INTRODUCTION TO BIOINFORMATICS
|
|
- Mariah Collins
- 5 years ago
- Views:
Transcription
1 Introducing the LINUX Operating System BecA-ILRI INTRODUCTION TO BIOINFORMATICS Mark Wamalwa BecA- ILRI Hub, Nairobi, Kenya h"p://hub.africabiosciences.org/ h"p:// 1
2 What is UNIX? A family of operating systems Multitasking IRIX Multiuser SOLARIS Runs more than one program at the same time. AIX Many different people can use A the busy system system at the can same be running time. LINUX several It is designed hundred to be or linked even to Digital thousands other computers UNIX of programs and to at allow the same people time. to work over a network. HP-UX The network IS the computer.... Networked 2
3 What is LINUX? Linus Torvalds n A freely available clone of the UNIX operating system for personal computers n Linux and Unix Time Sharing OPS: allow multiple users to use the system simultaneously Unix: developed in 1969 at Bell-Labs Linux is similar to Unix in some aspects 3
4 What does UNIX do? unix> help users Press ENTER to continue: UNIX Kernel X Xprog The Computer X Console The Pointy, User Controls Disk X Shell Interaction Window clicky storage programs access (or command program. System to the line) hardware. Run Allows Graphical Any Many Memory from number different the the interface user of shell users, to interact (point, can directly click, use typically Use Prevents any one drag, number with accessing programs drop the of etc.) computer actively programs the by at a interfering typing and system Network time methods commands. from enabled with adapter remote to access each other. system machines Provides The Can shell use from many interprets different any easy programs number way these ways for of at Modem programmers and once remote instructs machines the to talk kernel at the to the same electronics. accordingly. time. Is Screen a separate program Controls Very Easier powerful to data use than storage but the can and shell be Keyboard protection. intimidating but less powerful 4
5 Logging in Log in from anywhere. You must Log Have have in graphical from a username anywhere output (login sent you have anywhere id) to use you a unix/linux permission have system permission Every This user identifies is a member you of to one the system or more so groups it can of users. manage your work properly. This helps the system manage different types of user properly. 5
6 Logging in Connect to the linux machine using: Putty WinSCP - open source SFTP (SSH File Transfer Protocol) SCP (Secure CoPy) client for Windows using SSH (Secure SHell). Connecting to Connected. Welcome Xterm to Genotyping by Sequencing (GBS) workshop Login: Telnet Secure Shell username Kermit Other terminal emulators Password: The system will be unavailable unix linux is doesn t case sensitive. show during p/w username on Ramadhan. the screen is not as You have new mail. the you same type your as Username password. or USERNAME username@hpc~> You may get some messages here from the system administrator. 6
7 Accessing HPC from Windows systems n n Two stage process: Connecting to the system via secure shell (ssh) login Getting a graphical connection that supports X-Windows ssh connection: Need third party software. Local suggestion use putty n Process is slightly more awkward than ideal because local putty is configured for the Sun UNIX environment. n Better download putty.exe from Just runs from your desktop n Alternative cygwin - a Linux-like environment for Windows
8 Using Local PuTTY - 1 Better choice This is necessary for all PuTTY installs.
9 Using Local PuTTY - 2 linux
10 Using PuTTY-3
11 PuTTY Terminal Screen
12 The shell or command line Several 1. The Prompt. different shells but they behave more or less the same interactive your username The prompt can be the customised machine your to you look present how location you wish are logged in to 12
13 The shell or command line 2. Commands ls -ald ls -ald *.txt *.txt The shell breaks the command up into individual words The first word is a command The subsequent boundary between words form words a list a of space. arguments to For the the command shell to treat a phrase that includes arguments spaces as a beginning single word, with put - are it in options quotes: 'my word' or "my word". * is a special character. It means any group of Options control how the program runs. characters (including none). The shell finds all the '-a -l -d' is equivalent to '-ald' filenames that match anything.txt and adds them to the list of arguments 13
14 More Special Characters *? " ' Any word single group delineation character. of characters including none. & > < `` $ \ ; Cause Pipe. Redirect the the a process commands to run input. the background Pass output, eg. from the eg. output a file to a instead file of the of the command keyboard. Backticks String Backslash. Semicolon or Dollar (not on the '). left as the input Take Treat Change Seperate to the the output commands next meaning word of the as typed of on a the the in right. command variable next together. character. and as write an argument out its value Some special characters can lose their special meaning if they are inside quotes. 14
15 Organisation "Everything is a file" An ordinary file contains data. A directory contains other files. A link is a file that is a shortcut to another file. There data are could many be an other image, types a document, of file. a set of This instructions is a folder (a on program) windows. or A any directory fixed information. can contain Files can other have directories more than (sub-directories.) one name, and be in different directories at the same time 15
16 Organisation of the file system / bin usr home etc The top of the file system is the directory '/', Several commonly subdirectories known as the under root the directory root directory username Any example file in the users file home system can directory be uniquely with identified a subdirectory by and describing several the files path to it from the root directory. Another subdirectory. prot letter project seq4 seq3 seq2 seq1 /home/username/prot 16
