Introduction to Linux

Robert Putnam
Research Computing, IS&T
[email protected]
Introduction to Linux - agenda
 What is Linux?
 The Bash shell
 I/O redirection (pipes, etc.)
 Navigating the file system
 Processes and job control
 Editors
 Hello,world in C
What is
Linux?

The Most Common

O/S Used By BU
Researchers When
Working on a
Server or
Computer Cluster
Where is Linux?
What is Linux?

http://en.wikipedia.org/wiki/Darwin_%28operating_system%29
What is Linux?
 Linux is a Unix* clone begun in 1991 and
written from scratch by Linus Torvalds with
assistance from a loosely-knit team of
hackers across the Net.
 64% of the world’s servers run some variant

of Unix or Linux. The Android phone and the

Amazon Kindle run Linux.

*kernel
What is Linux?
Linux + GNU Utilities = Free Unix

 a set of programs written

 Linux is an O/S core by Richard Stallman and
written by Linus others. They are the GNU
Torvalds and others utilities.
AND http://www.gnu.org/
What is Linux?
gcc
 Bird’s eye view:
wc bash emacs

multitasking

tcsh
device grep
cat
access
Hardware file
system

sh

Kernel awk
sort

Shell

Utilities
What is Linux?
“Small programs that do one thing well”

 From The Unix Programming Environment,

Kernighan and Pike:
… at its heart is the idea that the power of a system comes
more from the relationships among programs than from the
programs themselves. Many UNIX programs do quite trivial
things in isolation, but, combined with other programs,
become general and useful tools.
What is Linux: Selected text
processing utilities
 awk Pattern scanning and processing language
 cat Display file(s)
 cut Extract selected fields of each line of a file
 diff Compare two files
 grep Search text for a pattern
 head Display the first part of files
 less Display files on a page-by-page basis
 od Dump files in various formats
 sed Stream editor (esp. search and replace)
 sort Sort text files
 split Split files
 tail Display the last part of a file
 tr Translate/delete characters
 uniq Filter out repeated lines in a file
 wc Line, word and character count
 tar File archive (similar to zip)
Connecting to a Linux Host – Windows Client
Software

 You need a “xterm” emulation –

software that emulates an “X”
terminal and that connects using the
“SSH” Secure Shell protocol.
◦ Windows
 Recommended: MobaXterm (http
://mobaxterm.mobatek.net/)
 Also available at BU, Xwin32
(http://www.bu.edu/tech/services/
support/desktop/distribution/xwindows/
xwin32/)
Connecting to a Linux Host – Mac OS
X Client Software

◦ Mac OS X
 “Terminal” is already installed
 Why? Darwin, the system on which Apple's Mac OS X
is built, is a derivative of 4.4BSD-Lite2 and FreeBSD.
In other words, the Mac is a Unix system!
 For X11 (graphics), see XQuartz
(http://xquartz.macosforge.org/landing/)
Connecting to a Linux Host -
Windows Client
 MobaXterm
◦ From Windows Desktop
 Double-click MobaXterm_Personal_6.5.exe
 Double-click saved session scc1.bu.edu [SSH]
 Login: <userID>
 Password: <password>
Connecting to a Linux Host -
Mac OS X Client
 Terminal
◦ Type ssh –X scc1.bu.edu or ssh –Y scc1.bu.edu
Get supplementary files
 At the command prompt, type the following:
◦ cd
◦ tar xf /tmp/linux-materials.tar
The Shell
 A shell is a computer program that interprets the commands
you type and sends them to the operating system. On Linux
systems (and others, like DOS/Windows), it also provides a
set of built-in commands and programming control
structures, environment variables, etc.
 Most Linux systems, including BU’s Shared Computing
Cluster, support at least two shells: TCSH and BASH. The
default shell for your account is BASH. (Which is best?
Caution: flame war potential here!)
 “BASH” = “Bourne-again Shell” (GNU version of ~1977 shell written by
Stephen Bourne)
Bash environment variables
 Variables are named storage locations. So-called
“environment variables” are conventionally used by
the shell to store information such as where it
should look for commands (i.e., the PATH).
Environment variables are shared with programs
that the shell runs.
 To see the current value of PATH, do:
◦ echo $PATH
 To see all currently defined environment variables
do:
◦ printenv
Using the Shell
 After you connect, type
◦ shazam # bad command
◦ whoami # my login
◦ hostname # name of this computer
◦ echo “Hello, world” # print characters to screen
◦ echo $HOME # print environment variable
◦ echo my login is $(whoami ) # replace $(xx) with program output
◦ date # print current time/date
◦ cal # print this month’s calendar
 Commands have three parts; command, options and parameters.
Example: cal –j 3 1999. “cal” is the command, “-j” is an option (or
switch), “3” and “1999” are parameters.
 Options have long and short forms. Example:
◦ date –u
◦ date --universal
What is the nature of the prompt?
What was the system’s response to the command?
Command History and Simple
Command Line Editing
 Try the history command
 Choose from the command history by using the
up ↑ and down ↓ arrows
 To redo your last command, try !!
 To go further back in the command history try !,
then the number as shown by history (e.g., !132).
Or, !ls, for example, to match the most recent ‘ls’
command.
 What do the left ← and right → arrow do on the
command line?
 Try the <Del> and <Backspace> keys
Help with Commands
 Type
◦ date –-help
◦ man date
◦ info date
 [And yes, you can always Google it]
 For a list of BASH built-in commands, just

