5/dist‑packages/tornado/platform/asyncio.py", line 112, in start
self.asyncio_loop.run_forever()
File "/usr/lib/python3.5/asyncio/base_events.py", line 340, in run_forever
raise RuntimeError('Event loop is running.')
RuntimeError: Event loop is running.
Traceback (most recent call last):
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/spyder/utils/ipython/start_kernel.py", line 241, in
main()
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/spyder/utils/ipython/start_kernel.py", line 237, in main
kernel.start()
File "/home/adityamagarde/.local/lib/python3.5/site‑packages/ipykernel/kernelapp.py", line 477, in start
ioloop.IOLoop.instance().start()
File "/usr/local/lib/python3.5/dist‑packages/tornado/platform/asyncio.py", line 112, in start
self.asyncio_loop.run_forever()
File "/usr/lib/python3.5/asyncio/base_events.py", line 340, in run_forever
raise RuntimeError('Event loop is running.')
RuntimeError: Event loop is running.

Please provide any additional information below
I recently installed jupyter. Even that isn't working I guess.

Version and main components

• Spyder Version: 3.2.3
• Python Version: 3.5.2
• Qt Versions: 4.8.7, PyQt4 (API v2) 4.11.4 on Linux

Dependencies

pyflakes >=0.6.0 :  1.6.0 (OK)
pycodestyle >=2.3:  2.3.1 (OK)
pygments >=2.0   :  2.2.0 (OK)
pandas >=0.13.1  :  0.17.1 (OK)
numpy >=1.7      :  1.13.3 (OK)
sphinx >=0.6.6   :  1.6.4 (OK)
rope >=0.9.4     :  0.10.7 (OK)
jedi >=0.9.0     :  0.11.0 (OK)
psutil >=0.3     :  5.3.1 (OK)
nbconvert >=4.0  :  5.3.1 (OK)
sympy >=0.7.3    :  None (NOK)
cython >=0.21    :  None (NOK)
qtconsole >=4.2.0:  4.3.1 (OK)
IPython >=4.0    :  6.2.1 (OK)
pylint >=0.25    :  1.7.4 (OK)

[adityamagarde]

I think I resolved the issue by downgrading the tornado version.

[CAM-Gerlach]

For the record, conda install tornado=4.5.3 should do the trick. Probably related to #6627 and its brethren.

[Tagar]

This seems to be a root cause for https://issues.apache.org/jira/browse/ZEPPELIN-3505

[xiaokunx]

downgrading tornado to 4.5.3 does not solve the problem, upgrading ipykernel from 4.6.1 to 4.8.2 solve the problem for me.

[Qberto]

Like @xiaokunx, downgrading tornado to 4.5.3 did not resolve the issue for me, while upgrading ipykernel solved the problem. conda upgrade ipykernel should do the trick.

[PistachioGuoguo]

conda upgrade ipykernel did help! But for Chinese using Tsinghua mirror will first have to conda config --remove-key channels to go back to default

[femiaiyeku]

Upgrading ipykernel worked for me
conda upgrade ipykernel

[meTchaikovsky]

Upgrading ipykernel worked for me
conda upgrade ipykernel

[mfschmidt]

Upgrading ipykernel worked for me, too.

pip install --upgrade ipykernel

[ccordoba12]

If you're using Anaconda, this needs to be

conda update ipykernel

[mullachv]

These were my versions, when I encountered the error:

$ conda list ipyker
# packages in environment at /anaconda/envs/dl3.6:
#
# Name                    Version                   Build  Channel
ipykernel                 4.5.2                    py36_0  
(dl3.6) $ 
(dl3.6) $ conda list tornado
# packages in environment at /anaconda/envs/dl3.6:
#
# Name                    Version                   Build  Channel
sockjs-tornado            1.0.3                    py36_0  
tornado                   5.1.1            py36h1de35cc_0  
(dl3.6) $ 
(dl3.6) $ conda list jupyter
# packages in environment at /anaconda/envs/dl3.6:
#
# Name                    Version                   Build  Channel
jupyter                   1.0.0                    py36_4  
jupyter_client            5.2.4                    py36_0  
jupyter_console           5.0.0                    py36_0  
jupyter_core              4.2.1                    py36_0  

What worked for me are to update ipykernel and then install tornado 4.5.3:

$conda update ipykernel
$conda install tornado=4.5.3

ipykernel is now 5.1.0 and tornado is 4.5.3, and my jupyter notebook works alright.

[xiaozhang8tuo]

THANKS

[okekec]

@mullachv Thank you for the detailed explanation, your code worked for me. I checked my versions first before upgrading both ipykernel and tornado.

[sliatecinos]

Upgrading ipykernel in Anaconda worked for me, too:

conda update ipykernel

But the Spyder stopped worked ...

(base) C:\Users\sliatecinos>spyder
Traceback (most recent call last):
  File "C:\Users\sliatecinos\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 3718, in main
    mainwindow = run_spyder(app, options, args)
  File "C:\Users\sliatecinos\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 3559, in run_spyder
    main.setup()
  File "C:\Users\sliatecinos\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 1010, in setup
    from spyder.plugins.ipythonconsole.plugin import IPythonConsole
  File "C:\Users\sliatecinos\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\plugin.py", line 52, in <module>
    from spyder.plugins.ipythonconsole.widgets import ClientWidget
  File "C:\Users\sliatecinos\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\widgets\__init__.py", line 16, in <module>
    from .debugging import DebuggingWidget
  File "C:\Users\sliatecinos\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\widgets\debugging.py", line 22, in <module>
    from IPython.core.inputtransformer2 import TransformerManager
ModuleNotFoundError: No module named 'IPython.core.inputtransformer2'

So I needed to upgrade IPython:

conda upgrade ipython

[jpthirumalai]

pip install --upgrade ipykernel
this worked, and brought up the "jupyter notebook"

[CAM-Gerlach]

@jpthirumalai If that worked, then your Spyder installation was likely contaminated with pip installed packages (assuming you installed it via Anaconda, as we recommend, and not pip in the first place) and things are likely to break again down the line. While Spyder itself supports installation via pip, if you run into machine-specific problems there isn't much we can do to help you with that other than recommending Anaconda, which avoids most of them. Also, I'm not sure why Jupyter Notebook has anything to do with this, unless you are using the spyder-notebook plugin for Spyder, since this is the Spyder repository not Jupyter.

Furthermore, if others try the same, they are likely to break their installs as well. Ergo, @ccordoba12 will likely want to hide the above comment, and you might want to make a final comment authoritatively stating the correct solution and then lock the thread, since the problem is resolved.