17 Organisation of the file system bin usr home etc / Any process is located somewhere in the filesystem The command 'pwd' will tell you where. username@hpc ~> pwd pwd print /home/username working dir prot username letter seq4 project seq3 seq2 seq1 '~' is a linux shortcut for 'your home directory' 17
18 Looking at the file system bin usr home etc 'ls' lists the files in a username directory or directories prot letter project Without There are an many argument, options ls to lists ls that all the allow files you that to don't select start and control with. in the the information current directory it presents. seq4 seq3 seq2 seq1 username@hpc~> ~> ls project prot project: letter project seq1 seq2 seq3 seq4 / 18
19 Moving around the file system bin usr home etc / You can move to a different directory with the command 'cd directory ' prot username letter project 'directory' is the directory seq4 to seq3 which seq2 you seq1 want to move. The name can be written as the username@hpc full path ~/project> ~> cd (from /home/username/project root) cd or.. as the relative path username@hpc (from ~/project> ~> your pwd current directory) pwd '..' means the parent directory. /home/username/project repeat using the relative path '.' means the current directory... 19
20 Changing the file system bin usr home etc / You can create a new subdirectory in the current directory with the command ' mkdir directory ' username prot letter project model seq4 seq3 seq2 seq1 username@hpc ~> username@hpc ~> mkdir model 20
21 Changing the file system bin usr home etc You can delete an empty username subdirectory with the command ' rmdir directory' prot letter project model You can delete a file You with can the delete a subdirectory and command ' rm file its contents ' with the command seq4 seq3 seq2 seq1 ' rm -rf directory ' username@hpc ~> rmdir model username@hpc ~> rm prot username@hpc~> rm -rf directory / 21
22 More about files: filenames Filenames can contain any normal text character including spaces and special characters. Filenames can be almost any length. It is best to stick to a-z, A-Z, If a filename contains _, -, and numbers. It is best a to special keep them character short or a space you may need as it saves to put typing. quotes around the whole path. Special characters in filenames can cause problems with some programs. 22
23 More about files: reading files You can print the contents of one or more files to the screen with the command: 'cat file1 file2...' You can view the contents of one or more files a cat prints the whole file at once, so a file page at a time on the screen with the command: longer than just a few lines will run off ' more the file1 top of your file2 screen....' You can print the first few lines of a file with the command: more will let you search through a file, go 'head file1 backwards file2 and forwards...' and has many other functions. The last few lines can be viewed with 'tail' 23
24 More about files: editing files You can change the content of text files and create new files with a text editor. Text editors edit text. They do not try to format the text like word processors. A novice friendly basic text editor used as standard on many systems. Start with the A powerful editing environment which can be command 'pico filename' programmed. It has many modes for auto layout A powerful of program editor which code. Start can be with somewhat the command confusing for 'emacs newcomers. filename' It is designed for rapid editing of text files and programming. Start with the command 'vi filename' PICO EMACS VI Others: kedit,gedit,kwrite etc.. 24
25 More about files: copying files You can copy a file with the command 'cp oldfilename newfilename' username@hpc ~> ls letter project username@hpc ~> cp letter draft If newfilename is a directory, then the file will be copied to 'newfilename/oldfilename' username@hpc ~> ls draft letter project username@hpc ~> mv oldfilename newfilename Warning: If a file called newfilename already exists The command then 'mv it will oldfilename be overwritten. newfilename' can be used to rename a file 25
26 More about files: permissions Every file is protected. Permissions determine who can read, write, or execute a given file. Owner Group World The user who owns the file Other users in the same group All the as other users who in the owns the system. file. Files can have read (-r), write (-w) or execute (-x) permission for each of the three types of user. 26
27 More about files: permissions You can view the permissions for a file by listing it in long format with the command 'ls -l filename' username@hpc ~> ls -l letter -rwxr--r-- 1 username users 6048 Aug 17 16:07 letter The letter l The The date Permissions file The the type: Permissions files was size for The for the last user for the owner modified everyone owners who The owns files group else name group the file - - ordinary file d - directory l - link (shortcut) 27
28 More about files: permissions You can change the permissions for a file with the command 'chmod change filename' change ls -l letter is the modification you want chmod to o-r make letter to the files permissions ls -l letter username@hpc ~> -rwxr--r-- 1 username users 6048 Aug 17 16:07 letter username@hpc ~> username@hpc ~> -rwxr For Permissions How username whom you are you being changing users are changed: changing 6048 permissions: permissions: Aug 17 16:07 letter username@hpc o r - - ~> other read remove permission these permissions g w + - group write add these permissions u x = - user execute set permissions (run) permission to this a - all 28
29 Introduction to Awk Awk is a convenient and expressive programming language that can be applied to a wide variety of computing and data manipulation tasks.
