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Introduction to the Linux Operating System

• Linux is a free and open source operating system for

computers

• Has wide usage in web servers. i.e. Google farms

• Popular in scientific computing and simulation community, In 2014 97% of

world’s fastest 500 computer systems run Linux!

• Developed in the 90’s and for most users it is very similar to Unix.

• Linux has many variants or ‘distributions’ because it is open source

• Most molecular simulation programs or packages run on Linux

Assignments require use of Linux

Linux Mascot

What is Linux

1 Acknowledgment: These lecture notes are based on notes of Prof. Tom Woo

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Computers in the Montpetit 142 Lab

1. The account you use to logon will be your uOttawa account

(Exchange email account).

2. You will have access to an H drive, the home drive on the uOttawa

environment. However, it is recommended that you copy any files you need

to a USB memory stick.

3. The Montpetit labs do not require an access card to enter and should

be open 24 hours a day. The building itself closes at 11 pm and opens at 6

am.

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Linux User Interface

• Linux was designed as a multi-user, networked Operating System (OS)

• Many user interfaces (or “shells”) exist

• Text based and graphical user interfaces (GUIs) are available

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Linux OS Environment

Kernel

Hardware

Shell Applications Utilities

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Text Based User Interfaces

• Most simulation packages run from the text based interface

• We will introduce you to the text based interfaces

• Text based interfaces are often called “command line interfaces”

Linux is difficult to learn at first, but powerful! 4

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The Wooki Computer Cluster

•your assignments will be performed on

Wooki

•To learn Linux accounts for all of you have been created on the Wooki

computer cluster.

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User Accounts on Wooki

Student Name username

Delphine Amellal damellal

Mehran Bagheri mbagheri

Katie Harriman kharriman

Andrew Hollingshead ahollingshead

Ryan MacDonell rmacdonell

Mackenzie Rack mrack

Rebeca Rondon rrondon

Peter Werhun pwerhun

Andrew White awhite

Yijue Xu yijuexu

Initial password: ilovechemistry

(change your password ASAP)

If you are not on this list please let me know right now! 6

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How to Log Into Wooki?

From a Windows PC:

• Use the Secure Shell SSH program (free)

• Installed on lab PCs, available for download from course website

1: click on

“Quick Connect”

Do this now

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2: Type in:

“Host Name” and

“User Name”

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Changing Your Password and Logging Out

[saman@wooki ~]$ passwd

Changing password for user saman.

Changing password for saman

(current) UNIX password:

- To change your password use the “passwd” command

- To log out use the ‘exit’ or ‘logout’ command

Do this now

(system will ask you for a new password)

Log in and log out of your account to check your new password

Do this now

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Accessing Wooki from Outside the University

- Wooki is not directly accessible from outside the University. One must

first SSH into a “gateway” or “portal” machine. This is for added

security.

- Using SSH installed on your home computer, use the following to login

information:

Host Name: gateway.science.uottawa.ca

User Name: woolab

Port Number: 22 (default)

The password is: Cluster2010!! (It is case sensitive)

The portal machine is simply another Linux machine. At the command prompt,

type in:

[woolab@gateway ~]$ ssh –X XXXX@wooki.chem.uolocal

where XXXX is the Wooki username you have been assigned.

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Linux File System – Absolute Directory Path

/

bin home tmp usr

twoo saman Student

name

project_A project_B

• Top most directory in Linux is the ‘/’ directory or the ‘root’ directory

• Students are first placed in your “HOME” directory i.e., /home/studentname

the full path to this directory is: /home/saman/project_B

•The location of the directory within the file system is called the PATH to

the directory (or file).

share

scratch

Work

folder

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Linux File System – Relative Directory Path

saman

project_A project_B

• When I log in, this is what I see:

The path to this directory relative to my home directory is: project_B

You need some basic knowledge of the Linux file system to move outside

your home directory.

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Absolute vs Relative Directory Paths

/

bin home tmp

twoo saman mary

project_A TEST

The full, absolute path of the TEST directory is: /home/saman/TEST

While in the ‘saman’ directory, one can simply

use the relative path:

cd TEST

‘..’ refers to a directory one level up (wherever you

may be), in this case the parent directory.

To go to the parent directory: cd ..

