Dead kernel

[NienkevandeLoosdrecht]

When I try to run the command lines of the exercise, I get the message: "the kernel appears to have died. It will restart automatically." But then nothing happens and if I retry it still doesn't work.

[nicolascouetard]

When I try to run the command lines of the exercise, I get the message: "the kernel appears to have died. It will restart automatically." But then nothing happens and if I retry it still doesn't work.

Got the same problem, it seems to be related to julia 1.4.1 since this error message doesn't appear with the python 3 where the kernel is working.
Under Linux Kubuntu 20.04

[Alexander-Barth]

I use Ubuntu 20.04 too (gnome version). In the julia command line can you run the following (https://github.com/JuliaLang/IJulia.jl#debugging-ijulia-problems):

ENV["IJULIA_DEBUG"]=true
using Pkg
Pkg.build("IJulia",verbose=true)

Can you paste the output of this previous command?

Then can you start jupyter-notebook from the terminal

jupyter-notebook  --debug assim_exercise.ipynb

or

/full/path/to/jupyter-notebook   --debug assim_exercise.ipynb

(by replacing /full/path/to/ with the directory containing jupyter-notebook).

There might be some helpful error message in the terminal why the kernel is crashing.

[Alexander-Barth]

I just updated the instruction above to increase the number of messages. These commands will (normally) generate a lot of screen output. Can you just copy paste them here.

[nicolascouetard]

I use Ubuntu 20.04 too (gnome version). In the julia command line can you run the following (https://github.com/JuliaLang/IJulia.jl#debugging-ijulia-problems):

ENV["IJULIA_DEBUG"]=true
using Pkg
Pkg.build("IJulia",verbose=true)

Can you paste the output of this previous command?
I got:

julia> ENV["IJULIA_DEBUG"]=true
true

julia> using Pkg

julia> Pkg.build("IJulia",verbose=true)
   Building Conda ─→ `~/.julia/packages/Conda/3rPhK/deps/build.log`
   Building IJulia → `~/.julia/packages/IJulia/DrVMH/deps/build.log`
[ Info: Installing Julia kernelspec in /home/ncouetard/.local/share/jupyter/kernels/julia-1.4
┌ Warning: JUPYTER=jupyter not found in PATH
└ @ Main ~/.julia/packages/IJulia/DrVMH/deps/build.jl:28"

Then can you start jupyter-notebook from the terminal

jupyter-notebook  --debug assim_exercise.ipynb

For this I got:

(base) ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ jupyter-notebook  --debug assim_exercise.ipynb
[C 22:45:23.404 NotebookApp] No such file or directory: /home/ncouetard/assim_exercise.ipynb
[D 22:45:23.404 NotebookApp] Exiting application: jupyter-notebook

or

/full/path/to/jupyter-notebook   --debug assim_exercise.ipynb

Since I've got 4 different "jupyter-notebook" in my personal directory, I replaced the path by all of them and I obtain:

(base) ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ /home/ncouetard/anaconda3/bin/jupyter-notebook   --debug assim_exercise.ipynb
[C 22:46:46.295 NotebookApp] No such file or directory: /home/ncouetard/assim_exercise.ipynb
[D 22:46:46.296 NotebookApp] Exiting application: jupyter-notebook
(base) ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ /home/ncoueta…/envs/py3/bin/jupyter-notebook   --debug assim_exercise.ipynb
bash: /home/ncoueta…/envs/py3/bin/jupyter-notebook: Aucun fichier ou dossier de ce type
(base) ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ /home/ncouetar…0.3-py37_0/bin/jupyter-notebook   --debug assim_exercise.ipynb
bash: /home/ncouetar…0.3-py37_0/bin/jupyter-notebook: Aucun fichier ou dossier de ce type
(base) ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ /home/ncouetar…0.3-py38_0/bin/jupyter-notebook   --debug assim_exercise.ipynb
bash: /home/ncouetar…0.3-py38_0/bin/jupyter-notebook: Aucun fichier ou dossier de ce type

(by replacing /full/path/to/ with the directory containing jupyter-notebook).

There might be some helpful error message in the terminal why the kernel is crashing.

[Alexander-Barth]

"Aucun fichier ou dossier de ce type": -> this is just that the file "assim_exercise.ipynb" is not yet downloaded. Can you decompress the files in this zip
https://github.com/Alexander-Barth/HF-radar-assim-exercise/archive/master.zip
cd into the folder where you should find a file assim_exercise.ipynb.

It seems that you run these commands inside an activated conda environment (as you command line starts with (base)). I usually keep them separate.

Can you try this?

• conda deactivate: this will unload the conda environment and the base should disappear for the current terminal windows (this is not a permanent change)

Then can you send me the output of these 3 commands?

