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Shell Scripting with Bash
Introduction to Shell Scripting with Bash Charles Jahnke Research Computing Services Information Services & Technology Topics for Today ● Introductions ● Basic Terminology ● How to get help ● Command-line vs. Scripting ● Variables ● Handling Arguments ● Standard I/O, Pipes, and Redirection ● Control Structures (loops and If statements) ● SCC Job Submission Example Research Computing Services Research Computing Services (RCS) A group within Information Services & Technology at Boston University provides computing, storage, and visualization resources and services to support research that has specialized or highly intensive computation, storage, bandwidth, or graphics requirements. Three Primary Services: ● Research Computation ● Research Visualization ● Research Consulting and Training Breadth of Research on the Shared Computing Cluster (SCC) Me ● Research Facilitator and Administrator ● Background in biomedical engineering, bioinformatics, and IT systems ● Offices on both CRC and BUMC ○ Most of our staff on the Charles River Campus, some dedicated to BUMC ● Contact: [email protected] You ● Who has experience programming? ● Using Linux? ● Using the Shared Computing Cluster (SCC)? Basic Terminology The Command-line The line on which commands are typed and passed to the shell. Username Hostname Current Directory [username@scc1 ~]$ Prompt Command Line (input) The Shell ● The interface between the user and the operating system ● Program that interprets and executes input ● Provides: ○ Built-in commands ○ Programming control structures ○ Environment -
CST8207 – Linux O/S I
Mounting a Filesystem Directory Structure Fstab Mount command CST8207 - Algonquin College 2 Chapter 12: page 467 - 496 CST8207 - Algonquin College 3 The mount utility connects filesystems to the Linux directory hierarchy. The mount point is a directory in the local filesystem where you can access mounted filesystem. This directory must exist before you can mount a filesystem. All filesystems visible on the system exist as a mounted filesystem someplace below the root (/) directory CST8207 - Algonquin College 4 can be mounted manually ◦ can be listed in /etc/fstab, but not necessary ◦ all mounting information supplied manually at command line by user or administrator can be mounted automatically on startup ◦ must be listed /etc/fstab, with all appropriate information and options required Every filesystem, drive, storage device is listed as a mounted filesystem associated to a directory someplace under the root (/) directory CST8207 - Algonquin College 5 CST8207 - Algonquin College 6 Benefits Scalable ◦ As new drives are added and new partitions are created, further filesystems can be mounted at various mount points as required. ◦ This means a Linux system does not need to worry about running out of disk space. Transparent ◦ No application would stop working if transferred to a different partition, because access to data is done via the mount point. ◦ Also transparent to user CST8207 - Algonquin College 7 All known filesystems volumes are typically listed in the /etc/fstab (static information about filesystem) file to help automate the mounting process If it is not listed in the /etc/fstab file, then all appropriate information about the filesystem needs to be listed manually at the command line. -
Windows Command Prompt Cheatsheet
Windows Command Prompt Cheatsheet - Command line interface (as opposed to a GUI - graphical user interface) - Used to execute programs - Commands are small programs that do something useful - There are many commands already included with Windows, but we will use a few. - A filepath is where you are in the filesystem • C: is the C drive • C:\user\Documents is the Documents folder • C:\user\Documents\hello.c is a file in the Documents folder Command What it Does Usage dir Displays a list of a folder’s files dir (shows current folder) and subfolders dir myfolder cd Displays the name of the current cd filepath chdir directory or changes the current chdir filepath folder. cd .. (goes one directory up) md Creates a folder (directory) md folder-name mkdir mkdir folder-name rm Deletes a folder (directory) rm folder-name rmdir rmdir folder-name rm /s folder-name rmdir /s folder-name Note: if the folder isn’t empty, you must add the /s. copy Copies a file from one location to copy filepath-from filepath-to another move Moves file from one folder to move folder1\file.txt folder2\ another ren Changes the name of a file ren file1 file2 rename del Deletes one or more files del filename exit Exits batch script or current exit command control echo Used to display a message or to echo message turn off/on messages in batch scripts type Displays contents of a text file type myfile.txt fc Compares two files and displays fc file1 file2 the difference between them cls Clears the screen cls help Provides more details about help (lists all commands) DOS/Command Prompt help command commands Source: https://technet.microsoft.com/en-us/library/cc754340.aspx. -