type the command ‘help’

(and see also ‘man bash’)
On using ‘man’ with ‘less’
 The ‘man’ command generally pipes its output
through a pager called ‘less’, which supports
many ways of scrolling through text:
◦ Space, f # page forward
◦ b # page backward
◦ < # go to first line of file
◦ > # go to last line of file
◦ / # search forward (n to repeat)
◦ ? # search backward (N to repeat)
◦ h # display help
◦ q # quit help
Plug: emacs has a man page
mode that is convenient.
I/O redirection with pipes
 Many Linux commands print to “standard
output”, which defaults to the terminal screen.
The ‘|’ (pipe) character can be used to divert or
“redirect” output to another program or filter.
◦w # show who’s logged on
◦ w | less # pipe into the ‘less’ pager
◦ w | grep ‘tuta’ # pipe into grep, which will print only
lines containing ‘tuta’
◦ w | grep –v ‘tuta’ # print only lines not containing
‘tuta’
◦ w | grep ‘tuta’ | sed s/tuta/scholar/g # replace all
‘tuta’ with ‘scholar’
More examples of I/O redirection
 Try the following (use up arrow to avoid retyping
each line):
◦ w | wc # count lines, words, and characters
◦ w | cut –d’ ‘ –f1 | less # extract first column, page with ‘less’
◦ w | cut –d’ ‘ –f1 | sort # sort users (with duplicates)
◦ w | cut –d’ ‘ –f1 | sort | uniq # eliminate duplicates
 We can also redirect output into a file:
◦ w | cut –d’ ‘ –f1 | sort | uniq > users
 Note that ‘awk’ can be used instead of ‘cut’:
◦ w | awk ‘{print $1;}’ | sort | uniq > users
 Quiz:
◦ How might we count the number of distinct users currently logged
in? For extra credit, how can we avoid over-counting by 2? (Hint:
use ‘tail’.)
The Linux File System
 The structure resembles an upside-down tree
 Directories (a.k.a. “folders” in Windows) are

collections of files and other directories.

 Every directory has a parent except for the

root directory.
 Many directories have subdirectories.
 Unlike Windows, with multiple drives and

