Introduction to Unix

2007 May

http://www.accre.vanderbilt.edu

Introduction to Unix 2

Outline

Overview of the Unix Operating System (slides 3-4)

Shell, CL, Basic Ops, Help, Special Characters (slides 5-15)

Files, Directories, & Access Rights (slides 16-17)

Defining Your Environment (slides 18-24)

Text Editors (slides 25)

Input/Output Redirection - Pipelines & Filters (slides 26-38)

Processes & Multitasking (slides 39-40)

Scripting (slides 41-44)

Compressing & Archiving (slides 45-46)

Getting Help from ACCRE (slide 47) ; O’Reilly books (slide 48)

screen, a nice Unix tool (slide 49)

Introduction to Unix 3

What is UNIX?

UNIX is an operating system like Windows orMac OS X

UNIX was originally created in 1971 by KenThompson and Dennis Ritchie of AT&T BellLabs

It was designed to be a portable, multitasking,multiuser operating system

UNIX is a “standard”, i.e. there isn't *a* UNIX,but multiple implementations of the UNIXdesign (Linux, BSD, Solaris, AIX, OS X)

Introduction to Unix 4

All UNIX's aren't the same

All UNIX's share a common design philosophyof simplicity

Each UNIX usually develops its own niche orspecialization

Mac OS X: “User-friendly” desktop• Red Hat Linux: “Easy” workstation, simple server

• Debian Linux: “Advanced” workstation and server

• FreeBSD: High-performance server

• OpenBSD: Security and network applications

Introduction to Unix 5

Unix Shell and CL The shell is an interpreter used to communicate with

the OS interactively on the command line (CL)

The cluster has two “flavors”: tcsh and bash. Onlinemanuals and FAQ:

http://www.gnu.org/software/bash/

http://www.tcsh.org/Home

For historical reasons, tcsh is the default shell for allusers on VAMPIRE (the ACCRE cluster)

If you wish to change your default shell, use the chshcommand on vmpsched

CL prompt> chsh -s /bin/bash

Introduction to Unix 6

CL Operations and Files

There are Unix commands (same function inany shell) and shell built-in commands

Commands entered at the CL prompt haveoptions and arguments

Files and directories are the primary abstractionin UNIX (similar to icons and folders inWindows)

Directories are files with information on theircontents

Some useful Unix commands for interactingwith files and directories:

Introduction to Unix 7

Basic Commands

• pwd - print working directory• ls - list contents of directories• mkdir - make (create) new directories• cd - change the current directory

• cp - copy files or directories• mv - move files or directories• rm - remove (delete) files or directories

• cat - concatenate file contents• more/less - scroll file contents• file - show file type

simple bash examples with CL editing

Introduction to Unix 8

Command Help

Unix traditionally includes instructions and helpfiles (manual pages) on most commands andAPI's and their options. To access a manpage:

CL prompt> man foo

For csh/tcsh and sh/bash built-in commands:

CL prompt> man builtin

Some commands have command line help (usagehints or --help)

Other sources of help: /usr/share/doc, Google

Introduction to Unix 9

Basic CL & Editing• <tab> complete filenames and commands on CL• up/down arrows scroll CL history• left/right scrolls back and forth on CL• history shell command lists CL history (also tcsh)

functionCL (event) repeat

(function described on next slide):

repeat most recent, but substitute new forfirst old^old^new^

repeat nth event (see history)!n

repeat nth previous event!-n

repeat last containing string!?string

repeat last starting with string!string

repeat previous command!!

Introduction to Unix 10

Basic CL & Editing

• “:” allows more complex CL editing, e. g., selectlast event containing specific word, replace word,then execute command:

CL prompt> !?old:s/old/new/

This repeats the last event containing old, butsubstitutes new for old

Introduction to Unix 11

Basic CL & Editing

temporary interrupt (can also send to background, slide38)

^Z

cancel current CL, return prompt^C

delete under cursor^D

delete to end of line^K

back 1 word<esc>B

back 1 character^B

forward 1 word<esc>F

forward 1 character^F

end of line^E

beginning of line^A

next line^N

previous line^P

function on command linekeystroke

Introduction to Unix 12

Files, Directories, SpecialCharacters

Files to care about• hidden (filenames begin with a dot, list with ls -a),

e. g., user initialization, .login, .bashrc, .cshrc, …• global initialization, e. g., /etc/bashrc• devices• symbolic links

/ = top root directory

A few special Unix shortcuts for file/directory names/paths:• ~ = expands word to your home directory path• ~username = home directory of any username• . = current directory• .. = parent directory

Introduction to Unix 13

Files, Directories, SpecialCharacters

Blank space

Shell executes command in background (slide 31)&

Quote following special character as normal string(e. g., filnames containing spaces, or slide 17)

\

Examples throughout presentation (esp. scripts)“ ` { } #

Separates commands (see slide 15);

more special characters

Used within [] denotes range of characters-

Enclose set of characters, match any one by position[ ]

Match any single character in filename?

