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Lecture 2 Unix Shell

The notes below are modified from the excellent Unix Shell tutorial that is freely available on the Software Carpentry website. I highly recommend checking out the full version for further reading. The material is being used here under the terms of the Creative Commons Attribution license.

What is Unix shell?

The Unix shell is both a command-line interface and a scripting language. With the shell, it is possible to invoke complicated programs like climate modeling or a simple command that create an empty directory. The most popular Unix Shell is Bash.

Several commands are frequently used to create, inspect, rename, and delete files and directories.

To get started, open a terminal using the OpenOnDemand Clusters: Amarel Cluster Shell Access. After entering your password, you will see the welcome message. 

(base) [xj103@amarel2 ~]$

The dollar sign is a prompt, which shows us that the shell is waiting for input.

xj103 is our username and amarel2 is the hostname. The username will be your NetID. The hostname indicates the node you're at. Here we are using login nodes (amarel1, amarel2, etc.). Cluster login nodes provide a shared environment where users can transfer data, build software, and prepare their calculations. Running applications on a shared login node or doing things that consume significant compute, memory, or network resources can unfairly impact other users. Please do not do that. Do not run your research applications on the login node. If you log into the terminal via a compute nodes, you will see the hostname as hal0001, hal0002 etc., which are nodes assigned to you for computation.

From now on, we will just use a $ to indicate the prompt.

To find out your username in general, you can use the command

$ whoami
xj103

and to find out your hostname

$ hostname
amarel2.amarel.rutgers.edu

Next, let's find out where we are by running a command called pwd (which stands for "print working directory"). At any moment, our current working directory is our current default directory, i.e., the directory that the computer assumes we want to run commands in unless we explicitly specify something else. Here, the computer's response is /home/xj103, which is the home directory of the user named xj103.

$ pwd

/home/xj103

To understand what a "home directory" is, let's have a look at how the file system as a whole is organized. For the sake of this example, we'll be illustrating the filesystem on Amarel. 

$ cd /

Now let's learn the command that will let us see the contents of our own filesystem. We can see what's in our home directory by running ls, which stands for "listing":

$ ls

On a Unix computer, at the top is the root directory that holds everything else. We refer to it using a slash character / on its own; this is the leading slash in /home/xj103.

Inside that directory are several other directories: bin (which is where some built-in programs are stored), lib (for the software "libraries" used by different programs), home (where users' personal directories are located), projects (where project data are stored), etc (system-wide configuration files), and so on.

Now let's go back to our home directory with ~ (tilde)

$ cd ~

ls prints the names of the files and directories in the current directory in alphabetical order, arranged neatly into columns. We can make its output more comprehensible by using the flag -F, which tells ls to add a trailing / to the names of directories:

$ ls -F

ls has lots of other options. To find out what they are, we can type:

$ man ls

man is the Unix "manual" command: it prints a description of a command and its options, and (if you're lucky) provides a few examples of how to use it. To navigate through the man pages, you may use the up and down arrow keys to move line-by-line. Quit the man pages by typing "q".

The command to change locations is cd followed by a directory name to change our working directory. cd stands for "change directory", which is a bit misleading: the command doesn't change the directory, it changes the shell's idea of what directory we are in.

Let's say we want to move to the Documents directory we saw above. We can use the following series of commands to get there:

$ cd Documents

These commands will move us from our home directory onto into the Documents directory. cd doesn't print anything, but if we run pwd after it, we can see that we are now in /home/xj103/Documents.

We now know how to go down the directory tree, but how do we go up?
There is a shortcut in the shell to move up one directory level that looks like this:

$ cd ..

.. is a special directory name meaning "the directory containing this one", or more succinctly, the parent of the current directory. Sure enough, if we run pwd after running cd .., we're back in /home/xj103:

$ pwd

/home/xj103

The special directory .. doesn't usually show up when we run ls. If we want to display it, we can give ls the -a flag:

$ ls -F -a

-a stands for "show all"; it forces ls to show us file and directory names that begin with ., such as .. (which, if we're in /home/xj103/Documents, refers to the /home/xj103 directory) As you can see, it also displays another special directory that's just called ., which means "the current working directory". It may seem redundant to have a name for it, but we'll see some uses for it soon.

Note that in most command line tools, multiple parameters can be combined with a single - and no spaces between the parameters: ls -F -a is equivalent to ls -Fa.

