Essentials for Scienti_c Computing:

Introduction to UNIX and Linux

Day 1
Ershaad Ahamed
TUE-CMS, JNCASR
May 2012
1 Operating Systems
Computers consist of one or more CPUs, memory and peripheral devices. The
CPU fetches instructions from memory and executes them. When a computer
boots up, the _rst instructions that it fetches and executes is from the BIOS.
These instructions direct the CPU in various stages to eventually load the op-
erating system and execute it. From that point onwards the operating system
(or speci_cally the kernel) runs at all times and has the following functions.
1. Hardware abstraction
2. Resource management and multitasking
3. Standardised interfaces
1.1 Hardware Abstraction
The manner in which hardware is instructed to perform their speci_c functions
is highly dependent on the hardware itself. This in turn depends on the man-
ufacturer, design and even the speci_c revision of the hardware in question. In
case we didn't have an OS, every programmer would have to know the exact
details of how to interact with the speci_c hardware on which their program
will run whenever they write a program.
1.2 Resource Management and Multitasking
On a computer which is running an operating system that supports multitasking
(which includes most modern OSes), several programs appear to be running
simultaneously although there may be only one or a few processors present.
This is called multitasking and is achieved by running each program for a short
amount of time on the CPU and quickly switching between them, giving the user
the illusion that all programs are executing concurrently. Multiple programs
running also means that they are sharing common resources such as memory
and even devices such as the video display. It is the operating system that
manages this sharing of resources and prevents rogue programs from disrupting
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the functioning of other programs especially by protecting each program's share
of memory from other running programs.
1.3 Standardised Interfaces
Programs or applications interact with the operating system by invoking func-
tions provided by the operating system called system calls. For example when
an application needs to open a _le, it invokes a speci_c system call with ap-
propriate parameters. The operating system then performs hardware speci_c
tasks that will eventually make the data of the _le available to the application
program. The speci_c names, parameters that need to be passed and return
values of these system calls constitutes the Application Programming Interface
(API) presented by the operating system to an application programmer. By
standardising these APIs, an application program's source code can be com-
piled unmodi_ed on all operating systems that present the same API regardless
of the speci_c vendor or version of the operating system and independent of the
hardware it is running on.
2 UNIX, Linux and the GNU Project
In the early 1970's, Ken Thompson, Dennis Ritchie and others began to design
and develop the UNIX operating system at AT&T Bell Labs. Work on UNIX
development continued into the 80's and by the 1990's several variants of the
UNIX operating system were developed by various entities, a notable one being
the Berkeley Software Distribution (BSD). The large number of variants even-
tually led to the creation of the IEEE POSIX standard which initially de_ned
the API, and eventually all aspects of the behaviour of a UNIX-like system in-
cluding commands, utilities and standard libraries. POSIX then evolved into
what is now the Single Unix Speci_cation (SUS).
In 1983, Richard Stallman initiated the GNU project aiming to create a
UNIX compatible software system consisting of free software. Free software
can be modi_ed, copied and redistributed without restriction. Several licenses
qualify for designation as free software. The GPL (GNU General Public License)
is the license adopted by the GNU project. In essence it dictates that the
source code of any software released under the GPL should be available without
restriction and that any modi_ed or derivative software will also be governed
by the GPL.
Linux began as a hobby kernel by Linus Torvalds in 1991. It aimed to be
POSIX compliant and was licensed under the GPL. The combination of Linux
kernel and GNU project software is what is now popularly known as Linux,
although it is more accurate to refer to it as GNU/Linux. Fedora, Ubuntu, SUSE
etc. are all distributions of the GNU/Linux operating system. Software from
the GNU project is extensive and includes everything from compilers for a large
number of languages to editors to complete desktop graphical user interfaces
(GUIs).
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3 Users and Groups
UNIX was designed around the concept of multiple users. Each user on a system
owns a set of _les. The owner can de_ne whether other users may view, modify
or execute (if they are scripts or executables) their _les. Users may be divided
into sets called groups. A user may be a member of several groups. Groups
allow users to allow speci_c permissions to members of a group to which they
belong.
In UNIX, users and groups are identi_ed by names which are mapped to
unique user and group ids respectively. Any _le on disk has a user and group
id associated with it, and this de_nes its ownership.
As special user exists on UNIX systems called the root user. The root user
has access to all _le and functions on the system. A person logs in as the
root user in order to perform system administration tasks such as con_guring
a network or changing operating system policy and settings. The root user can
edit _les critical to the functioning of the system and can delete all _les on the
system, while normal users can only edit _les that are owned by them or for
which they are given write permissions.
4 Processes
Once the programmer has written the source code in a programming language
(like C or FORTRAN), it is compiled into machine code that is ready to be
executed. This machine code executable when stored on disk is called a program.
When a program is executed, the operating system reads it from disk and loads
all or parts of the program into main memory. From there it initiates the
execution of these instructions by the CPU and the program becomes a process.
Each process in a UNIX system is identi_ed by a process ID. A process may
have a limited lifetime or may run for the entire duration the system is up.
processes may be in a \running", \stopped" or \sleeping" state.
5 Files (from the point of view of processes)
A process may open a number of _les for input or output. In the UNIX design
_les need not necessarily need to be data stored on disk. They may be a network
device or even a sound device. This is one of the abstractions built into the
UNIX design. The operating system can present any device (real or virtual) to
an application program as a regular _le.
Three _les are always opened whenever a process is started. They are the
standard input, standard output and standard error (stdin, stdout and stderr).
these _les do not exist on disk.
6 Directory Layout, Pathnames and Symbolic
Links
In UNIX all _les are stored within directories (folders). UNIX uses a hierarchical
directory structure similar to other operating systems. In UNIX all directories
are subdirectories of the uppermost level root directory represented by `/'.
