''Unix is user friendly --

It's just picky about who it's friends are...''

-- Unknown, seen in .sigs around the world

Basics of the Unix/Linux

EnvironmentShells and Your Unix Environment

What is a shell?Traditional user interface with the unix

operating system…it interprets your typing

A scripting program that controls the syntax at the command line interface

Just as there are many flavors of unix and unix-like systems, there are many types of shells

Common Shells

BourneShell

Bourne Again Shell

TENEXC shell

C ShellKornShell

shBourne shell

the original Unix shell

Pro: Flexible and powerful scripting shell

Con: Not interactive or particularly user friendly

cshC shell

designed for the BSD Unix system

syntax closely follows C programming

Pro: easy for C programmers to learn and comes with many interactive features such as file completion and aliases

Con: not as flexible or powerful a scripting language

kshKorn shell

derived from the Bourne shell so has a shared syntax

job control taken from the C shell

bashBourne-Again shell

Combines the “best” of sh, ksh, and csh

Default shell on Linux and Mac OSX operating systems

Pro: Flexible and powerful scripting language with all the interactive features of csh plus command completion

This shell is great for complicated GMT scripts

tcshTENEX C shell

Default shell of the CERI unix environment

Pro: User friendly on the command line & it is what your CERI account environment is set up to use

Con: It is not as suitable for long and involved scripts

It is perfectly good for most daily geophysics work on the command line & most faculty here use it on a daily basis so there are many experts around

What is my shell?env $SHELL will echo your current login shell to

the screen

to switch your shell in a single terminal window, simply type the name of the preferred shell

the command line also usually indicates which shell family you are using

$ -- bash, sh, or ksh> or % -- csh, tcsh

Useful features of tcsh & bash

file completion: you can key the tab button to complete the name of a long file

history: list the previous commands entered during the active session

% history1139 11:19 ls | more | tail -n5 >> directory.list

up and down arrow keys: allow you to move up and down through previous commands

right and left arrow keys: allow you to edit command lines without starting from scratch

!XXX: reruns the command labeled XXX in the history list% !1139ls | more | tail -n5 >> directory.list

The Unix EnvironmentMitch has set up the basic CERI environment

so that everyone can access the standard geophysics packages available on the Sun system

But what does this mean?your environment is composed of a number of

environment variables which provide important information to the operating system

since you generally want the computer to behave the same way everyday, these environment variables are setup in configuration files accessed at login

What are your environment variables?

env: prints the current environment variables to the screen

HOME & SHELLHOME: this environment variable controls what

other unix commands consider your base or home directory

this is how “%cd “ knows which directory to go to

% echo $HOME/gaia/home/hdeshon

SHELL: this variable stores your default shell% echo $SHELL/usr/bin/tcsh

*these environment variables should not be changed by the user

PATHPATH: tells the shell where to find applications

and/or executable files

%echo $PATH

/gaia/smeagol/local/passcal.2006/bin:/gaia/smeagol/local/gmt/GMT4.2.1/bin:/opt/local/bin:/opt/local/sbin:/opt/csw/bin:/opt/csw/sbin:/ceri/local/bin:/usr/sbin:/ceri/local/sbin:/gaia/home/stbisrat/bin:/usr/local/bin:/opt/Studio/SUNWspro/bin:/opt/Studio/SUNWspro/prod/bin:/opt/sfw/bin:/usr/bin:/usr/dt/bin:/usr/openwin/bin:/bin:/usr/ucb:/usr/ccs/bin:/usr/local/teTeX/bin/sparc-sun-solaris2.8:/gaia/smeagol/local/bin

The : is used to separate each full path name

When a command is called from the command line, the shell will search through this list of paths, in order, until it finds the first instance

How does PATH work?If you are working a program to do least squares

analysis and decide to call it “ls,” what will happen when you enter the command “ls”?

It depends on your PATH variable.

When the shell goes looking through your path for an executable file named “ls”, it will run the first one it finds.

If the directory containing your least squares program (executable file), “ls”, is in your path

Before

the directory containing the Unix list command, “ls”, it will run your program and you will not be

able (at least simply) to get a listing of your directory!

If the directory containing your least squares program, “ls”, is in your path

AFTER

the directory containing the Unix list command, “ls”, it will run the Unix ls command and you will

not be able (at least simply) to run your program!

