1. California State University Fresno
Essential Linux
Harinder Bawa
California State University Fresno

2. Editors In order to do many tasks you will have to use an editor
Edit Code
Control analysis/programs
In the linux world these all edit text files
Word is not an editor
Can run at the command line, or in window
5/19/2018
Dr. Harinder Bawa

3. Choice of an editor Nearly always available Don’t require xwindows
Command line editors vi
vim
pico/nano
Xwindow editors
Xemacs/emacs
nedit
Nearly always available
Don’t require xwindows
fast
Not very powerful and
no access to mouse
5/19/2018
Dr. Harinder Bawa

4. vi Editor The most readily available
Generally installed as standard on all systems
Quite powerful
But difficult to use or at least get used to
Some people swear by vi
Its important to know some basics in case vi is the only option for a particular task.
5/19/2018
Dr. Harinder Bawa

5. Basic commands of vi vi filename (open file to edit)
Two modes of operation
Insert mode: Used for typing ( after typing i)
Command mode:- used to issue commands(Esc + command)
:q to quit without saving (!q= quit & discard changes)
u = undo the last change
x = Delete a character; dd= delete full line
:wq to quit after saving
5/19/2018
Dr. Harinder Bawa

6. vi: Cheat sheet
5/19/2018
Dr. Harinder Bawa

7. Editing a file using pico or nano
Type “pico” or “nano” at the prompt
5/19/2018
Dr. Harinder Bawa

8. Editing a file using pico
To save use “ctrl-x”
5/19/2018
Dr. Harinder Bawa

9. Compiling a C++ Program
To compile a c++ program, use the g++ command. “g++ helloworld.cpp”
Provided there are no errors, this will create an executable file called a.out.
If you want to name your executable file, use the -o flag to specify a name. “g++ helloworld.cpp -o helloworld.out”

10. Running a C++ Program
Running a c++ program is easy, just type in the name of the executable file!
“a.out”
There could be a minor issue however. If for some reason, that doesn’t work, try preceding the name with a ./
“./a.out”

11. OTHERS WAY TO DISPLAY A FILE CONTENTS AND SEARCH INSIDE IT
5/19/2018
Dr. Harinder Bawa

12. Displaying a file Various ways to display a file in Unix cat less/more
head
tail
5/19/2018
Dr. Harinder Bawa

13. Command: cat Dumps an entire file to standard output
Good for displaying short, simple files
5/19/2018
Dr. Harinder Bawa

14. Command: less/more
“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
The file contents are displayed by ‘cat’ command. The contents will scroll off the screeen, when the file contents are more than one screen page. The file contents are displayed page by page with the use of ‘more’ command.
5/19/2018
Dr. Harinder Bawa

15. 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
5/19/2018
Dr. Harinder Bawa

16. Command: head Here’s an example of using “head”: 5/19/2018
Dr. Harinder Bawa

17. Command: tail Same as head, but shows the last lines 5/19/2018
Dr. Harinder Bawa

18. Pipes and Redirection
Programs can output to other programs called “piping
Command > file- Redirect output to a file
Command>>file- Append output to an existing file
Command<file- Get input from a file, eg sort<file.txt
Command<file1>file2- Get input from file1, and write to file2
Command | command- Pipe one command to another
5/19/2018
Dr. Harinder Bawa

19. Searching grep pattern files- search for pattern in files
grep -r pattern dir- search recursively for pattern in dir
Command | grep pattern- search for pattern in the output of command
locate file- find all instances of file
5/19/2018
Dr. Harinder Bawa

20. A few examples of piping
5/19/2018
Dr. Harinder Bawa

21. 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
5/19/2018
Dr. Harinder Bawa

22. A few examples of piping
5/19/2018
Dr. Harinder Bawa

23. Command: grep
To search files in a directory for a specific string use “grep”
5/19/2018
Dr. Harinder Bawa

24. Command: diff To compare to files for differences use “diff”
Try: diff /dev/null hello.txt
/dev/null is a special address -- it is always empty, and anything moved there is deleted
5/19/2018
Dr. Harinder Bawa

25. LINUX SHELLS & ITS SCRIPTING
5/19/2018
Dr. Harinder Bawa

26. Shells The shells is a part of the interface for control of linux
There are a number of options, the two most common are:
tc (or c) shell (tcsh)
bourne shell (bash)
Change your shell with chsh
Pick a shell and stick to it, but can be useful for a new account somewhere.
5/19/2018
Dr. Harinder Bawa

