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Lecture 2- the Linux operating
system
CLI (Command line Interface) vs
GUI (Graphical User Interface)
PHYS 5P10— Introduction To Scientific Computing
PHYS 5P10— Introduction To Scientific Computing
• Linux is a Unix clone written from scratch by Linus
Torvalds with assistance from a loosely-knit team of
hackers across the Net.
• Unix is a multitasking, multi-user computer operating
system originally developed in 1969 by a group of
AT&T employees at Bell Labs.
• 64% of the world’s servers run some variant of Unix
or Linux. The Android phone and the Kindle run Linux.
PHYS 5P10— Introduction To Scientific Computing
What is Linux?
Linux + GNU Utilities = Free Unix
• Linux is an O/S core
written by Linus Torvalds
and others AND
What is Linux?
• a set of small programs
written by Richard
Stallman and others. They
are the GNU utilities.
http://www.gnu.org/
Linux Has Many Distributions
The computers that we use have redhat.
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Linux/Unix Architecture
What is Linux?
“Small programs that do one thing well”
These are all programs/tasks that can be run from the command line:
•
• Kernel: The heart of the operating system
 It interacts with hardware.
 Memory management, task scheduling and
file management.
• Shell: The utility that processes your requests.
 the shell interprets the command and calls
the program that you want.
• Commands and Utilities:
 Eg: cp, mv, cat and grep etc.
• Files and Directories:
 All data in UNIX is organized into files.
 All files are organized into directories.
 These directories are organized into a treelike structure called the filesystem.
PHYS 5P10— Introduction To Scientific Computing
In order to interact with the system using the command
line, one must open a terminal window :
• Network: ssh, scp, ping, telnet, nslookup, wget
• Shells: BASH, TCSH, alias, watch, clear, history, chsh, echo, set,
setenv, xargs
• System Information: w, whoami, man, info, which, free, echo,
date, cal, df, free, man, info
• Command Information: man, info
• Symbols: |, >, >>, <, &, >&, 2>&1, ;, ~, ., .., $!, !:<n>, !<n>
• Filters: grep, egrep, more, less, head, tail
• Hotkeys: <ctrl><c>, <ctrl><d>
• File System: ls, mkdir, cd, pwd, mv, ln, touch, cat, file, find, diff,
cmp, /net/<hostname>/<path>, mount, du, df, chmod, find
• File Editors: vim,emacs, gedit
PHYS 5P10— Introduction To Scientific Computing
In order to interact with the system using the command
line one must open a terminal window :
Window in which commands are entered
PHYS 5P10— Introduction To Scientific Computing
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UNIX: The Shells
• The “Shell” is simply another program which provides
a basic human-OS interface.
• Shells can run interactively or as a shell script
• Two main ‘flavors’ of Shells:
• Bourne created what is now known as the standard shell:
“sh”, or “bourne shell”. It’s syntax roughly resembles Pascal.
It’s derivatives include “ksh” (“korn shell”) and now, the
most widely used, “bash” (“bourne shell”), which is what
we use.
• One of the creators of the C language implemented the
shell to have a “C-programming” like syntax. This is called
“csh” or “C-shell”. Today’s most widely used form is the
very popular “tcsh”.
PHYS 5P10— Introduction To Scientific Computing
The Linux File System
UNIX Shell
The shell sits between you and the operating
system, acting as a command interpreter.
It reads your terminal input and translates the
commands into actions taken by the system. The
shell is analogous to command.com in DOS.
When you log into the system you are given a
default shell.
When the shell starts up it reads its startup files
and may set environment variables, command
search paths, and command aliases, and executes
any commands specified in these files.
PHYS 5P10— Introduction To Scientific Computing
Unix/Linux File System
NOTE: Unix file names
are CASE SENSITIVE!
• file system is a hierarchical directory structure
• The structure resembles an upside down tree
• Directories are collections of files and other directories.
The structure is recursive with many levels.
• Every directory has a parent except for the root directory.
• Many directories have children directories.
• Unlike Windows, with multiple drives and multiple file
systems, a Linux system only has ONE file system.
