Linux

What is Linux

● Unix-like computer operating system assembled under the

model of free and open-source software development and distribution.

● These operating systems share the Linux kernel.

○ Typically have the GNU utilities

● Comes in several “distributions” to serve different purposes.

What is Linux gcc

wc emacs
● Bird’s eye view bash

multitasking

tcsh
cat device file grep
access
Hardware system
sh

Kernel awk
sort

Shell

Utilities
Who is Linux

&
● Linux is an O/S core originally
written by Linus Torvalds. Now ● A set of programs written by
almost 10,000 developers Richard Stallman and others.
including major technology They are the GNU utilities.
companies like Intel and IBM.
When is Linux?

~1991
Where is Linux

● World Wide Web

○ 67% of the world’s web-servers run Linux (2016)

● Research/High-Performance Compute
○ Google, Amazon, NSA, 100% of TOP500 Super-computers.

● Modern Smartphones and devices

○ The Android phone
○ Amazon Kindle
○ Smart TVs/Devices
Connecting
Let’s use Linux
Local System

Remote Server
Connection Protocols and Software
Remote Connections: Remote Graphics: Data Transfer:
Secure SHell X-Windowing Secure File Transfer Protocol
(SSH) (X, X-Win) (SFTP)

Other protocols too, but let’s start with these.

Connecting from Different Platforms

SSH X-Win SFTP

Microsoft MobaXterm
Windows https://mobaxterm.mobatek.net

Apple Terminal XQuartz Cyberduck

macOS (Built in) https://www.xquartz.org https://cyberduck.io

Terminal X11 Various

Linux
(Built in) (Built in) (Built in)

SCC Help: http://www.bu.edu/tech/support/research/system-usage/getting-started

Microsoft Windows
You need software that emulates an “X” terminal and
that connects using the “SSH” Secure Shell protocol.

● Recommended: MobaXterm
○ Download: http://mobaxterm.mobatek.net/

● Alternatives:
○ SSH/X-Windows: X-Win32
https://www.bu.edu/tech/services/support/desktop/distribution/xwindows/
○ SFTP: Filezilla
https://filezilla-project.org/

SCC Help: http://www.bu.edu/tech/support/research/system-usage/getting-started/connect-ssh

 Built in!
Apple macOS Apple macOS is built on
Darwin -- a derivative of
4.4BSD-Lite2 and FreeBSD
● SSH: Terminal
○ Built in to macOS
Applications > Utilities > Terminal

● X-Windows: XQuartz
○ Download: https://www.xquartz.org/
○ Note: This install requires a logout.

● SFTP: Your choice

○ Filezilla: https://filezilla-project.org/ (Cross-platform, open-source)
○ Cyberduck: https://cyberduck.io (macOS native, drag-and-drop)
○ Many others
Linux
● SSH: Terminal
○ Built in to Linux
Applications > System > Terminal

● X-Windows: X11
○ Built in to Linux
○ Use your package manager.

● SFTP: Your choice

○ Usually has one Built in.
○ Alternate: Filezilla (https://filezilla-project.org/)

SCC Help: http://www.bu.edu/tech/support/research/system-usage/getting-started/connect-ssh

Connecting
● Use your Shared Computing Cluster account if you have one.

● Tutorial accounts if you need one.

○ Username:
Tutorial credentials blocked for print.
○ Password: This box disappears during presentation

[local_prompt]$ ssh username@scc1.bu.edu

username@scc1.bu.edu’s Password:
[username@scc1 ~]$
Get supplementary files
● At the command prompt, type the following:

[username@scc1 ~]$ cd ~
[username@scc1 ~]$ tar xf /scratch/linux-materials.tar
[username@scc1 ~]$ ls
c data haystack scripts
 Linux Interaction
Shell, Prompt, Commands and System Use
Linux: The Shell
● Program that interprets commands and sends them to the OS

● Provides:
○ Built-in commands
○ Programming control structures
○ Environment variables

● Linux supports multiple shells.

○ The default on SCC is Bash.
“Bash” = “Bourne-again Shell”
(GNU version of ~1977 shell written by Stephen Bourne)
Linux: The “prompt”

Your Username Current Directory

[username@scc1 ~]$

The System Name Input

( In Linux “ ~ ” is a shorthand for your home directory. )

Linux: Command Basics

[username@scc1 ~]$ command --option argument

● Command: Command/program that does one thing

● Options: Change the way a command does that one thing

○ Short form: Single-dash and one letter e.g. ls -a
○ Long form: Double-dash and a word e.g. ls --all

● Argument: Provides the input/output that the command interacts with.