These then, are the basic commands for navigating the filesystem on your computer: pwd, ls and cd. Let's explore some variations on those commands. What happens if you type cd on its own, without giving a directory? 

$ cd

How can you check what happened? pwd gives us the answer! 

$ pwd

/home/xj103

It turns out that cd without an argument will return you to your home directory, which is great if you've gotten lost in your own filesystem. 

$ cd

Check that we've moved to the right place by running pwd and ls -F

If we want to move up one level from the data directory, we could use cd ... But there is another way to move to any directory, regardless of your current location.

So far, when specifying directory names, or even a directory path (as above), we have been using relative paths. When you use a relative path with a command like ls or cd, it tries to find that location from where we are, rather than from the root of the file system.

However, it is possible to specify the absolute path to a directory by including its entire path from the root directory, which is indicated by a leading slash. The leading / tells the computer to follow the path from the root of the file system, so it always refers to exactly one directory, no matter where we are when we run the command.

This allows us to move to our examples directory from anywhere on the filesystem. To find the absolute path we're looking for, we can use pwd and then extract the piece we need to move to examples. 

$ pwd

$ cd /home/xj103/Documents/

Run pwd and ls -F to ensure that we're in the directory we expect.

Two More Shortcuts

The shell interprets the character ~ (tilde) at the start of a path to mean "the current user's home directory". For example, if my home directory is /home/xj103, then ~/rcaes is equivalent to /home/xj103/rcaes. This only works if it is the first character in the path.

Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in, which is faster than having to remember, then type, the full path. This is a very efficient way of moving back and forth between directories. The difference between cd .. and cd - is that the former brings you up, while the latter brings you back. You can think of it as the Last Channel button on a TV remote.

Tab Completion

Typing the full path to directories and files can be slow and annoying. Fortunately, we have "tab completion" to help us. Try typing cd Doc and then press the <tab>. The system will try to "auto complete" your command. Pressing tab twice brings up a list of all the files, and so on. This is called tab completion, and we will see it in many other tools as we go on.

Key Points:

  • "The file system is responsible for managing information on the disk."
  • "Information is stored in files, which are stored in directories (folders)."
  • "Directories can also store other directories, which forms a directory tree."
  • "cd path changes the current working directory."
  • "ls path prints a listing of a specific file or directory; ls on its own lists the current working directory."
  • pwd prints the user's current working directory.
  • whoami shows the user's current identity.
  • / on its own is the root directory of the whole file system.
  • A relative path specifies a location starting from the current location.
  • An absolute path specifies a location from the root of the file system.
  • Directory names in a path are separated with '/' (forward slash) on Unix, but '\\' (backslash) on Windows.
  • '..' means 'the directory above the current one'; '.' on its own means 'the current directory'.
  • Most files' names are something.extension. The extension isn't required, and doesn't guarantee anything, but is normally used to indicate the type of data in the file.
  • Most commands take options (flags) which begin with a '-'.

Working with Files and Directories

We now know how to explore files and directories, but how do we create them in the first place? Let's go back to our home directory and use ls -F to see what it contains:

$ cd
$ pwd

/home/xj103/

Let's create a new directory called thesis using the command mkdir thesis (which has no output):

$ mkdir thesis

As you might guess from its name, mkdir means "make directory". Since thesis is a relative path (i.e., doesn't have a leading slash), the new directory is created in the current working directory:

$ ls -F

Good names for files and directories

Complicated names of files and directories can make your life painful when working on the command line. Here we provide a few useful tips for the names of your files.

  1. Don't use whitespaces.

    Whitespaces can make a name more meaningful but since whitespace is used to break arguments on the command line is better to avoid them on name of files and directories. You can use - (dash) and _ (underscore) instead of whitespace.

  2. Don't begin the name with - (dash).

    Commands treat names starting with - as options.

  3. Stick with letters, numbers, . (period), - (dash) and _ (underscore).

    Many other characters have special meanings on the command line. We will learn about some of these during this lesson. There are special characters that can cause your command to not work as expected and can even result in data loss.

If you need to refer to names of files or directories that have whitespace or another non-alphanumeric character, you should surround the name in quotes ("").

