Shell Script Getopts Example
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Glibc and System Calls Documentation Release 1.0
Glibc and System Calls Documentation Release 1.0 Rishi Agrawal <[email protected]> Dec 28, 2017 Contents 1 Introduction 1 1.1 Acknowledgements...........................................1 2 Basics of a Linux System 3 2.1 Introduction...............................................3 2.2 Programs and Compilation........................................3 2.3 Libraries.................................................7 2.4 System Calls...............................................7 2.5 Kernel.................................................. 10 2.6 Conclusion................................................ 10 2.7 References................................................ 11 3 Working with glibc 13 3.1 Introduction............................................... 13 3.2 Why this chapter............................................. 13 3.3 What is glibc .............................................. 13 3.4 Download and extract glibc ...................................... 14 3.5 Walkthrough glibc ........................................... 14 3.6 Reading some functions of glibc ................................... 17 3.7 Compiling and installing glibc .................................... 18 3.8 Using new glibc ............................................ 21 3.9 Conclusion................................................ 23 4 System Calls On x86_64 from User Space 25 4.1 Setting Up Arguements......................................... 25 4.2 Calling the System Call......................................... 27 4.3 Retrieving the Return Value...................................... -
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 -
Chapter 4 Programming in Perl
Chapter 4 Programming in Perl 4.1 More on built-in functions in Perl There are many built-in functions in Perl, and even more are available as modules (see section 4.4) that can be downloaded from various Internet places. Some built-in functions have already been used in chapter 3.1 and some of these and some others will be described in more detail here. 4.1.1 split and join (+ qw, x operator, \here docs", .=) 1 #!/usr/bin/perl 2 3 $sequence = ">|SP:Q62671|RATTUS NORVEGICUS|"; 4 5 @parts = split '\|', $sequence; 6 for ( $i = 0; $i < @parts; $i++ ) { 7 print "Substring $i: $parts[$i]\n"; 8 } • split is used to split a string into an array of substrings. The program above will write out Substring 0: > Substring 1: SP:Q62671 Substring 2: RATTUS NORVEGICUS • The first argument of split specifies a regular expression, while the second is the string to be split. • The string is scanned for occurrences of the regexp which are taken to be the boundaries between the sub-strings. 57 58 CHAPTER 4. PROGRAMMING IN PERL • The parts of the string which are matched with the regexp are not included in the substrings. • Also empty substrings are extracted. Note, however that trailing empty strings are removed by default. • Note that the | character needs to be escaped in the example above, since it is a special character in a regexp. • split returns an array and since an array can be assigned to a list we can write: splitfasta.ply 1 #!/usr/bin/perl 2 3 $sequence=">|SP:Q62671|RATTUS NORVEGICUS|"; 4 5 ($marker, $code, $species) = split '\|', $sequence; 6 ($dummy, $acc) = split ':', $code; 7 print "This FastA sequence comes from the species $species\n"; 8 print "and has accession number $acc.\n"; splitfasta.ply • It is not uncommon that we want to write out long pieces of text using many print statements. -
The Clon User Manual the Command-Line Options Nuker, Version 1.0 Beta 25 "Michael Brecker"
The Clon User Manual The Command-Line Options Nuker, Version 1.0 beta 25 "Michael Brecker" Didier Verna <[email protected]> Copyright c 2010{2012, 2015, 2017, 2020, 2021 Didier Verna Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided also that the section entitled \Copy- ing" is included exactly as in the original. Permission is granted to copy and distribute translations of this manual into an- other language, under the above conditions for modified versions, except that this permission notice may be translated as well. Cover art by Alexis Angelidis. i Table of Contents Copying ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 1 1 Introduction :::::::::::::::::::::::::::::::::::::::::::::::::::: 3 2 Installation:::::::::::::::::::::::::::::::::::::::::::::::::::::: 5 3 Quick Start ::::::::::::::::::::::::::::::::::::::::::::::::::::: 7 3.1 Full Source :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 7 3.2 Explanation ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 7 4 Using Clon :::::::::::::::::::::::::::::::::::::::::::::::::::: 11 4.1 Synopsis Definition ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 11 4.1.1 Synopsis Items ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 11 4.1.1.1 Text :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -
Bash Shell Scripts
Bash Shell Scripts Writing Bash shell scripts Bash shell scripts are text files Text files most efficiently built with programming editors (emacs or vi) File must be executable and in search path chmod 700 my_script PATH environment variable may not include .! An example shell script: #!/bin/bash #My first script echo "Hello World!" Bash Shell Scripts Writing Bash shell scripts Compile a Verilog file with vlog #!/bin/bash if [ ! d work ] ; then echo work does not exist, making it vlib work fi if [ ! s adder.v ] ; then vlog adder.v fi work directory must exist before compilation Get scripts via wget, eg: wget http://web.engr.oregonstate.edu/~traylor/ece474/script --- Bash Shell Scripts Writing Bash shell scripts File attribute checking #!/bin/bash if [ ! s junk_dir ] ; then mkdir junk_dir fi Spaces around brackets are needed! File attribute checking d exists and is a directory e, a file exists f exists and is a regular file s file exists and is not empty --- Bash Shell Scripts Writing Bash shell scripts Compile Verilog then run a simultion #!/bin/bash if [ ! -d "work" ] ; then vlib work fi if [ -s "adder.v" ] ; then vlog adder.v #runs simulation with a do file and no GUI vsim adder -do do.do quiet c else echo verilog file missing fi --- Bash Shell Scripts Writing Bash shell scripts vsim command and arguments vsim entity_name do dofile.do quiet -c -quiet (do not report loading file messages) -c (console mode, no GUI) -do (run vsim from a TCL do file) +nowarnTFMPC (don’t warn about mismatched ports, scary) +nowarnTSCALE (don’t warn about timing mismatches) Try vsim help for command line arguements --- Bash Shell Scripts Writing Bash Shell Scripts (TCL Script) In another text file, we create a TCL script with commands for the simulator. -
Tcl/Tk for Xspecta Michael Flynn Tcl: Tcl (Ie Tool Command Language)
Tcl/Tk for XSPECTa Michael Flynn Tcl: Tcl (i.e. Tool Command Language) is an open source scripting language similar to other modern script languages such as Perl or Python. It is substantially more powerful than UNIX/LINUX/POSIX shell script languages such as the Bourne Shell (sh), the C Shell (csh), or the Korn Shell (https://en.wikipedia.org/wiki/Shell_script). Tcl and its associated graphical user interface toolkit, Tk, were developed by John Ousterhout of the University of California. Ousterhout's group subsequently continued development of Tcl/Tk while at Sun Microsystems and later at Scriptics. Continued development is now done by an open source project team. The language has been popular for developing graphic applications and is available as public domain software for almost all computer systems (Linux, Windows and MacOS). Installation: Tcl/Tk software can be found at: http://www.activestate.com/activeTcl Binary Windows installers are available from this site for both 32 and 64 bit systems as a Free Community Edition. The lab modules were last validated with Version 8.6.4.1 but more recent versions should not be problematic. Unless Tcl has already been installed on the system being used, download and install the software from ActiveState. The installer should be run with administrative privileges. On Windows7, you should right click and 'run as administrator'. Installing with elevated privilege will allow the registry changes that map Tcl extensions and will configure the un-installer database, making later removal of ActiveTcl easier. The ActiveState default installation directory is C:/Tcl. During the installation, the installer will ask if you want this changed. -
Bash Crash Course + Bc + Sed + Awk∗
Bash Crash course + bc + sed + awk∗ Andrey Lukyanenko, CSE, Aalto University Fall, 2011 There are many Unix shell programs: bash, sh, csh, tcsh, ksh, etc. The comparison of those can be found on-line 1. We will primary focus on the capabilities of bash v.4 shell2. 1. Each bash script can be considered as a text file which starts with #!/bin/bash. It informs the editor or interpretor which tries to open the file, what to do with the file and how should it be treated. The special character set in the beginning #! is a magic number; check man magic and /usr/share/file/magic on existing magic numbers if interested. 