UKUI: a Lightweight Desktop Environment Based on Pluggable
2016 International Conference on Artificial Intelligence and Computer Science (AICS 2016) ISBN: 978-1-60595-411-0 UKUI: A Lightweight Desktop Environment Based on Pluggable Framework for Linux Distribution Jie YU1, Lu SI1,*, Jun MA1, Lei LUO1, Xiao-dong LIU1, Ya-ting KUANG2, Huan PENG2, Rui LI1, Jin-zhu KONG2 and Qing-bo WU1 1College of Computer, National University of Defense Technology, Changsha, China 2Tianjin KYLIN Information Technology Co., Ltd, Tianjin, China *[email protected] *Corresponding author Keywords: Desktop environment, Ubuntu, User interface. Abstract. Ubuntu is an operating system with Linux kernel based on Debian and distributed as free and open-source software. It uses Unity as its default desktop environment, which results in more difficulties of usage for Microsoft Windows users. In this paper, we present a lightweight desktop environment named UKUI based on UbuntuKylin, the official Chinese version of Ubuntu, for Linux distribution. It is designed as a pluggable framework and provides better user experience during human-computer interaction. In order to evaluate the performance of UKUI, a set of testing bench suits were performed on a personal computer. Overall, the results showed that UKUI has better performance compared with Unity. Introduction Linux is a freely available operating system (OS) originated by Linux Torvalds and further developed by thousands of others. Typically, Linux is packaged in a form known as a Linux distribution for both desktop and server use. Some of the most popular mainstream Linux distributions are Red Hat [1], Ubuntu [2], Arch [3], openSUSY [4], Gentoo [5], etc. There are several desktop environments available for nowadays modern Linux distributions, such as XFCE [6], GNOME [7], KDE [8] and LXDE [9]. -
Linux Tutorial Last Updated: September 29 2021 for Windows Users
VLAAMS SUPERCOMPUTER Innovative Computing CENTRUM for A Smarter Flanders Linux Tutorial Last updated: September 29 2021 For Windows Users Authors: Jasper Devreker (UGent), Ewan Higgs (UGent), Kenneth Hoste (UGent) Acknowledgement: VSCentrum.be Audience: This document is a hands-on guide for using the Linux command line in the context of the UGent HPC infrastructure. The command line (sometimes called ’shell’) can seems daunting at first, but with a little understanding can be very easy to use. Everything you do startsatthe prompt. Here you have the liberty to type in any commands you want. Soon, you will be able to move past the limited point and click interface and express interesting ideas to the computer using the shell. Gaining an understanding of the fundamentals of Linux will help accelerate your research using the HPC infrastructure. You will learn about commands, managing files, and some scripting basics. Notification: In$ commands this tutorial specific commands are separated from the accompanying text: These should be entered by the reader at a command line in a terminal on the UGent-HPC. They appear in all exercises preceded by a $ and printed in bold. You’ll find those actions ina grey frame. Button are menus, buttons or drop down boxes to be pressed or selected. “Directory” is the notation for directories (called “folders” in Windows terminology) or specific files. (e.g., “/user/home/gent/vsc400/vsc40000”) “Text” Is the notation for text to be entered. Tip: A “Tip” paragraph is used for remarks or tips. They can also be downloaded from the VSC website at https://www.vscentrum.be. -
File System, Files, and *Tab /Etc/Fstab
File system, files, and *tab File system files directories volumes, file systems mounting points local versus networked file systems 1 /etc/fstab Specifies what is to be mounted where and how fs_spec: describes block special device for remote filesystem to be mounted fs_file: describes the mount point fs_vfstype: describes the type of file system fs_mntops: describes the mount options associated with the filesystem 2 /etc/fstab cont. fs_freq: used by the dump command fs_passno: used by fsck to determine the order in which checks are done at boot time. Root file systems should be specified as 1, others should be 2. Value 0 means that file system does not need to be checked 3 /etc/fstab 4 from blocks to mounting points metadata inodes directories superblocks 5 mounting file systems mounting e.g., mount -a unmounting manually or during shutdown umount 6 /etc/mtab see what is mounted 7 Network File System Access file system (FS) over a network looks like a local file system to user e.g. mount user FS rather than duplicating it (which would be a disaster) Developed by Sun Microsystems (mid 80s) history for NFS: NFS, NFSv2, NFSv3, NFSv4 RFC 3530 (from 2003) take a look to see what these RFCs are like!) 8 Network File System How does this actually work? server needs to export the system client needs to mount the system server: /etc/exports file client: /etc/fstab file 9 Network File System Security concerns UID GID What problems could arise? 10 Network File System example from our raid system (what is a RAID again?) Example of exports file from -
