UNIX & Linux

Introduction to UNIX

The internet is full of useful UNIX/Linux tutorials; this is just one more, but hopefully it will be brief yet thorough enough to learn the basics of using UNIX/Linux insofar as will be needed for the remainder of this documentation. The contents of this tutorial are adapted from an online UNIX tutorial by Michael Stonebank.

Introduction to the UNIX and UNIX-Like Operating Systems

What is UNIX/Linux?

UNIX is an operating system which was first developed in the 1960s, and has been under constant development ever since. By operating system, we mean the suite of programs which make the computer work. It is a stable, multi-user, multi-tasking system for servers, desktops and laptops.

UNIX systems also have a graphical user interface (GUI) similar to Microsoft Windows which provides an easy to use environment. However, knowledge of UNIX is required for operations which aren’t covered by a graphical program, or for when there is no windows interface available, for example, in a ssh session.

Types of UNIX

There are many different versions of UNIX, although they share common similarities. The most popular varieties of UNIX are GNU/Linux and macOS. Within the “Linux” category, there are a multitude of flavors: Debian (Ubuntu, Mint, Crunchbang), RedHat (RHEL, Fedora, CentOS), SuSE, etc.

The UNIX operating system

The UNIX operating system is made up of three parts; the kernel, the shell, and the programs.

The kernel

The kernel of UNIX is the hub of the operating system: it allocates time and memory to programs and handles the filestore and communications in response to system calls.

As an illustration of the way that the shell and the kernel work together, suppose a user types

$ rm myfile

(which has the effect of removing the file myfile). The shell searches the filestore for the file containing the program rm, and then requests the kernel, through system calls, to execute the program rm on myfile. When the process rm myfile has finished running, the shell then returns the UNIX prompt $ to the user, indicating that it is waiting for further commands.

The shell

The shell acts as an interface between the user and the kernel. When a user logs in, the login program checks the username and password, and then starts another program called the shell. The shell is a command line interpreter (CLI). It interprets the commands the user types in and arranges for them to be carried out. The commands are themselves programs: when they terminate, the shell gives the user another prompt.

The adept user can customize his/her own shell, and users can use different shells on the same machine. Users will typically have the TCSH shell or Bash shell by default (Bash is typically the default on modern Linux distributions).

These shells have certain features to help the user inputting commands:

• Filename Completion - By typing part of the name of a command, filename or directory and pressing the [Tab] key, the tcsh and bash shells will complete the rest of the name automatically. If the shell finds more than one name beginning with those letters you have typed, it will beep, prompting you to type a few more letters before pressing the [Tab] key again.

• History - The shell keeps a list of the commands you have typed in. If you need to repeat a command, use the cursor keys to scroll up and down the list or type history for a list of previous commands.

Files and processes

Everything in UNIX is either a file or a process.

A process is an executing program identified by a unique PID (process identifier).

A file is a collection of data. They are created by users using text editors, running compilers etc.

Examples of files:

• a document (report, essay etc.);

• the text of a program written in some high-level programming language;

• instructions comprehensible directly to the machine and incomprehensible to a casual user, for example, a collection of binary digits (an executable or binary file);

• a directory, containing information about its contents, which may be a mixture of other directories (subdirectories) and ordinary files.

The Directory Structure

All the files are grouped together in the directory structure. The file-system is arranged in a hierarchical structure, like an inverted tree. The top of the hierarchy is traditionally called root (written as a slash /)

UNIX directory structure example

In the diagram above, we see that the directory ee51vn contains two sub-directories (docs and pics) and a file called report.doc.

The full path to the file report.doc is /home/its/ug1/ee51vn/report.doc.

Moving Around the Filesystem

Listing files and directories

ls (list)

When you first login, your current working directory is your home directory. Your home directory has the same name as your user-name, e.g. rkalescky, and it is where your personal files and subdirectories are saved.

