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.

Caches on Alps

On Alps, $HOME is small and $SCRATCH (capstor) has a 1 million inode quota that cache-heavy tools exhaust by themselves: a uv cache is ~80k files, a GT4Py build cache ~25k. lib/hostinfo.sh therefore points every cache at the flash-backed iopsstor scratch, which has no inode limit and is the right filesystem for many small files:

/iopsstor/scratch/cscs/$USER/cache   # $DOTFILES_CACHE_ROOT, = $XDG_CACHE_HOME
├── pip  uv  matplotlib  numba  cupy  gt4py
└── tmp                                        # $TMPDIR

XDG_CACHE_HOME covers everything that follows the spec (gh, fontconfig, pyright, the Claude CLI); PIP_CACHE_DIR, UV_CACHE_DIR, MPLCONFIGDIR, NUMBA_CACHE_DIR, CUPY_CACHE_DIR, GT4PY_BUILD_CACHE_DIR and TMPDIR are set individually because those tools ignore it. Export DOTFILES_CACHE_ROOT before the rc file runs to put the whole tree somewhere else.

Scratch is subject to the CSCS cleanup policy, so everything under that root must be regenerable. Check the quota that motivates this with quota.

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
tmux.conf	~/.tmux.conf	tmux configuration
gitconfig	~/.gitconfig	git config: delta pager, LFS filters, push defaults
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.

Git

gitconfig holds everything that is the same everywhere. The identity is not in it: the last line includes ~/.gitconfig.local, which is per machine and not tracked, so the work and personal machines can commit under different addresses. Write it by hand on a new machine, git silently ignores a missing include:

cat > ~/.gitconfig.local <<'EOF'
[user]
    email = you@example.com
    name = Your Name
EOF

The pager is delta || less, because delta is not installed on the clusters and an unconditional pager = delta breaks git log there. install_tools.sh installs delta on the Debian/Ubuntu/WSL machines.

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 currently set there

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.