Leveraging better machines for Jupyter-Julia workshops

Background

I haven’t ever actually worked with julia before, however, some of the talks and workshops at this year’s Juliacon'21 were of great (applied) interest to me so I decided to follow along. In doing so, since my laptop is woefully inadequate for working through some of the materials (DFT), I decided to augment the installation instructions with remote machine usage notes.

Assumptions

The following gentle assumptions should not actually be much of a practical hurdle for this post, namely:

  • You have a remote machine which runs some variant of Linux
    • No nix is assumed unfortunately
    • Should be capable of running micromamba
  • Some code snippets assume a user-modifiable directory in the $PATH
    • Typically I assume something like export PATH=$HOME/.local/bin:$PATH

The code snippets arise in the context of the DFT workshop1, but are applicable across all the talks. Additionally, the snippets will assume no forks but in practice it is best to clone modifiable forks of these repositories so your mutations last forever.

Paths and Directories

For me, I use the following layout:

export jc21=$HOME/Git/Github/Julia/juliacon21
mkdir -p $jc21
cd $jc21
git clone git@github.com:mfherbst/juliacon_dft_workshop.git

Environment

We will start by setting up a micromamba environment. This is probably the most copied snippet on my site.

Now we can start with the (non-julia) scaffolding:

cd $jc21
micromamba create -p ./.jc21tmp pymatgen python==3.8 jupyterlab pip ipython
micromamba activate $(pwd)/.jc21tmp

We need to grab a stable juia version which we will use jill.py for:

pip install jill
jill install

For all workshops, we need a kernel to work with jupyterhub which we get in a straightforward way with an interactive julia session.

# julia
using Pkg
Pkg.add("IJulia")

Exposing Access

To make sure we can access our remote server we can use ngrok 2 or ssh forwarding 3.

wget https://bin.equinox.io/c/4VmDzA7iaHb/ngrok-stable-linux-amd64.zip
unzip ngrok-stable-linux-amd64.zip
mv ngrok $HOME/.local/bin
ngrok authtoken <token>
ngrok http 8888

We have assumed again, that $HOME/.local/bin is in our path. tmux is optional, but it is fantastic for all headless setups.It is probably better to not do this on your login / head node, and with ngrok we don’t need to care about how deeply nested we are in terms of exposing the tunnel, so just grab an interactive job. Assuming tmux then, the workflow is simply:

ssh mysuperhpc
# 6.5 hours on 1 node
srun -N 1 -t 6:30:00 --pty /bin/bash
# Or whatever configuration works for you
tmux new -s jc21 # enter an environment
cd $jc21
micromamba activate $(pwd)/.jc21tmp
jupyter lab --ServerApp.allow_remote_access=1 \
    --ServerApp.open_browser=False --port=8889
# Ctrl+B --> : --> split-pane
ngrok http 8889

Where the jupyter lab options are self evident and circumvent having to generate a configuration file. The second pane does not need to be run from the same location naturally. With this, pointing a local browser anywhere to the ngrok URL will bring you control over your remote machine and we’re off to the races.

Now we get a standard server with the appropriate kernel and can continue working through the workshops.

Conclusions

I’m not jumping on the julia bandwagon. I still reach for C++ or Fortran or even Python; but JuliaCon is why I need to be conversant with julia. It is used for fantastic applied use-cases, and being practically able to follow along and hack around existing code is important, even if I’m not interested in it as a programming language per-say. In general these instructions could be generalized to other workflows/workshops/kernels etc. etc., so it helps to have it written down too. Keep in mind that some system admins will take umbrage at running servers like this.


  1. Most of my existing experience with other codes like Quantum Espresso were at CECAM events with VMs… so it wouldn’t be fair to plunge into dftk on my laptop ↩︎

  2. Alan Shreve is a fantastic person and ngrok blows all competition out of the water, great student pricing too ↩︎

  3. This is a very good resource about setting up the SSH chain required, but ngrok just works across nodes too ↩︎