If you are in the ‘TEST’ directory you can do the following to go directly

into the ‘project_A’ directory

cd ../project_A

To go back to your home directory, no matter what directory you are in

you can use: cd 12

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Basic File System Commands

Command Meaning

ls Displays a list of files in the

current working directory

cd directory_name change directories

pwd display present working directory

Try making a directory called ‘TEST’ and going into the directory

mkdir directory_name make a new directory

rm filename delete a file

rmdir directory_name delete a directory

file filename display the file type

mv file1 file2 rename or move file1 into file2

cp file1 file2 copy or replace file1 into file2

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A directory: /scratch/CHM4390

has been created for the course. Linux course and assignment files will

be placed there.

There is a directory called: Linux_Intro

Copy this file to your HOME directory.

cp /scratch/CHM4390/Linux_Intro/propene.out .

or you can ‘cd’ into the directory

cd /scratch/CHM4390/Linux_Intro

cp propene.out /home/XXXX/

TIP: File names can be auto-completed by pressing the ‘TAB’ key.

The ‘.’ means

the current

directory.

In that directory there is a file called: propene.out

‘XXXX’ is your

username

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/

bin home tmp usr

twoo saman Student A

project_A project_B

share

scratch

Gnuplot Assignment

1 Linux_Intro

scratch

CHM4390

propene.out

Wooki Directory Structure

1) cp /scratch/CHM4390/Linux_Intro/propene.out .

2) cd /scratch/CHM4390/Linux_Intro

cp propene.out /home/XXXX/

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File Properties

•Linux files have owners and different read/write privileges

Try the command ‘ls –al’

[saman@wooki ~]$ ls -al

total 28

drwx------ 2 saman woolab 4096 Jan 6 22:09 .

drwxr-xr-x 60 root root 4096 Jan 6 22:28 ..

-rw-r--r-- 1 saman woolab 24 Jan 6 22:09 .bash_logout

-rw-r--r-- 1 saman woolab 176 Jan 6 22:09 stuff.text

drwxr-xr-x 6 saman woolab 4096 Jan 7 15:12 project_A

owner group size creation

date

file name file permission

codes

•Linux file names are all case sensitive

current directory

parent directory

•Linux file names do not need extensions like in Windows i.e. ‘.exe’ but

they are often used.

•Do not use spaces in your file names! 16

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Getting Help

man command • lists the ‘man’ or manual pages for the command

example: man ls

info command • lists the ‘info’ pages for the command

• info is more informative than man for beginner

What if you don’t know the command?

apropos keyword •will search a database of relevant commands

• search the internet

•use the ‘apropos’ command

“ls –al” or “ls –a –l” •most Linux commands have options.

• ‘-’ or ‘--‘ designates an command line

option

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How to View Text Files: Display Commands

Command Meaning

cat file1 lists contents of file1 to screen

more file1 pages through file1 use spacebar to go to next page

head [-number] file1 display the first 10 (or number of) lines of a file

tail [-number] file1 display the last 10 (or number of) lines of a file

•WARNING: Files that are not text files, for example executable

programs, will output gibberish if you try to read their content.

•Press ‘Ctrl-c’ to exit if there is a problem during reading a file

Try viewing the ‘propene.out’ file

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How to Create and Edit Files?

•We will need to edit ‘input’ files to define the systems for simulations.

•Point-and-click editors like MS Word are not available through the command

line interface.

The ‘Nano’ text editor

•The ‘nano’ editor is an easy to use text editor

•You will need to learn to use ‘nano’ or another editor to complete the

assignments for this course

•Another text editor available on Linux is ‘vi’, but nano is the much

more user friendly.

• It is essential in Linux to learn how to use a text editor.

•nano is sometimes called ‘pico’. nano is actually an open source

clone of the editor ‘pico’.

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The ‘Nano’ text editor basics

• starting ‘nano’ [saman@wooki ~]$ nano filename

if filename does not exist, it will be created

nano propene.out do this now

Navigation and Moving the Cursor inside a file with nano

•Use the arrow keys, PgDn and PgUp keys to move

Ctrl-a move to beginning of the line

Ctrl-e move to the end of the line

Ctrl-v page forward

Ctrl-y page backward

Other navigation commands in nano

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•To insert text, simply move the cursor to the point you want to and then start

typing.

Editing Text

backspace delete a single character ‘backward’

Ctrl-r insert a file at cursor position (prompt will appear)

Ctrl-k cut or delete an entire line

Ctrl-u paste

•To select a portion of a line or more than one line for cutting:

1. use the ‘Ctrl-^’ (Ctrl+Shift+6) to mark the beginning of the text

2. Move the cursor to select the text from the ‘marked’ point.

Other editing commands

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The nano Menu

Nano always has the contextual menu at the bottom of the screen

The ‘^’ or caret symbol means ‘Ctrl-’. Thus, ‘^G’ means press the Ctrl key while

pressing the ‘G’ key. (lowercase ‘g’ works)

There is ‘Help’ menu that you should explore.