To find out what is in your home directory, type

$ ls

The ls command lists the contents of your current working directory.

Unix Terminal - running the ls command

There may be no files visible in your home directory, in which case, the UNIX prompt will be returned. Alternatively, there may already be some files inserted by the System Administrator when your account was created.

ls does not, in fact, cause all the files in your home directory to be listed, but only those ones whose name does not begin with a dot (.) Files beginning with a dot (.) are “hidden” files and usually contain important program configuration information. They are hidden because you should not change them unless you are very familiar with UNIX.

To list all files in your home directory including those whose names begin with a dot, type

$ ls -a

As you can see, ls -a lists files that are normally hidden.

Unix Terminal - running the ls -a command

ls is an example of a command which can take options: -a is an example of an option. The options change the behaviour of the command. There are online manual pages that tell you which options a particular command can take, and how each option modifies the behaviour of the command. (See later in this tutorial).

Making Directories

mkdir (make directory)

We will now make a subdirectory in your home directory to hold the files you will be creating and using in the course of this tutorial. To make a subdirectory called unixstuff in your current working directory type

$ mkdir unixstuff

To see the directory you have just created, type

$ ls

Or to see what is inside of the directory unixstuff, type

$ ls unixstuff

Changing to a different directory

cd (change directory)

The command cd directory means change the current working directory to directory. The current working directory may be thought of as the directory you are in, i.e. your current position in the file-system tree.

To change to the directory you have just made, type

$ cd unixstuff

Type ls to see the contents (which should be empty).

Exercise

Make another directory inside the unixstuff directory called backups.

The directories . and ..

While still in the unixstuff directory, type

$ ls -a

As you can see, in the unixstuff directory (and in all other directories), there are two special directories called . and ..

. <. (the current directory)>

In UNIX, . means the current directory, so typing

$ cd .

there is a space between cd and .

means stay where you are (in the unixstuff directory).

This may not seem very useful at first, but using . as the name of the current directory will save a lot of typing, as we shall see later in the tutorial.

.. (the parent directory)

The other “special” directory in UNIX, .., refers to the parent of the current directory, so typing

$ cd ..

will take you one directory up the hierarchy (back to your home directory). Try it now.

typing cd with no argument always returns you to your

home directory. This is very useful if you somehow get lost in the file-system.

Pathnames

pwd (print working directory)

Pathnames enable you to work out where you are in relation to the whole file-system. For example, to find out the absolute pathname of your home-directory, type cd to get back to your home-directory and then type

$ pwd

which should give you something like this,

/users/rkalescky

Suppose you were on the computer from our example UNIX directory structure figure (reproduced again below). There, typing pwd in the ee51vn sub-directory would produce

/home/its/ug1/ee51vn

which means that ee51vn is in the sub-directory ug1, which in turn is located in the its sub-directory, which is in the home sub-directory, which is in the top-level root directory called /.

UNIX directory structure example

Exercise

Use the commands cd, ls and pwd to explore the file-system.

(Remember, if you get lost, type cd by itself to return home).

More about home directories and pathnames

Understanding pathnames

Go back to your home-directory and then type

$ ls unixstuff

to list the contents of your unixstuff directory. Now type

$ ls backups

You will get a message like this

/bin/ls: cannot access backups: No such file or directory

The reason is, backups is not in your current working directory. To use a command on a file (or directory) not in the current working directory (the directory you are currently in), you must either cd to the correct directory, or specify its full pathname. To list the contents of the backups directory that we made earlier, you must instead type

$ ls unixstuff/backups

~ (your home directory)

Home directories can also be referred to by the tilde character, ~. It can be used to specify paths starting at your home directory. So typing

$ ls ~/unixstuff

will list the contents of your unixstuff directory, no matter where you currently are in the file-system.

What do you imagine that

$ ls ~

would list? What do you think that

$ ls ~/..

would list?