2. Each script (assume you created “scriptname.sh file) can be invoked by command <dir>/scriptname.sh in console, where <dir> is absolute or relative path to the script directory, e.g., ./scriptname.sh for current directory. If it has #! as the first line it will be invoked by this command, otherwise it can be called by command bash <dir>/scriptname.sh. Notice: to call script as ./scriptname.sh it has to be executable, i.e., call command chmod 555 scriptname.sh before- hand. 3. Variable in bash can be treated as integers or strings, depending on their value. There are set of operations and rules available for them. For example: #!/bin/bash var1=123 # Assigns value 123 to var1 echo var1 # Prints ’var1’ to output echo $var1 # Prints ’123’ to output var2 =321 # Error (var2: command not found) var2= 321 # Error (321: command not found) var2=321 # Correct var3=$var2 # Assigns value 321 from var2 to var3 echo $var3 # Prints ’321’ to output -
16.5. Getopt — Parser for Command Line Options — Python V2.6.4
Navigation • index • modules | • next | • previous | • Python v2.6.4 documentation » • The Python Standard Library » • 16. Generic Operating System Services » 16.5. getopt — Parser for command line options¶ This module helps scripts to parse the command line arguments in sys.argv. It supports the same conventions as the Unix getopt() function (including the special meanings of arguments of the form ‘-‘ and ‘--‘). Long options similar to those supported by GNU software may be used as well via an optional third argument. A more convenient, flexible, and powerful alternative is the optparse module. This module provides two functions and an exception: getopt.getopt(args, options[, long_options])¶ Parses command line options and parameter list. args is the argument list to be parsed, without the leading reference to the running program. Typically, this means sys.argv[1:]. options is the string of option letters that the script wants to recognize, with options that require an argument followed by a colon (':'; i.e., the same format that Unix getopt() uses). Note Unlike GNU getopt(), after a non-option argument, all further arguments are considered also non-options. This is similar to the way non-GNU Unix systems work. long_options, if specified, must be a list of strings with the names of the long options which should be supported. The leading '--' characters should not be included in the option name. Long options which require an argument should be followed by an equal sign ('='). Optional arguments are not supported. To accept only long options, options should be an empty string. Long options on the command line can be recognized so long as they provide a prefix of the option name that matches exactly one of the accepted options. -
Research Computing and Cyberinfrastructure Team
Research Computing and CyberInfrastructure team ! Working with the Linux Shell on the CWRU HPC 31 January 2019 7 February 2019 ! Presenter Emily Dragowsky KSL Data Center RCCI Team: Roger Bielefeld, Mike Warfe, Hadrian Djohari! Brian Christian, Emily Dragowsky, Jeremy Fondran, Cal Frye,! Sanjaya Gajurel, Matt Garvey, Theresa Griegger, Cindy Martin, ! Sean Maxwell, Jeno Mozes, Nasir Yilmaz, Lee Zickel Preface: Prepare your environment • User account ! # .bashrc ## cli essentials ! if [ -t 1 ] then bind '"\e[A": history-search-backward' bind '"\e[B": history-search-forward' bind '"\eOA": history-search-backward' bind '"\eOB": history-search-forward' fi ! This is too useful to pass up! Working with Linux • Preamble • Intro Session Linux Review: Finding our way • Files & Directories: Sample work flow • Shell Commands • Pipes & Redirection • Scripting Foundations • Shell & environment variables • Control Structures • Regular expressions & text manipulation • Recap & Look Ahead Rider Cluster Components ! rider.case.edu ondemand.case.edu University Firewall ! Admin Head Nodes SLURM Science Nodes Master DMZ Resource ! Data Manager Transfer Disk Storage Nodes Batch nodes GPU nodes SMP nodes Running a job: where is it? slide from Hadrian Djohari Storing Data on the HPC table from Nasir Yilmaz How data moves across campus • Buildings on campus are each assigned to a zone. Data connections go from every building to the distribution switch at the center of the zone and from there to the data centers at Kelvin Smith Library and Crawford Hall. slide -
Lecture 17 the Shell and Shell Scripting Simple Shell Scripts