30 Awk n Works well on record-type data n Reads input file(s) a line at a time n Parses each line into fields n Performs user-defined tests against each line, performs actions on matches
31 Other Common Uses n Input validation Every record have same # of fields? Do values make sense (negative time, hourly wage > $100, etc.)? n Filtering out certain fields n Searches Who got a zero on lab 3? Who got the highest grade? n Many others (it's late)
32 Invocation n Can write little one-liners on the command line (very handy): print the 3 rd field of every line: $ awk '{ print $3 }' input.txt n Execute an awk script file: $ awk f script.awk input.txt n Or, use this sha-bang as the first line, and give your script execute permissions: #!/bin/awk -f
33 Form of an AWK program n AWK programs are entries of the form: pattern { action } pattern some test, looking for a pattern (regular expressions) or C-like conditions n if null, actions are applies to every line action a statement or set of statements n if not provided, the default action is to print the entire line, much like grep
34 Awk Features n Patterns can be regular expressions or C like conditions. n Each line of the input is matched against the patterns, one after the next. If a match occurs the corresponding action is performed. n Input lines are parsed and split into fields, which are accessed by $1,,$NF, where NF is a variable set to the number of fields. The variable $0 contains the entire line, and by default lines are split by white space (blanks, tabs)
35 Variables n Not declared, nor typed n No character type Only strings and floats (support for ints) n $n refers to the nth field (where n is some integer value) # prints each field on the line for( i=1; i<=nf; ++i ) print $i
36 Some Built-in Variables n FS the input field separator n OFS the output field separator n NF # of fields; changes w/each record n NR the # of records read (so far). So, the current record #. n $0 the entire input line
37 Getting help You can get help on a command by using the command ' man command' If you do not know This what will bring a command up the is manual called, page use the option '-k' and to show get it a list to you of commands screen by screen that may be relevant 'man -k word' Try using the options This will '-h', find '-help', all manual or pages '--help' if you containing can't find word the man in the page. short description of the command. 37
38 Exercise: Filter SNPS Go to and run these commands in your home directory a) mkdir snp_data b) cd snp_data c) wget d) wget e) ls -alh f) grep '^23\ ^25\ ^26 Africa55K_10Pops.bim > AfricaAll_Pops_non_autosomal.rsids g) awk '{if ($1 > 22) print $2}' Africa55K_10Pops.bim > Africa55K_10Pops.xchrsnps 38
39 Example Print those employees who actually worked $ awk '$3>0 {print $1, $2*$3}' emp.data Kathy 40 Mark 100 Mary 121 Susie 76.5 $ cat emp.data Beth Dan Kathy Mark Mary Susie
40 Acknowledgement n SANBI (David Martin) n BSK Adapted from SANBI & Bioinformatics Society of Kenya/BSK 40
41 Useful literature 'Learning the UNIX operating system', O'Reilly press. Questions? 'UNIX Quickguide hpc 41
Introduction: What is Unix?
Introduction Introduction: What is Unix? An operating system Developed at AT&T Bell Labs in the 1960 s Command Line Interpreter GUIs (Window systems) are now available Introduction: Unix vs. Linux Unix
More informationIntroduction to UNIX. Logging in. Basic System Architecture 10/7/10. most systems have graphical login on Linux machines
Introduction to UNIX Logging in Basic system architecture Getting help Intro to shell (tcsh) Basic UNIX File Maintenance Intro to emacs I/O Redirection Shell scripts Logging in most systems have graphical
More informationPerl and R Scripting for Biologists
Perl and R Scripting for Biologists Lukas Mueller PLBR 4092 Course overview Linux basics (today) Linux advanced (Aure, next week) Why Linux? Free open source operating system based on UNIX specifications
More informationA Brief Introduction to the Linux Shell for Data Science
A Brief Introduction to the Linux Shell for Data Science Aris Anagnostopoulos 1 Introduction Here we will see a brief introduction of the Linux command line or shell as it is called. Linux is a Unix-like
More informationIntroduction to the Linux Command Line
Introduction to the Linux Command Line May, 2015 How to Connect (securely) ssh sftp scp Basic Unix or Linux Commands Files & directories Environment variables Not necessarily in this order.? Getting Connected
More informationChapter-3. Introduction to Unix: Fundamental Commands
Chapter-3 Introduction to Unix: Fundamental Commands What You Will Learn The fundamental commands of the Unix operating system. Everything told for Unix here is applicable to the Linux operating system
More informationUsing UNIX. -rwxr--r-- 1 root sys Sep 5 14:15 good_program
Using UNIX. UNIX is mainly a command line interface. This means that you write the commands you want executed. In the beginning that will seem inferior to windows point-and-click, but in the long run the
More informationcommandname flags arguments
Unix Review, additional Unix commands CS101, Mock Introduction This handout/lecture reviews some basic UNIX commands that you should know how to use. A more detailed description of this and other commands
More informationUser Guide Version 2.0
User Guide Version 2.0 Page 2 of 8 Summary Contents 1 INTRODUCTION... 3 2 SECURESHELL (SSH)... 4 2.1 ENABLING SSH... 4 2.2 DISABLING SSH... 4 2.2.1 Change Password... 4 2.2.2 Secure Shell Connection Information...