multiple file systems, a Unix/Linux system

only has ONE file system.
The Linux File System
A Typical Linux File System
Navigating the File System
 Essential navigation commands:
◦ pwd print current directory
◦ ls list files
◦ cd change directory
Navigating the File System
 We use “pathnames” to refer to files and directories in the
Linux file system. There are two types of pathnames:
◦ Absolute – the full path to a directory or file; begins with /
◦ Relative – a partial path that is relative to the current working
directory; does not begin with /
 Special characters interpreted by the shell for filename
expansion:
◦ ~ your home directory (e.g., /usr1/tutorial/tuta1)
◦ . current directory
◦ .. parent directory
◦ * wildcard matching any filename
◦ ? wildcard matching any character
◦ TAB try to complete (partially typed) filename
Navigating the File System
 Examples:
◦ cd /usr/local/lib # change directory to /usr/local/lib
◦ cd ~ # change to home directory (could also
just type ‘cd’)
◦ pwd # print working (current) directory
◦ cd ..
◦ cd / (root directory)
◦ ls –d pro* # (a listing of only the directories starting
with “pro”)
The ls Command
 Useful options for the “ls” command:
◦ ls -a List all files, including hidden files
beginning with a period “.”
◦ ls -ld * List details about a directory and not its
contents
◦ ls -F Put an indicator character at the end of
each name
◦ ls –l Simple long listing
◦ ls –lR Recursive long listing
◦ ls –lh Give human readable file sizes
◦ ls –lS Sort files by file size
◦ ls –lt Sort files by modification time (very useful!)
Some Useful File Commands
 cp [file1] [file2] copy file
 mkdir [name] make directory
 rmdir [name] remove (empty) directory
 mv [file] [destination] move/rename file
 rm [file] remove (-r for recursive)
 file [file] identify file type
 less [file] page through file
 head -n [file] display first n lines
 tail -n [file] display last n lines
 ln –s [file] [new] create symbolic link
 cat [file] [file2…] display file(s)
 tac [file] [file2…] display file in reverse order
 touch [file] update modification time
 od [file] display file contents, esp. binary
Manipulating files and directories
 Examples:
◦ cd (also takes you to your home directory like cd ~)
◦ mkdir test
◦ cd test
◦ echo ‘Hello everyone’ > myfile.txt
◦ echo ‘Goodbye all’ >> myfile.txt
◦ less myfile.txt
◦ mkdir subdir1/subdir2 (FAILS)
◦ mkdir -p subdir1/subdir2 (Succeeds)
◦ mv myfile.txt subdir1/subdir2
◦ cd ..
◦ rmdir test (FAILS)
◦ rm –rf test (Succeeds)
Symbolic links
 Sometimes it is helpful to be able to access a
file from multiple locations within the
hierarchy. On a Windows system, we might
create a “shortcut.” On a Linux system, we
can create a symbolic link:
◦ mkdir foo # make foo directory
◦ touch foo/bar # create empty file
◦ ln –s foo/bar . # create link in current dir.
Finding a needle in a haystack
 The ‘find’ command has a rather unfriendly syntax, but can be
exceedingly helpful for locating files in heavily nested
directories.
 Examples:
◦ find . –name my-file.txt # search for my-file.txt in .
◦ find ~ -name bu –type d # search for “bu” directories in ~
◦ find ~ -name ‘*.txt’ # search for “*.txt in ~
 Quiz:
◦ Can you use find to locate a file called “needle” in your
haystack directory?
◦ Extra credit: what are the contents of the “needle” file?
File access permissions
 Linux files have a set of associated permissions
governing read, write, and execute status for
the owner, members of the owner’s group, and
everyone else. To see a file’s permissions, use
the –l flag to ls:
[tuta0@scc1 ~]$ touch foo
[tuta0@scc1 ~]$ ls -l foo
-rw-r--r-- 1 tuta0 tutorial 0 Sep 4 10:25 foo

group
owner other
Changing file access permissions
with chmod
 We can change a file’s access permissions with
the chmod command. There are a couple of
distinct ways to use chmod. With letters,
u=owner, g=group, o=other, a = all
r=read, w=write, x=execute:
[tuta0@scc1 ~]$ chmod ug+x foo
[tuta0@scc1 ~]$ ls -l foo
-rwxr-xr-- 1 tuta0 tutorial 0 Sep 4 10:03 foo
[tuta0@scc1 ~]$ chmod a-x foo
[tuta0@scc1 ~]$ ls -l foo
-rw-r--r-- 1 tuta0 tutorial 0 Sep 4 10:03 foo
Changing file access permissions
with chmod (cont.)
 The chmod command also works with the following
mappings, read=4, write=2, execute=1, which are
combined like so:
[tuta0@scc1 ~]$ ls -l foo
-rw-r--r-- 1 tuta0 tutorial 0 Sep 4 10:20 foo
[tuta0@scc1 ~]$ chmod 660 foo
[tuta0@scc1 ~]$ ls -l foo
-rw-rw---- 1 tuta0 tutorial 0 Sep 4 10:20 foo
(4+2=6)