Lecture 17 The Shell and Shell Scripting In this lecture • The UNIX shell • Simple Shell Scripts • Shell variables • File System commands, IO commands, IO redirection • Command Line Arguments • Evaluating Expr in Shell • Predicates, operators for testing strings, ints and files • If-then-else in Shell • The for, while and do loop in Shell • Writing Shell scripts • Exercises In this course, we need to be familiar with the "UNIX shell". We use it, whether bash, csh, tcsh, zsh, or other variants, to start and stop processes, control the terminal, and to otherwise interact with the system. Many of you have heard of, or made use of "shell scripting", that is the process of providing instructions to shell in a simple, interpreted programming language . To see what shell we are working on, first SSH into unix.andrew.cmu.edu and type echo $SHELL ---- to see the working shell in SSH We will be writing our shell scripts for this particular shell (csh). The shell scripting language does not fit the classic definition of a useful language. It does not have many of the features such as portability, facilities for resource intensive tasks such as recursion or hashing or sorting. It does not have data structures like arrays and hash tables. It does not have facilities for direct access to hardware or good security features. But in many other ways the language of the shell is very powerful -- it has functions, conditionals, loops. It does not support strong data typing -- it is completely untyped (everything is a string). But, the real power of shell program doesn't come from the language itself, but from the diverse library that it can call upon -- any program. -
Introduction to Shell Programming Using Bash Part I
Introduction to shell programming using bash Part I Deniz Savas and Michael Griffiths 2005-2011 Corporate Information and Computing Services The University of Sheffield Email [email protected] [email protected] Presentation Outline • Introduction • Why use shell programs • Basics of shell programming • Using variables and parameters • User Input during shell script execution • Arithmetical operations on shell variables • Aliases • Debugging shell scripts • References Introduction • What is ‘shell’ ? • Why write shell programs? • Types of shell What is ‘shell’ ? • Provides an Interface to the UNIX Operating System • It is a command interpreter – Built on top of the kernel – Enables users to run services provided by the UNIX OS • In its simplest form a series of commands in a file is a shell program that saves having to retype commands to perform common tasks. • Shell provides a secure interface between the user and the ‘kernel’ of the operating system. Why write shell programs? • Run tasks customised for different systems. Variety of environment variables such as the operating system version and type can be detected within a script and necessary action taken to enable correct operation of a program. • Create the primary user interface for a variety of programming tasks. For example- to start up a package with a selection of options. • Write programs for controlling the routinely performed jobs run on a system. For example- to take backups when the system is idle. • Write job scripts for submission to a job-scheduler such as the sun- grid-engine. For example- to run your own programs in batch mode. Types of Unix shells • sh Bourne Shell (Original Shell) (Steven Bourne of AT&T) • csh C-Shell (C-like Syntax)(Bill Joy of Univ. -
Simple Shell Scripting for Scientists
Simple Shell Scripting for Scientists Day Three Julian King Bruce Beckles University of Cambridge Computing Service 1 Introduction • Who: ! Julian King, Unix Support, UCS ! Bruce Beckles, e-Science Specialist, UCS • What: ! Simple Shell Scripting for Scientists course, Day Three ! Part of the Scientific Computing series of courses • Contact (questions, etc): ! [email protected] • Health & Safety, etc: ! Fire exits • Please switch off mobile phones! [email protected] Simple Shell Scripting for Scientists: Day Three 2 As this course is part of the Scientific Computing series of courses run by the Computing Service, all the examples that we use will be more relevant to scientific computing than to system administration, etc. This does not mean that people who wish to learn shell scripting for system administration and other such tasks will get nothing from this course, as the techniques and underlying knowledge taught are applicable to shell scripts written for almost any purpose. However, such individuals should be aware that this course was not designed with them in mind. 2 What we don’t cover • Different types of shell: ! We are using the Bourne-Again SHell (bash). • Differences between versions of bash • Very advanced shell scripting – try one of these courses instead: ! “Python: Introduction for Absolute Beginners” ! “Python: Introduction for Programmers” [email protected] Simple Shell Scripting for Scientists: Day Three 3 bash is probably the most common shell on modern Unix/Linux systems – in fact, on most modern Linux distributions it will be the default shell (the shell users get if they don’t specify a different one).