Match any character in filename*

wildcards

N. b., best to avoid using these characters in filenames

Introduction to Unix 14

Files, Directories, SpecialCharacters

E. g., globbing (expanding wildcard to match pattern):

CL prompt> ls -1 *file1file2~file3

CL prompt> ls ?ile1file1

CL prompt> ls file[1-2]file1

CL prompt> ls file[a-z0-9]~file2~

Introduction to Unix 15

Multiple commands and ;

You can use the “;” operator to append manycommands on one line:

CL prompt> date ; uptime

Tue May 8 11:41:26 CDT 2007

11:41 up 8 days, 22:26, 1 user, load averages:0.81 0.69 0.67

Introduction to Unix 16

File Permissions

Files/directories have an owner and a group

The owner can grant read/write/executepermissions to three groups (the user, the user'sgroup, and all others on the system)

prompt> ls -l /home/usernametotal 16drwxr-xr-x 2 username group 8192 May 1 15:59 certs/drwxr-xr-x 3 username group 8192 Sep 15 17:28 classes/

Introduction to Unix 17

File Permissions

These permissions are modified by the chmodcommand, e. g. :

CL prompt> chmod g+rx file

permits other users in the owner’s group toread and execute file

Introduction to Unix 18

Startup Files, Variables, Aliases

Two types, environment and shell, can be(re)initialized at any time.

If defined in .login, environment variablesare set upon login

If defined in shell run command files (e. g.,.bashrc, .cshrc, .tcshrc), shellvariables set upon each instance of shell

Frequently used variables should be set inthese files

Introduction to Unix 19

Startup Files, Variables, Aliases

default when spawned by other programsEDITOR

login nameUSER

terminal typeTERM

default printerPRINTER

directories containing commandsPATH

operating systemOSTYPE

name of computerHOST

home directory pathHOME

screen for X windows displayDISPLAY

machine architectureARCH

functionname

A few common variables common to both shells:

Introduction to Unix 20

Startup Files, Variables, Aliases

Important environment variables:

• PATH - points to executables

• LD_LIBRARY_PATH – points to libraries

Reference a variable with $ or ${}

echo and printenv commands:

CL prompt> echo $PATHCL prompt> echo ${PATH}CL prompt> printenv PATH

Introduction to Unix 21

Setting Variables

To assign a value to a variable (shells have different syntax):

Example of adding to your PATH:

rehash lets shell know PATH was just updated

set FOO = “bar”

setenv FOO “bar”tcsh

export FOO=bar

FOO=bar ; export FOObash

set path = ( $path $home/bin:/directory2 )

setenv PATH “${PATH}:${HOME}/bin:/directory2”tcsh

export PATH=$PATH:$HOME/bin:/directory2bash

Introduction to Unix 22

Setting Variables

Example of setting a new variable to the outputvalue of a command:

CL prompt> current_date_time=`date`CL prompt> echo $current_date_timeMon Apr 23 14:15:35 CDT 2007

Another example (note pwd vs. $PWD):CL prompt> echo "I am in `pwd` on $HOST”I am in /home/username on vmps08CL prompt> echo "I am in $PWD on $HOST”I am in /home/username on vmps08

Introduction to Unix 23

Setting Command Aliases

Shorten frequently used or lengthy commands:• tsch syntax:

alias rm 'rm -i’

• bash syntax:alias rm='rm -i’

• other useful aliases:alias cp='cp -i'alias mv='mv -i'alias ls='ls --color-tty -F'alias ll='ls -laF'

Introduction to Unix 24

Setting Command Aliases

Return to default:

• “backslash” temporarily returns to default:

\rm junk

• unalias returns default for rest of session:unalias rm

rm junk

Introduction to Unix 25

Text Editors on Cluster

Fairly basic:

Nano (http://www.nano-editor.org/)

More advanced:

Vim (http://www.vim.org/)

Emacs (http://www.gnu.org/software/emacs/)

Create/edit a new file example.txt

Introduction to Unix 26

Input/Output Redirection

Most programs have three I/O streams:

• stdin – standard input

• stdout – standard output

• stderr – standard error.

