Introduction to Basic Linux | Tufts Technology Services

Introduction to Basic Linux

Delilah MaloneyHigh Performance Computing (HPC) Specialist

Research TechnologyTufts Technology Services

[email protected]@tufts.edu

Linux

• Introduction• Basic Linux Commands in CLI with exercises• System• Directories & Files

Linux

• Operation System, just like Unix, Windows or OS X.

Linux

• Operation System, just like Unix, Windows or OS X.• Linux was created in 1991 by Linus Torvalds as a free and open

source alternative to Minix, another Unix clone that was predominantly used in academic settings.

Linux

• Hobby

Linux

• Hobby

Ø 75% stock exchange

Linux

• Hobby


Ø Web servers

Linux

• Hobby


Ø Web servers

Ø Electronic devices

Linux

• Hobby


Ø Web servers

Ø Electronic devices

Ø 95% Supercomputers and ALL of the TOP500s

Command Line Interface

Graphical User Interface

Type Alone

q If you have access to Tufts HPC cluster:• Terminal (from Linux or Mac)• ssh [email protected]

• OnDemand Web Interface (from Windows)• https://ondemand.cluster.tufts.edu• Clusters à Tufts HPC Shell Access

q If you haven’t get your access to Tufts HPC cluster:• CentOS terminal online by Coding Group : • https://www.tutorialspoint.com/unix_terminal_online.ph

p • Some of the commands may not be available

Commands

q Basic structure of Linux commands:§ command§ command options § command options arguments

q Two versions of options: Short (-a) and/or Long (--all)q Most of the options can Mix and Match!q The wildcard “*” (asterisk or star)q Execute “./”q Run commands from a file “source” or “.”q Case Sensitive!

§ “File” and “file” are different files!

Tips & Tricks

q Tabq Control + A & Control + Eq Control + Cq The arrow keys are your friend (Up & Down)q Put your most used set of commands in a script

System

How to get user information:• whoami

Ø Display username

System


Ø Display username• groups

Ø Display the groups you belong to

System



Ø Display the groups you belong to• id

Ø Display your username and groups

System



Ø Display the groups you belong to• id

Ø Display your username and groups• getent group name_of_the_group

Ø Display the members’ usernames in a group

System

To get information about your system:Memory information:• free –g or –m or -h

Ø Display host memory (RAM) spec in GB/MB/human readable

System



• quotaØ Display storge/memory quota

System




• showquotaØ Unique to Tufts HPC clusterØ Display home directory quota and project space quota

System




• showquotaØ Unique to Tufts HPC clusterØ Display home directory quota and project space quota

• du -shØ Display disc usage summary in human readable form

System

To get information about your system:System information:• hostname < –i >

Ø Display system hostnameØ Display IP address of the host

System



• lscpu <–e=[list]>Ø Display CPU information (compact)Ø Display selected CPU information

System




• cat /proc/cpuinfoØ Display CPU information (Individually)

System




• cat /proc/cpuinfoØ Display CPU information (Individually)

• nproc < --all >Ø Number of available processors

Help!

Most commands have a manual, if not, most of them have help:• man command

Ø Display command manual• man –k keyword

Ø Search all manuals based on keyword• command –h or --help

Ø Help info

...And Google helps!

System

Try it out yourself!• whoami• group• Id• free –h• quota• showquota (on Tufts HPC Cluster)• hostname• lscpu• cat /proc/cpuinfo• nproc• man <any command>• <command> --help

Directory & File

Navigate in the system, editing files, working with directories, .etc. • mkdir dir_name

Ø Create a directory

Directory & File

Navigate in the system, editing files, working with directories, .etc. • mkdir dir_name

Ø Create a directory • rm file_name

Ø Remove a file• rm –r or -rf dir_name

Ø Remove a directory with it’s contents• rmdir

Ø Remove an empty directory

Directory & File

Navigate in the system, actions in directory level:• pwd

Ø Show current directory path

Directory & File

Navigate in the system, actions in directory level:• pwd

Ø Show current directory path• cd directory_path

Ø Go the “directory_path” location• cd ~ or cd

Ø Go to home directory• cd ..

Ø Go up a level of the directory• cd –

Ø Go back to the last directoryyou were in

Directory & File

Listing directory contents:• ls

Ø Display contents in the current directory

Directory & File

Listing directory contents:• ls

Ø Display contents in the current directory• ls –a

Ø Display ALL contents in the current directory• ls –l

Ø Display long listing of the contents• ls –d */

Ø Display directory entries only• ls –r or –t or –X or –R or .etc

Ø Display in reverse order/sort by time/sort by extension/recursively

Directory & File

Text editors:• nano• vi• vim• emacs• atom• geany• brackets• Kwrite• sublime• gedit• OnDemand!

Directory & File

Try it out yourself!• cd ~• ls• mkdir test1 test2• ls• rmdir test2• ls• cd test1• pwd• nano file1.txt• Hello World

• ls

Directory & File

Navigate in the system, editing files, working with directories, .etc. The object that you work on:• cp file1 file2 or dir

Ø Copy file1 to file2• cp –r dir1 dir2

Ø Copy dir1 to dir2 with contents

Directory & File

Navigate in the system, editing files, working with directories, .etc. The object that you work on:• cp file1 file2 or dir


Ø Copy dir1 to dir2 with contents• mv file1 file2

Ø Rename file1 as file2

Directory & File

Navigate in the system, editing files, working with directories, .etc. The object that you work on:• cp file1 file2



Ø Rename file1 as file2• ln –s dir_path new_dir_path

Ø Create a symbolic link to dir_path

Directory & File

Navigate in the system, editing files, working with directories, .etc. The object that you work on:• cp file1 file2



Ø Rename file1 as file2• ln –s dir_path new_dir_path

Ø Create a symbolic link to dir_path• nl –b a file1

Ø Number lines in file1,including the empty lines.

