Jupyter-Kernels

Steps to setup multiple kernels with Jupyter

Installing Jupyter

pip install jupyter
pip install  ipykernel

Installing other kernels

Bash

pip install bash_kernel
python -m bash_kernel.install

Octave

sudo apt-get install octave
pip install octave_kernel
python -m octave_kernel.install

Julia

Install julia by following steps in http://julialang.org/downloads/platform.html for ubuntu run bellow commands

sudo add-apt-repository ppa:staticfloat/juliareleases
sudo add-apt-repository ppa:staticfloat/julia-deps
sudo apt-get update
sudo apt-get install julia
sudo apt-get install libnettle4

Run this in Julia

Pkg.add("IJulia")

Scala

sudo apt-get install scala
sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer
export SCALA_HOME=/usr/local/share/scala
export PATH=$PATH:$SCALA_HOME/bin
export JAVA_HOME=/usr/lib/jvm/java-8-oracle
wget "https://oss.sonatype.org/content/repositories/snapshots/sh/jove/jove-scala-cli_2.11/0.1.1-1-SNAPSHOT/jove-scala-cli_2.11-0.1.1-1-SNAPSHOT.tar.gz"
tar -xvzf jove-scala-cli_2.11-0.1.1-1-SNAPSHOT.tar.gz
cd jove-scala-cli-0.1.1-1-SNAPSHOT/bin
./jove-scala --kernel-spec

R

sudo add-apt-repository ppa:marutter/rrutter
sudo apt-get update
sudo apt-get install r-base r-base-dev
sudo apt-get install libzmq3-dev libcurl4-openssl-dev

Run this in R

install.packages("devtools")
install.packages('RCurl')
library(devtools)
install_github('armstrtw/rzmq')
install_github('IRkernel/repr')
install_github('IRkernel/IRdisplay')
install_github('IRkernel/IRkernel')
IRkernel::installspec()

Python 3

sudo apt-get install python3-pip
sudo pip3 install -U ipython
sudo pip3 install jupyter_client
sudo pip3 install ipykernel
sudo ipython3 kernelspec install-self

To add any virtual environment

Activate your python virtual environment to be added before if virtual wraper present then

workon MyVEnviron

else

source ~/Envs/MyVEnviron/bin/activate

once the virtual environment is active run bellow code

pip install jupyter
python -m ipykernel install --user --name MyVEnviron --display-name "Python (MyVEnviron)"
deactivate

replace MyVEnviron with your virtual environment name

Matlab

You must have Matlab installed on your system - Duke has a site licesne so you should be able to get it.

pip install pymatbridge
pip install matlab_kernel
python -m pymatbridge.install
python -m matlab_kernel.install

Installing extensions

Spell-checking

! ipython install-nbextension https://bitbucket.org/ipre/calico/downloads/calico-spell-check-1.0.zip

Notebook sections

! ipython install-nbextension https://bitbucket.org/ipre/calico/downloads/calico-document-tools-1.0.zip

To configure slide view in Jupyter notebook

git clone https://github.com/ahmadfaizalbh/RISE.git
cd RISE
python setup.py install

To setup you Jupyter notebook in server

genrate configuration file

jupyter notebook --generate-config

Using SSL for encrypted communication

genrate self signed ssl cirtificate

openssl req -x509 -nodes -days 365 -newkey rsa:1024 -keyout mykey.key -out mycert.pem

Preparing a hashed password

run this in jupyter console

In [1]: from notebook.auth import passwd
In [2]: passwd()
Enter password:
Verify password:
Out[2]: 'sha1:67c9e60bb8b6:9ffede0825894254b2e042ea597d771089e11aed'

Edit config file (~/.jupyter/jupyter_notebook_config.py) and uncomment bellow mentioned lines and add appropriate value

c = get_config()
c.IPKernalApp.pylab = 'inline'
# Set options for certfile, ip, password, and toggle off browser auto-opening
c.NotebookApp.certfile = u'/absolute/path/to/your/certificate/mycert.pem'
c.NotebookApp.keyfile = u'/absolute/path/to/your/certificate/mykey.key'
# Set ip to '*' to bind on all interfaces (ips) for the public server
c.NotebookApp.ip = '*'
c.NotebookApp.notebook_dir = u'/home/pynb/pynb'
c.NotebookApp.open_browser = False
c.NotebookApp.password = u'sha1:bcd259ccf...<your hashed password here>'
c.NotebookApp.port = 9999

now every thing is configured run jupyter notebook to start notebook in server

To Set jupyter notebook as Background process

do any one of bellow and restart your server

To put it in background and run as root

add bellow lines to /etc/rc.local

export JAVA_HOME=/usr/lib/jvm/java-8-oracle jupyter notebook exit 0

#### To put it in background and run as some other user (USER) with less permisiion
>  add bellow lines to `/etc/rc.local` also remember to change `USER`with appropriate username
>  ```
su USER -c 'export JAVA_HOME=/usr/lib/jvm/java-8-oracle;jupyter  notebook'
exit 0

To put it in background and run as some other user with less permisiion and a seperate virtual environment

set up vertual environment inside the user (USER) directry and install Jupyter inside this environment add bellow lines to /etc/rc.local also remember to change USERwith appropriate username in bellow case I have asumed that your environments in folder /home/USER/Envs and your environment name is MyVEnviron please change these appropriately

su USER -c 'export JAVA_HOME=/usr/lib/jvm/java-8-oracle;export WORKON_HOME=/home/USER/Envs;source /home/USER/Envs/MyVEnviron/bin/activate;/home/USER/Envs/MyVEnviron/bin/jupyter notebook;deactivate' exit 0

once server restarts wait for a minute and then try in your browser [https://your server IP:9999]() , your browser may show security warning please go to advance options and accept certificate. and then refresh your page it will prompt for password, enter the one used to genrate hashed password.

# Done!