• The Linux Standard Base (LSB) specifies the structure of a
Linux file system.
/home/mary/
/home/john/portfolio/
The Path
PHYS 5P10— Introduction To Scientific Computing
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Typical Linux directories
Pathnames
• /bin System binaries, including the command shell
bin
• /boot Boot-up routines
boot
• /dev Device files for all your peripherals
dev
etc
• /etc System configuration files
home
• /home User directories
lib
• /lib Shared libraries and modules
• /lost+found Lost-cluster files, recovered from a disk-check
lost+found
/
misc
• /mnt Mounted file-systems
mnt
• /opt Optional software
opt
•/proc Kernel-processes pseudo file-system
proc
• /root Administrator’s home directory
• /sbin System administration binaries
• Absolute Pathnames
• In the previous tree
/users/usern/file1 is
an absolute
pathname
• Relative pathnames
• If you are already in
the users directory,
the relative
pathname for file1 is
usern/file1
root
sbin
tmp
•/usr User-oriented software
usr
• /var Various other files: mail, spooling and logging
var
PHYS 5P10— Introduction To Scientific Computing
More on UNIX paths
 “~” (tilda) points to the user’s home directory.
Useful if you are logging into a workstation with
many users.
 Many of the other paths are inaccessible and
unimportant to you
 ~ is the default working directory when you log in.
 If you are user “usern”, then /users/usern/file1 is the
same as ~/file1.
 “.” refers to the current directory
 “..” refers to the parent directory.
PHYS 5P10— Introduction To Scientific Computing
UNIX Commands
A command is a program which interacts with the
kernel to provide the environment and perform the
functions called for by the user.
A command can be: a built-in shell command; an
executable shell file, known as a shell script; or a
source compiled, object code file.
The shell is a command line interpreter. The user
interacts with the kernel through the shell. You can
write ASCII (text) scripts to be acted upon by a
shell.
 If you are in /users/usern/, then ../ refers to /users/.
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Basic Commands
Command
Anatomy of a Linux Command
Meaning
ls (-artlh)
list files and directories
mkdir
make a directory
cd directory
change to named directory
pwd
display the path of the current directory
mv file1 file2
move or rename file1 to file2
cp file1 file2
copy file1 and call it file2
rm file
remove a file
rmdir
remove a directory
cat file
display a file
less file
display a file one page a time
head/tail file
display the first/last few lines of a file
PHYS 5P10— Introduction To Scientific Computing
$ ls -l -r -s
/tmp
 ls (command or utility or program)
 -l -r -s (options, or flags –control the flavors of the
command)
 /tmp (argument – what is been operated on)
PHYS 5P10— Introduction To Scientific Computing
Navigation
Directory and file operations
• Commands: cd, ls, and pwd
• Create a new directory
cd /
cd /tmp
ls
ls q*
pwd
ls -l
cd ~
• mkdir mydir1
• Create a new file in a directory
• cd mydir1
• gedit file1.txt
• Copy a file
• cp file1.txt file1_copy.txt
• Delete a file or directory
• rm file1_copy.txt
• rm -r folder1
PHYS 5P10— Introduction To Scientific Computing
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Directory and file operations
• Rename a file or folder
• mv file1.txt file12.txt
• mv folder1 folder2
• Move file from one folder to another
• mv folder1/file1.txt folder2
• Compress files
• gzip, and gunzip
Command History and Simple
Command Line Editing
• Try the history command
• Try <Ctrl><r> (only works in BASH shell)
• Choose from the command history by using the up ↑
and down ↓ arrows
• What do the left ← and right → arrow do on the
command line?
• Try the <Del> and <Backspace> keys
PHYS 5P10— Introduction To Scientific Computing
PHYS 5P10— Introduction To Scientific Computing
Command: ls
Command: ls
• ls has many options
• More useful options for the “ls” command:
•
•
•
•
•
-l long list (displays lots of info)
-t sort by modification time
-S sort by size
-h list file sizes in human readable format
-r reverse the order
• “man ls” for more options
• Options can be combined: “ls -ltr”
PHYS 5P10— Introduction To Scientific Computing
• ls -a List all file including hidden file 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 –lh Give human readable file sizes
• ls –lS Sort files by file size
• ls –lt Sort files by modification time
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Wildcards
Creating files in Unix/Linux
• You can substitute the * as a wildcard symbol
for any number of characters in any filename.