Directory & File

• clearØ Clear the terminal screen

Directory & File


• Command 1 | command 2Ø Use output of command 1 as the input of command 2

Directory & File


• Command 1 | command 2Ø Use output of command 1 as the input of command 2

• Command > fileØ Save output to file

• Command >> fileØ Append output to file

• Command 2> fileØ Redirect error message to file

• Command < fileØ Use data from file as input of command

Directory & File

Work with text files:• cat file_name

Ø Display file content• less file_name

Ø Display a long text file per page at a time• more file_name

Ø Display a long text file per page at a time

Directory & File

Work with text files:• cat file_name

Ø Display file content• less file_name

Ø Display a long text file per page at a time• more file_name

Ø Display a long text file per page at a time• head file_name

Ø Display first 10 lines of a file• tail file_name

Ø Display last 10 lines of a file

Directory & File

Try it out yourself!• cp file1.txt file2.txt• mv file2.txt newfile2.txt• ln –s link dir• seq 1 2 100 > file3.txt• less file3.txt• Seq 2 2 100 >>file3.txt• head file3.txt• tail file3.txt• Typenonsense 2> error.err• cat error.err• Seq 2 3 100 | tail

Directory & File

Work with text files:• paste <-s> file1 file2 > file3

Ø Combine lines in file1 and file2, save output to file3

Directory & File


Ø Combine lines in file1 and file2, save output to file3• csplit file line_number <–f prefix>

Ø Split file at the end of line_number and name the output files as prefix00 prefix01

Directory & File




• fold –w width –s file1Ø Wrap each line to fit in a specific width (default 80), break

at space

Directory & File




• fold –w width –s file1Ø Wrap each line to fit in a specific width (default 80), break

at space• diff file1_name file2_name• sdiff file1_name file2_name

Ø Difference between two filesØ Side by side comparison

Directory & File

Searching for something? Look no further:• grep pattern file

Ø Search text for specific pattern• grep –i pattern file

Ø Search with case insensitive pattern• grep --color pattern file

Ø High pattern in search result• grep –r pattern dir

Ø Search pattern recursively. • grep –c pattern file

Ø Count the matching case

Directory & File

Searching for something? Look no further:• find dir_name –name file_name

Ø Find file “file_name” in directory dir_name• find dir_name –atime or -mmin n

Ø The file was last accessed more than n days or minutes ago• find dir_name –iname file_name

Ø Search for file_name ignore case• find dir_name –executable

Ø Search for executable files• which

Ø List the path for a commad

Directory & File

Navigate in the system, editing files, working with directories, .etc. The object that you work on:• wget file_url

Ø Download file from web

Directory & File

Navigate in the system, editing files, working with directories, .etc. The object that you work on:• wget file_url

Ø Download file from web• tar –cf or -xf file_list or file.tar

Ø Compress or Extract files • gzip (-l) file_name

Ø Compress file to .gz (with info)• gzip –d or gunzip file.gz

Ø Decompress file.gz• unzip file.zip

Ø Decompress file.zip

Directory & File

Changing permissions!• chmod permissions file_name

Ø permissions:o u: user(owner) g: group o: otherso r: read (4) w: write (2) x: execute (1) o No permission (0)

Ø chmod u=rwx,g=rx,o=r file_nameØ chmod 754 file_name

o User have the right to read, write, and executeo Group members have the right to read and executeo Others have the right to read

Ø chmod +x file_nameo Executable for owner and group

Directory & File

Changing owner and group!• chown ownername file/dir

Ø Change the owner of a file or directoryØ Use –R for recursively change ownership under a directory

• chown :groupname file/dir• chgrp groupname file/dir

Ø Change the group of a file or directoryØ Use –R for recursively change group under a directory

Tips & Tricks

q Change the permission of your scriptØ chmod +x script.sh

q Create aliases for common commandsØ alias mybook=“echo cat in the hat”Ø alias interact=“srun -p interactive –n 1 --pty --x11=first --

mem=8G bash”

Directory & File

Try it out yourself!• paste –s file1.txt file3.txt > file13.txt• fold file13.txt –w 60• grep --color 9 file3.txt• which wget• chmod +x file3.txt

More Information:

Wiki:• go.tufts.edu/cluster OR • https://wikis.uit.tufts.edu/confluence/display/TuftsUITResear

chComputing/Homego to High Performance Compute Cluster/Linux

Linux Reference:• https://linoxide.com/guide/linux-command-shelf.html• https://www.howtoforge.com/linux-commands/

Google it!

https://linoxide.com/guide/linux-command-shelf.html

https://www.howtoforge.com/linux-commands/

Contact RT-TTS

If you have any questions regarding to Tufts HPC cluster access or usage,Please feel free to contact us at:

[email protected]

Introduction to Basic Linux | Tufts Technology Services

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