Jupyter Notebook Server

Instructions for Using Julia via the Jupyter Notebook server in the ICDS ACI Portal

1. Setup Julia kernel to work with ICDS-ACI (only needs to be done once per user)
2. Start a Jupyter Notebook session on ACI
3. Clone your Github Repository on ACI (only need to do once per repository)

Setup Julia kernel to work with ACI’s Jupyter notebook server

• Browse to portal.aci.ics.psu.edu
• Login (if necessary)
• Click Interactive Apps on top menu
• Before using Julia on ACI for the first time
  • Choose ACI Interactive Desktop
  • Click Launch
  • Wait while your job starts
  • Once the Launch noVNC in new tab button appears, click it
• Open a terminal via second button on bottom toolbar
• Run the following code in the terminal

module load python/3.6.3-anaconda5.0.1
cd work
mkdir julia_depot
# Setup a Julia package depot in your ACI work directory
cd julia_depot
export JULIA_DEPOT_PATH=$PWD
echo "export JULIA_DEPOT_PATH=$PWD" >> ~/.bashrc
cd ..

# Install Julia in your work directory
mkdir julia_install
cd julia_install/
wget https://julialang-s3.julialang.org/bin/linux/x64/1.0/julia-1.0.2-linux-x86_64.tar.gz
tar -xf julia-1.0.2-linux-x86_64.tar.gz
cd julia-1.0.2

# Setup paths so Julia can be found
export PATH=$PWD/bin:$PATH
export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$PWD/lib/julia:$LD_LIBRARY_PATH
echo "export PATH=$PWD/bin:$PATH" >> ~/.bashrc
echo "export LD_LIBRARY_PATH=$PWD/lib:$LD_LIBRARY_PATH" >> ~/.bashrc
echo "export LD_LIBRARY_PATH=$PWD/lib/julia:$LD_LIBRARY_PATH" >> ~/.bashrc

# Setup IJulia and a few packages that we'll be using lots
julia -e 'using Pkg; Pkg.add(["IJulia","Weave","NBInclude"])'

# Create ssh-keys
ssh-keygen -t rsa -b 4096  # follow prompts, default location should be ok
cat ~/.ssh/id_rsa.pub

• If this is your first time using git, then enter something for your name and email (you may wish to use your github id rather than your real name, and a non-email address like nobody@nowhere.org).

git config --global user.email "nobody@nowhere.org"
git config --global user.name "Your Github Id"

• Authorize your ssh-keys on GitHub, following these instructions but manually copying the key rather than using xclip (i.e., starting from step 2)
• Shutdown the session and close the browser window/tab with the ACI Interactive Desktop
• Go back to the “My Interactive Sessions” tab in the ACI Portal, click “Delete” for this Sessions and confirm.

Start a Jupyter notebook session on ACI

Each time in the future you want to start a Jupyter notebook session on ICDS-ACI

• Browse to portal.aci.ics.psu.edu
• Login (if necessary)
• Click Interactive Apps on top menu
• Choose Jupyter Notebook
  • Select:
    • Anaconda version: 5.0.1-3.6.3
    • Allocation: Open
    • Number of hours: 1 hour
    • Node type: ACI-i
  • Click Launch
  • Wait while your job starts
• Once the Connect to Jupyter Notebook Server button appears, click it
  • Near the upper right, there’s a New button, from which you can create a new blank notebook or access a terminal or text editor. By default, Python will be the only language avaliable. It is possible to connect other languages to Jupyter. See (#setup-julia) for info on setting up Julia.
  • If you’d like to create a blank notebook, then choose New.Julia 1.0.2 (or whatever kernel you like and have installed)
  • A new browser tab should open where you can work with a notebook interactively.
  • Do your work, remembering to save your notebook after key edits and before you quite.
• When you’re done, close notebook tabs and click logout in upper right (of the Jupyter server session).
• Go back to the “My Interactive Sessions” tab in the ACI Portal, click “Delete” for this Sessions and confirm.

Clone your github repository to begin a new project

• Request a Jupyter notebook session on ACI (see above)
• While waiting for it to start, let’s get the url for the repo to be cloned.
  • Navigate to the github repository you’ll be using.
  • Click Clone or download.
  • If it says “Clone with https”, click “Use ssh”.
  • Click the clipboard icon to copy the url onto your clipboard
• Return to your browser tab with “My Interactive Sessions”.
• Hopefully, there’s now a Connect to Jupyter Notebook Server button. Click it
• Go to the newly opened tab, you’ll have a Jupyter Notebook Server.
• Find New button and choose Terminal
• In the new terminal tab, clone your github repo by running

git clone REPO_URL  # where REPO_URL is what you'll paste from the clipboard

• Change into the directory that was created for the repository (we’ll call REPO_DIR) and setup all the packge dependancies required.

cd REPO_DIR
julia -e 'using Pkg; Pkg.activate("."); Pkg.instantiate(); '

• Go back to the browser tab with your Jupyter notebook server running.
• Click the directory name of the repository that you just installed.
• Open a Jupyter notebook (file ending in .ipynb) in that repo, or use the New button to create a new one.
• Do your work in the Jupyter notebook.
• When you’re done with a notebook, save it and close the tab.