• If you type just * after a command, it stands for
all files in the current directory:
lpr * will print all files
• You can mix the * with other characters to form
a search pattern:
ls a*.txt
end in “.txt”
will list all files that start with “a”
•
•
Requires the use of an Editor
Various Editors:
Can open these from the GUI
1) gedit
as well as from the command
2) emacs
line
3) vi
and
• The “?” wildcard stands for any single character:
cp draft?.doc
will copy draft1.doc, draft2.doc,
draftb.doc, etc.
PHYS 5P10— Introduction To Scientific Computing
Opening gedit from the GUI:
PHYS 5P10— Introduction To Scientific Computing
Displaying a text file
• Various ways to display a file in Unix
•
•
•
•
•
PHYS 5P10— Introduction To Scientific Computing
cat
more
head
tail
less
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Command: cat
• Dumps an entire file to standard output
• Good for displaying short, simple files
Command: more
• Dumps an entire file to standard output, but one
screen at a time
• Press on the tab to display the next screen of output
PHYS 5P10— Introduction To Scientific Computing
Command: head
• “head” displays the top part of a file
• By default it shows the first 10 lines
• -n option allows you to change that
• “head -n50 file.txt” displays the first 50 lines of
file.txt
Command: tail
• “tail” displays the bottom part of a file
• Works similarly to head
PHYS 5P10— Introduction To Scientific Computing
Command: less
File Commands
• “less” displays a file, allowing forward/backward
movement within it
• Copying a file: cp
• Move or rename a file: mv
• Remove a file: rm
• return scrolls forward one line, space one page
• y scrolls back one line, b one page
• use “/” to search for a string
• Press q to quit
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Command: rm
File permissions
• To remove a file “recursively”: rm –r
• Used to remove all files and directories
• Be very careful, deletions are permanent in
Unix/Linux
• Each file in Unix/Linux has an associated permission
level
• This allows the user to prevent others from
reading/writing/executing their files or directories
• Use “ls -l filename” to find the permission level of that
file
PHYS 5P10— Introduction To Scientific Computing
PHYS 5P10— Introduction To Scientific Computing
File and Directory Ownership and
Permissions
File System Ownership and
Permissions
• Try
• All files and directories have a individual and a group
ownership.
• All files and directories have read (r), write (w), and
execute (x) permissions assigned as octets to the
individual owner (u), the group (g) owner and all
others (o) that are logged into the system.
• You can change permissions if you are the individual
owner or a member of the group.
• Only root can change ownership.
•
•
•
•
•
•
•
•
•
•
•
•
cd
touch myfile (create file)
mkdir mydir (create directory)
ls –l myfile (examine file)
ls –ld mydir (examine directory)
chmod g+w myfile (add group write permission)
ls –l myfile
chmod ugo+x myfile (add user, group and other execute permission)
ls –l myfile
chmod ugo+w mydir (add user, group and other write permission)
ls –ld mydir
chmod a-w (a=ALL, remove user, group and other write permission)
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Permission levels
• “r” means “read only” permission
• “w” means “write” permission
• “x” means “execute” permission
Command: chmod
• If you own the file, you can change it’s permissions with
“chmod”
• Syntax: chmod [user/group/others/all]+[permission] [file(s)]
• Below we grant execute permission to all:
• In case of directory, “x” grants permission to list directory
contents
A file must be converted to executable before it
can be run as a program.
PHYS 5P10— Introduction To Scientific Computing
File Permissions
PHYS 5P10— Introduction To Scientific Computing
UNIX: More Standard Commands
echo: print out a string
echo “$HOME is where I want to be”
whereis: Show where a file can be found
printenv: Display all environment variables
grep: Get Regular Expression and Print
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UNIX: More Standard Commands
Whereis command is helpful to locate binary, source and manual pages of
commands in the Linux system. It is very simple utility and provides several
options which are given below with examples.