More informationLab Working with Linux Command Line
Introduction In this lab, you will use the Linux command line to manage files and folders and perform some basic administrative tasks. Recommended Equipment A computer with a Linux OS, either installed
More informationCSCI 2132 Software Development. Lecture 4: Files and Directories
CSCI 2132 Software Development Lecture 4: Files and Directories Instructor: Vlado Keselj Faculty of Computer Science Dalhousie University 12-Sep-2018 (4) CSCI 2132 1 Previous Lecture Some hardware concepts
More informationIntroduction to Linux. Fundamentals of Computer Science
Introduction to Linux Fundamentals of Computer Science Outline Operating Systems Linux History Linux Architecture Logging in to Linux Command Format Linux Filesystem Directory and File Commands Wildcard
More informationIntroduction to Linux for BlueBEAR. January
Introduction to Linux for BlueBEAR January 2019 http://intranet.birmingham.ac.uk/bear Overview Understanding of the BlueBEAR workflow Logging in to BlueBEAR Introduction to basic Linux commands Basic file
More informationSession 1: Accessing MUGrid and Command Line Basics
Session 1: Accessing MUGrid and Command Line Basics Craig A. Struble, Ph.D. July 14, 2010 1 Introduction The Marquette University Grid (MUGrid) is a collection of dedicated and opportunistic resources
More informationUoW HPC Quick Start. Information Technology Services University of Wollongong. ( Last updated on October 10, 2011)
UoW HPC Quick Start Information Technology Services University of Wollongong ( Last updated on October 10, 2011) 1 Contents 1 Logging into the HPC Cluster 3 1.1 From within the UoW campus.......................
More informationUnix Introduction to UNIX
Unix Introduction to UNIX Get Started Introduction The UNIX operating system Set of programs that act as a link between the computer and the user. Developed in 1969 by a group of AT&T employees Various
More informationPhysics REU Unix Tutorial
Physics REU Unix Tutorial What is unix? Unix is an operating system. In simple terms, its the set of programs that makes a computer work. It can be broken down into three parts. (1) kernel: The component
More informationIntroduction to Linux Workshop 1
Introduction to Linux Workshop 1 The George Washington University SEAS Computing Facility Created by Jason Hurlburt, Hadi Mohammadi, Marco Suarez hurlburj@gwu.edu Logging In The lab computers will authenticate
More informationHistory. Terminology. Opening a Terminal. Introduction to the Unix command line GNOME
Introduction to the Unix command line History Many contemporary computer operating systems, like Microsoft Windows and Mac OS X, offer primarily (but not exclusively) graphical user interfaces. The user
More informationMills HPC Tutorial Series. Linux Basics I
Mills HPC Tutorial Series Linux Basics I Objectives Command Line Window Anatomy Command Structure Command Examples Help Files and Directories Permissions Wildcards and Home (~) Redirection and Pipe Create
More informationIntroduction to the UNIX command line
Introduction to the UNIX command line Steven Abreu Introduction to Computer Science (ICS) Tutorial Jacobs University s.abreu@jacobs-university.de September 19, 2017 Overview What is UNIX? UNIX Shell Commands
More informationOutline. Structure of a UNIX command
Outline Structure of Unix Commands Command help (man) Log on (terminal vs. graphical) System information (utility) File and directory structure (path) Permission (owner, group, rwx) File and directory
More informationEECS Software Tools. Lab 2 Tutorial: Introduction to UNIX/Linux. Tilemachos Pechlivanoglou
EECS 2031 - Software Tools Lab 2 Tutorial: Introduction to UNIX/Linux Tilemachos Pechlivanoglou (tipech@eecs.yorku.ca) Sep 22 & 25, 2017 Material marked with will be in your exams Sep 22 & 25, 2017 Introduction
More informationIntroduction of Linux
Introduction of Linux 阳 oslab2018_class1@163.com 寅 oslab2018_class2@163.com PART I Brief Introduction Basic Conceptions & Environment Install & Configure a Virtual Machine Basic Commands PART II Shell
More informationContents. Note: pay attention to where you are. Note: Plaintext version. Note: pay attention to where you are... 1 Note: Plaintext version...