They all default to the console ("console"means the keyboard for the input and thescreen for the output)

Introduction to Unix 27

Input/Output Redirection

To redirect stdout of a program to a file:bash: myprogram 1> output.log

tcsh: myprogram > output.log

To redirect stderr of a program to a file: bash: myprogram 2> error.log

To redirect both stdout and stderr to same file (ordermatters): bash: myprogram > combined.log 2>&1

To redirect both stdout and stderr separately:(myprogram >output.log) >&error.log

Introduction to Unix 28

Input/Output Redirection

( comm > ofile ) >& efilestdout/err to 2 files

comm < ifile > ofile 2> efilestderr to third file

comm < ifile > filecomm < ifile > fileredirect stdin/out

comm <<ccomm <<cstdin until “c”

comm >> ofile 2>&1comm >>& ofilestdout/err to end

comm 2>> ofilestderr to end of file

comm >> ofilecomm >> ofilestdout to end of file

comm < ifilecomm < ifilestdin from file

comm >ofile 2>&1

comm &> ofilecomm >& ofilestdout/err to file

comm 2> filestderr to file

comm > filecomm >ofilestdout to file

bashtcshfunction

Introduction to Unix 29

Input/Output Redirection

Example of “>>” operator to appendinformation to a file:

prompt> date > foo

prompt> cat fooWed Aug 31 17:27:52 CDT 2005

prompt> date >> foo

prompt> cat fooWed Aug 31 17:27:52 CDT 2005Wed Aug 31 17:27:56 CDT 2005

Introduction to Unix 30

Input/Output Redirection

Use of single back quotes to substitute in thevalue of another command:

Compare to slides 14 and 22:

prompt> ls `find . -name “file[a-z0-9]~”`file2~

prompt> echo `find . -name “file[a-z0-9]~”`file2~

Introduction to Unix 31

Input/Output Redirection

script to redirect CL stdin/out to recordsession to a file (however, formatting not sonice)

To redirect output to “nowhere” use the nulldevice, /dev/null

To redirect stdout to null device (tcsh/bash):myprogram >/dev/null

To redirect stdout and stderr to null (bash):myprogram >/dev/null 2>/dev/null

Introduction to Unix 32

I/O Redirection - Pipes/Filters

Pipelines are a set of processes chained by their standardstreams, so that the stdout of each process feeds directlyas the stdin of the next.

Pipelines are defined using the “|” character.

E. g., use a pipe and tee to direct output of echo toboth stdout and to a file:

prompt> echo "Hello World" | tee output.txt

comm 2>&1 | comm2comm |& comm2pipe stdout/err to comm2

comm | comm2comm | comm2pipe stdout to comm2

bashtcshfunction

Introduction to Unix 33

I/O Redirection - Pipes/Filters

Commands can be used as filters which take the outputof a program and modify it. E. g., use a pipe to countwords from the output of echo:

prompt> echo "Hello World" | wc -w2

Very useful filters include:• grep - Pattern matching• sed - Search and Replace• cut - Print specific columns• sort - Sort alphabetically / numerically• uniq - Remove duplicate lines from a file

Introduction to Unix 34

I/O Redirection - Pipes/Filters

grep example:

prompt> cat example.txtHello WorldGoodbye World

prompt> cat example.txt | grep HelloHello World

prompt> cat example.txt | grep -v HelloGoodbye World

Introduction to Unix 35

I/O Redirection - Pipes/Filters

sed example:

prompt> cat example.txtHello WorldGoodbye World

prompt> cat example.txt | sed “s/Hello/Goodbye/g”Goodbye WorldGoodbye World

Introduction to Unix 36

I/O Redirection - Pipes/Filters

cut example:

prompt> cat example.txt1,Hello,World2,Goodbye,World

prompt> cat example.txt | cut -d "," -f 2-Hello,WorldGoodbye,World

Introduction to Unix 37

I/O Redirection - Pipes/Filters

sort example:

prompt> cat example.txt2 Goodbye1 Hello2 Goodbye

prompt> cat example.txt | sort -n1 Hello2 Goodbye2 Goodbye

Introduction to Unix 38

I/O Redirection - Pipes/Filters

uniq example:

prompt> cat example.txt2 Goodbye1 Hello2 Goodbye

prompt> cat example.txt | sort -n | uniq1 Hello2 Goodbye

Introduction to Unix 39

Processes and Multitasking

To run a program in the background, use the “&”character (or “^Z” followed by “bg”):

prompt> myprogram &[1] 7895

myprogram is now running in the background asprocess id (PID) 7895

Whenever your process finishes, it will print“Done” to the console.

