Introduction to the

Linux Command Line
Ken Weiss
HITS Computational Research Consulting Division
 A word from our sponsor…
This class is brought to you courtesy of:

Advanced Research Computing – Technical Services
ARC‐TS

For more information please click on:
http://arc‐ts.umich.edu

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 Roadmap
The command shell
Navigating the filesystem
Basic commands & wildcarding
Shell redirection & pipelining
Editing text files
Permissions
Processes
Environment variables and customizing your session

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 Course Text

William E Shotts, Jr.,
“The Linux Command Line: A 
Complete Introduction,”
No Starch Press, January 2012.

Download Creative Commons Licensed version at 
http://downloads.sourceforge.net/project/linuxcommand
/TLCL/13.07/TLCL‐13.07.pdf.  
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 The command shell

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 What you are used to using

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 What you will be using

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 The command shell
The command shell is an application that reads command lines 
from the keyboard and passes them to the Linux operating 
system to be executed.
When you login to a remote Linux system, using a tool like 
ssh, you will automatically be connected to a shell.
Your computing session is kept separate from other user’s 
computing sessions, because they are “enclosed” in a 
“shell”.
On your desktop, laptop, or tablet, you may have to find and 
execute a terminal emulator application to bring up a shell in 
a window.
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 The command shell

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http://askubuntu.com/questions/161511/are-the-linux-utilities-parts-of-the-kernel-shell
 The command line
A basic way of interacting with a Linux system
Execute commands
Create files and directories
Edit file content
Access the web
Copy files to and from other hosts
Run HPC jobs

… do things you can’t do from the conventional point‐
and‐click Graphical User Interface (GUI)

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 Why command line?
1. Linux was designed for the command line
2. You can create new Linux commands using the command 
line, without programming
3. Many systems provide only the command line, or poorly 
support a GUI interface
• Such as most HPC systems
4. Many things can be accomplished only through the 
command line
• Much systems administration & troubleshooting
5. You want to be cool

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 Connecting via ssh
Terminal emulators
Linux and Mac OS X
Start Terminal
Use ssh command
Windows
U-M Compute at the U (Get Going)
http://its.umich.edu/computing/computers-software/compute
PuTTY
http://www.chiark.greenend.org.uk/~sgtatham/putty/

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 Logging in to a host
We will be using the host: linux‐training.arc‐ts.umich.edu for 
our class.
For Mac or other Linux workstation, from a terminal window 
type:   ssh uniqname@linux‐training.arc‐ts.umich.edu
On a PC, start PuTTY. In the 
“Host Name (or IP address)” box
type: 
linux‐training.arc‐ts.umich.edu
Click on the “Open” button.
Once connected, you will see:
“login as:”. Type in your
uniqname and press: enter
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 Logging in to a host
You will be prompted:
“uniqname@linux‐training.arc‐ts.umich.edu's password:”
Enter your Level 1 password and press enter.
You are now logged into a shell on the linux‐training host
Your shell prompt looks like this:
uniqname@training:~$

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 The shell prompt
The “uniqname@training:~$“ is the shell prompt
This means the shell is waiting for you to type 
something
Format can vary, usually ends with “$” , “%” or “#”
If $ or %, you have a normal shell
This shell has your privileges
If #, you have a so‐called “root shell”
This shell has administrator privileges
You can do a great deal of irreversible damage

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 Typing into the shell
Basic input line editing commands
Backspace erases previous character
Left and right arrow move insertion point on the line
Control‐c interrupts whatever command you started and returns 
you to the shell prompt (usually)
Control‐u erases the line from the beginning to the cursor
Control‐k erases the line from the cursor to the end
Enter executes the line you typed
Up and down arrow will access your command history
Type “exit” and press Enter without the quotes to exit the shell
Click the red "close" icon at the top of the Terminal window to close 
it (on a Mac)

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 Lab 1
Task:  Enter some basic commands
~$ date
~$ id
~$ ps
~$ df ‐kh
~$ who
~$ top # type Control‐c or q to exit
~$ history