In the Help menu the ‘Meta’ symbol (M) means press the ‘Esc’ key then

press the key. E.g. ‘M-g’ means press the Esc key then press the ‘g’ key.

Don’t hold down the Esc key while pressing the ‘g’.

Esc-g or M-g Go to a specific line number

Esc-/ or M-/ Go to the end of the file

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Saving and Quitting

Ctrl-o save. Nano prompts you for file name

Ctrl-x exit. Nano prompts you to save work if changes were

made since the last save.

Searching for Text

Ctrl-w Search for specific text

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Copying and Pasting with SecureShell

One can also copy and paste with the SecureShell program. You can do

this any time in Linux, not just when running ̀ nano`.

To copy:

1. Highlight text with mouse.

2. Right-click and select copy from the menu

or

3. Click on “copy” icon on Secure Shell toolbar

Please note the standard Windows keyboard shortcuts Ctrl-c, Ctrl-v are

disabled in Secure Shell because these have special meaning in Linux.

To paste:

1. Right-click and select paste from the menu.

Please note you cannot paste anywhere on the screen in the Secure Shell

window. Pasting is equivalent to typing in with the keyboard. Recall we

are using a text based interface and it doesn’t know about your

‘Windows’ mouse and cursor. 24

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Text Editor Exercise

One of the simulation packages we will use is called ‘DL_POLY’.

There are 3 input files that DL_POLY requires

CONTROL, CONFIG, and FIELD

Examples of these files have been placed in /scratch/CHM4390

A. Make a directory called “Problem_1” in your home directory and copy

these files in this directory. Also copy the FIELD_VDW file from

/scratch/CHM4390.

B. The CONTROL input file has some of the set-up parameters for an MD

simulation. The present file has the temperature and pressure of the

simulation set to 250 K and 0.001013 kbar (1 atm), respectively. Make a new

file called CONTROL2 which has the temperature and pressure set to 300 K

and 0.1 kbar.

There are also parts C and D for this exercise, see course website.

(available on the course website, not graded)

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/scratch/CHM4

390

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‘Environment Variables’ in Linux

•An “Environment variable” is an entity that changes its value.

•Software can use environment variables to determine specific

information about the computer or user preferences.

e.g. $HOME = /home/saman

environment variable

changes, depending on the user

•User can change environment variables

•Environment variables are referenced with the ̀ $`

$DEFAULT_PRINTER

$BASIS_SETS

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‘Environment Variables’ in Linux

How to Display an Environment Variable (the echo command)

[saman@wooki ~]$ echo $HOME

/home/saman

[saman@wooki ~]$ echo $PATH

/usr/local/bin:/usr/bin:/usr/X11R6/bin:/binc

How to Define or Change an Environment Variable (the export command)

[saman@wooki ~]$ export MYNAME=“Saman”

[saman@wooki ~]$ echo $MYNAME

saman

•We will use environment variables sparingly in the course but it is an

important Linux concept.

no ‘$’ sign when

defining

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The ‘$PATH’ Environment Variable

• $PATH is an important environment variable.

PATH defines a list of directories to search through when looking for a

command to execute

•When you run a Linux command, such as ‘ls’, it actually executes a

program or script from a directory which is accessed by the PATH.

[saman@wooki ~]$ echo $PATH

/usr/local/bin:/usr/bin:/usr/X11R6/bin:/home/saman/bin

•We will not work with the environment variable $PATH much, but the

$PATH is an important concept in Linux for future reference.

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Other Linux Tricks and Tips

One can scroll through a history of your commands to repeat them more

easily or even search your command history:

• File names can be auto-completed by pressing the ‘TAB’ key.

•To edit the command, use the arrow keys (,) to move the cursor,

the Ctrl-d or ‘Backspace’ to delete a character.

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•The last 100 commands used can be seen by using the history command

• Commands can be recalled using the up and down arrow keys (, ).

