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3 Linux

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13 views35 pages

3 Linux

Uploaded by

majir61269
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Linux

T: +27 51 401 9111 | E: [email protected] | www.ufs.ac.za


Contents
• Introduction
• Linux User Interfaces
• Linux File System
• Linux Terminal Demonstration
Introduction
Linux
• Unix-like operating system
• GNU/Linux
⚫ GNU system packages with Linux Kernel

• Standard operating system for HPC / Servers / etc.


• Community driven, open-source and free to use and distribute
• Thus, many flavors or distributions
Linux Advantages & Disadvantages
• Advantages
⚫ Free to use and distribute

⚫ Bugs are found and fixed quicker

⚫ Transparency natural fit for scientists

• Disadvantages
⚫ Software compilation – not user friendly

⚫ Not Windows
Linux Distributions
• Linux Mint (https://linuxmint.com/)

• Pop!_OS (https://pop.system76.com/)

• Fedora (https://getfedora.org/)

• Ubuntu (https://ubuntu.com/)

• Hanna Montana Linux (http://hannahmontana.sourceforge.net/)


Linux User Interfaces
Linux User Interfaces
• Two main types
⚫ Graphical User Interface (GUI)

⚫ Text Interface (Terminal)

• Main HPC interface → Text Interface


Linux GUIs
• Many options
• Desktop Managers
⚫ GNOME

⚫ KDE Plasma

⚫ XFCE

⚫ Cinnamon

⚫ ETC
Linux Mint with Cinnamon
Garuda Linux with KDE Plasma
Rocky Linux with GNOME3
Terminal – Terminal Emulators
Linux File System
Linux File system
• File System
⚫ Collection of methods OS uses to manage data on a storage device such as hard
disks
• Partition Types:
⚫ NTFS, FATx (Microsoft)
⚫ Ext4 (Linux)
⚫ HFS (Apple)
• Windows can only read NTFS and FATx partition / not Ext4
• Linux can read most partition types
• Files and directories organized differently from Windows
Windows File System
Windows File System
Linux File system
• All storage devices amalgamated into one root file system
• Top directory --> Root or /
• Storage devices mounted in directories within /
• Home directories --> / home / <username>
⚫ Users have full permissions in their own home directories
⚫ No write permissions in system directories
⚫ More secure
• File extensions for your convenience and not important in Linux
Linux File system
Linux File system
Linux File system
File and directory paths

Windows Linux

I: \ Fantasy /media/leon/MOVIES/Fantasy

Drive Directory Directory mount point Directory


Letter
Linux Terminal Demonstration
Introduction
• Use terminal commands to navigate and perform actions
• Each terminal command is usually a stand-alone program
• Common interfaces with most CLI commands / programs
⚫ Positional arguments: cp <source> <destination>
⚫ Options/Flags can be in long form or short hand
⚫ Long form: --help
⚫ Short hand: -h
⚫ Using (-h) or (--help) --> most cases --> show how to use command/program
⚫ Using man <command> will display the command’s manual
Navigation in the Linux
• Short-cuts:
⚫ / : Root Directory
⚫ . : Present Working Directory (PWD)
⚫ .. : One directory above the PWD
⚫ ~ : Home directory for the current user
⚫ - : Previous directory (only used with cd)
• pwd
• ls
• cd
• find
Performing File Operations
• mkdir

• touch

• cp

• mv

• rm
Viewing File Contents
• cat

• more

• less

• head

• tail
Miscellaneous Commands
• tar

• screen
Regular Expressions
• Patterns that match strings

• Can become complex very quickly → gentle introduction

• Steps for crafting a regular expression:

• Identify common patterns

• Write the regular expression based on common pattern

• Test the regular expression


Identifying Patterns
• Example: The following files are generated by an experiment:
• foo_stats.txt
• foo_seq1.fasta
• foo_seq2.fasta
• foo_seq3.fasta
• foo_timings.fasta
• hpc_job.error
• hpc_job.output
• hpc_job.nodes
• hpc_job.txt
Regular Expressions
• Example: The following files are generated by an experiment:
• foo_stats.txt
• foo_seq1.fasta
• foo_seq2.fasta
• foo_seq3.fasta
• foo_timings.fasta
• hpc_job.error
• hpc_job.output
• hpc_job.nodes
• hpc_job.txt
Regular Expressions
• Example: The following files are generated by an experiment:
• foo_stats.txt
• foo_seq1.fasta
• foo_seq2.fasta
• foo_seq3.fasta
• foo_timings.fasta
• hpc_job.error
• hpc_job.output
• hpc_job.nodes
• hpc_job.txt
Regular Expressions
• Example: The following files are generated by an experiment:
• foo_stats.txt
• foo_seq1.fasta
• foo_seq2.fasta
• foo_seq3.fasta
• foo_timings.fasta
• hpc_job.error
• hpc_job.output
• hpc_job.nodes
• hpc_job.txt
Writing regular expressions
Element Definition Example
Character set or class Characters retaining their The prefix foo
literal meaning
Modifiers Expand or narrow the Asterisk (*) expands
text to match selection to all characters
Anchors Indicates the location Caret (^) indicates that
from where to match the pattern should be at
the beginning of the text

* Note that Anchors can only be used with tools such as grep and sed
Writing regular expressions - Example
• List all files that start with the prefix foo

• $ ls foo*

• List all files that end with the .fasta extension

• $ ls *.fasta

• Copy all files that start with the prefix hpc_job

• $ cp hpc_job* new_directory

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