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 Navigating the filesystem

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 Linux Filesystem Concepts

Files are stored in a directory (think: folder)

Directories may contain other directories as
well as files
A hierarchy of directories is called a directory
tree
A directory tree (a connected graph with no
cycles) has a single, topmost root directory
A directory tree, rooted at the system root
directory “/”, is called a filesystem

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 A Linux Filesystem

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 Linux Filesystem Concepts
A file is accessed using its path name
Absolute path name
/dir1/dir2/…/dirn/filename
/usr/X11R6/bin
Relative path name
current‐working‐directory/filename
bin
Every shell maintains a notion of a current working directory
Initialized at login to your home directory
Changed via cd command
Two special directories
. refers to the current directory
.. refers to the current directory’s  parent directory
Many ways to get “home”
~ refers to your home directory
$HOME is a synonym for ~
~username refers to a user’s home directory
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 Basic commands

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 Prerequisites
Some fundamental commands:
~$ file file # what kind of file is file?
~$ cat file # display contents of text file
~$ less file # paginate text file
~$ man command # get info about command

Exercise:  figure out how to make the date command 
display the date in Coordinated Universal Time (UTC)

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 Navigating the filesystem
Some fundamental commands:
~$ pwd # print working directory
~$ cd dir # make dir the current working directory
~$ cd  # cd to your home dir
~$ cd ~cja # cd to cja’s home dir
~$ mkdir dir # create directory dir
~$ rmdir dir # remove (empty) directory dir
~$ rm ‐fR dir # remove directory dir (empty or not)
~$ tree # display dir tree

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 Lab 2
Task:  navigate the file system
Commands:
~$ cd  # make your home directory 
the current working directory
~$ pwd # print working directory
~$ mkdir foo # create directory foo
~$ cd foo # cd to the foo directory
~$ mkdir bar # create directory bar
~$ cd .. # go up one level in the directory tree 
~$ tree foo # display foo’s directory tree.
(Use tree ‐A in PuTTY)

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 Listing info on files
ls – list information about files
~$ ls # list contents of cur dir
~$ ls dir # list contents of dir
~$ ls ‐l # list details of files in cur dir
including access, owner & group,
size, and last‐modified time
~$ ls ‐t # list newest files first
~$ ls ‐R dir # list all files in tree dir
~$ ls ‐lt dir # options can be combined
~$ ls ‐hl dir # list all files in human readable 
format

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 Working with files
These commands manipulate files
~$ mv big large # rename file big to large
~$ cp big large # copy file big to large
~$ cp ‐r dir1 dir2 # copy dir tree dir1 to dir2
~$ cp f1 f2 dir # copy file1 and file2 to directory dir
~$ mkdir dir # create empty directory dir
~$ rmdir dir # remove empty directory dir
~$ rm file # remove file file
~$ rm ‐r dir # remove directory tree dir

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 Lab 3
Exercise:
Create a directory named tutorial in your home 
directory.  In that directory, create a directory named 
sample and a directory named test .  Create a file 
named msg in directory test that contains a copy of the 
file /etc/os‐release.
Extra credit:  Make the last‐modified time of your copy 
identical to that of /etc/os‐release.  Hint:  look at the 
options of the copy command

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 Permissions

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 File Permissions
Three permission bits, aka mode bits
Files: Read, Write, EXecute
Directories: List, Modify, Search
Three user classes
User (File Owner), Group, Other
man chmod

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 File Permissions

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http://www.csit.parkland.edu/~smauney/csc128/fig_permissions.jpg
 File Permissions, examples

‐rw‐‐‐‐‐‐‐ cja lsait 40 Oct 1 12:03 foo.bz2

file read and write rights for the owner, no access for
anyone else
chmod u=rw,g=r,o= file
‐rw‐r‐‐‐‐‐ cja lsait 40 Oct 1 12:03 foo.bz2
file read and write rights for the owner, read for
members of the lsait group and no access for others
drwxr‐x‐‐x cja lsait 4096 Oct  1 12:15 bar
list, modify, and search for the owner, list and search
for group, and execute only for others