Moving around the filesystem – summary

Command	Meaning
ls	list files and directories
ls -a	list all files and directories (including hidden ones)
mkdir	make a directory
cd directory	change to named directory
cd	change to home-directory
cd ~	change to home-directory
cd ..	change to parent directory
pwd	display the path of the current directory

Manipulating Files and Directories

Copying Files

cp (copy)

cp file1 file2 is the command which makes a copy of file1 in the current working directory and calls it file2.

What we are going to do now, is to take a file stored in an open access area of the file system, and use the cp command to copy it to your unixstuff directory.

First, go to your unixstuff directory.

$ cd ~/unixstuff

Then at the UNIX prompt, type,

$ cp /usr/include/sys/types.h types.h

The above command means copy the file types.h from the /usr/include/sys directory to the current directory, keeping the name the same.

You can accomplish the same thing by typing

$ cp /usr/include/sys/types.h .

Like the previous command, it directs the computer to copy the file types.h from the /usr/include/sys directory to the current directory, ., without changing the file name.

Exercise

Create a backup of your types.h file by copying it to a file called types.bak.

Moving files

mv (move)

To move a file from one place to another, use the mv command. This has the effect of moving rather than copying the file, so you end up with only one file rather than two. The calling sequence is of the form mv file1 file2 which results in moving file1 to file2.

This can be helpful when moving a file from one directory to another. We are now going to move the file types.bak to your backup directory.

First, change directories to your unixstuff directory (can you remember how?). Then, inside the unixstuff directory, type

$ mv types.bak backups/.

Type ls and ls backups to see if it has worked.

The mv command can also be used to rename a file, by moving the file to the same directory, but giving it a different filename.

Removing files and directories

rm (remove), rmdir (remove directory)

To delete (remove) a file, use the rm command. As an example, we are going to create a copy of the types.h file then delete it.

Inside your unixstuff directory, type

$ cp types.h tempfile.txt
$ ls
$ rm tempfile.txt
$ ls

(after rm tempfile.txt you may need to answer “y” at the prompt and hit [Enter] before continuing).

These commands first copied the file types.h to a copy called tempfile.txt, then showed you the list of files in this directory (notice the new file), then deleted tempfile.txt, and finally showed you the updated list of files in this directory.

You can use the rmdir command to remove a directory (make sure it is empty first). Try to remove the backups directory:

$ rmdir backups

Notice that you cannot remove the directory, since UNIX will not let you remove a non-empty directory.

Exercise

Create a directory called tempstuff using mkdir, then remove it using the rmdir command.

Displaying the contents of a file on the screen

clear (clear screen)

Before you start the next section, you may want to clear the terminal window of the previous commands so the output of the following commands can be clearly understood.

At the prompt, type

$ clear

This will clear all text and leave you with the $ prompt at the top of the window.

cat (concatenate)

The command cat can be used to display the contents of a file to the screen. Type:

$ cat types.h

As you can see, the file is longer than than the size of the window, so it scrolls past making it difficult to read the file from the beginning.

less (view file contents)

The command less writes the contents of a file onto the screen one page at a time. Type

$ less types.h

Press the [space-bar] if you want to see another page, and type [q] if you want to quit reading.

As you can see, less can be more useful for reading long files than cat.

head (view top of file)

The head command writes the first ten lines of a file to the screen.

First clear the screen then type

$ head types.h

Then type

$ head -3 types.h

What difference did the -3 do to the head command?

tail (view bottom of file)

The tail command writes the last ten lines of a file to the screen.

Clear the screen and type

$ tail types.h

17. Can you figure out how to view the last 15 lines of this file?

Searching the contents of a file

Simple searching using less

Using less, you can search though a text file for a keyword (pattern). For example, to search through types.h for the word long, type

$ less types.h

then, still in less, type a forward slash [/] followed by the word you want to search for,

/long

As you can see, less finds and highlights the keyword. Type [n] to search for the next occurrence of the word. Type [q] to quit the search.

grep <grep (file search)> (don’t ask why it is called grep)

grep is one of many standard UNIX utilities. It searches files for specified words or patterns. First clear the screen, then type

$ grep long types.h

As you can see, grep has printed out each line of the file types.h that contains the word long.