Contents Note: pay attention to where you are........................................... 1 Note: Plaintext version................................................... 1 Hello World of the Bash shell 2 Accessing
More informationCS Fundamentals of Programming II Fall Very Basic UNIX
CS 215 - Fundamentals of Programming II Fall 2012 - Very Basic UNIX This handout very briefly describes how to use Unix and how to use the Linux server and client machines in the CS (Project) Lab (KC-265)
More informationA Brief Introduction to Unix
A Brief Introduction to Unix Sean Barag Drexel University March 30, 2011 Sean Barag (Drexel University) CS 265 - A Brief Introduction to Unix March 30, 2011 1 / 17 Outline 1 Directories
More informationUnix/Linux Basics. Cpt S 223, Fall 2007 Copyright: Washington State University
Unix/Linux Basics 1 Some basics to remember Everything is case sensitive Eg., you can have two different files of the same name but different case in the same folder Console-driven (same as terminal )
More informationUnix File System. Class Meeting 2. * Notes adapted by Joy Mukherjee from previous work by other members of the CS faculty at Virginia Tech
Unix File System Class Meeting 2 * Notes adapted by Joy Mukherjee from previous work by other members of the CS faculty at Virginia Tech Unix File System The file system is your interface to: physical
More informationComputer Systems and Architecture
Computer Systems and Architecture Stephen Pauwels Computer Systems Academic Year 2018-2019 Overview of the Semester UNIX Introductie Regular Expressions Scripting Data Representation Integers, Fixed point,
More informationTHE HONG KONG POLYTECHNIC UNIVERSITY Department of Electronic and Information Engineering
THE HONG KONG POLYTECHNIC UNIVERSITY Department of Electronic and Information Engineering ENG224 Information Technology Part I: Computers and the Internet Laboratory 2 Linux Shell Commands and vi Editor
More informationGetting Started with UNIX
Getting Started with UNIX What is UNIX? Boston University Information Services & Technology Course Number: 4000 Course Instructor: Kenny Burns Operating System Interface between a user and the computer
More informationCS CS Tutorial 2 2 Winter 2018
CS CS 230 - Tutorial 2 2 Winter 2018 Sections 1. Unix Basics and connecting to CS environment 2. MIPS Introduction & CS230 Interface 3. Connecting Remotely If you haven t set up a CS environment password,
More informationUNIX. The Very 10 Short Howto for beginners. Soon-Hyung Yook. March 27, Soon-Hyung Yook UNIX March 27, / 29
UNIX The Very 10 Short Howto for beginners Soon-Hyung Yook March 27, 2015 Soon-Hyung Yook UNIX March 27, 2015 1 / 29 Table of Contents 1 History of Unix 2 What is UNIX? 3 What is Linux? 4 How does Unix
More informationComputer Systems and Architecture
Computer Systems and Architecture Introduction to UNIX Stephen Pauwels University of Antwerp October 2, 2015 Outline What is Unix? Getting started Streams Exercises UNIX Operating system Servers, desktops,
More informationIntroduction to Unix The Windows User perspective. Wes Frisby Kyle Horne Todd Johansen
Introduction to Unix The Windows User perspective Wes Frisby Kyle Horne Todd Johansen What is Unix? Portable, multi-tasking, and multi-user operating system Software development environment Hardware independent
More informationShell Programming Overview
Overview Shell programming is a way of taking several command line instructions that you would use in a Unix command prompt and incorporating them into one program. There are many versions of Unix. Some
More informationUnix Filesystem. January 26 th, 2004 Class Meeting 2
Unix Filesystem January 26 th, 2004 Class Meeting 2 * Notes adapted by Christian Allgood from previous work by other members of the CS faculty at Virginia Tech Unix Filesystem! The filesystem is your interface
More informationUnix Workshop Aug 2014
Unix Workshop 2014 5 Aug 2014 What is Unix Multitasking, multiuser operating system Often the OS of choice for large servers, large clusters Unix Around You You re probably familiar with these: Linux Solaris
More informationCS 215 Fundamentals of Programming II Spring 2019 Very Basic UNIX
CS 215 Fundamentals of Programming II Spring 2019 Very Basic UNIX This handout very briefly describes how to use Unix and how to use the Linux server and client machines in the EECS labs that dual boot
More informationIntroduction to Linux. Woo-Yeong Jeong Computer Systems Laboratory Sungkyunkwan University
Introduction to Linux Woo-Yeong Jeong (wooyeong@csl.skku.edu) Computer Systems Laboratory Sungkyunkwan University http://csl.skku.edu What is Linux? A Unix-like operating system of a computer What is an
More informationCENG 334 Computer Networks. Laboratory I Linux Tutorial
CENG 334 Computer Networks Laboratory I Linux Tutorial Contents 1. Logging In and Starting Session 2. Using Commands 1. Basic Commands 2. Working With Files and Directories 3. Permission Bits 3. Introduction
More informationCSCE 212H, Spring 2008, Matthews Lab Assignment 1: Representation of Integers Assigned: January 17 Due: January 22
CSCE 212H, Spring 2008, Matthews Lab Assignment 1: Representation of Integers Assigned: January 17 Due: January 22 Manton Matthews January 29, 2008 1 Overview The purpose of this assignment is to become
More informationEssential Linux Shell Commands
Essential Linux Shell Commands Special Characters Quoting and Escaping Change Directory Show Current Directory List Directory Contents Working with Files Working with Directories Special Characters There
More informationWorking with Basic Linux. Daniel Balagué
Working with Basic Linux Daniel Balagué How Linux Works? Everything in Linux is either a file or a process. A process is an executing program identified with a PID number. It runs in short or long duration
More informationOperating Systems. Copyleft 2005, Binnur Kurt
3 Operating Systems Copyleft 2005, Binnur Kurt Content The concept of an operating system. The internal architecture of an operating system. The architecture of the Linux operating system in more detail.
