Navigating the Linux Shell

This guide provides an introduction to essential Linux shell commands for navigating and interacting with the filesystem, especially within a typical cluster login environment. The shell is provides a command-line interface (CLI) that allows users to communicate with the system by typing commands. On Triton/Pegasus, the default shell is Bash.

Users input commands into the shell, which executes them and displays the output. Commands may include options (also called flags) to modify behavior, and arguments to specify targets or inputs. To scroll through previously entered commands, use the up/down arrow keys.

Below is a collection of commonly used Linux shell commands, along with detailed explanations and examples. Remember that Linux is case-sensitive—“name” is different from “NAME”, “Name”, “nAMe”, and so on. To stop a running process and return to the prompt, press CTRL-C (on Windows) or Command-C (on macOS).

Check Your Current Shell with echo

The echo command displays text or variable values in the terminal. In Linux, variables are referenced using a leading dollar sign ($). For instance, the variable $SHELL stores the path to your default shell. To view it, you can pass the variable to echo. Variables can also be embedded within strings, as shown below.

[username@pegasus ~]$ echo $SHELL
/bin/bash
[username@pegasus ~]$ echo "My shell is $SHELL"
My shell is /bin/bash

List All Environment Variables with env

To view a complete list of your environment variables, use the env command. To organize the output in alphabetical order, combine it with sort as shown. The pipe (|) command is used to connect multiple commands in sequence, passing the output of one as the input to the next.

[username@pegasus ~]$ env
MODULE_VERSION_STACK=3.2.10
LC_PAPER=en_US.utf8
HOSTNAME=login4
SHELL=/bin/bash
...
[username@pegasus ~]$ env | sort
...

Check Your Current Directory with pwd

Linux uses directories, which are equivalent to folders in other operating systems. When you log in, you are placed in your home directory by default. The tilde (~) symbol is a shorthand for this location. The pwd (print working directory) command outputs the absolute path of your current location in the filesystem, beginning at the root directory (/).

[username@pegasus ~]$ pwd
/nethome/username

List Directory Contents with ls

Running the ls command without any arguments displays the contents of your current directory. Note: if this is your first login, your home directory may appear empty. Items that begin with a d in their permissions are directories.

[username@pegasus ~]$ ls
example_file1  example_file2  testdir1

To inspect a specific directory, provide its path as an argument to ls. In the example below, testdir1 is located in the home directory and contains one file: testdir1_file1.

[username@pegasus ~]$ ls testdir1
testdir1_file1

You can press the TAB key while typing a name to automatically complete it. If multiple possibilities exist, a list will appear. Continue typing more characters and press TAB again until completion succeeds.

You can learn more about command flags and usage by accessing the Linux manual pages using:

[username@pegasus ~]$ man topic or command

Use the arrow keys, Page Up, or Page Down to scroll. Press SPACE to view additional content, and type q to quit.

To display more detailed file information, use ls with flags like -lh:

[username@pegasus ~]$ ls -lh
total 0
-rw-r--r-- 1 username ccsuser  54  example_file1
-rw-r--r-- 1 username ccsuser 476  example_file2
drwxr-xr-x 2 username ccsuser 512  testdir1
...

Explanation of ls -lh flags:

• -l: Long listing format (includes size, owner, permissions, etc.)

• -h: Human-readable file sizes (e.g., 1K, 234M, 2G)

Other useful ls options include:

• -a: Include hidden files (starting with .)

• -d: Show directory details instead of listing contents

• -1 (number 1): Output one entry per line

• -R: Recursively display subdirectory contents

• -S: Sort files by size

• -X: Sort files alphabetically by extension

• -m: Display output as a comma-separated list

* Hidden files include . (current directory) and .. (parent directory). These shortcuts are useful in relative paths:

[username@pegasus testdir1]$ ls -a
.  ..  testdir1_file1
[username@pegasus testdir1]$ ls ..
example_file1  example_file2  testdir1

Move Between Directories with cd

Use the cd (change directory) command to navigate the filesystem. The provided path can be absolute (starting with /) or relative to your current location.

[username@pegasus ~]$ cd testdir1
[username@pegasus testdir1]$

Some useful cd patterns:

• cd or cd ~: Return to your home directory

• cd ..: Move up to the parent directory

• cd -: Return to the previous directory and display it

Visualize Directory Structure with tree

Pegasus includes the tree utility, which shows a recursive, indented listing of files and directories. This can be more informative than ls, especially for visualizing nested directories.

[username@pegasus ~]$ tree -vC
.
|-- example_file1
|-- example_file2
|-- testdir1
    `-- testdir1_file1

1 directory, 3 files

Explanation of tree -vC flags:

• -v: Sort contents alphanumerically by type

• -C: Enable colored output for better visibility

Other helpful tree flags include:

• -a: Display hidden files

• -d: Show directories only

• -r: Reverse the sorting order

• -L number: Limit the depth of displayed directory levels

Locate Commands with which

The which command shows the full path of a command executable by searching directories listed in your $PATH environment variable. Use which to verify if a command is installed and to find its location.

[username@pegasus ~]$ which bash
/bin/bash
[username@pegasus ~]$ which vim
/usr/bin/vim
[username@pegasus ~]$ which python
/share/opt/python/2.7.3/bin/python