Linux environment

Chanderprabhu Jain College of Higher Studies & School of Law
Plot No. OCF, Sector A-8, Narela, New Delhi – 110040
(Affiliated to Guru Gobind Singh Indraprastha University and Approved by Govt of NCT of Delhi & Bar Council of India)
Linux environment
BCA – VI
Paper Code 306

Introduction: What is Unix?
• An operating system
• Developed at AT&T Bell Labs in the 1960’s
• Command Line Interpreter
• GUIs (Window systems) are now available

Introduction: Unix vs. Linux
• Unix was the predecessor of Linux
• Linux is a variant of Unix
– So is Mac OS X, so much of this tutorial applies to
Macs as well
• Linux is open source
• Most of the machines you’ll use in the
Bioinformatics program are running the Linux
OS

Introduction: Why Unix/Linux?
• Linux is free
• It’s fully customizable
• It’s stable (i.e. it almost never crashes)
• These characteristics make it an ideal OS for
programmers and scientists

Connecting to a Unix/Linux system
• Open up a terminal:

Connecting to a Unix/Linux system
• Open up a terminal:
The “prompt”
The current directory (“path”)
The host

What exactly is a “shell”?
• After logging in, Linux/Unix starts another program
called the shell
• The shell interprets commands the user types and
manages their execution
• The shell communicates with the internal part of the operating
system called the kernel
• The most popular shells are: tcsh, csh, korn, and bash
• The differences are most times subtle
• For this tutorial, we are using bash

Help!
• Whenever you need help with a command
type “man” and the command name

Help!

Unix/Linux File System
/home/john/portfolio/
/home/mary/
The Path
NOTE: Unix file names
are CASE SENSITIVE!

Command: pwd
• To find your current path use “pwd”

Command: cd
• To change to a specific directory use “cd”

Command: cd
• “~” is the location of your home directory

Command: cd
• “..” is the location of the directory below
current one

Command: ls
• To list the files in the current directory use “ls”

Command: ls
• ls has many options
– -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”

Command: ls -ltr
• List files by time in reverse order with long listing

General Syntax: *
• “*” can be used as a wildcard in unix/linux

Command: mkdir
• To create a new directory use “mkdir”

Command: rmdir
• To remove and empty directory use “rmdir”

Creating files in Unix/Linux
• Requires the use of an Editor
• Various Editors:
1) nano / pico
2) vi
3) emacs

Displaying a file
• Various ways to display a file in Unix
– cat
– less
– head
– tail

Command: cat
• Dumps an entire file to standard output
• Good for displaying short, simple files

Command: less
• “less” displays a file, allowing
forward/backward movement within it
– 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

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: head
• Here’s an example of using “head”:

Command: tail
• Same as head, but shows the last lines

File Commands
• Copying a file: cp
• Move or rename a file: mv
• Remove a file: rm

Command: cp
• To copy a file use “cp”

Command: mv
• To move a file to a different location use “mv”

Command: mv
• mv can also be used to rename a file

Command: rm
• To remove a file use “rm”

Command: rm
• To remove a file “recursively”: rm –r
• Used to remove all files and directories
• Be very careful, deletions are permanent in
Unix/Linux

File permissions
• 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

Permission levels
• “r” means “read only” permission
• “w” means “write” permission
• “x” means “execute” permission
– In case of directory, “x” grants permission to list
directory contents

File Permissions
User (you)Chanderprabhu Jain College of Higher Studies & School of Law

File Permissions
Group

File Permissions
“The World”

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:

Running a program (a.k.a. a job)
• Make sure the program has executable
permissions
• Use “./” to run the program

Running a program: an example
• Running the sample perl script “hello_world.pl”

Ending a program
• To end a program use “ctrl-c”. To try it:

Command: ps
• To view the processes that you’re running:

Command: top
• To view the CPU usage of all processes:

Command: kill
• To terminate a process use “kill”