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 Lab 4
Task:  copy sample files for further exercises
Commands:
~$ cd  # make your home directory 
the current working directory
~$ pwd # print working directory to verify you
are in your home directory
~$ mkdir training # create directory training
~$ cd training # cd to the training directory
~$ cp ‐rf /data/examples/IntroLinux/. . 
# copies sample files to training directory

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 Compression, archiving & 
wildcards

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 Compressing and archiving
These commands compress and archive files
~$ gzip foo # compress foo to foo.gz
~$ gunzip foo # uncompress foo.gz to foo
~$ bzip2 foo # better compress foo to foo.bz2
~$ bunzip2 foo # uncompress foo.bz2 to foo

~$ tar ‐cf foo.tar bar   # archive subtree bar in file foo.tar

~$ tar ‐xf foo.tar # restore archive from file foo.tar
~$ tar ‐tf foo.tar # list files in archive file foo.tar
~$ tar ‐zcf foo.tgz bar  # archive and compress
~$ tar ‐jcf foo.tjz bar  # archive and compress better

Exercise:  Archive and compress the files in the training directory to a file 
named examples_train.tgz

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 Wildcards
The shell accepts wildcarded arguments
This is also called "shell globbing"
Wildcards:
? Matches a single character
* Matches zero or more characters
[chars] Matches any of the chars
[c1‐c2] Matches chars ‘c1’ through ‘c2’
[^chars] Matches any but the chars
~$ ls foo.? # match files named foo.x, where x 
is any character
~$ echo *.[cs] # echo files that end in .c or .s
~$ mv [o‐z]* save # move files starting with o through
z to directory save
~$ echo [^A‐Z]? # ??? 

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 Shell redirection & 
pipelining

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 Shell redirection
A Linux command can have its inputs and outputs redirected
~$ ls >myfiles # put list of files in current
directory into file myfiles
~$ ls >>filelist # add list of files in current
directory to end of file filelist
~$ sort <grocery.list # sort lines from file grocery.list
~$ sort <<EOF  # sort lines entered at keyboard
whiskey # (this is a “here document”)
bravo
tango
EOF
~$ wc ‐l </etc/os‐release >~/mycounts
# count number of lines from file
/etc/os‐release and put result in
file mycounts in my home directory

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 More Linux commands
More useful Linux tool commands
~$ grep string # show lines of input containing
string
~$ tail # show last few lines of input
~$ head # show first few lines of input
~$ sort # sort the input
~$ du ‐sh # report the size of the current directory
~$ du ‐sh dir # report the size of directory dir
~$ who # gives a list of the users currently
logged in
~$ cut ‐cxx‐yy # keep the output from a command starting 
at the xx character in the line and ending
at the yy character

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 Shell pipelining
A Linux command can have its output connected to the 
input of another Linux command
~$ ls | wc –l # count files in current
directory
~$ last | grep reboot # when did we reboot?

Exercises:
How many users are currently logged in? 
How many unique user IDs are currently logged in? 

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 Editing text files

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 Editing text files

Simple editor
nano
"What you see is what you get” editor
Simple to learn if you want to get started quickly
No mouse support. Arrow keys for navigation
Supported editors
vi or vim
emacs
Powerful but more complex
If you have time and inclination to become proficient,
spend time here

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 Text files
Watch out for source code or data files 
written on Windows systems
Use these tools to analyze and convert source 
files to Linux format
file
dos2unix
unix2dos

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 File Transfers

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 File Transfers
Eventually, you will need to move/copy files to and from your computer and a 
server/workstation/cluster. You can do this using the secure copy command (scp) in a terminal 
window.
To transfer files (i.e. foobar.txt) FROM your local host TO a remote host use:
~$ scp foobar.txt [email protected]:/some/remote/directory

To transfer files (i.e. foobar.txt) FROM a remote host TO your local host use:
~$ scp [email protected]:foobar.txt /some/local/directory
To copy a directory, repeat as above adding the ‐r flag. (~$ scp ‐r … )