 Quiz: What number would denote readable and

executable by owner and group, but just readable
by other?
Bash startup files – dot files
 When bash is started when you log in, a
number of startup files are read. Some are
system files (and are protected), but others
are in your home directory and can be edited
if you wish to customize your environment.
These files generally start with ‘.’, and are
hidden from view unless you use the –a
switch to ls. Try typing ‘ls –al’ now.
.bash_profile, .bashrc, alias
 View .bash_profile (with less, or cat).
◦ This file is executed when you log in.
◦ Note that PATH is set here.
 View .bashrc
◦ This file is executed when a new shell is created.
◦ Note this line: alias rm='rm –i’ (ask for confirmation when
deleting files)
 To remove the alias, edit .bashrc (e.g., with gedit or
emacs or vim) and comment out the alias by placing ‘#’
at the beginning of the line. This will take effect the next
time a bash shell is created. (For an immediate effect,
type ‘unalias rm’.) Type ‘which rm’ or ‘type rm’ to see
whether the alias is currently in effect. To see all current
aliases, type ‘alias’.
Processes and job control
 As we interact with Linux, we create numbered
instances of running programs called “processes.”
You can use the ‘ps’ command to see a listing of
your processes (and others!). To see a long listing,
for example, of all processes on the system try:
◦ ps -ef
 To see all the processes owned by you and other
members of the class, try:
◦ ps –ef | grep tuta
 To see the biggest consumers of CPU, use the top
command (which refreshes every few seconds):
◦ top
Foreground/background
 Thus far, we have run commands at the
prompt and waited for them to complete. We
call this running in the “foreground.” It is
also possible, using the “&” operator, to run
programs in the “background”, with the result
that the shell prompts immediately without
waiting for the command to complete:
◦ $ mycommand &
◦ [1] 54356 -------- process id
◦ $
Process control
 To get experience with process control, let’s
look at the “countdown” script, in your scripts
folder:
◦ cd ~/linux-materials/scripts
◦ cat countdown
 Make the script executable with chmod:
◦ chmod +x countdown
 First, run it for a few seconds, then kill with
Control-C.
Process control
 Now, let’s try running it in the background
with &:
◦ countdown 20 &
 The program’s output is distracting, so
redirect it to a file:
◦ countdown 20 > c.txt &
 Type ‘ps’ to see your countdown process.
 Also, try running ‘jobs’ to see any jobs

running in the background from this bash

shell.
Process control
 To kill the job, use the ‘kill’ command, either
with the five-digit process id:
◦ kill 56894 #for example
 Or, you can use the job number, with ‘%’:
◦ kill %1 #for example
Backgrounding a running job with
C-z and ‘bg’
 Sometimes you start a program, then decide
you want to run it in the background. Here’s
how:
◦ countdown 200 > c.out
◦ Press C-z to suspend the job.
◦ Type ‘bg’ at the command prompt.
◦ The job is now running in the background. To
bring it back to the foreground, type ‘fg’ at the
command prompt.
Regular expressions
 Many Linux tools, such as grep and sed, use
strings that describe sequences of characters.
These strings are called regular expressions.
(In fact, grep is an acronym for “general
regular expression parser”.) Here are some
examples:
◦ ^foo # line begins with “foo”
◦ bar$ # line ends with “bar”
◦ [0-9]\{3\} # 3-digit number
◦ .*a.*e.*i.*o.*u.* # words with vowels in order*

*to apply this against a dictionary, run

~/linux-materials/scripts/vowels.sh
File Editors
 emacs
◦ Swiss-army knife, has modes for all major languages, and can
be customized ad infinitum (with Emacs lisp). Formerly steep
learning curve has been reduced with introduction of menu
and tool bars. Can be used under Xwindows or not.
 vim
◦ A better version of ‘vi’ (an early full-screen editor). In the right
hands, is efficient, fast. Still popular among systems
programmers. Non-Xwindows.
 gedit
◦ Notepad-like editor with some programming features (e.g.,
keyword highlighting). Requires Xwindows.
 Nano
◦ Lightweight editor. Non-Xwindows.
“Hello, world” in C
 cd to “~/linux-materials/c”, and read hello.c
into your editor of choice.
 Modify the text on the printf line between “[“

and “]” and save the file.

 Produce an executable file called “hello” by

compiling the program with gcc:

◦ gcc –o hello hello.c
 Run the program at the command line:
◦ hello
 Optional: modify countdown script to run hello
program
Obtaining the Supplementary Course
Material
 In browser, search for “SCV tutorials” (or go to
http://www.bu.edu/tech/support/research/training
-consulting/live-tutorials
/), scroll to Introduction to Linux and select “Cheat
Sheets”.
 See also other Linux tutorials:
◦ http://www.tutorialspoint.com/unix/
◦ Edx Linux intro [Google “edx linux”]
◦ http://www.cse.sc.edu/~okeefe/tutorials/unixtut/
Questions?