“Linux at the Command Line” Don Johnson of BU IS&T We’Ll Start with a Sign in Sheet
“Linux at the Command Line” Don Johnson of BU IS&T We’ll start with a sign in sheet. We’ll end with a class evaluation. We’ll cover as much as we can in the time allowed; if we don’t cover everything, you’ll pick it up as you continue working with Linux. This is a hands-on, lab class; ask questions at any time. Commands for you to type are in BOLD The Most Common O/S Used By BU Researchers When Working on a Server or Computer Cluster Linux is a Unix clone begun in 1991 and written from scratch by Linus Torvalds with assistance from a loosely-knit team of hackers across the Net. 64% of the world’s servers run some variant of Unix or Linux. The Android phone and the Kindle run Linux. a set of small Linux is an O/S core programs written by written by Linus Richard Stallman and Torvalds and others others. They are the AND GNU utilities. http://www.gnu.org/ Network: ssh, scp Shells: BASH, TCSH, clear, history, chsh, echo, set, setenv, xargs System Information: w, whoami, man, info, which, free, echo, date, cal, df, free Command Information: man, info Symbols: |, >, >>, <, ;, ~, ., .. Filters: grep, egrep, more, less, head, tail Hotkeys: <ctrl><c>, <ctrl><d> File System: ls, mkdir, cd, pwd, mv, touch, file, find, diff, cmp, du, chmod, find File Editors: gedit, nedit You need a “xterm” emulation – software that emulates an “X” terminal and that connects using the “SSH” Secure Shell protocol. ◦ Windows Use StarNet “X-Win32:” http://www.bu.edu/tech/support/desktop/ distribution/xwindows/xwin32/ ◦ Mac OS X “Terminal” is already installed Why? Darwin, the system on which Apple's Mac OS X is built, is a derivative of 4.4BSD-Lite2 and FreeBSD. -
The Linux Command Line
The Linux Command Line Fifth Internet Edition William Shotts A LinuxCommand.org Book Copyright ©2008-2019, William E. Shotts, Jr. This work is licensed under the Creative Commons Attribution-Noncommercial-No De- rivative Works 3.0 United States License. To view a copy of this license, visit the link above or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042. A version of this book is also available in printed form, published by No Starch Press. Copies may be purchased wherever fine books are sold. No Starch Press also offers elec- tronic formats for popular e-readers. They can be reached at: https://www.nostarch.com. Linux® is the registered trademark of Linus Torvalds. All other trademarks belong to their respective owners. This book is part of the LinuxCommand.org project, a site for Linux education and advo- cacy devoted to helping users of legacy operating systems migrate into the future. You may contact the LinuxCommand.org project at http://linuxcommand.org. Release History Version Date Description 19.01A January 28, 2019 Fifth Internet Edition (Corrected TOC) 19.01 January 17, 2019 Fifth Internet Edition. 17.10 October 19, 2017 Fourth Internet Edition. 16.07 July 28, 2016 Third Internet Edition. 13.07 July 6, 2013 Second Internet Edition. 09.12 December 14, 2009 First Internet Edition. Table of Contents Introduction....................................................................................................xvi Why Use the Command Line?......................................................................................xvi -
Filesystem Hierarchy Standard
Filesystem Hierarchy Standard LSB Workgroup, The Linux Foundation Filesystem Hierarchy Standard LSB Workgroup, The Linux Foundation Version 3.0 Publication date March 19, 2015 Copyright © 2015 The Linux Foundation Copyright © 1994-2004 Daniel Quinlan Copyright © 2001-2004 Paul 'Rusty' Russell Copyright © 2003-2004 Christopher Yeoh Abstract This standard consists of a set of requirements and guidelines for file and directory placement under UNIX-like operating systems. The guidelines are intended to support interoperability of applications, system administration tools, development tools, and scripts as well as greater uniformity of documentation for these systems. All trademarks and copyrights are owned by their owners, unless specifically noted otherwise. Use of a term in this document should not be regarded as affecting the validity of any trademark or service mark. Permission is granted to make and distribute verbatim copies of this standard provided the copyright and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this standard under the conditions for verbatim copying, provided also that the title page is labeled as modified including a reference to the original standard, provided that information on retrieving the original standard is included, and provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this standard into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the copyright holder. Dedication This release is dedicated to the memory of Christopher Yeoh, a long-time friend and colleague, and one of the original editors of the FHS. -