More informationIntroduction to Unix: Fundamental Commands
Introduction to Unix: Fundamental Commands Ricky Patterson UVA Library Based on slides from Turgut Yilmaz Istanbul Teknik University 1 What We Will Learn The fundamental commands of the Unix operating
More informationOperating Systems 3. Operating Systems. Content. What is an Operating System? What is an Operating System? Resource Abstraction and Sharing
Content 3 Operating Systems The concept of an operating system. The internal architecture of an operating system. The architecture of the Linux operating system in more detail. How to log into (and out
More informationIntroduction to Linux Part 1. Anita Orendt and Wim Cardoen Center for High Performance Computing 24 May 2017
Introduction to Linux Part 1 Anita Orendt and Wim Cardoen Center for High Performance Computing 24 May 2017 ssh Login or Interactive Node kingspeak.chpc.utah.edu Batch queue system kp001 kp002. kpxxx FastX
More informationLinux Command Line Primer. By: Scott Marshall
Linux Command Line Primer By: Scott Marshall Draft: 10/21/2007 Table of Contents Topic Page(s) Preface 1 General Filesystem Background Information 2 General Filesystem Commands 2 Working with Files and
More informationIntroduction to Linux
Introduction to Linux Mukesh Pund Principal Scientist, NISCAIR, New Delhi, India History In 1969, a team of developers developed a new operating system called Unix which was written using C Linus Torvalds,
More informationCS197U: A Hands on Introduction to Unix
CS197U: A Hands on Introduction to Unix Lecture 3: UNIX Operating System Organization Tian Guo CICS, Umass Amherst 1 Reminders Assignment 2 is due THURSDAY 09/24 at 3:45 pm Directions are on the website
More informationCrash Course in Unix. For more info check out the Unix man pages -orhttp://www.cs.rpi.edu/~hollingd/unix. -or- Unix in a Nutshell (an O Reilly book).
Crash Course in Unix For more info check out the Unix man pages -orhttp://www.cs.rpi.edu/~hollingd/unix -or- Unix in a Nutshell (an O Reilly book). 1 Unix Accounts To access a Unix system you need to have
More informationCSE 303 Lecture 2. Introduction to bash shell. read Linux Pocket Guide pp , 58-59, 60, 65-70, 71-72, 77-80
CSE 303 Lecture 2 Introduction to bash shell read Linux Pocket Guide pp. 37-46, 58-59, 60, 65-70, 71-72, 77-80 slides created by Marty Stepp http://www.cs.washington.edu/303/ 1 Unix file system structure
More informationUnix Basics. Benjamin S. Skrainka University College London. July 17, 2010
Unix Basics Benjamin S. Skrainka University College London July 17, 2010 Overview We cover basic Unix survival skills: Why you need some Unix in your life How to get some Unix in your life Basic commands
More informationEECS2301. Lab 1 Winter 2016
EECS2301 Lab 1 Winter 2016 Lab Objectives In this lab, you will be introduced to the Linux operating system. The basic commands will be presented in this lab. By the end of you alb, you will be asked to
More informationUnix L555. Dept. of Linguistics, Indiana University Fall Unix. Unix. Directories. Files. Useful Commands. Permissions. tar.
L555 Dept. of Linguistics, Indiana University Fall 2010 1 / 21 What is? is an operating system, like DOS or Windows developed in 1969 by Bell Labs works well for single computers as well as for servers
More informationOverview LEARN. History of Linux Linux Architecture Linux File System Linux Access Linux Commands File Permission Editors Conclusion and Questions
Lanka Education and Research Network Linux Architecture, Linux File System, Linux Basic Commands 28 th November 2016 Dilum Samarasinhe () Overview History of Linux Linux Architecture Linux File System
More informationIntroduction to Linux
Introduction to Linux M Tech CS I 2015-16 Arijit Bishnu Debapriyo Majumdar Sourav Sengupta Mandar Mitra Login, Logout, Change password $ ssh, ssh X secure shell $ ssh www.isical.ac.in $ ssh 192.168 $ logout,
More informationCHAPTER 1 UNIX FOR NONPROGRAMMERS
CHAPTER 1 UNIX FOR NONPROGRAMMERS The man command is used to display the manual entry associated with word entered as argument. The -k option is used displays a list of manual entries that contain entered
More informationVirtual Machine. Linux flavor : Debian. Everything (except slides) preinstalled for you. https://www.virtualbox.org/
Virtual Machine Anyone have problems installing it? VM: Virtual Box - allows you to run a different operating system within the current operating system of your machine. https://www.virtualbox.org/ Linux
More informationBrief Linux Presentation. July 10th, 2006 Elan Borenstein
Brief Linux Presentation July 10th, 2006 Elan Borenstein History 1965 - Bell Labs (AT&T), GE and MIT Project to develop a new (multiuser, multitasking) operating system - MULTICS. (not successful) History
More informationWelcome to getting started with Ubuntu Server. This System Administrator Manual. guide to be simple to follow, with step by step instructions
Welcome to getting started with Ubuntu 12.04 Server. This System Administrator Manual guide to be simple to follow, with step by step instructions with screenshots INDEX 1.Installation of Ubuntu 12.04
More informationIntroduction to Linux
Introduction to Linux Prof. Jin-Soo Kim( jinsookim@skku.edu) TA Sanghoon Han(sanghoon.han@csl.skku.edu) Computer Systems Laboratory Sungkyunkwan University http://csl.skku.edu Announcement (1) Please come
