Our Linux Work Environment

A repository with information about current packages and software we use on linux clusters and workstations.

The key files are here with conda packages and R packages. We are not currently relying much on python. We have C++ code to compile within R packages.

Interactive Mode

They key pieces for interactive development (and bug squashing) for me are neovim, tmux, htop, ripgrep.

Editor

For interactive work I tend to use neovim installed via AppImage because conda only has old versions. This is done by hand and requires changing the path in .zshrc:

export PATH=$HOME/usr/bin:$PATH

And I use a fork of the kickstart.nvim set of plugins to make neovim understand R and LaTeX etc.

Zsh

I use zsh and the oh my zsh system:

export ZSH="$HOME/.oh-my-zsh"

To Use on the Campus Cluster

To test, on the campus cluster cd to /projects/illinois/las/pol/jwbowers and run interactive.sh. This is a wrapper around an srun call to get on a particular node (see note about why inside script.) Once the interactive job is launched, do

$ singularity run <name-of-sif>

which should put you in a container with an Oh My Zsh-style prompt