Or has it ????

Try typing

$ grep LONG types.h

Note that the grep command is case sensitive; it distinguishes between LONG and long.

To ignore upper/lower case distinctions, use the -i option, i.e. type

$ grep -i long types.h

To search for a phrase or pattern, you must enclose it in single quotes (the apostrophe symbol). For example to search for long int you would type

$ grep -i 'long int' types.h

Some of the other options of grep are:

-v display those lines that do NOT match

-n precede each matching line with the line number

-c print only the total count of matched lines

Try some of them and see how the results differ. Don’t forget, you can combine options to do more than just one thing at a time. For example, the number of lines without the words long or LONG is

$ grep -ivc long types.h

wc (word count)

A handy little utility is the wc command, short for word count. To do a word count on types.h, type

$ wc -w types.h

To find out how many lines the file has, type

$ wc -l types.h

Manipulating files and directories – summary

Command	Meaning
cp file1 file2	copy file1 and call it file2
mv file1 file2	move or rename file1 to file2
rm file	remove a file
rmdir directory	remove a directory
cat file	display a file
less file	display a file a page at a time
head file	display the first few lines of a file
tail file	display the last few lines of a file
grep ‘keyword’ file	search a file for keywords
wc file	count number of lines/words/characters in file

Redirection, Pipes, Wildcards and Getting Help

Redirection

Most processes initiated by UNIX commands write to the standard output (that is, they write to the terminal screen), and many take their input from the standard input (that is, they read it from the keyboard). There is also the standard error, where processes write their error messages, by default, to the terminal screen.

We have already seen one use of the cat command to write the contents of a file to the screen.

Now type cat without specifing a file to read

$ cat

Then type a few words on the keyboard and press the [Return] key.

Finally hold the [Ctrl] key down and press [d] (written as ^D for short) to end the input.

What has happened?

If you run the cat command without specifing a file to read, it reads from standard input (the keyboard), and on receiving the ‘end of file’ character (^D), copies the input to standard output (the screen).

In UNIX, we can redirect both the standard input (stdin) and the standard output (stdout) of commands.

Redirecting the Output <> (redirecting output)>

We use the > symbol to redirect the output of a command. For example, to create a file called list1 containing a list of fruit, type

$ cat > list1

Then type in the names of some fruit. Press [Return] after each one.

pear
banana
apple
^D        # this means press [Ctrl] and [d] to stop

What happens is the cat command reads the standard input (the keyboard) and the > redirects the output, which normally goes to the screen, into a file called list1

To read the contents of the new file, use cat or less.

Exercise

Using the above method, create another file called list2 containing the following fruit: orange, plum, mango, grapefruit. Read the contents of the new file, list2.

Appending to a file <>> (appending output)>

The double greater-than symbol >> appends standard output to a file. So to add more items to the existing file list1, type

$ cat >> list1

Then type in the names of more fruit

peach
grape
orange
^D

To read the contents of the file, type

$ cat list1

You should now have two files: list1 contains six fruit, while list2 contains four.

We will now use the cat command to join (concatenate) list1 and list2 into a new file called biglist. Type

$ cat list1 list2 > biglist

What this is doing is reading the contents of both files list1 and list2 in turn, then outputing the text to the file biglist

To read the contents of this new file, type

$ cat biglist

Redirecting the Input << (redirecting input)>

We use the < symbol to redirect the input of a command.

The command sort alphabetically or numerically sorts a list. Type

$ sort

Then type in the names of some animals. Press [Return] after each one.

dog
cat
bird
ape
^D

The output will be

ape
bird
cat
dog

Using < you can redirect the input to come from a file rather than the keyboard. For example, to sort the list of fruit, type

$ sort < biglist

and the sorted list will be output to the screen.