For more information about any command, use man or info (e.g. “man ls”)
Commands: Hands-On

● After you connect, type

○ whoami # my login
○ hostname # name of this computer
○ echo “Hello, world” # print characters to screen
○ echo $HOME # print environment variable
○ echo my login is $(whoami) # replace $(xx) with program output
○ date # print current time/date
○ cal # print this month’s calendar
○ shazam # bad command
Commands: Hands-On Options
● Commands have three parts; command, options and arguments/parameters.

Example: cal –j 3 1999. “cal” is the command, “-j” is an option (or switch), “3”
and “1999” are arguments/parameters.

[username@scc1 ~]$ cal -j 3 1999

Commands

“Small programs that do one thing well”

● The Unix Programming Environment, Kernighan and Pike

… at its heart is the idea that the power of a system comes more from the
relationships among programs than from the programs themselves. Many
UNIX programs do quite trivial things in isolation, but, combined with other
programs, become general and useful tools.
Commands: Selected text processing utilities
● awk Pattern scanning and processing language
● cat Display file(s)
● cut Extract selected fields of each line of a file
Just a few of the
● diff Compare two files commands for
● grep Search text for a pattern text processing
● head Display the first part of files
● less Display files on a page-by-page basis
● sed Stream editor (esp. search and replace)
● sort Sort text files
● split Split files
● tail Display the last part of a file
● tr Translate/delete characters
● uniq Filter out repeated lines in a file
● wc Line, word and character count
Variables and Environment Variables

● Variables are named storage locations.

○ USER=augustin
○ foo=“this is foo’s value”

● “Environment variables” are variables used and shared by the shell

○ For example, $PATH tells the system where to find commands.

● Environment variables are shared with programs that the shell runs.
Bash variables
● To create a new variable, use the assignment operator ‘=‘

[username@scc1 ~]$ foo=“this is foo’s value”

● The foo variable can be printed with echo

[username@scc1 ~]$ echo $foo

this is foo’s value

● To make $foo visible to programs run by the shell (i.e., make it an

“environment variable”), use export:
[username@scc1 ~]$ export foo
Environment Variables
● To see all currently defined environment variable, use printenv:
[username@scc1 ~]$ printenv
HOSTNAME=scc1
TERM=xterm-256color
SHELL=/bin/bash
HISTSIZE=1000
TMPDIR=/scratch
SSH_CLIENT=168.122.9.131 37606 22
SSH_TTY=/dev/pts/191
USER=cjahnke
MAIL=/var/spool/mail/cjahnke
PATH=/usr3/bustaff/cjahnke/apps/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
PWD=/usr3/bustaff/cjahnke/linux-materials
LANG=C
MODULEPATH=/share/module/bioinformatics:/share/module/chemistry
SGE_ROOT=/usr/local/ogs-ge2011.11.p1/sge_root
HOME=/usr3/bustaff/cjahnke
Command History and Command Line Editing
● Try the history command
● Choose from the command history using the up ↑ and down ↓ arrows
● To redo your last command, try !!
● To go further back in the command history try !, then the number as shown
by history (e.g., !132). Or, !ls, for example, to match the most recent ‘ls’
command.
● What do the left ← and right → arrow do on the command line?
● Try the <Del> and <Backspace> keys
Help with Commands
● Type
○ date –-help
○ man date
○ info date
.
● BASH built-ins
○ A little different from other commands
○ Just type the command ‘help’
○ Or ‘man bash’
On using ‘man’ with ‘less’
● The man command outputs to a pager called less, which supports
many ways of scrolling through text:
○ Space, f # page forward
○ b # page backward
○ < # go to first line of file
○ > # go to last line of file
○ / # search forward (n to repeat)
○ ? # search backward (N to repeat)
○ h # display help
○ q # quit help
I/O Redirection
I/O redirection with pipes
● Many Linux commands print to “standard output”, which defaults to
the terminal screen. The ‘|’ (pipe) character can be used to divert or
“redirect” output to another program or filter.
○ w # show who’s logged on
○ w | less # pipe into the ‘less’ pager
○ w | grep ‘tuta’ # pipe into grep, print lines containing ‘tuta’
○ w | grep –v ‘tuta’ # print only lines not containing ‘tuta’
○ w | grep ‘tuta’ | sed s/tuta/scholar/g
# replace all ‘tuta’ with ‘scholar’
More examples of I/O redirection
● Try the following (use up arrow to avoid retyping each line):
○ w | wc # count lines
○ w | cut –d ‘ ’ –f1 | sort # sort users
○ w | cut –d ‘ ’ –f1 | sort | uniq # eliminate duplicates
● We can also redirect output into a file:
○ w | cut –d ‘ ’ –f1 | sort | uniq > users
● Note that ‘awk’ can be used instead of ‘cut’:
○ w | awk ‘{print $1;}’ | sort | uniq > users
● Quiz:
○ How might we count the number of distinct users currently logged in?
For extra credit, how can we avoid over-counting by 2? (Hint: use ‘tail’.)
The Filesystem
The Linux File System
● The structure resembles an upside-down tree
● Directories (a.k.a. folders) are collections of files and other directories.
● Every directory has a parent except for the root directory.
● Many directories have subdirectories.
Navigating the File System