More informationh/w m/c Kernel shell Application s/w user
Structure of Unix h/w m/c Kernel shell Application s/w. user While working with unix, several layers of interaction occur b/w the computer h/w & the user. 1. Kernel : It is the first layer which runs on
More informationParallel Programming Pre-Assignment. Setting up the Software Environment
Parallel Programming Pre-Assignment Setting up the Software Environment Authors: B. Wilkinson and C. Ferner. Modification date: Aug 21, 2014 (Minor correction Aug 27, 2014.) Software The purpose of this
More informationPractical Session 0 Introduction to Linux
School of Computer Science and Software Engineering Clayton Campus, Monash University CSE2303 and CSE2304 Semester I, 2001 Practical Session 0 Introduction to Linux Novell accounts. Every Monash student
More informationCS4350 Unix Programming. Outline
Outline Unix Management Files and file systems Structure of Unix Commands Command help (man) Log on (terminal vs. graphical) System information (utility) File and directory structure (path) Permission
More informationIntroduction to Linux
Introduction to Linux Prof. Jin-Soo Kim( jinsookim@skku.edu) TA - Dong-Yun Lee (dylee@csl.skku.edu) Computer Systems Laboratory Sungkyunkwan University http://csl.skku.edu What is Linux? A Unix-like operating
More informationUnix/Linux Operating System. Introduction to Computational Statistics STAT 598G, Fall 2011
Unix/Linux Operating System Introduction to Computational Statistics STAT 598G, Fall 2011 Sergey Kirshner Department of Statistics, Purdue University September 7, 2011 Sergey Kirshner (Purdue University)
More informationThe Unix Shell & Shell Scripts
The Unix Shell & Shell Scripts You should do steps 1 to 7 before going to the lab. Use the Linux system you installed in the previous lab. In the lab do step 8, the TA may give you additional exercises
More informationExamples: Directory pathname: File pathname: /home/username/ics124/assignments/ /home/username/ops224/assignments/assn1.txt
ULI101 Week 03 Week Overview Absolute and relative pathnames File name expansion Shell basics Command execution in detail Recalling and editing previous commands Quoting Pathnames A pathname is a list
More informationUNIX File Hierarchy: Structure and Commands
UNIX File Hierarchy: Structure and Commands The UNIX operating system organizes files into a tree structure with a root named by the character /. An example of the directory tree is shown below. / bin
More informationTable Of Contents. 1. Zoo Information a. Logging in b. Transferring files 2. Unix Basics 3. Homework Commands
Table Of Contents 1. Zoo Information a. Logging in b. Transferring files 2. Unix Basics 3. Homework Commands Getting onto the Zoo Type ssh @node.zoo.cs.yale.edu, and enter your netid pass when prompted.
More informationIntroduction to Linux
Introduction to Linux The command-line interface A command-line interface (CLI) is a type of interface, that is, a way to interact with a computer. Window systems, punched cards or a bunch of dials, buttons
More informationFiles
http://www.cs.fsu.edu/~langley/cop3353-2013-1/reveal.js-2013-02-11/02.html?print-pdf 02/11/2013 10:55 AM Files A normal "flat" file is a collection of information. It's usually stored somewhere reasonably
More informationUnix Essentials. BaRC Hot Topics Bioinformatics and Research Computing Whitehead Institute October 12 th
Unix Essentials BaRC Hot Topics Bioinformatics and Research Computing Whitehead Institute October 12 th 2016 http://barc.wi.mit.edu/hot_topics/ 1 Outline Unix overview Logging in to tak Directory structure
More informationIntroduction to Linux
Introduction to Linux University of Bristol - Advance Computing Research Centre 1 / 47 Operating Systems Program running all the time Interfaces between other programs and hardware Provides abstractions
More informationScripting Languages Course 1. Diana Trandabăț
Scripting Languages Course 1 Diana Trandabăț Master in Computational Linguistics - 1 st year 2017-2018 Today s lecture Introduction to scripting languages What is a script? What is a scripting language
More informationCISC 220 fall 2011, set 1: Linux basics
CISC 220: System-Level Programming instructor: Margaret Lamb e-mail: malamb@cs.queensu.ca office: Goodwin 554 office phone: 533-6059 (internal extension 36059) office hours: Tues/Wed/Thurs 2-3 (this week
More informationCHE3935. Lecture 1. Introduction to Linux
CHE3935 Lecture 1 Introduction to Linux 1 Logging In PuTTY is a free telnet/ssh client that can be run without installing it within Windows. It will only give you a terminal interface, but used with a
More informationConnecting to ICS Server, Shell, Vim CS238P Operating Systems fall 18
Connecting to ICS Server, Shell, Vim CS238P Operating Systems fall 18 By Aftab Hussain (Adapted from Claudio A. Parra s Slides for Fall 18 CS-143A) October 5 2018 University of California, Irvine Andromeda
More informationCSE Linux VM. For Microsoft Windows. Based on opensuse Leap 42.2
CSE Linux VM For Microsoft Windows Based on opensuse Leap 42.2 Dr. K. M. Flurchick February 2, 2017 Contents 1 Introduction 1 2 Requirements 1 3 Procedure 1 4 Usage 3 4.1 Start/Stop.................................................