Graphical, drag‐and‐drop scp programs are available for Windows and Mac platforms. 
(WinSCP – Windows, Cyberduck – Mac)
Demonstration
I will Copy the file headtail.txt from the training directory to /home/kgweiss
directory using SCP on the remote host flux‐xfer.arc‐ts.umich.edu
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 Processes

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 Processes
Modern operating systems are usually multitasking, meaning that
they create the illusion of doing more than one thing at once by
rapidly switching from one executing program to another. The
Linux kernel manages this through the use of processes. Processes
are how Linux organizes the different programs waiting for their
turn at the CPU.
On Linux, every program runs in a process
You can examine these processes

man ps
ps
ps ax
top

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 Processes

You can signal a running process

To stop it, or "kill" it

man kill

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 Additional commands
~$ quota ‐Q ‐s $USER # show disk quota for $USER
~$ grep “sometext” somefile # find & print sometext if found
in somefile
~$ history # displays last n commands entered
(execute again with !###)
~$ clear # clears the screen
~$ diff ‐w file1 file2 # compare file1 with file2 
ignoring all white space
~$ which command # prints the full path to command
~$ acommand | tee filename # takes the results from acommand and 
prints them to the screen and to 
the file filename
(Use tee –a to append to filename)
~$ source filename # reads and executes the commands contained 
in filename

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 Environment Variables and 
Customizing Your Session

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 Environment Variables
An environment variable is a named object that contains data used by 
one or more applications. In simple terms, it is a variable with a name 
and a value.
The convention in Linux is for the environment variable to be all 
uppercase letters.
To use an environment variable, prefix the variable name with $
You can see the value of an environment variable by typing: 
~$ echo $VARIABLENAME
You can see all the environment variables defined for your session 
by typing: ~$ env
You can set an environment variable by typing: 
~$ export VARIABLENAME = value

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 Common Environment
Variables
USER # $USER ‐‐> user login name
PATH # $PATH ‐‐> a list of  
directories to look into for programs
and files
HISTSIZE # $HISTSIZE ‐‐> number of commands
to keep in history
HOSTNAME # $HOSTNAME ‐‐> fully enumerated host name
HOME # $HOME ‐‐> home directory of the user
TERM # $TERM ‐‐> terminal type
SHELL # $SHELL ‐‐> shell type you are using

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 Customizing Your Session
You can modify certain aspects of your session to do your work in 
terms that are easier/more useful for you. See chapter 11 in Schott’s 
book
Changes can be made in ~/.bashrc file.
It is recommended that you use an external file, (in our class, 
~/training/.custom) and then source it from the .bashrc file
You can:
Set an alias
Export an environment variable
Change directories
Execute a Linux command or an external program
Exercises
1) Modify the .custom file in the training directory creating a new alias named ‘llh’ 
that gives a directory listing in human readable file sizes
2) Create a new environment variable CLASS that points to your training directory
3) Source this file and see if your customizations worked
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 Any Questions?
Ken Weiss
Health Information Technology & Services
[email protected]
arc‐workshop‐[email protected]
734 763 7503

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 References
1. http://en.wikipedia.org/wiki/History_of_Linux
2. http://www.openbookproject.net/tutorials/getdown/unix/lesson2.html
3. William E Shotts, Jr., “The Linux Command Line: A Complete Introduction,” No Starch 
Press, January 2012.  Download Creative Commons Licensed version at 
http://downloads.sourceforge.net/project/linuxcommand/TLCL/13.07/TLCL‐13.07.pdf.  
4. Learning the nano editor
1. The nano text editor ‐ https://www.lifewire.com/beginners‐guide‐to‐nano‐editor‐
3859002
2. Beginners guide to nano ‐ http://www.howtogeek.com/howto/42980/the‐
beginners‐guide‐to‐nano‐the‐linux‐command‐line‐text‐editor/
5. Learning the VI editor
1. VIM Adventures ‐ http://vim‐adventures.com/
2. Graphical cheat sheet ‐ http://www.viemu.com/vi‐vim‐cheat‐sheet.gif
3. Interactive VIM tutorial ‐ http://www.openvim.com/

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 Have a Nice Day

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