● Essential navigation commands:

○ pwd print current directory
○ ls list files
○ cd change directory
Navigating the File System

We use pathnames to refer to files and directories in the Linux file system.

● There are two types of pathnames:

○ Absolute – The full path to a directory or file; begins with /
○ Relative – A partial path that is relative to the current working directory;
does not begin with /
Navigating the File System

● Special characters interpreted by the shell for filename expansion:

○ ~ your home directory (e.g., /usr1/tutorial/tuta1)
○ . current directory
○ .. parent directory
○ * wildcard matching any filename
○ ? wildcard matching any character
○ TAB try to complete (partially typed) filename
Navigating the File System

● Examples:
○ cd /usr/local Change directory to /usr/local/lib
○ cd ~ Change to home directory (could just type ‘cd’)
○ pwd Print working (current) directory
○ cd .. Change directory to the “parent” directory
○ cd / Change directory to the “root”
○ ls –d pro* Listing of only the directories starting with “pro”
The ls Command
● Useful options for the “ls” command:
○ ls -a List all files, including hidden files beginning with a “.”
○ ls -ld * List details about a directory and not its contents
○ ls -F Put an indicator character at the end of each name
○ ls –l Simple long listing
○ ls –lR Recursive long listing
○ ls –lh Give human readable file sizes
○ ls –lS Sort files by file size
○ ls –lt Sort files by modification time (very useful!)
Some Useful File Commands
● cp [file1] [file2] copy file
● mkdir [name] make directory
● rmdir [name] remove (empty) directory
● mv [file] [destination] move/rename file
● rm [file] remove (-r for recursive)
● file [file] identify file type
● less [file] page through file
● head -n N [file] display first N lines
● tail -n N [file] display last N lines
● ln –s [file] [new] create symbolic link
● cat [file] [file2…] display file(s)
● tac [file] [file2…] display file in reverse order
● touch [file] update modification time
● od [file] display file contents, esp. binary
Manipulating files and directories
● Examples:
○ cd # The same as cd ~
○ mkdir test
○ cd test
○ echo ‘Hello everyone’ > myfile.txt
○ echo ‘Goodbye all’ >> myfile.txt
○ less myfile.txt
○ mkdir subdir1/subdir2 # Fails. Why?
○ mkdir -p subdir1/subdir2 # Succeeds
○ mv myfile.txt subdir1/subdir2
○ cd ..
○ rmdir test # Fails. Why?
○ rm –rf test # Succeeds
Symbolic links
● Sometimes it is helpful to be able to access a file from multiple locations
within the hierarchy. On a Windows system, we might create a “shortcut.” On
a Linux system, we can create a symbolic link:

○ mkdir foo # make foo directory

○ touch foo/bar # create empty file
○ ln –s foo/bar . # create link in current dir.
Finding a needle in a haystack
● The find command has a rather unfriendly syntax, but can be exceedingly
helpful for locating files in heavily nested directories.

● Examples:
○ find ~ -name bu –type d # search for “bu” directories in ~
○ find . –name my-file.txt # search for my-file.txt in .
○ find ~ -name ‘*.txt’ # search for “*.txt” in ~

● Quiz:
○ Can you use find to locate a file called “needle” in your haystack directory?
○ Extra credit: what are the contents of the “needle” file?
Processes & Job Control
Processes and Job Control
● As we interact with Linux, we create numbered instances of running programs
called “processes.” You can use the ‘ps’ command to see a listing of your
processes (and others!). To see a long listing, for example, of all processes
on the system try:

[username@scc1 ~]$ ps -ef

● To see all the processes owned by you and other members of the class, try:

[username@scc1 ~]$ ps -ef | grep tuta

Processes and job control
● Use “top” to see active processes.
Tasks: 408 total, 1 running, 407 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.3%us, 0.1%sy, 0.0%ni, 99.6%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 99022756k total, 69709936k used, 29312820k free, 525544k buffers
Swap: 8388604k total, 0k used, 8388604k free, 65896792k cached

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND

7019 root 20 0 329m 137m 4852 S 4.0 0.1 217:01.56 sge_qmaster
38246 isw 20 0 88724 2764 1656 S 0.7 0.0 0:01.28 sshd
41113 cjahnke 20 0 13672 1512 948 R 0.7 0.0 0:00.03 top
2324 root 20 0 0 0 0 S 0.3 0.0 0:21.82 kondemand/2
7107 nobody 20 0 89572 10m 2400 S 0.3 0.0 2:18.05 gmond
27409 theavey 20 0 26652 1380 880 S 0.3 0.0 0:34.84 tmux
1 root 20 0 25680 1604 1280 S 0.0 0.0 0:05.74 init
2 root 20 0 0 0 0 S 0.0 0.0 0:00.07 kthreadd
3 root RT 0 0 0 0 S 0.0 0.0 0:00.89 migration/0
4 root 20 0 0 0 0 S 0.0 0.0 0:01.72 ksoftirqd/0
5 root RT 0 0 0 0 S 0.0 0.0 0:00.00 stopper/0

(refreshes every 2 seconds)

Foreground/background
● Thus far, we have run commands at the prompt and waited for them
to complete. We call this running in the “foreground.”
● Use the “&” operator, to run programs in the “background”,
○ Prompt returns immediately without waiting for the command to complete:

[username@scc1 ~]$ mycommand &

[1] 54356 ← process id
[username@scc1 ~]$
Process Control Practice
● Let’s look at the “countdown” script, in your scripts folder for practice

[username@scc1 ~]$ cd ~/scripts

[username@scc1 ~]$ cat countdown

● Make the script executable with chmod:

[username@scc1 ~]$ chmod +x countdown

● First, run it for a few seconds, then kill with Control-C.

[username@scc1 ~]$ ./countdown 100
100
99
98
^C ← Ctrl-C = (^C)
Process control
● Now, let’s try running it in the background with &:
[username@scc1 ~]$ ./countdown 60 &
[1] 54355
[username@scc1 ~]$
60
59

● The program’s output is distracting, so redirect it to a file:

[username@scc1 ~]$ countdown 60 > c.txt &
[1] 54356
[username@scc1 ~]$
Process control
● Type ‘ps’ to see your countdown process.

● Also, try running ‘jobs’ to see any jobs running in the background from this
bash shell.

● To kill the job, use the ‘kill’ command, either with the five-digit process id:
○ kill 54356

● Or, you can use the job number (use ‘jobs’ to see list) with ‘%’:
○ kill %1
Backgrounding a running job with C-z and ‘bg’
● Sometimes you start a program, then decide to run it in the background.

[username@scc1 scripts]$ ./countdown 200 > c.out

^Z ← Ctrl-Z = (^Z)
[1]+ Stopped ./countdown 200 > c.out

[username@scc1 scripts]$ bg
[1]+ ./countdown 200 > c.out &

[username@scc1 scripts]$ jobs

[1]+ Running ./countdown 200 > c.out &

[username@scc1 scripts]$
Editors
Regular expressions
● Many Linux tools, such as grep and sed, use strings that describe sequences
of characters. These strings are called regular expressions.
Here are some examples:

○ ^foo # line begins with “foo”

○ bar$ # line ends with “bar”
○ [0-9]\{3\} # 3-digit number
○ .*a.*e.*i.*o.*u.* # words with vowels in order*
File Editors
● gedit
○ Notepad-like editor with some programming features (e.g., syntax highlighting). Requires
X-Windows.
● nano
○ Lightweight editor. Non-Xwindows.
● emacs
○ Swiss-army knife, has modes for all major languages, and can be customized. Formerly steep
learning curve has been reduced with introduction of menu and tool bars. Can be used under
Xwindows or not.
● vim
○ A better version of ‘vi’ (an early full-screen editor). Very fast, efficient. Steep learning curve.
Popular among systems programmers. Terminal or X-Windows.
Creating and Running Code
“Hello, world” in C
● cd to “~/c”, and read hello.c into your editor of choice.
● Modify the text on the printf line between “[“ and “]” and save the file.
● Produce an executable file called “hello” by compiling the program with gcc:

[username@scc1 ~]$ gcc –o hello hello.c

● Run the program at the command line:

[username@scc1 ~]$ ./hello