$ whereis open
open: /bin/open /usr/share/man/man1/open.1.gz /usr/share/man/man2/open.2.gz
If we want to locate binary of Linux command, use “-b” option.
$ whereis -b whereis
whereis: /usr/bin/whereis /usr/bin/X11/whereis
• wc: (word count) simply counts the number of words,
lines, and characters in the file(s).
wc [-clw] [file1 file2 ... fileN]
• The three parameters, clw, stand for character, line, and
word respectively, and tell wc which of the three to count.
• cmp: compares two files.
• The first must be listed on command line, while the second
is either listed as the second parameter or is read in form
standard input.
• cmp is very simple, and merely tells you where the two files
first differ.
cmp file1 [ file2]
PHYS 5P10— Introduction To Scientific Computing
UNIX: More Standard Commands
• One of the most complicated standard unix commands is
called diff.
• The GNU version of diff has over twenty command line
options. It is a much more powerful version of cmp and
shows you what the differences are instead of merely
telling you where the first one is.
diff file1 file2
• touch will update the time stamps of the files listed on
the command line to the current time.
PHYS 5P10— Introduction To Scientific Computing
UNIX: More Standard Commands
•
•
•
•
•
•
•
•
•
time
date
test
tee
sdiff
sort
gzip
gunzip
strings
How long your program took to run
print out current date/time
Compare values, existence of files, etc
Replicate output to one or more files
Report differences side-by-side
Sort a file line by line
Compress a file
Uncompress it
Print out ASCII strings from a (binary)
• If a file doesn’t exist, touch will create it.
PHYS 5P10— Introduction To Scientific Computing
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The tar command
The following command writes the output only to
the file and not to the screen.
$ ls > file
The following command (with the help of tee
command) writes the output both to the screen
(stdout) and to the file.
$ ls | tee file
Multiple files
$ ls | tee file1 file2 file3
PHYS 5P10— Introduction To Scientific Computing
The tar command
Once you have an archive, you can extract it with the tar
command. The following command will extract the contents
of archive.tar.gz to the current directory.:
tar -xzvf archive.tar.gz
It’s the same as the archive creation command we used
above, except the -x switch replaces the -c switch. This
specifies you want to extract an archive instead of create
one.
You may want to extract the contents of the archive to a
specific directory. You can do so by appending the -C switch
to the end of the command. For example, the following
command will extract the contents of the archive.tar.gz file to
the /tmp directory:
tar -xzvf archive.tar.gz -C /tmp
PHYS 5P10— Introduction To Scientific Computing
Use the following command to compress an entire directory
or a single file on Linux. It’ll also compress every other
directory inside a directory you specify–in other words, it
works recursively:
tar -czvf name-of-archive.tar.gz /path/to/directory-or-file
Here’s what those switches actually mean:
-c: Create an archive.
-z: Compress the archive with gzip.
-v: Display progress in the terminal while creating the
archive, also known as “verbose” mode. The v is always
optional in these commands, but it’s helpful.
-f: Allows you to specify the filename of the archive.
PHYS 5P10— Introduction To Scientific Computing
Control characters
• You type Control characters by holding down
the ‘control’ key while also pressing the
specified character.
• While you are typing a command:
• ctrl-W erases the previous word
• ctrl-U erases the whole command line
• Control commands that work (almost) any time
• ctrl-S suspends (halts) output scrolling up on your terminal
screen
• ctrl-Q resumes the display of output on your screen
• ctrl-C will abort any program
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Setting the path:
Help with Commands
At the shell prompt, type:
PATH=$PATH:/path/to/dir1; export PATH
Export works like set
• Type
• man command
• help command
• info command
• And “Yes,” you can always Google it
$ export MYAPP=1
Verify that the environment variable is set properly using the echo command.
$ echo $MYAPP 1
To export variables permanently, you can add the export command in any of the
following start-up files
:~/.profile
~/.bash_profile
/etc/profile
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