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The `/' is also the symbol for separating elements in a pathname. An abso-
lute pathname speci_es how to reach a particular _le or directory from the root
directory. For example,.
`/home/user/thesis.txt'
6.1 Relative and Absolute Pathnames
If a pathname is speci_ed without a leading `/', then it is a relative path.
Relative pathnames are interpreted as relative to the current working directory.
Picture it as an absolute pathname that is constructed by joining the current
working directory and the relative pathname.
Every directory has two special subdirectories named `.' and `..'. `.' is
equivalent to the current working directory and `..' is equivalent to the parent
of the current working directory.
6.2 Symbolic Links
Symbolic links are _les on a disk that point to other _les (shortcuts to Win-
dows users). Deleting a symbolic link does not delete the _le that it points to.
Symbolic links take up very little actual space on the disk. One use of symbolic
links is the make a direct link to a _le that has a very long pathname. Symbolic
links are created with the ln command.
7 Basic Commands
7.1 The Bash Shell
In operating system, the shell is the interactive interface presented to the user.
The user interacts with the shell in order to achieve speci_c tasks, and the shell
in turn communicates with the operating system kernel. The shell is thus a
layer of abstraction that hides details of the underlying operating system and
presents a uniform and convenient way for the user to interact with the OS.
The most common text mode shell for Linux based operating systems is the
Bash shell. The Bash shell presents the user with a programmable interface
along with several built-in commands. If you need to get a shell on a Linux
system running a graphical front end, you usually need to open the `terminal'
menu item. The Bash shell presents a prompt to the user when it is ready to
accept commands. A user prompt may look like the following.
ershaad@strobe:~$
or
[ershaad@n138 ~]$
And a root prompt will be similar to
root@strobe:~#
or
[root@n138 ~]#
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Notice the # at the end of the prompt for the root user. As we mentioned above,
the root user can a_ect the working of the system and therefore, this account
should be used with caution.
7.2 ls Command and the Current Working Directory
The ls command lists the contents of the current working directory. The current
working directory for a session of the shell can be found by entering the pwd
command. Files that begin with a period `.' are hidden _les and do not appear
in the output of the ls command. In order to view all _les including hidden
_les pass the -a command line option to ls ls -a.
Command line options may have a long and a short form. The corresponding
long option for -a is --all, so that you would type ls --all to see the full
listing of _les. Short options can be strung together or supplied separately. Like
ls -l -t or ls -lt. The same cannot be done with long options. Both long
and short options can be used in the same command ls -t --all.
Most commands usually print a usage summary when passed either of the
-h or --help options. In order to get detailed usage of a command, the man
page can be referred. It is an online documentation that can be viewed from
the shell. To view the man page of the cp command simply type man cp at the
shell prompt. The _rst few lines of the cp man page looks like.
CP(1) User Commands NAME
cp - copy files and directories
SYNOPSIS
cp [OPTION]... [-T] SOURCE DEST
cp [OPTION]... SOURCE... DIRECTORY
cp [OPTION]... -t DIRECTORY SOURCE...
DESCRIPTION
Copy SOURCE to DEST, or multiple SOURCE(s) to DIRECTORY.
The words in CAPS or in the form <word> or in italics means that they
need to be substituted with an appropriate word which may be a _lename or
keyword. In the above example SOURCE needs to be replaced with the path
of the source _le. Words or options within square brackets `[]' are optional. If
a `|' symbol separates one or more words or options like -r|-s, it means only
one of them may be speci_ed at a time. An ellipsis `. . . ' after a word means
that more can be speci_ed. In the above man page SOURCE... means one or
more source _les can be speci_ed separated by spaces.
7.3 Essential Commands
_ pwd
Print the present working directory
_ cd
Change the current working directory
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cd [dir]
cd /home/ershaad/workdir
cd workdir
_ rm
Delete _le(s)
rm draftfile.txt
rm -r tempdir
_ cp
Copy _les
cp thesis.tex thesiscopy.tex
cp -r datadir datadircopy
_ mv
Move or rename _les
mv oldfilename.txt newfilename.txt
mv /home/ershaad/olddirname /home/backup/newdirname
mv myfile.txt ..
_ mkdir
Create a directory
mkdir newdir
mkdir -p newdir/newsubdir/subsubdir
_ cat
Write the concatenation of contents to stdout
cat file1.txt
cat file1.txt file2.txt
_ less
View the contents of _les
less readme.txt
_ file
Information on the type of a _le
file image01.jpg
_ find
Search for _les based on criteria
find sourcedir -name "*.f90"
_ locate
Search for _lename within index of _les
locate workreport.doc
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_ chmod
Manage permissions for a _le
chmod u+x file.sh
chmod go-rwx file.txt
chmod o-w file.txt
_ gzip
Compress a _le
gzip bigfile.dat
_ gunzip
Uncompress a _le
gunzip bigfile.dat.gz
_ tar
Create/Extract an archive
tar -cvf homebackup.tar /home/ershaad
tar -czvf homebackup.tar.gz /home/ershaad
tar -xvf homebackup.tar
tar -xzvf homebackup.tar.gz
_ df
Summary of space on _lesystems
df -h
_ exit
Exit the shell
_ head, tail
Print the _rst/last few lines of a _le
head bankstatement.txt
head -n 15 bankstatement.txt
tail bankstatement.txt
tail -n 12 bankstatement.txt
_ du
Find how much disk space a directory is using
du -sh Downloads
_ date
Print or set the system date/time
_ grep
Print lines in _le that match some pattern
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grep orange fruits.txt
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