• which python
• which python3
• which jupyter

Then start julia and retype:

ENV["IJULIA_DEBUG"]=true
using Pkg
Pkg.build("IJulia",verbose=true)
using IJulia
IJulia.notebook()

After this in a separate terminal window, can you run the command find ~ -name jupyter and send me the output?

[nicolascouetard]

"Aucun fichier ou dossier de ce type": -> this is just that the file "assim_exercise.ipynb" is not yet downloaded. Can you decompress the files in this zip
https://github.com/Alexander-Barth/HF-radar-assim-exercise/archive/master.zip
cd into the folder where you should find a file assim_exercise.ipynb.

It seems that you run these commands inside an activated conda environment (as you command line starts with (base)). I usually keep them separate.

Can you try this?

* `conda deactivate`: this will unload the conda environment and the `base` should disappear for the current terminal windows (this is not a permanent change)

Then can you send me the output of these 3 commands?

* `which python`

ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ which python
/usr/bin/python

* `which python3`

ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ which python3
/usr/bin/python3

* `which jupyter`

ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ which jupyter
Don't have any output for this line

Then start julia and retype:

ENV["IJULIA_DEBUG"]=true
using Pkg
Pkg.build("IJulia",verbose=true)
using IJulia
IJulia.notebook()

After this in a separate terminal window, can you run the command find ~ -name jupyter and send me the output?

ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ find ~ -name jupyter
/home/ncouetard/anaconda3/envs/py3/bin/jupyter
/home/ncouetard/anaconda3/envs/py3/etc/jupyter
/home/ncouetard/anaconda3/envs/py3/share/jupyter
/home/ncouetard/anaconda3/bin/jupyter
/home/ncouetard/anaconda3/etc/jupyter
/home/ncouetard/anaconda3/share/jupyter
/home/ncouetard/anaconda3/pkgs/_ipyw_jlab_nb_ext_conf-0.1.0-py37_0/etc/jupyter
/home/ncouetard/anaconda3/pkgs/jupyter_core-4.6.1-py37_0/bin/jupyter
/home/ncouetard/anaconda3/pkgs/widgetsnbextension-3.5.1-py37_0/etc/jupyter
/home/ncouetard/anaconda3/pkgs/widgetsnbextension-3.5.1-py37_0/share/jupyter
/home/ncouetard/anaconda3/pkgs/jupyter_core-4.6.3-py38_0/bin/jupyter
/home/ncouetard/anaconda3/pkgs/ipykernel-5.1.4-py37h39e3cac_0/share/jupyter
/home/ncouetard/anaconda3/pkgs/widgetsnbextension-3.5.1-py38_0/etc/jupyter
/home/ncouetard/anaconda3/pkgs/widgetsnbextension-3.5.1-py38_0/share/jupyter
/home/ncouetard/anaconda3/pkgs/r-irkernel-1.1-r36h6115d3f_1/share/jupyter
/home/ncouetard/anaconda3/pkgs/jupyterlab-1.2.6-pyhf63ae98_0/etc/jupyter
/home/ncouetard/anaconda3/pkgs/jupyterlab-1.2.6-pyhf63ae98_0/share/jupyter
/home/ncouetard/anaconda3/pkgs/ipykernel-5.1.4-py38h39e3cac_0/share/jupyter
/home/ncouetard/anaconda3/pkgs/r-irkernel-0.5-r3.2.2_1a/share/jupyter
/home/ncouetard/.julia/conda/3/bin/jupyter
/home/ncouetard/.julia/conda/3/etc/jupyter
/home/ncouetard/.julia/conda/3/share/jupyter
/home/ncouetard/.julia/conda/3/pkgs/widgetsnbextension-3.5.1-py37_0/etc/jupyter
/home/ncouetard/.julia/conda/3/pkgs/widgetsnbextension-3.5.1-py37_0/share/jupyter
/home/ncouetard/.julia/conda/3/pkgs/jupyter_core-4.6.3-py37_0/bin/jupyter
/home/ncouetard/.julia/conda/3/pkgs/ipykernel-5.1.4-py37h39e3cac_0/share/jupyter
/home/ncouetard/.local/share/jupyter

[Alexander-Barth]

OK, thanks. This look good so far. Can you try to go one step further and open the downloaded notebook following these steps?

• conda deactivate
• start julia and type

using IJulia
IJulia.notebook()

• a browser window should open with a notebook session
• In the notebook session, navigate to the folder containing assim_exercise.ipynb and open assim_exercise.ipynb
• Choose run all from the menu

If you see any errors can you paste them here?

[nicolascouetard]

It still doesn't work. It's written "connected to the kernel" but a few seconds after I got "the kernel appears to have died. It will restart automatically."

