The .bashrc file

Setting up the .bashrc file.

Motivation #

Every time you open a new shell on the CCB cluster, you are given a new session in a Bash environment in your Terminal application.

In those new sessions, you may find yourself repetitively typing the same set of commands to set up the environment of that session before you are able to work.

The file ~/.bashrc is a Shell script that Bash runs whenever it is started interactively. As such, this file is often edited to include commands that users wish to execute every time they log in, without the need to explicitly type them every time.

However, you want to be mindful of the commands that you add in this file, as the automatic execution of those commands may have unintended consequences on the running of other programs (e.g., remote desktop applications).

New accounts on the CCB cluster are created with a initial copy of ~/.bashrc file. It is common for the file to evolve over time, as many programs suggest additions as part of their installation and setup procedures.

The ~/.bashrc file is a hidden file – its name starts with a . (dot) symbol – so it will only be listed by the ls command with the -a option.

In this page, we provide an example that contains elements specific to the WIMM CCB cluster, as well as aliases and optional elements that may not be relevant to all users.

Contents #

Please carefully read the comments and review the elements that are relevant to you. You may choose to replace the entire contents of your .bashrc file, or select portions of the example below.

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# User specific aliases and functions
alias emacs='emacs -nw'
alias R='R --no-save'

### Load environment modules
# Load the latest version of Git (system version is old)
module load git/2.31.1

Explanation #

Comments #

First, it is important to clarify that, in the contents above, all the lines that start with the # symbol are purely comments that are only added for information purposes and future reference, without any impact on the functionality of the file.

/etc/bashrc #

The first chunk of code – repeated below – executes a script that sets up system-wide functions and aliases. That script is exclusively and safely managed by system administrators, and it is highly recommended to keep this as the first bit of code in your ~/.bashrc file at all times.

if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

Aliases #

The next chunk of code uses the alias command to create aliases. Aliases are essentially shortcuts that condense arbitrarily complex (sequences of) commands as single-word keywords, reducing keystrokes and improving speed and efficiency.

While the alias command can be used to define shortcuts interactively in the Bash session, aliases are most commonly defined in the ~/.bashrc file, to make them available as soon as users open a new shell.

In this example:

• We change the meaning of the emacs command to automatically apply the option -nw (synonym to --no-window-system). This force the Emacs editor to open within the terminal rather than attempting to open it as a GUI (i.e., windowed) application.
• We change the meaning of the R command to automatically apply the option --no-save. This forces the R program to discard the workspace at the end of each session instead of offering to interactively save the workspace to a file. Large workspaces – that contain many objects or large data sets – can significantly increase the time that it takes for R sessions to start and end (up to several minutes).

alias emacs='emacs -nw'
alias R='R --no-save'

Other common aliases include:

• la, to list all files (including hidden files) in long form, with human readable file sizes, and file type indicators.

alias la='ls -alhF'

• Overriding the rm command to force an interactive prompt before every removal.

alias rm='rm -i'

Modules #

The next chunk of code uses the module command to put a version of the git program on the PATH that is more recent than the version originally installed with the operating system.

module load git/2.31.1