Ardpower Documentation Release V1.2.0
ardPower Documentation Release v1.2.0 Anirban Roy Das Sep 27, 2017 Contents 1 Introduction 1 2 Screenshot 3 3 Documentaion 5 3.1 Overview.................................................5 3.2 Installation................................................7 3.3 Usage................................................... 12 4 Indices and tables 13 i ii CHAPTER 1 Introduction Its a custom Oh-My-Zsh Theme inspired by many custom themes suited for a perfect ZSH Environment under Byobu with Tmux Backend. 1 ardPower Documentation, Release v1.2.0 2 Chapter 1. Introduction 3 ardPower Documentation, Release v1.2.0 CHAPTER 2 Screenshot 4 Chapter 2. Screenshot CHAPTER 3 Documentaion You can also find PDF version of the documentation here. Overview We will start with understanding the individual components of an entire CLI. Generally we don’t put much attention to what we do. We just fire up a terminal or some say sheel and start typing our commands and get the result. That’s all. But there are a lot of things that goes behind all this. Terminal The very first component is the Terminal. So what is a Terminal? A terminal emulator, terminal application, term, or tty for short, is a program that emulates a video ter- minal within some other display architecture. Though typically synonymous with a shell or text terminal, the term terminal covers all remote terminals, including graphical interfaces. A terminal emulator inside a graphical user interface is often called a terminal window.A terminal window allows the user access to a text terminal and all its applications such as command-line interfaces (CLI) and text user interface (TUI) applications. -
UNIX X Command Tips and Tricks David B
SESUG Paper 122-2019 UNIX X Command Tips and Tricks David B. Horvath, MS, CCP ABSTRACT SAS® provides the ability to execute operating system level commands from within your SAS code – generically known as the “X Command”. This session explores the various commands, the advantages and disadvantages of each, and their alternatives. The focus is on UNIX/Linux but much of the same applies to Windows as well. Under SAS EG, any issued commands execute on the SAS engine, not necessarily on the PC. X %sysexec Call system Systask command Filename pipe &SYSRC Waitfor Alternatives will also be addressed – how to handle when NOXCMD is the default for your installation, saving results, and error checking. INTRODUCTION In this paper I will be covering some of the basics of the functionality within SAS that allows you to execute operating system commands from within your program. There are multiple ways you can do so – external to data steps, within data steps, and within macros. All of these, along with error checking, will be covered. RELEVANT OPTIONS Execution of any of the SAS System command execution commands depends on one option's setting: XCMD Enables the X command in SAS. Which can only be set at startup: options xcmd; ____ 30 WARNING 30-12: SAS option XCMD is valid only at startup of the SAS System. The SAS option is ignored. Unfortunately, ff NOXCMD is set at startup time, you're out of luck. Sorry! You might want to have a conversation with your system administrators to determine why and if you can get it changed. -
Useful Commands in Linux and Other Tools for Quality Control
Useful commands in Linux and other tools for quality control Ignacio Aguilar INIA Uruguay 05-2018 Unix Basic Commands pwd show working directory ls list files in working directory ll as before but with more information mkdir d make a directory d cd d change to directory d Copy and moving commands To copy file cp /home/user/is . To copy file directory cp –r /home/folder . to move file aa into bb in folder test mv aa ./test/bb To delete rm yy delete the file yy rm –r xx delete the folder xx Redirections & pipe Redirection useful to read/write from file !! aa < bb program aa reads from file bb blupf90 < in aa > bb program aa write in file bb blupf90 < in > log Redirections & pipe “|” similar to redirection but instead to write to a file, passes content as input to other command tee copy standard input to standard output and save in a file echo copy stream to standard output Example: program blupf90 reads name of parameter file and writes output in terminal and in file log echo par.b90 | blupf90 | tee blup.log Other popular commands head file print first 10 lines list file page-by-page tail file print last 10 lines less file list file line-by-line or page-by-page wc –l file count lines grep text file find lines that contains text cat file1 fiel2 concatenate files sort sort file cut cuts specific columns join join lines of two files on specific columns paste paste lines of two file expand replace TAB with spaces uniq retain unique lines on a sorted file head / tail $ head pedigree.txt 1 0 0 2 0 0 3 0 0 4 0 0 5 0 0 6 0 0 7 0 0 8 0 0 9 0 0 10