jupyter: Jupyter running wrong python kernel

@takluyver off course, as you thought there was an override of the kernels. The output of jupyter kernelspec list was,

Available kernels:
  python3    /home/damejia/.local/share/jupyter/kernels/python3
  python2    /usr/local/share/jupyter/kernels/python2

The kernel for python3 located in /home/damejia/.local/share/jupyter/kernels/python3 was incorrectly configured. The kernel.json read,

{
 "argv": [
  "python",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "display_name": "Python 3",
 "language": "python"
}

So it called the wrong python version (python points to Python 2.7 in my machine). I just removed the /home/damejia/.local/share/jupyter/kernels/ path and now jupyter kernelspec list shows,

Available kernels:
  python2    /usr/local/share/jupyter/kernels/python2
  python3    /usr/local/share/jupyter/kernels/python3

And under a Python3 kernel in Jupyter the output of,

import sys
sys.version

baheves as expected,

'3.5.3 (default, Jan 19 2017, 14:11:04) \n[GCC 6.3.0 20170118]'

I’m not sure why this happened, I’ve been using Jupyther for about a year without problems so far. I hope this thread can help anyone. I guess It’s closed 👍

I also encountered a similar error. Jupyter notebook installation in my Ubuntu 17.04 cloud machine had issues selecting the right kernel. This is what I did to solve this issue.

Step 1: Install all the necessary dependencies: For Python2: $sudo apt-get install python-setuptools python-dev build-essential $sudo easy_install pip

$python2 -m pip --version

$python2 -m pip install ipykernel $sudo python2 -m ipykernel install --user $pip install -U jupyter ipython

For Python3: $sudo apt-get install python3-setuptools python3-dev build-essential $sudo apt-get install python3-pip

$python3 -m pip --version

$sudo python3 -m pip install ipykernel $sudo python3 -m ipykernel install --user $sudo pip3 install -U jupyter ipython

Step 2: Find the python executable locations for each version of Python and available kernels for Jupyter:

For Python2: $python

import sys print sys.executable The output for me was: /usr/bin/python

For Python3: $python3

import sys print (sys.executable) The output for me was: /usr/bin/python3

To get the list of available kernels:

$jupyter kernelspec list

The output for me was: Available kernels: python2 /home/info/.local/share/jupyter/kernels/python2 python3 /home/info/.local/share/jupyter/kernels/python3

Step 3: Update the kernel.json file with the correct location pointers to python executable

For Python2: $sudo nano /usr/local/share/jupyter/kernels/python2/kernel.json

Eg:

{ “display_name”: “Python 2”, “language”: “python”, “argv”: [ “/usr/bin/python”,
“-m”, “ipykernel_launcher”, “-f”, “{connection_file}” ] }

For Python3: $sudo nano /usr/local/share/jupyter/kernels/python3/kernel.json

{ “display_name”: “Python 3”, “language”: “python”, “argv”: [ “/usr/bin/python3”,
“-m”, “ipykernel_launcher”, “-f”, “{connection_file}” ] }

Step 4: Restart Jupyter and toggle kernels to see if python versions are selected correctly in the back-end.

Quick update

Hi everyone, i’m writing this update since it could help diagnose the problem. So, after a fresh install of the Debian OS (testing, the weekly build for this week),

Linux ibuki 4.11.0-1-amd64 #1 SMP Debian 4.11.6-1 (2017-06-19) x86_64 GNU/Linux

Module Versions Installed via pip with dependencies, pip3 install --upgrade pip jupyter ipython

So far, the versions installed are,

Jupyter version 4.3.0 (via PIP3) Python 3.5.4rc1 from the Debian repos Ipython3 6.1.0 (via PIP3)

Once the installation was made via pip3, the kernel for Python3 was automatically installed at /usr/local/share/jupyter/kernels/python3 and read the wrong python version again as initially reported

Solution

Proceeded to install the corresponding kernel as root with the command, ipython3 kernel install

Can you check jupyter kernelspec list to see if there’s another kernel spec overriding the one you found?

This is still an open and annoying problem - I have two python 3.6 environments set up for different projects (that is, after all, the whole point of having conda environments in the first place). It seems that the kernelspec will only allow one of them to be the python 3.6 kernel. That seems like an architectural mistake - each environment should know about the kernels associated with it. Or am I mistaken? Is there a way to handle multiple python versions aside from manually modifying the kernel file each time (ugh…)?

Quick update

Hi everyone, i’m writing this update since it could help diagnose the problem. So, after a fresh install of the Debian OS (testing, the weekly build for this week),

Linux ibuki 4.11.0-1-amd64 #1 SMP Debian 4.11.6-1 (2017-06-19) x86_64 GNU/Linux

Module Versions Installed via pip with dependencies, pip3 install --upgrade pip jupyter ipython

So far, the versions installed are,

Jupyter version 4.3.0 (via PIP3) Python 3.5.4rc1 from the Debian repos Ipython3 6.1.0 (via PIP3)

Once the installation was made via pip3, the kernel for Python3 was automatically installed at /usr/local/share/jupyter/kernels/python3 and read the wrong python version again as initially reported

Solution

Proceeded to install the corresponding kernel as root with the command, ipython3 kernel install

Actually this solution helped me. I followed exactly and got resolved.

You probably want to ask that on a binder repo, also you should not need to do that on a binder, it should install the kernel automatically.

Same issue - changing the default on Mint to 3.6 from 2.7 broke Jupyter as described.

@rahulremanan’s solution worked for me - editing the kernel.json file to point directly at python 2.7 and python 3.6. Checked separate kernels in the same run copy of Jupyter and the outputs are now in line with expectation.

$ jupyter kernelspec list --json { “kernelspecs”: { “python3”: { “resource_dir”: “/home/trent/.local/share/jupyter/kernels/python3”, “spec”: { “argv”: [ “python”, “-m”, “ipykernel_launcher”, “-f”, “{connection_file}” ], “env”: {}, “display_name”: “Python 3”, “language”: “python” } } } }

$ stat /usr/bin/python File: /usr/bin/python -> /usr/bin/python2

I explicitly installed this with python3, and even Jupyter knows it’s python3

$ sudo find / -iname ‘kernel.json’ ~/.local/share/jupyter/kernels/python3/kernel.json

Yet, it completely ignored the fact that a python3 interpreter was used, and instead tries to use 2.7. Changing argv[0] to the correct path (/usr/bin/python3) in the kernel.json file fixed this (well maybe, I still get an error in Atom/Hydrogen but the output indicates the kernel started).

I’m having a similar problem on binder. I’ve used this in postBuild:

python2 -m pip install ipykernel --user
python2 -m ipykernel install --user

I’ve also tried replacing python2 with /usr/bin/python and python2.7 and /usr/bin/python2.7, but in all cases I get the same broken kernel.json:

{
 "display_name": "Python 2",
 "language": "python",
 "argv": [
  "python",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ]
}

Strangely, when I run the exact same command in the terminal on the binder instance itself, the kernel.json is overwritten with the correct argv and everything works:

{
 "display_name": "Python 2",
 "language": "python",
 "argv": [
  "/usr/bin/python2",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ]
}

Any idea how to fix this in the binder setup?

Thanks @rahulremanan, as you suggested, I just changed {“argv”: [“python”,… ]} to {“argv”: [“python3”,… ]} and it worked. I’m not sure how it got set incorrectly, since it was fine before I upgraded jupyter notebook.

@minrk could this be a result of trying to install the kernelspec as a data file in the Python package installation? I notice that it’s using the new generic python in the kernel.json.