Environment variables

A brief introduction to environment variables.

Motivation

A variable is a named place in a computer’s memory that stores a particular piece of information (e.g., number, string).

Environment variables are variables defined and available in the shell’s environment. Those variables can be accessed by any program that runs in the shell. They can be accessed using the $ (dollar) symbol, followed by the name of the environment variable (e.g., $USER).

Once logged into the CCB cluster, a number of environment variables are set in the Bash session. Existing environment variables can be modified, and new environment variables can be defined at runtime, including from the ~/.bashrc file while the login shell is executed.

Some environment variables are identical for all users on the cluster, other are derived from the username, and users can also set environment variables themselves. Many programs require certain environment variables to be set for their good functioning.

In this page, we describe some of the built-in environment variables, with a brief description of their purpose and advice on best practices.

Built-in variables

$HOME

The $HOME environment variable is set for each user to their own home directory.

The echo command can be used to display the value of $HOME.

echo $HOME

The ‘HOME’ environment variable.

The $HOME environment variable can also be used in commands. For instance, users can list the contents of their home directory as follows.

ls $HOME

$USER

The $USER environment variable is set for each user to their own username.

The echo command can be used to display the value of $USER.

echo $USER

The ‘USER’ environment variable.

For instance, users create a directory named after their own username as follows. This is particularly useful to use a consistent naming of personal directories that is guaranteed to avoid any conflict with other usernames.

mkdir $USER

$PATH

The $PATH environment variable is unquestionably one of the most important environment variables.

The $PATH is stored as a colon-separated (: symbol) character string that represents the list of directories that are searched – in the given order – to find executable files that are invoked by users and their scripts.

As such:

  • Commands may fail if the directory where they are stored is not listed in the $PATH.
  • Users may need to modify their $PATH to add directories that contain commands they wish to use.
  • Users may need to modify their $PATH to remove directories that contain command they do not wish to use (e.g., when a command is defined in multiple directories).
echo $PATH

The ‘PATH’ environment variable.

Whenever possible, we recommend using the module command to add and remove programs (i.e., modules) from the $PATH.

For instance:

module rm git/2.31.1

Modify the ‘PATH’ environment variable using the module command.

As an alternative, users may not need to modify their $PATH if they provide the full path to the executable file that they wish to run. However, this approach requires many more keystrokes, and is more prone to typographical mistakes.

For instance:

/package/git/2.31.1/libexec/git-core/git status

$TMPDIR

The $TMPDIR environment variable is set globally to the location of a directory that user should use to store temporary files.

For instance, users can create new temporary directories and files in that directory as follows:

mkdir $TMPDIR/new_temp_dir
touch $TMPDIR/new_temp_file

The ‘TMPDIR’ environment variable.

Note that $TMPDIR is the same for all users. To avoid clashes of directories and file names with other users, we recommend creating and using the subdirectory with your own username first.

For instance:

mkdir $TMPDIR/$USER
mkdir $TMPDIR/$USER/new_temp_dir
touch $TMPDIR/$USER/new_temp_dir/new_temp_file

Custom variables

Motivation

Environment variables are not restricted to built-in variable names. Users can define any number of custom environment variable names.

Some programs expect users to define additional environment variables, controlling the behaviour of the program without passing arguments explicitly on the command line.

Expert users may also define custom environment variables for their own purposes (e.g., store a value commonly used on the command line or in their own scripts).

$TMP

The $TMP environment variable is not set by default.

Some programs may expect the value of this variable to be a character string indicating the location of an existing directory that can be used to store temporary files during their execution.

We recommend setting the value of $TMP to $TMPDIR.

We also recommend defining that environment variable in the ~/.bashrc file, so that the environment variable is immediately set in every Bash session.

In the example below, we define $TMP interactively at the prompt only for demonstration purposes:

export TMP="$TMPDIR"

Defining the ‘TMP’ environment variable.

← The .bashrc file
Advanced configuration →