Introduction to UNIX - Part 2: Getting Started

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Obtaining a user account

As already mentioned, before you can do anything on a UNIX system you must have a user account. This is usually obtained by introducing yourself to your friendly neighborhood system administrator and asking them to create an account for you. If you make a good impression, you will be asked for some information and the account will be created within a matter of minutes. If not, homemade cookies have been known to be an effective motivational instrument. ;-)

Structural Biology has an online form that collects the necessary information to create your account. Send mail to that introduces yourself (we need to know who you are!) and explains why you need an account. Access to the aforementioned online form will subsequently be provided.

Similarly, you can sign up for an account on the ACCRE cluster via a web form linked off the ACCRE main page.

Logging in

Once you have been given a user account, you can get started. The first step is to log in by providing a valid username and password to the system. This will grant you some level of access to the system depending on how you log in. There are essentially two types of logins: console (local) logins and remote logins:

  • Console login:

    In the practical sense, the term "console" is just a fancy word for the display and input devices that are directly attached to a UNIX system. Logging in at the console means that you are physically sitting at the machine and will log in via the mouse, keyboard, and display that are attached to the system.

    When you sit at the console, you should see the login window on the screen (if the screen is blank, move the mouse or press the shift key on the keyboard to wake up the display). The exact details of the login window will vary between the different flavors of UNIX, but at the very least you will see a place to enter your username. Note: Some systems may require you to point your mouse over the login window before the keyboard is activated in that window.

    1. Type your username at the appropriate place in the login window

    2. Press "enter" to bring you to the password field (Note: Some systems may require you to press "tab" to move to the password field).

    3. Type your password into the password field. You will not see your password as it is being typed, so type carefully. Also keep in mind that UNIX systems are case-sensitive. That means that if your password is "ImaDork3", you must type exactly "ImaDork3" to preserve the pattern of lower case and capital letters. "imadork3" and "IMADORK3" would be completely different passwords to UNIX.

    4. Once you've typed your password, press enter (or click the appropriate action button if present on the login window). If you've typed everything correctly, you will be granted access. The login screen will disappear and be replaced with the system's Graphical User Interface or "GUI" (covered in the next part of this introduction).

    Once you have completed these steps, your user is the "owner" of the console. As such, you have control over the input devices, the display, and its contents. Remote users or systems will be unable to access any of these resources without your permission.

  • Remote login:

    I've already mentioned that UNIX is a multi-user networked operating system. As such, you are able to log in to remote systems and do work right alongside other users without leaving your office or kicking the other users off (you do, however, have to remember that you are sharing system resources with all the users who are currently logged on).

    Remote logins are also known as "shell access". We will talk more about the UNIX shell later, but for now just keep in mind that the shell is a place where you give instructions to a UNIX system (like starting a program or deleting a file) via a command-line interface. When performing a remote login, it is assumed that you are already logged in to the console of a local UNIX machine (or perhaps a PC) and wish to gain shell access on a remote UNIX machine.

    In order to proceed, you should know the fully qualified domain name of the system you wish to remotely log in to. The fully qualified domain name is a combination of the hostname and the domain name of a system. Every properly configured UNIX system has both a hostname and a domain name.

    1. Start a UNIX shell (covered later) and make that window active.

    2. You will now use a program called "ssh" (short for "Secure SHell") to log in to the remote system. At the shell prompt (%), you would type, for example:

      % ssh

      and press enter. In the example above, you would be connected to the system with hostname "reef" in the domain "" as user "jake".

      Systems in structural biology have a domain name of "". Often, you will be connecting between machines that reside in the same domain. In this case the domain name can usually be left off. For example, if you were on a system in the domain "" and wanted to remotely log in to the machine called "reef" you could type:

      % ssh jake@reef

      or if your username is the same on both machines you can leave out that part, too:

      % ssh reef

    3. In any case, ssh will connect to the system and ask for user jake's password. Type the password (remember about case-sensitivity) and press enter. If you were successful, a shell will be started for you on the remote system and you will get a command prompt. You can now give the remote system commands via the remote shell's command-line interface.

What Now?

Now you know the difference between console and remote logins as well as how to perform both actions. You know that once you perform a console login, you are immediately presented with the system's Graphical User Interface (GUI) and that once you perform a remote login, you are immediately presented with the remote system's shell (command-line) interface. The GUI and the shell will be discussed in the following two sections.

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