[Alexander-Barth]

As a last try, can you do these steps

• run conda deactivate
• cd path where path contains the downloaded notebooks
• run /home/ncouetard/.julia/conda/3/bin/jupyter kernelspec list
• run /home/ncouetard/.julia/conda/3/bin/jupyter notebook --debug assim_exercise.ipynb
• select Cell -> Run all in the notebook

Can you paste the output of the terminal and possible error message?

If this still does not work, please then I suggest you to use the binder service:

https://github.com/Alexander-Barth/HF-radar-assim-exercise#using-binder

[nicolascouetard]

ncouetard@ncouetard-ZenBook-13-UX331UAL:~$ cd /home/ncouetard/HF-radar-assim-exercise
ncouetard@ncouetard-ZenBook-13-UX331UAL:~/HF-radar-assim-exercise$ /home/ncouetard/.julia/conda/3/bin/jupyter kernelspec list
Available kernels:
  julia-1.4    /home/ncouetard/.local/share/jupyter/kernels/julia-1.4
  python3      /home/ncouetard/.julia/conda/3/share/jupyter/kernels/python3

ncouetard@ncouetard-ZenBook-13-UX331UAL:~/HF-radar-assim-exercise$ /home/ncouetard/.julia/conda/3/bin/jupyter --debug assim_exercise.ipynb
Traceback (most recent call last):
  File "/home/ncouetard/.julia/conda/3/bin/jupyter", line 11, in <module>
    sys.exit(main())
  File "/home/ncouetard/.julia/conda/3/lib/python3.7/site-packages/jupyter_core/command.py", line 247, in main
    command = _jupyter_abspath(subcommand)
  File "/home/ncouetard/.julia/conda/3/lib/python3.7/site-packages/jupyter_core/command.py", line 134, in _jupyter_abspath
    'Jupyter command `{}` not found.'.format(jupyter_subcommand)

I tried Binder and it works so I'll follow there. Thank you for having trying to solve my issue.

[mutiarizqydiani]

I use Ubuntu 20.04 too (gnome version). In the julia command line can you run the following (https://github.com/JuliaLang/IJulia.jl#debugging-ijulia-problems):

ENV["IJULIA_DEBUG"]=true
using Pkg
Pkg.build("IJulia",verbose=true)

Can you paste the output of this previous command?

Then can you start jupyter-notebook from the terminal

jupyter-notebook  --debug assim_exercise.ipynb

or

/full/path/to/jupyter-notebook   --debug assim_exercise.ipynb

(by replacing /full/path/to/ with the directory containing jupyter-notebook).

There might be some helpful error message in the terminal why the kernel is crashing.

Does it apply for Windows? I have the same issue with the kernel and this method doesn't seem to be working for my computer

[Alexander-Barth]

I noticed a typo in my instructions. It should have been this (with the notebook)

/home/ncouetard/.julia/conda/3/bin/jupyter notebook --debug assim_exercise.ipynb

I tried Binder and it works so I'll follow there. Thank you for having trying to solve my issue.

Yes, luckily there is binder that you can use. The caveat is that Binder will close your session after about 10 minutes. Let's try to keep the binder notebook busy during the lecture :-)

[Alexander-Barth]

@mutiarizqydiani , yes the instructions are essentially the same on windows (the path names are a bit different, /path/to/file becomes e.g. c:\path\to\file).

A source of trouble can be an always activated conda environment (even if this seems not the be the issue of your colleague) or some outdated libraries in your system Path.

Here is how you see the Path variable in windows.
https://docs.telerik.com/teststudio/features/test-runners/add-path-environment-variables

It would be useful if you can paste the value of Path variable here.

You should not have a directory called miniconda, anaconda, ... there.

[NienkevandeLoosdrecht]

@mutiarizqydiani , yes the instructions are essentially the same on windows (the path names are a bit different, /path/to/file becomes e.g. c:\path\to\file).

A source of trouble can be that you have an always activated conda environment (even if this seems not the be the issue of your colleague) or some outdated libraries in your system Path.

Here is how you see the Path variable in windows.
https://docs.telerik.com/teststudio/features/test-runners/add-path-environment-variables

It would be useful if you can paste the value of Path variable here.

You should not have a directory called miniconda, anaconda, ... there.

I have a MacBook, is it the same?

[Alexander-Barth]

On a Mac (like Linux), you can get the content of the system PATH by open a terminal and type

echo $PATH

Check if jupyter is already installed with

which  jupyter

Ideally, it should return nothing. In this case IJulia will install a "private" jupyter server.

A MacBook behaves essentially the same as Linux / Kubuntu 20.04.