I - Intro to Unix and Bash Shell

UNIX

UNIX is a text-oriented operating system (OS) originally developed at Bell Labs during the 1960s. Two versions of this OS are dominant today, Linux and macOS.

Strictly speaking, “Linux” refers just to the kernel, which is the part of an operating system that manages the hardware interfaces. On top of the kernel sits a number of utilities that enable users and applications to interact with the kernel.

Linux is the operating system most widely used at HPC facilities, internet servers, and the majority of financial trading system worldwide. A version of Linux powers Android systems.

macOS is based on a slightly different version of Unix.

Shell

In all version of Unix, the shell is a program that interprets commands and acts as an interface between the user and the kernel.

Multiple shells are available. In Linux systems, the default is the bash shell. MacOS formerly defaulted to bash as well, but has recently switched to zsh.

The shell displays a prompt, which indicates that it is ready to accept commands. In this tutorial, we will utilize the dollar sign $ as the prompt; yours may be different, and later in this tutorial we will learn how to customize it to your preferences.

To determine your current shell, at the prompt type

$echo $SHELL

It is important to keep in mind that Unix in general and the shell in particular is case-sensitive. The commands LS and ls would not be the same.

Logging In

Logging into a remote UNIX based system requires a program generally called a client. The options for the client depends on your OS.

SSH

Command line access through a terminal on your computer is based on the ssh or Secure Shell protocol. It is

• Encrypted
• Available on most UNIX systems

Your ssh client communicates with the ssh server program running on the remote system. Once established, the connection is secure even if the network is insecure.

Example

If your computer is a macOS or Linux system, you log in with

ssh -Y mst3k@login.hpc.virginia.edu

Throughout this tutorial we will use mst3k as our example user ID. You should substitute your own. The option -Y allows access to graphical applications and requires that an X11 server application must be installed on your computer. This should be the default for Linux, but macOS users must install XQuartz before this command-line option will be useful.

Graphical Applications

The command-line secure shell is not the only option for accessing the HPC system. Windows users in particular may wish to use other methods, since although ssh is available for it, Windows is not particularly friendly to command lines.

Open OnDemand (OOD)

Open OnDemand is a Web-based interface to the system. It provides a graphical file-management interface and access to several popular applications running on the compute nodes. A simple terminal that opens on a loginnode is also provided. See the introduction in our basic tutorial.

FastX

FastX is a Web-based graphical interface to a loginnode. It is also covered in the introduction.

MobaXterm (Windows)

MobaXterm combines an ssh client, a sftp client for file transfers, and an X11 server into a single bundle. More details are available at our Website or in the introduction.

Running Shell Commands

The syntax of Unix commands is not completely standardized but in general follow the pattern of a two or three-letter abbreviation followed by command-line options, which are single-letter options preceded by one hyphen or multiple-letter options with two hyphens. Many commands also take arguments.

$cmd -o  --option  argument

Example

Invoke the utility rm to delete a file.

$rm myfile

In this example, the shell issues a request to the kernel to delete myfile. The kernel then communicates with the software that manages file storage to execute the operation.

When it is complete the shell then returns the UNIX prompt to the user, indicating that it is waiting for further commands.

Running Our First Command

Let’s run our first command. Into a terminal type

$pwd
/home/mst3k

This command stands for print working directory. It prints the name of the folder in which the shell is currently working.

Navigating the Bash Shell

Modern shells provide useful “hotkey” commands that can save considerable typing. The “control-” notation means that the Ctrl (control) key and the following key should be depressed at the same time.

Function	Key
Tab completion: expand typed string to as far as it has a unique name.	tab
Search for earlier command	control-r
Move to the beginning of the line	control-a
Move to the end of the line	control-e
Clear the screen	clear or control-l

Bash History

When using bash you may use its built-in history mechanism to save yourself some keystrokes.

Function	Key
scroll through the previous commands you have typed	up arrow
if already scrolled back, scroll to more recent commands	down arrow
edit text on a line	right or left arrow

Logging Out

To log out of a shell, type exit

$exit

This logs you out of your current terminal window. If that is a login window, for example your ssh shell, it will log you out of the system entirely.