dotfiles

Shell, vim and ssh configuration shared across the HPC systems and personal machines I work on. One repo, symlinked into $HOME, with the per-machine differences resolved at shell startup instead of by keeping separate branches.

Install

git clone --recursive git@github.com:mjaehn/dotfiles.git ~/git/dotfiles
cd ~/git/dotfiles

./install_tools.sh                    # local + IAC only; skips apt where there is no root
./install_oh_my_zsh_plugins_theme.sh  # oh-my-zsh + plugins + powerlevel10k
./install.sh                          # symlink everything into $HOME
exec zsh

Then run :PluginInstall inside vim once to build the vim plugins.

On a cluster without a system zsh (balfrin), run ./install_zsh_user.sh first to compile one into ~/local.

install.sh is safe to re-run; it only refreshes symlinks.

install_tools.sh installs Miniforge into ~/miniforge3 and builds the default conda environment (the one the shells auto-activate) from conda_packages. To pull in new packages afterwards, add them there and run:

mamba install -n default -c conda-forge --file conda_packages

Machines

Host detection lives in lib/hostinfo.sh and sets DOTFILES_HOST (the machine) and DOTFILES_CLUSTER (the site). Everything else keys off those two variables.

DOTFILES_HOST	DOTFILES_CLUSTER	Matched on	Notes
santis	alps	santis*	CSCS, uenv + Lmod
balfrin	alps	balfrin*	CSCS/MeteoSwiss, Tcl modules, locally built zsh
clariden	alps	clariden*	CSCS
eiger	alps	eiger*	CSCS
euler	eth	eu*	ETH; stays in bash, the module command misbehaves under zsh
levante	dkrz	levante*	DKRZ; non-interactive sessions stop early
co2	iac	co2	ETH IAC server
atmos	iac	atmos	ETH IAC server
iac-laptop	local	iacpc*	work laptop
home-pc	local	desktop*	personal desktop
surface	local	surfacepro*	personal laptop, WSL2 on aarch64

Hostnames are lowercased before matching, so SurfacePro11, IACPC-42 and DESKTOP-ABC all match. On Alps, $CLUSTER_NAME is used as a fallback because inside a uenv the hostname is generic.

conda is only bootstrapped where it is actually used: co2, atmos, and the three local machines. The clusters use modules or uenv instead. All of them use $HOME/miniforge3; since co2 and atmos share a filesystem, running install_tools.sh on either one provisions both.

Layout

Path	Linked to	Purpose
lib/hostinfo.sh	—	host/cluster detection and per-host environment
lib/common.sh	—	environment, aliases and functions for both shells
lib/conda.sh	—	conda bootstrap, where conda is used
bashrc	~/.bashrc	bash prompt and the hand-off to zsh
zshrc	~/.zshrc	oh-my-zsh, powerlevel10k, zsh options
aliases.zsh	~/.oh-my-zsh/custom/aliases.zsh	the few zsh-only additions
profile	~/.profile	minimal login-shell setup
vimrc	~/.vimrc	vim configuration
config	~/.ssh/config	ssh hosts, grouped by site
p10k.zsh	~/.p10k.zsh	powerlevel10k prompt, generated
vim-extensions/	~/.vim/vim-extensions/	vim plugins, git submodules
keybindings.json	not linked	VS Code keybindings, see below

lib/ is not symlinked. bashrc and zshrc resolve their own symlink back to this repo and source lib/ from there.

Anything shared between bash and zsh belongs in lib/, not in one of the rc files. That includes the machine-specific aliases, so both shells behave the same everywhere.

Shells

bashrc execs into zsh on every interactive machine except Euler, and except inside Slurm jobs. Euler sets DOTFILES_USE_ZSH=0 because its module command does not work properly under zsh.

Git aliases use the oh-my-zsh names (gst, gco, gl, gp, ...). zsh gets them from the plugin; lib/common.sh defines the same ones for bash so the two shells match. The pretty graph log is gll.

VS Code

keybindings.json restores the usual ctrl+a/c/x/v/z/y/f/h and tab-indent behaviour when the Vim extension is active. It is not symlinked, because VS Code stores its settings outside $HOME on WSL. Copy it into your VS Code user directory by hand.

Vim plugins

Quick cheat sheet for the plugins in vim-extensions/ (managed via Vundle, see vimrc for the full Plugin list and custom mappings).

Plugin	Purpose	Key bindings
NERDTree	File tree	ff toggle/reveal current file (custom); o open; t new tab; i/s split/vsplit; R refresh
ctrlp.vim	Fuzzy file/buffer finder	<C-p> open; <C-j>/<C-k> navigate; <C-t>/<C-v>/<C-s> open in tab/vsplit/split; <C-f>/<C-b> switch mode
vim-gitgutter	Git diff markers in the sign column	]c/[c next/prev hunk; <leader>hs stage hunk; <leader>hu undo hunk; <leader>hp preview hunk
indentLine	Indent guides	:IndentLinesToggle
vim-rainbow	Rainbow parentheses	:RainbowToggle
lightline.vim	Status line	none, purely visual
vim-autotag	Regenerates ctags on save	none, automatic (disabled on Euler/Levante, too slow on those filesystems)
vim-fugitive	Git wrapper	:Git/:G status window (- stage/unstage, cc commit, dv diff); :Gdiffsplit; :Git blame
vim-surround	Change surrounding pairs/quotes/tags	ds<char> delete; cs<old><new> change; ys<motion><char> add; S wrap visual selection
vim-commentary	Toggle comments	gcc current line; gc + motion (e.g. gcap); gc in visual mode
tagbar	ctags sidebar	tl<space> toggle (custom); inside: <CR>/o jump to tag, p preview
ale	Async lint/build checks	:ALENext/:ALEPrevious cycle errors; :ALEFix run fixers; sign column shows severity
vim-tmux-navigator	Seamless vim/tmux pane movement	<C-h/j/k/l> move between vim splits and tmux panes; needs matching bindings in tmux.conf, not present in this repo

Adding a machine

1. Add a case arm to lib/hostinfo.sh matching the lowercased hostname, setting DOTFILES_HOST and DOTFILES_CLUSTER.
2. Put machine-specific environment in the per-host case further down the same file; put machine-specific aliases in the machine-specific section of lib/common.sh.
3. Add it to the conda case in lib/conda.sh only if that machine uses conda.
4. Add a row to the table above.
5. Check it:

   zsh -c 'source lib/hostinfo.sh; echo $DOTFILES_HOST $DOTFILES_CLUSTER'

License

GPL-3.0, see LICENSE.