Input/Output Redirection (“piping”)
• Programs can output to other programs
• Called “piping”
• “program_a | program_b”
– program_a’s output becomes program_b’s input
• “program_a > file.txt”
– program_a’s output is written to a file called “file.txt”
• “program_a < input.txt”
– program_a gets its input from a file called “input.txt”

A few examples of piping

Command: wc
• To count the characters, words, and lines in a
file use “wc”
• The first column in the output is lines, the
second is words, and the last is characters

Command: grep
• To search files in a directory for a specific
string use “grep”

What is a Regular Expression?
• Pattern to match all or part of a line of text
– Expressed in a formal, albeit weird, language
– For example:
^.*:Mike
matches lines that start (^) with any string (.*) and contain a colon
followed by Mike
• ^, . and * are called meta characters
– They do not represent themselves, but have other special meaning.
• :, M, i, k and e are normal characters
– The do represent themselves
55

Where are
Regular Expressions Used?
• Special commands that “know” about them
– Vi-Uses them in searching for a string: /regexp/
• Uses them in substitite command: s/regexp/replace/sed
– Edit a file (like vi) as a filter in a pipeline
… | sed editing-commands | …
– grep , fgrep (fixed grep) , egrep (extended grep)
• Print lines of a file that match a regexp
– awk
• Process input files looking for lines that match a regexp and
processing those lines
56

Regular expression
• A regular expression is a pattern of characters
used for describing sets of strings
• A pattern or sequence of characters
– Upper and lower case
– Digits
– Space, underscore, etc
• Metacharacters
57

Basic Regular Expressions
• Patterns that match a single character
– All regular letters match themselves
a b z T Q 0 1 9
– . (a single dot) matches any single character except
newline.
• In awk, dot can match newline also
• (like ? in filename generation)
– A set of characters that matches any single character from
the set (just like filename generation)
[aeiou]
[a-z0-9]
[A-Za-z-]
[a-m]
58

Metacharacter
* Matches 0 or more occurrences of the
preceding char
[…] Matches any one of characters enclosed
between the brackets.
- dash indicates a range when inside sq bkts.
[^ - negates what's inside brackets]
59

Metacharacter (con’t)
- backslash - escape character - just like before.
– . means match a dot
– This means is a meta character
– means match
Positional indicators:
• ^ anchor to beginning of line
• $ anchor to end of line
60

• "Some people, when confronted with a Unix
problem, think ‘I know, I’ll use sed.’ Now they
have two problems.”
-
61

Regular expression examples
• Peach
• a*c
– cxxx, acxxx, aaacxxxx
• a.c
– a+c, abc, match, a3c
• [tT]he
– The, the
• Ch[^0-9]
– Chapter, Chocolate
• ^the
– Start with the
• Friends$
– End with Friends
62

Regular expression examples
• L..e
• $[0-9]*.[0-9]
• ^[0-9]file.dat
• [^0-9]file.dat
• MM-DD-YY or MM/DD/YY
– [0-1][0-9][-/][0-3][0-9][-/][0-9][0-9]
63

Named classes of characters
• [0-9] ---OR --- [[:digit:]]
• [a-z] --- OR --- [[:lower:]]
• [A-Z] --- OR --- [[:upper:]]
• [a-zA-Z] --- OR --- [[:alpha:]]
• [a-zA-Z0-9] ---OR --- [[:alnum:]]
• egrep ‘^[[:lower:]]*$’
64

Extended Metacharacter (egrep and awk)
Available in egrep and awk NOT in vi, sed, grep or fgrep
? matches zero or one occurrence of the preceding
char
+ Matches 1 or more occurrences of the preceding
char
| Specifies that either the preceding or following
regular expression can be matched
( ) Groups regular expressions
65

Examples
• “.*” matches all characters between the quotations
• ^$ matches blank lines
• ^.*$ matches the entire line
• Big( Computer)?
• Compan(y|ies) # note: the | is a pipe symbol
• SSN: [0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9][0-9][0-9]
• grep ‘.H[123]’ ch0[12]
– ch01: .H1 “Contents of Distribution Tape”
– ch02: .H2 “A Quick Tour”
66