To output the sorted list to a file, type

$ sort < biglist > slist

Use cat to read the contents of the newly-created file slist.

Pipes <| (pipes)>

To see who is logged into the system along with you, type

$ who

One method to get a sorted list of those names is to type,

$ who > names.txt
$ sort < names.txt

This is a bit slow (two whole steps) and you have to remember to remove the temporary file names when you have finished. As truly lazy/efficient technophiles, what you really want to do is connect the output of the who command directly to the input of the sort command. This is exactly what pipes do. The symbol for a pipe is the vertical bar |.

For example, typing

$ who | sort

will give the same result as above, but quicker and cleaner.

To find out how many users are logged on, you can type

$ who | wc -l

Exercise

Using two pipes, display all lines of list1 and list2 containing the letter “p”, and sort the result.

Wildcards

The * <* (wildcard)> wildcard

The character * is called a wildcard, and will match against none or more character(s) in a file (or directory) name. For example, in your unixstuff directory, type

$ ls list*

This will list all files in the current directory starting with the characters “list”

Try typing

$ ls *list

This will list all files in the current directory ending with “list”

The ? <? (wildcard)> wildcard

The character ? will match exactly one character, So ?ouse will match files like house and mouse, but not grouse.

Try typing

$ ls ?list

File Editing

While it is technically possible to create text files using cat and redirection, these tools are inadequate for creating/editing program text files. A wide variety of text editors exist within the Linux ecosystem; a brief overview of the main editors installed on ManeFrame is given here:

• GEdit – This is a simple graphical text editor that should be familiar to Windows users, since it uses the same keyboard shortcuts as Windows programs (copy/cut/paste/save/find/quit). Newer versions even support syntax highlighting in source code files. GEdit may be launched at the command line via the command gedit

• Nano – This is another simple text editor, but it runs inside the terminal, so it can be used with broken X11-forwarding or with slow network connections. While the keyboard shortcuts differ from Windows, they are listed at the bottom of the screen. Nano may be launched with the command nano.

• Emacs – This is a full-featured editor, that may either be launched as a graphical editor (emacs) or within the terminal (emacs -nw). The keyboard shortcuts differ from Windows, but when launched graphically there are clickable menus.

• VI – This is another full-featured editor that runs within the terminal (vi). Graphical variants of VI exist as well (e.g. gvim) but do not seem to be installed on ManeFrame. The keyboard shortcuts are different from all other editors, and no menu system is available.

I recommend that new users start with GEdit and/or Nano, and

move on to Emacs or VI after they are comfortable with Linux.

Filename conventions

We should note here that a directory is merely a special type of file. So the rules and conventions for naming files apply also to directories.

In naming files, characters with special meanings such as /, *, &, % and , should be avoided. Also, it is best to avoid using spaces within names. The safest way to name a file is to use only alphanumeric characters, that is, letters and numbers, together with _ (underscore) and . (dot).

Good filenames	Bad filenames
project.txt	project
my_big_program.c	my big program.c
fred_dave.doc	fred & dave.doc

File names conventionally end with a dot followed by a group of letters indicating the contents of the file, although this is not at all required in Linux. For example, all files consisting of C code may be named with the ending .c, for example, prog1.c. Then in order to list all files containing C code in your home directory, you need only type ls ~/*.c

Getting Help

On-line Manuals

There are built-in manuals which give information about most commands. The manual pages <man (manual)> tell you which options a particular command can take, and how each option modifies the behaviour of the command. Type “man command” to read the manual page for a particular command.

For example, to find out more about the wc (word count) command, type

$ man wc

Alternatively

$ whatis wc

gives a one-line description <whatis (brief manual)> of the command, but omits any information about options etc.

