Dotfiles and workflows

Dotfiles (e.g. .bashrc) provide a way to customise your environment by defining environment variables and aliases. For a beginner's guide on customising your .bashrc file, see

It is often tempting to load modules or define environment variables used in your workflows. We strongly recommend against doing so for several reasons:

  • Dotfiles may silently break old workflows: It may become impossible to reproduce old results by running an old job script because your dotfile has since changed. By the time you realise, many years may have passed, and the previous setup requirements may be long forgotten.

  • Complex dotfile setups often lead to conflicts between workflows: Everybody eventually runs more than one type of job. Placing your setup in your dotfile prevents you from keeping your workflows separate.

  • Errors in your dotfiles may prevent you from logging in or transferring files: For example, any output will prevent rsync from working. This is especially problematic when scripts in your dotfiles are shared between project members, as their changes may break your environment.

Always define your environment variables and setup in the batch script.


Many of the issues that users commonly encounter result from problems with their dotfiles.

Common problems

X11 forwarding and VNC servers

Some modules, especially ones that provide X11 support, may set environment variables that interfere with other applications that use X11 forwarding.

If you are encountering errors when using X11 forwarding, try removing all module loads from your dotfiles.


"Emacs is delicate and sensitive like a little flower, and won't work if you mess with its libs".

Emacs depends on many system libraries. When other modules are also loaded, they may switch out those libraries to ones incompatible with Emacs. The solution is to use Emacs in it's own window with no modules loaded, and to load modules and run things in a separate window to the editor. Alternatively, you can fire up the editor, leave it up and running, and then load modules for other things.

If you an encountering errors when using Emacs, try removing all module loads from your dotfiles.