Introduction to Unix 40

Processes and Multitasking

To check on the status of your jobs running onthe system, use the ps command

prompt> ps -a PID TTY TIME CMD 8095 pts/3 00:00:00 ps

You can get an expanded list by typingps agux, or by using the top command

Use uptime to check the load average (howhard system is working) on slowly respondingmachines

Introduction to Unix 41

Simple Shell Scripting

String unix commands into a shell script.#/bin/csh N. b., not a comment on line 1

To execute:tsch: prompt> source myscript01.csh

bash: prompt> . ./myscript01.sh

Or run as executable:prompt> chmod u+x myscript01.csh

prompt> myscript01.csh

prompt> ./myscript01.csh (if not in path)

Introduction to Unix 42

Simple Shell Scripting

Simple bash programming: myscript02.sh#!/bin/sh# define variablelist="Mercury Venus Earth Mars Jupiter Saturn Uranus

Neptune”# initiate counteri=1# for loopfor planet in $listdo echo "planet $i is $planet" # Print to STDOUT i=`expr $i + 1` # Increment counterdone

Execute it:prompt> chmod u+x myscript02.sh ; ./myscript02.sh

Introduction to Unix 43

More on Variables

Can also define conditional variables:

If VAR, use its value else usealternate_value and exit if in shellscript; if alternate_value also emptyprint print msg to stderr

${VAR:?alternate_value}

If VAR, use alternate_value${VAR:+alternate_value}

If VAR, use its value else usealternate_value and set VAR=alternate_value

${VAR:=alternate_value}

If VAR defined, use its value else usealternate_value${VAR:-alternate_value}

resultformat

Introduction to Unix 44

More on Variables

Example bash uses of conditional variables:

prompt> echo $VAR $ERROR

prompt> echo ${ERROR:?”An error was found”}bash: ERROR: An error was found

prompt> ERROR=TRUE

prompt> echo ${ERROR:+”An error was found”}An error was found

prompt> echo ${ERROR:-”An error was found”}TRUE

prompt> echo ${ERROR:=”An error was found”}TRUE

Introduction to Unix 45

Compressing and Archiving

There are several ways you can compress files toreduce disk usage or transfer time.

The “Windows” way is using the zip and unzipcommands:prompt> ls -alh testfile1 testfile2-rw-r--r-- root root 1.0M testfile1-rw-r--r-- root root 1.0M testfile2

prompt> zip testfile.zip testfile1 testfile2

prompt> ls -alh testfile.zip-rw-r--r-- root root 2.4K testfile.zip

Introduction to Unix 46

Compressing and Archiving

Traditional UNIX archiving tools, tar and gzip.

tar takes a number of files/directories andcombines them into a single file

gzip takes combined archive and compresses it:

tar -c file1 file2 ... | gzip -9 > archive.tgz

Or simply:tar -zc archive.tgz file1 file2 …

To extract files from a tar archive:tar xfzp archive.tgz

Introduction to Unix 47

Getting Help from ACCRE

ACCRE website FAQ and Getting Started pages:

www.accre.vanderbilt.edu/support

ACCRE helpdesk:

www.accre.vanderbilt.edu/support/contact/submit_RT.php

accre-forum mailing list

Office hours at ACCRE M-F 4-5 PM

Introduction to Unix 48

Give UNIX a try!

There are several free flavors of UNIX available:

•Fedora: http://www.fedora.redhat.com

•Debian: http://www.debian.org

•FreeBSD: http://www.freebsd.org

•Ubuntu: http://www.ubuntu.com

O’Reilly has excellent desktop reference materials (I. e., books):

http://www.oreilly.com/

(E. g., “Linux in a Nutshell”, “Class Shell Scripting”, …)

O’Reilly pocket guides also very useful quick references (Linux OS,shells, editors, …)

\

Introduction to Unix 49

Screen

Another useful unix tool with remote session Tutorial :

… Log onto cluster noting the gateway (i. e., vmpsxx) …prompt> screenprompt> nano junk.txt

… While in editor, close window …

… Must log back onto node you were on, i. e.,vmpsxx.accre.vanderbilt.edu …

… Find SCREEN process ID (PID) …prompt> ps augx | grep <your user name>prompt> screen -R <PID>

… Your process is Restored where you left off …