Apropos <apropos (command search)>

When you are not sure of the exact name of a command, “apropos keyword” will give you the commands with keyword in their manual page header. For example, try typing

$ apropos copy

Redirection, pipes, wildcards and help – summary

Command	Meaning
command > file	redirect standard output to a file
command >> file	append standard output to a file
command < file	redirect standard input from a file
command1 | command2	pipe the output of command1 to the input of command2
cat file1 file2 > file0	concatenate file1 and file2 to file0
sort	sort data
who	list users currently logged in
*	match any number of characters
?	match one character
man command	read the online manual page for a command
whatis command	brief description of a command
apropos keyword	match commands with keyword in their man pages

Permissions and Security

File system security (access rights)

In your unixstuff directory, type

$ ls -l

The -l stands for ‘long’ listing. You will see that you now get lots of details about the contents of your directory, similar to the example below.

File and directory access rights

Each file (and directory) has associated access rights, which may be found by typing ls -l. Also, ls -lg gives additional information as to which group owns the file (beng95 in the following example):

-rwxrw-r-- 1 ee51ab beng95 2450 Sept29 11:52 file1

In the left-hand column is a 10 symbol string consisting of the symbols d, r, w, x, -, and, occasionally, s or S. If d is present, it will be at the left hand end of the string, and indicates a directory: otherwise - will be the starting symbol of the string.

The 9 remaining symbols indicate the permissions, or access rights, and are taken as three groups of 3.

• The left group of 3 gives the file permissions for the user that owns the file (or directory) (ee51ab in the above example);

• the middle group gives the permissions for the group of people to whom the file (or directory) belongs (eebeng95 in the above example);

• the rightmost group gives the permissions for all other users.

The symbols r, w, etc., have slightly different meanings depending on whether they refer to a simple file or to a directory.

Access rights on files

• r (or -), indicates read permission (or otherwise), that is, the presence or absence of permission to read and copy the file

• w (or -), indicates write permission (or otherwise), that is, the permission (or otherwise) to change a file

• x (or -), indicates execution permission (or otherwise), that is, the permission to execute/run a file, where appropriate

Access rights on directories

• r allows users to list files in the directory

• w means that users may delete files from the directory or move files into it

• x means the right to access files in the directory. This implies that you may read files in the directory provided you have read permission on the individual files.

So, in order to read a file, you must have execute permission on the directory containing that file, and hence on any directory containing that directory as a subdirectory, and so on, up the tree.

Some examples

Permissions	Meaning
-rwxrwxrwx	a file that everyone can read, write and execute (and delete)
-rw-------	a file that only the owner can read and write - no-one else can read or write and no-one has execution rights (e.g. your mailbox file)
drwxr-x---	a directory that the owner can read/write/enter, that the group can read/enter, but others are denied access
drwx--x--x	a directory that the owner may read/write/enter, and all others can enter (but do nothing else)

Changing access rights

chmod (change permissions)

Only the owner of a file can use chmod to change the permissions of a file. The options of chmod are as follows

Symbol	Meaning
u	user
g	group
o	other
a	all
r	read
w	write (and delete)
x	execute (and access directory)
	add permission
	take away permission

For example, to remove read write and execute permissions on the file biglist for the group and others, type

$ chmod go-rwx biglist

This will leave the other permissions unaffected.

To give read and write permissions on the file biglist to all,

$ chmod a+rw biglist

Alternatively, you may use a three-digit number to specify the access permissions. The numerical values for the permissions are

Read	Write	Execute
4	2	1

Add up the desired permissions for the user to form the first digit, add up the desired permissions for the group to form the second digit, and add up the desired permissions for others to form the third digit.

For example, to grant read and write permissions to the user (4+2=6), read permissions (4) to the group, and no permissions to others (0), for the file biglist, use the command

$ chmod 640 biglist

Exercise

Try changing access permissions on the file types.h and on the directory backups.

Use ls -l to check that the permissions have changed.