Open another shell without

having to log in. (Try now)

Transfer files between Linux

and Windows. (Try now)

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X-windows Server

• graphics application runs on

this machine

• sends graphics information

over internet to the client

X-windows Client

• X-windows client software

interprets graphics information

• displays graphics

X-Windows: The Linux Networked Graphics System

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• Many computers running Linux (including Wooki) do not have monitors

• One needs to send display (graphical information to a computer with a monitor

• The remote computer you use to log in to Wooki has the ‘monitor’

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Setting up your PC to be a X-Windows Client

•MobaXterm is free X-windows client software for Windows XP/Vista/7

• For your Windows laptop or home computer you can

download and install MobaXterm from the website:

http://mobaxterm.mobatek.net/

• First, close any open SSH secure shell windows that are open.

• In Montpetit Hall , launch MobaXterm from the ‘Start’ menu, launch pad.

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Click here

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• Launch a new Secure Shell window with the X11 tunneling turned on.

• Do this by selecting it with the settings window:

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To test whether X-Windows is working log into Wooki and type xeyes

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If X-Windows is properly activated, you should see a pair of eyes show up

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X-windows can ‘tunnel’ through the UOttawa Firewall (gateway machine)

such that you can use X-windows to Wooki from outside of campus.

X-Windows Thru the Portal from Off-Campus

1. Launch MobaXterm on your home computer.

2. Secure Shell to ‘gateway.science.uottawa.ca’ using the ‘woolab’ account

with the X11 tunneling turned on in the SSH window.

3. When logged onto the portal machine ssh into Wooki using the ‘-X’ option:

[woolab@gateway ~]$ ssh -X saman@wooki.chem.uolocal

Now when you run X-windows programs on Wooki, they should be

redirected through the portal machine to your off-campus computer.

- Graphical application may run very slowly off campus!

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Allows graphical data to be transferred during the session

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gnuplot: A powerful graphics program

gnuplot is a command-line driven plotting program available on Linux.

It can be used to quickly plot simple data, while at the same time being

extremely powerful.

http://www.gnuplot.info.

It can easily perform least squares fitting of data to specific functions that

Excel cannot.

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Starting Gnuplot

To use gnuplot, make sure that an X-windows session is active

[saman@wooki ~]$ gnuplot

gnuplot>

A gnuplot prompt will appear:

gnuplot> f(x) = 2*x + 5*sin(x)

gnuplot> plot f(x)

gnuplot> set xrange [0:20]

gnuplot> set yrange [0:30]

gnuplot> set xlabel ‘x-axis name’

gnuplot> set ylabel ‘y-axis name’

gnuplot> set grid

gnuplot> replot

Try the following plot settings

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Plotting Styles

gnuplot> plot f(x) with dots

gnuplot> plot f(x) with points

gnuplot> set pointsize 4

gnuplot> plot f(x) with boxes

gnuplot> plot f(x) with impulses

To Remove the Legend

gnuplot> unset key

To Reset the Plot Settings

gnuplot> reset

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•Commands can be recalled using the up and down arrow keys (, ).

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Plotting Numerical Data from a File

gnuplot> plot ‘filename’ using 1:2

Numerical data stored in columns within a

file can be plotted.

1.0320 6.2074 38.5313

2.0640 8.5465 73.0424

3.0960 6.7056 44.9651

4.1280 4.2160 17.7746

5.1600 5.2054 27.0960

6.1920 10.6029 112.4220

7.2240 17.2849 298.7689

which columns to ‘use’

gnuplot> plot ‘filename’ using 1:2 with linespoints

to change the style

One can plot more than one function

gnuplot> plot ‘filename’ using 1:2 with linespoints, f(x)

separate with commas

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Fitting Data to a Function

gnuplot> g(x) = a + b*x

Gnuplot performs least squares fitting to both linear and non-linear functions.

gnuplot> fit g(x) ‘/scratch/CHM4390/Gnuplot/linear.dat’ via a,b

gnuplot> plot g(x),‘/scratch/CHM4390/Gnuplot/linear.dat’

Any function can be fit too. Here sometimes, one needs to provide a good

initial guess for the parameters.

gnuplot> b = 5.42 gnuplot> fit g(x) ‘filename’ via a,b

(Note to perform fitting, you need to start gnuplot in a directory that you

have write permission)

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Output of Fitting Data to a Function

Full output of fitting procedure is given in fit.log

Values of fit

parameters

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Gnuplot Exercise

Hand out is part of gnuplot tutorial on course website.

Since the Penguin is the Linux mascot….

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Gnuplot Exercise

ba pd d /

cm

P / kPa

Least squares fit this distance versus

pressure data:

Find best fit parameters, ‘a’ and ‘b’.

/scratch/CHM4390/Gnuplot/penguin.dat

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gnuplot> g(x) = a*x**b