To force your least squares executable in the current (working) directory to run

%./ls

To force the unix ls command to run

%/bin/ls

MANPATHMANPATH: tells the shell where to find the manual

pages read using the man command

%echo $MANPATH

/gaia/smeagol/local/passcal.2006/man:/gaia:smeagol/local/gmt/GMT4.2.1/man:/opt/local/man:/ceri/local/man:/usr/dt/man:/usr/man:/usr/openwin/share/man:/usr/local/man:/opt/SUNWspro/man:/opt/sfw/man:/usr/local/teTeX/man:/gaia/smeagol/local/man:/opt/csw/man

If you do a man on a command and the shell can’t find a manual page (and you are sure the man page exists), this environment variable may not be set correctly

HOST & REMOTEHOSTHOST: the name of the machine you are

currently logged into

REMOTEHOST: the name of the machine you are sitting in front of, if different

% echo $HOST $REMOTEHOST

enigma sailfish2.ceri.memphis.edu

SSH Related VariablesSSH_CLIENT: the IP (internet protocol) address of

the HOST machine

SSH_CONNECTION: the IP address of the HOST machine and the REMOTEHOST machine

% echo $SSH_CLIENT $SSH_CONNECTION

141.225.156.223 52372 22

141.225.156.223 52372 141.225.157.75 22

Modifying your current shell environment

If you mess up modifying the environment in your current window – you may “break” your current window (shell).

This is generally not a problem on the sun, mac, etc.

The environment is local to that window/shell.

Just close it and open another window.

set

set: sets csh shell variablesA typical tcsh set command is

%set history=100

This would save the last 100 commands on the history list.

The bash equivalent is simply%history=100

setenvsetenv: the csh command to change

environment settings.

% setenv PATH {$PATH}:/gaia/home/hdeshon/scripts

this adds the directory ‘~/scripts’ to the end of the environment variable PATH within the active window

The bash equivalent is simply%PATH=$PATH:/gaia/home/hdeshon/scripts

setenv can be run on the command line, from within a local configuration file (.cshrc or .login), or in a shell script.

When run without specifying an environment variable, it will print all environment variables to the screen

Making your own environment variables

• Anytime you want a global definition of something, you can create your own global environment variable

%setenv LATESTRTVEL rtvel4_9305_5bv19

Modifying your default environment

It will get old changing everything to the way you want it each time you log in/open a new window/start a new shell. And this being Unix, there is a (easy) way to set up your own personal environment.

The setup of your personal environment (personal changes/preferences for how you want the shell to work for you) is stored in shell configuration files, aka dot files

.cshrc or .bashrc

There is also a file .login, but it is not likely you will have to change it (it get’s used when you log in, not each time you start a shell)

setenv PATH ${PATH}:/gaia/home/hdeshon/scripts

setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/gaia/home/hdeshon/fftw-2.1.5/lib

setenv PRINTER 3876_grad

set filec #explicitly turns on file completion

set noclobber #turns on no clobber, which keeps redirect > from #overwriting files unless the ! is specified

set history=500 #keep the last 500 commands in the history list

alias l 'ls -F'

.cshrc

PATH=/usr/local/sod-2.2.2/bin:$ANTELOPE/bin:$PATH

export PATH

.bashrc

some warningsIf you need to modify your environment

configuration file (.cshrc, .bashrc), do so with care

Always leave two terminal windows open (prior to making any changes) in case you mess your file up so completely and break your active window, you have another window open to delete the offending file

Always backup the file you before modifying it!

Aliasesalias: creates a pseudonym or nickname for a

common command or series of commandsAnything you find yourself typing repeatedly can

be set to an aliasAnything you find yourself frequently mis-typing

can be set to an alias

unalias: unset the alias

alias and unalias can be run within a terminal window for short-term usage or set in your configuration files for long-term usage

Aliases examplesalias settitlebar 'echo -n "^[]2;$CWD^G"'

alias cwdcmd 'set PROMPT="[${USER}@`hostname`] $CWD% "'

alias cd 'chdir \!* && cwdcmd && settitlebar’

alias howmuch 'du -sk .’

alias h 'history’

alias m more

alias mroe more

alias l 'ls -F'

alias c clear

alias src source

Sourcesource: executes configuration files

If you change your configuration file, you will need to execute the changes in all open terminal windows for the changes to take effect. They automatically will take effect when new terminal windows are opened.

%nedit ~/.cshrc you’ve used NEdit to make file changes

%source ~/.cshrc