Repetition Examples
• Consider a file named text containing:
We're off to see the wizard.
The wonderful wizard of oz.
What a wonderful wizard he was.
The end.
• Try the following commands and explain the
output:
egrep 'f+' text
grep 'ff*' text
grep 'f{2}' text
egrep 'z?' text
67

Some More Examples
• A price: $[0-9]*.[0-9][0-9]
• A filename, at the start of a line, that starts with a digit
^[0-9]file.dat
• A filename, anyplace in the line, that starts with a non-digit
[^0-9]file.dat
• A social security number
[0-9]{3}-[0-9]{2}-[0-9]{4}
• From 4 to 6 digits: [0-9]{4, 6}
• A date - MM-DD-YY or MM/DD/YY:
[0-1][0-9][-/][0-3][0-9][-/][0-9][0-9]
• A line containing only upper case letters:
^[A-Z]*$
68

Replacement in sed and vi
• Applies to substitute command:
– s/regexp/replacement/
– Replacement string can contain the metacharacter
‘&’ which means the string that was matched
• Try this
STRING=“Start Again”
echo $STRING | sed 's/Again/& &/'
69

Process and Thread
• Process
– Execution context
– Program code
– Resources
– Associated threads
• Threads: units of execution
• Process and threads are objects

Thread Scheduling

Linux Architecture
• Monolithic kernel
– Contains modular components, however
• UNIX-like or UNIX-based operating system
• Six primary subsystems:
– Process management
– Interprocess communication
– Memory management
– File system management
• VFS: provides a single interface to multiple file systems
– I/O management
– Networking

Linux Kernel Architecture

Process and Thread Organization

Process information

System Calls
• Interface between user-level processes and
hardware devices.
– CPU, memory, disks etc.
• Make programming easier:
– Let kernel take care of hardware-specific issues.
• Increase system security:
– Let kernel check requested service via syscall.
• Provide portability:
– Maintain interface but change functional
implementation.

POSIX APIs
• API = Application Programmer Interface.
– Function defn specifying how to obtain service.
– By contrast, a system call is an explicit request to kernel made via a
software interrupt.
• Standard C library (libc) contains wrapper routines that make system calls.
– e.g., malloc, free are libc routines that use the brk system call.
• POSIX-compliant = having a standard set of APIs.
• Non-UNIX systems can be POSIX-compliant if they offer the required set of
APIs.

Linux System Calls (1)
Invoked by executing int $0x80.
– Programmed exception vector number 128.
– CPU switches to kernel mode & executes a kernel function.
• Calling process passes syscall number identifying system
call in eax register (on Intel processors).
• Syscall handler responsible for:
– Saving registers on kernel mode stack.
– Invoking syscall service routine.
– Exiting by calling ret_from_sys_call().

Linux System Calls (2)
• System call dispatch table:
– Associates syscall number with corresponding
service routine.
– Stored in sys_call_table array having up to
NR_syscall entries (usually 256 maximum).
– nth entry contains service routine address of
syscall n.

Initializing System Calls
• trap_init() called during kernel initialization
sets up the IDT (interrupt descriptor table) entry
corresponding to vector 128:
– set_system_gate(0x80, &system_call);
• A system gate descriptor is placed in the IDT,
identifying address of system_call routine.
– Does not disable maskable interrupts.
– Sets the descriptor privilege level (DPL) to 3:
• Allows User Mode processes to invoke exception handlers
(i.e. syscall routines).

The system_call() Function
• Saves syscall number & CPU registers used by
exception handler on the stack, except those
automatically saved by control unit.
• Checks for valid system call.
• Invokes specific service routine associated
with syscall number (contained in eax):
– call *sys_call_table(0, %eax, 4)
• Return code of system call is stored in eax.

Linux environment

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