More informationCS246 Spring14 Programming Paradigm Notes on Linux
1 Unix History 1965: Researchers from Bell Labs and other organizations begin work on Multics, a state-of-the-art interactive, multi-user operating system. 1969: Bell Labs researchers, losing hope for
More informationINSE Lab 1 Introduction to UNIX Fall 2017
INSE 6130 - Lab 1 Introduction to UNIX Fall 2017 Updated by: Paria Shirani Overview In this lab session, students will learn the basics of UNIX /Linux commands. They will be able to perform the basic operations:
More informationUnix as a Platform Exercises + Solutions. Course Code: OS 01 UNXPLAT
Unix as a Platform Exercises + Solutions Course Code: OS 01 UNXPLAT Working with Unix Most if not all of these will require some investigation in the man pages. That's the idea, to get them used to looking
More informationLinux/Cygwin Practice Computer Architecture
Linux/Cygwin Practice 2010 Computer Architecture Linux Login Use ssh client applications to connect (Port : 22) SSH Clients zterm ( http://www.brainz.co.kr/products/products4_2.php ) Putty ( http://kldp.net/frs/download.php/3411/hangulputty-0.58.h2.exe
More informationLec 1 add-on: Linux Intro
Lec 1 add-on: Linux Intro Readings: - Unix Power Tools, Powers et al., O Reilly - Linux in a Nutshell, Siever et al., O Reilly Summary: - Linux File System - Users and Groups - Shell - Text Editors - Misc
More informationUnix and C Program Development SEEM
Unix and C Program Development SEEM 3460 1 Operating Systems A computer system cannot function without an operating system (OS). There are many different operating systems available for PCs, minicomputers,
More informationCS 2400 Laboratory Assignment #1: Exercises in Compilation and the UNIX Programming Environment (100 pts.)
1 Introduction 1 CS 2400 Laboratory Assignment #1: Exercises in Compilation and the UNIX Programming Environment (100 pts.) This laboratory is intended to give you some brief experience using the editing/compiling/file
More informationLinux Training. for New Users of Cluster. Georgia Advanced Computing Resource Center University of Georgia Suchitra Pakala
Linux Training for New Users of Cluster Georgia Advanced Computing Resource Center University of Georgia Suchitra Pakala pakala@uga.edu 1 Overview GACRC Linux Operating System Shell, Filesystem, and Common
More informationComputer Architecture Lab 1 (Starting with Linux)
Computer Architecture Lab 1 (Starting with Linux) Linux is a computer operating system. An operating system consists of the software that manages your computer and lets you run applications on it. The
More informationExploring UNIX: Session 3
Exploring UNIX: Session 3 UNIX file system permissions UNIX is a multi user operating system. This means several users can be logged in simultaneously. For obvious reasons UNIX makes sure users cannot
More informationCSE 390a Lecture 3. Multi-user systems; remote login; editors; users/groups; permissions
CSE 390a Lecture 3 Multi-user systems; remote login; editors; users/groups; permissions slides created by Marty Stepp, modified by Jessica Miller and Ruth Anderson http://www.cs.washington.edu/390a/ 1
More informationThis is Lab Worksheet 3 - not an Assignment
This is Lab Worksheet 3 - not an Assignment This Lab Worksheet contains some practical examples that will prepare you to complete your Assignments. You do not have to hand in this Lab Worksheet. Make sure
More informationWhen talking about how to launch commands and other things that is to be typed into the terminal, the following syntax is used:
Linux Tutorial How to read the examples When talking about how to launch commands and other things that is to be typed into the terminal, the following syntax is used: $ application file.txt
More informationIntroduction to UNIX command-line II
Introduction to UNIX command-line II Boyce Thompson Institute 2017 Prashant Hosmani Class Content Terminal file system navigation Wildcards, shortcuts and special characters File permissions Compression
More informationUsing LINUX a BCMB/CHEM 8190 Tutorial Updated (1/17/12)
Using LINUX a BCMB/CHEM 8190 Tutorial Updated (1/17/12) Objective: Learn some basic aspects of the UNIX operating system and how to use it. What is UNIX? UNIX is the operating system used by most computers
More informationIntroduction to Linux
Introduction to Linux Prof. Jin-Soo Kim( jinsookim@skku.edu) TA - Kisik Jeong (kisik@csl.skku.edu) Computer Systems Laboratory Sungkyunkwan University http://csl.skku.edu What is Linux? A Unix-like operating
More informationIntroduc)on to Linux Session 2 Files/Filesystems/Data. Pete Ruprecht Research Compu)ng Group University of Colorado Boulder
Introduc)on to Linux Session 2 Files/Filesystems/Data Pete Ruprecht Research Compu)ng Group University of Colorado Boulder www.rc.colorado.edu Outline LeHover from last week redirec)on Filesystem layout
More information