27. Linux Command Line Interface
Linux shells: A shell is a command interpreter that allows you to type commands from the keyboard to interact with the operating system kernel.
■ sh (Bourne Shell) The sh shell was the earliest shell, being developed for UNIX back in the late 1970s.
■ bash (Bourne-Again Shell) The bash shell is an improved version of the sh shell and is one of the most popular shells today. It’s the default shell used by most Linux distributions.
■ csh (C Shell) The csh shell was originally developed for BSD UNIX. It uses a syntax that is very similar to C programming.
■ tsch The tsch shell is an improved version of the C Shell. It is the default shell used on FreeBSD(Berkeley Software Distribution) systems.
■ zsh (Z Shell) The Z Shell is an improved version of the bash shell.
5/19/2018
Dr. Harinder Bawa

28. Environment variables
Much of your linux environment is set by environment variables
These are access via the $sign
eg $HOST
To view your environment use env
Prints out all your environment variables
Use echo to view an individual one
echo $HOST or echo $HOME
5/19/2018
Dr. Harinder Bawa

29. Setting environment variables
You can set your environment variables using
export (bash shell)
export ROOTSYS=/user/local/root
setenv(tc shell)
setenv ROOTSYS /user/local/root
This creates the variable if it doesn’t already exist or updates if it does
Typically the environment variables you set yourself will be to tell programs where to find things.
5/19/2018
Dr. Harinder Bawa

30. Your PATH Your path is an environment variable
$PATH (check by echo $PATH)
It contains all the directories that your OS will look in to find the programs you want to run
The path should contain “.” to ensure that you don’t need to specify it while running local program
Entries are separated by “:”
Update your path with
setenv PATH /newdir:$PATH
5/19/2018
Dr. Harinder Bawa

31. Adding/Modifying the “PATH”
5/19/2018
Dr. Harinder Bawa

32. Bash Shell Startup
When a bash shell is started, it automatically executes commands stored in certain files.
There are three kinds of shells:
5/19/2018
Dr. Harinder Bawa

33. Note: Hidden files
If you try the ls command in your home directory, you will (probably) notice that the file .bash_profile is not listed. Filenames that begin with a period are hidden by default. You can use the
ls –a command
will show hidden files as well as non-hidden files.
5/19/2018
Dr. Harinder Bawa

34. Ubuntu Variance
When you open an interactive terminal session in Ubuntu, the sequence described on the preceding slide is NOT followed by default.
In particular, ~/.bash_profile is not executed automatically, and therefore changes you make to it will not be effective.
There is a simple fix for the issue:
- open a terminal session and go to Edit/Profile Preferences
- select the Title and Command tab
- check the box for “Run command as a login shell”
In fact, in my Ubuntu installation, ~/.bash_profile did not exist initially; I had to create it with editor.
5/19/2018
Dr. Harinder Bawa

35. ~/.bash_profile
You should use ~/.bash_profile to set changes to the PATH variable because ~/.bash_profile is only executed once.
Here is a sample ~/.bash_profile
And you know how to add PATH. Right?
5/19/2018
Dr. Harinder Bawa

36. A sample ~/.bashrc
alias commands are a convenient way to create mnemonics(memory) for specialized execution of system commands.
5/19/2018
Dr. Harinder Bawa

37. Setup atlas environment in lxplus
5/19/2018
Dr. Harinder Bawa

38. Remote communication
Most of your analysis is unlikely to be on your local machine. You need to login to bigger computing clusters e.g CERN’s “lxplus.cern.ch” or FresnoState “t3head.atlas.fresnostate.edu” provided you have account in that!
Advantage
Large Processing nodes for jobs
Remote data storage for experiments
Remote code repositories & databases .
5/19/2018
Dr. Harinder Bawa

39. ssh/scp
ssh is used to securely log in to remote systems, successor to telnet
ssh options
ssh
Type “exit” to log out of session
5/19/2018
Dr. Harinder Bawa

40. ssh/scp
scp is used to copy files to/from remote systems, syntax is similar to cp:
scp [local path] file path]
scp options file
or scp options
5/19/2018
Dr. Harinder Bawa

41. Exercise-1 Download http://zimmer.csufresno.edu/~hbawa/ubuntu.txt
Print number of words in the file
Print number of lines in a file
Command to scp transfer the file to your lxplus area
login to lxplus and move the file to /tmp/username dir.
Scp transfer file from lxplus /tmp/username to your current working dir.
5/19/2018
Dr. Harinder Bawa

42. Exercise-2
Download simple c++ code from
Open using any editor (vi /pico)
Remove second line and correct indentations.
Save the file
Compile using both c++ and g++ compiler
Make executable name “myoutput”
Run and print the output
5/19/2018
Dr. Harinder Bawa

43. Brain Teaser
How to save the output text on the screen in a file named “screen.txt”.
5/19/2018
Dr. Harinder Bawa