Understanding the Linux CLI

Sessions

Each time you log in to the system, you start an interactive shell session. An interactive shell session is kept alive for as long as you keep it open. You can exit the session with the command exit or by pressing Ctrl+D.

File structure

The Linux file structure is structured in a tree-like fashion. Every file and directory on the system can be referenced absolutely or relatively to the current working directory.

The file tree

The directory /home/domain/user/subdirectory can thus be broken up into: /, home, domain, user.

Note that the first / is the root, and the following directories are subdirectories to each other.

Referencing paths

We can reference file paths in two ways. Suppose we want to list the files in /home/domain/user/subdirectory

Relatively: If we are standing in user, we can call ls -l subdirectory
Absolutely: Regardless of where we are standing, we can ls -l /home/domain/user/subdirectory

Commands

ls: list files in the current directory
ls -al: list all files in the current directory (including dotfiles).
pwd: print the current working directory
cd: change directory (if no input is given, go to $HOME)
cd mydir: change directory to mydir (if no input is given, go to $HOME)
mkdir: create (make) directory
rm: remove file
rm -r: remove directory
rmdir: remove directory
cp: copy file
cp -r: copy file (or directory) recursively (including all it's subdirectories)
mv target-file target-location: move file
mv old-filename new-filename: rename file (think about this, as if you are editing the filepath)
touch filename: create an empty file
cat filename: print file content
head filename: print the first 5 lines of a file
head -n 2 filename: print the first 2 lines of a file
tail filename: print the last 5 lines of a file
tail -n 2 filename: print the last 2 lines of a file
tail -f filename: print the last 5 lines of a file continously (follow newly written lines)

Tips and tricks

Use tab completion as much as you can. This is both easier and decreases the risk of mistyping.
Avoid using spaces when naming files and directories.

Variables

Variables are attached to your shell session and are stored in memory.

Some variables are set, when you log into your session, eg. $HOME, $USER, $PATH. Others can be set by the user to interact with programs, or to be referenced in scripts.

Call the command env to see which variables are loaded into your current shell session.

Variable assignment can be done in the following manner:

var="hello world"

Variables can be printed with

❯ echo $var
hello world

Prepending export to the assignment makes the variable accessible to child processes. This can be useful if you are delegating a job to a compute node.

Additional info on calling commands

Commands can either be shell builtins or programs. This can be checked with the command type:

❯ type echo
echo is a shell builtin

❯ type ls
ls is /bin/ls

For the most part it is not important to be able to distinguish between them, but it is important to understand that in most cases commands are programs, which we can execute because the system knows where to find them.

This is important to understand because operating an HPC system involves jumping between nodes and software containers, whereby the software environment changes, and we may want to confirm that we are indeed calling the correct command or the correct path.

In Linux, programs can be made available in two ways:

1: We can call them because they are located in one of the directories in the $PATH variable.

Consider the following:

We can call squeue
which squeue will return /usr/local/bin/squeue
echo $PATH will verify that /usr/local/bin is indeed in $PATH

2: We can call them by referencing their paths.

If a program is not in $PATH, we can execute it by referencing it's path:

Calling /bin/ls is equivalent to calling ls
If we are standing in /bin, calling ./ls is equivalent to calling ls.

This can be useful for calling a specific version of a program or for verifying that you are indeed calling the program, you intend to call.