Since we've just created the thesis directory, there's nothing in it yet:

$ ls -F thesis

Let's change our working directory to thesis using cd. We then create a blank new file called draft.txt using the touch command:

$ cd thesis
$ touch draft.txt

Now we can edit the file in JupyterLab's text editor. Let's type in a few lines of text. Once we're happy with our text, we save the file, and return to the shell.

ls now shows that we have created a file called draft.txt:

$ ls
draft.txt

Let's tidy up by running rm draft.txt:

$ rm draft.txt

This command removes files (rm is short for "remove"). If we run ls again, its output is empty once more, which tells us that our file is gone:

$ ls

Deleting Is Forever

The Unix shell doesn't have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do). Instead, when we delete files, they are unhooked from the file system so that their storage space on disk can be recycled. Tools for finding and recovering deleted files do exist, but there's no guarantee they'll work in any particular situation, since the computer may recycle the file's disk space right away.

Let's re-create that file and then move up one directory to /home/xj103 using cd ..:

$ touch draft.txt
$ cd ..

If we try to remove the entire thesis directory using rm thesis, we get an error message:

$ rm thesis

rm: cannot remove `thesis`: Is a directory

This happens because rm by default only works on files, not directories.

To really get rid of thesis we must also delete the file draft.txt. We can do this with the recursive option for rm:

$ rm -r thesis

With Great Power Comes Great Responsibility

Removing the files in a directory recursively can be very dangerous operation. If we're concerned about what we might be deleting we can add the "interactive" flag -i to rm which will ask us for confirmation before each step

 $ rm -r -i thesis
 rm: descend into directory ‘thesis’? y
 rm: remove regular file ‘thesis/draft.txt’? y
 rm: remove directory ‘thesis’? y

This removes everything in the directory, then the directory itself, asking at each step for you to confirm the deletion.

Let's create that directory and file one more time.

$ mkdir thesis
$ touch thesis/draft.txt
$ ls thesis

draft.txt

draft.txt isn't a particularly informative name, so let's change the file's name using mv, which is short for "move":

$ mv thesis/draft.txt thesis/quotes.txt

The first parameter tells mv what we're "moving", while the second is where it's to go. In this case, we're moving thesis/draft.txt to thesis/quotes.txt, which has the same effect as renaming the file. Sure enough, ls shows us that thesis now contains one file called quotes.txt:

$ ls thesis

quotes.txt

One has to be careful when specifying the target file name, since mv will silently overwrite any existing file with the same name, which could lead to data loss. An additional flag, mv -i (or mv --interactive), can be used to make mv ask you for confirmation before overwriting.

Just for the sake of consistency, mv also works on directories

Let's move quotes.txt into the current working directory. We use mv once again, but this time we'll just use the name of a directory as the second parameter to tell mv that we want to keep the filename, but put the file somewhere new. (This is why the command is called "move".) In this case, the directory name we use is the special directory name . that we mentioned earlier.

$ mv thesis/quotes.txt .

The effect is to move the file from the directory it was in to the current working directory. ls now shows us that thesis is empty:

$ ls thesis

Further, ls with a filename or directory name as a parameter only lists that file or directory. We can use this to see that quotes.txt is still in our current directory:

$ ls quotes.txt

quotes.txt

The cp command works very much like mv, except it copies a file instead of moving it. We can check that it did the right thing using ls with two paths as parameters --- like most Unix commands, ls can be given multiple paths at once:

$ cp quotes.txt thesis/quotations.txt
$ ls 

quotes.txt   thesis/quotations.txt

To prove that we made a copy, let's delete the quotes.txt file in the current directory and then run that same ls again.

$ rm quotes.txt
$ ls quotes.txt thesis/quotations.txt

ls: cannot access quotes.txt: No such file or directory
thesis/quotations.txt

This time it tells us that it can't find quotes.txt in the current directory, but it does find the copy in thesis that we didn't delete.

Key Points

  • cp old new copies a file.
  • mkdir path creates a new directory.
  • mv old new moves (renames) a file or directory.
  • rm path removes (deletes) a file.
  • Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.
  • The shell does not have a trash bin: once something is deleted, it's really gone.
  • Depending on the type of work you do, you may need a more powerful text editor than Nano.

Learning More

The goal of this lesson was to familiarize you with the basics of working with files and directories. There is a lot more to the unix shell and filexsystem than what we have covered here! To ge deeper with self study, we recommend the excellent Software Carpentry Unix Shell Lesson, on which the above material was based.