An Introduction to the C Shell
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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 -
Name Synopsis Description
Perl version 5.10.0 documentation - vmsish NAME vmsish - Perl pragma to control VMS-specific language features SYNOPSIS use vmsish; use vmsish 'status';# or '$?' use vmsish 'exit'; use vmsish 'time'; use vmsish 'hushed'; no vmsish 'hushed'; vmsish::hushed($hush); use vmsish; no vmsish 'time'; DESCRIPTION If no import list is supplied, all possible VMS-specific features areassumed. Currently, there are four VMS-specific features available:'status' (a.k.a '$?'), 'exit', 'time' and 'hushed'. If you're not running VMS, this module does nothing. vmsish status This makes $? and system return the native VMS exit statusinstead of emulating the POSIX exit status. vmsish exit This makes exit 1 produce a successful exit (with status SS$_NORMAL),instead of emulating UNIX exit(), which considers exit 1 to indicatean error. As with the CRTL's exit() function, exit 0 is also mappedto an exit status of SS$_NORMAL, and any other argument to exit() isused directly as Perl's exit status. vmsish time This makes all times relative to the local time zone, instead of thedefault of Universal Time (a.k.a Greenwich Mean Time, or GMT). vmsish hushed This suppresses printing of VMS status messages to SYS$OUTPUT andSYS$ERROR if Perl terminates with an error status. and allowsprograms that are expecting "unix-style" Perl to avoid having to parseVMS error messages. It does not suppress any messages from Perlitself, just the messages generated by DCL after Perl exits. The DCLsymbol $STATUS will still have the termination status, but with ahigh-order bit set: EXAMPLE:$ perl -e"exit 44;" Non-hushed error exit%SYSTEM-F-ABORT, abort DCL message$ show sym $STATUS$STATUS == "%X0000002C" $ perl -e"use vmsish qw(hushed); exit 44;" Hushed error exit $ show sym $STATUS $STATUS == "%X1000002C" The 'hushed' flag has a global scope during compilation: the exit() ordie() commands that are compiled after 'vmsish hushed' will be hushedwhen they are executed. -
Using the GNU Compiler Collection (GCC)
Using the GNU Compiler Collection (GCC) Using the GNU Compiler Collection by Richard M. Stallman and the GCC Developer Community Last updated 23 May 2004 for GCC 3.4.6 For GCC Version 3.4.6 Published by: GNU Press Website: www.gnupress.org a division of the General: [email protected] Free Software Foundation Orders: [email protected] 59 Temple Place Suite 330 Tel 617-542-5942 Boston, MA 02111-1307 USA Fax 617-542-2652 Last printed October 2003 for GCC 3.3.1. Printed copies are available for $45 each. Copyright c 1988, 1989, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004 Free Software Foundation, Inc. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with the Invariant Sections being \GNU General Public License" and \Funding Free Software", the Front-Cover texts being (a) (see below), and with the Back-Cover Texts being (b) (see below). A copy of the license is included in the section entitled \GNU Free Documentation License". (a) The FSF's Front-Cover Text is: A GNU Manual (b) The FSF's Back-Cover Text is: You have freedom to copy and modify this GNU Manual, like GNU software. Copies published by the Free Software Foundation raise funds for GNU development. i Short Contents Introduction ...................................... 1 1 Programming Languages Supported by GCC ............ 3 2 Language Standards Supported by GCC ............... 5 3 GCC Command Options ......................... -
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. -
Introduction to Linux by Lars Eklund Based on Work by Marcus Lundberg
Introduction to Linux By Lars Eklund Based on work by Marcus Lundberg ● What is Linux ● Logging in to UPPMAX ● Navigate the file system ● “Basic toolkit” What is Linux ● The Linux Operating system is a UNIX like UNIX compatible Operating system. ● Linux is a Kernel on which many different programs can run. The shell(bash, sh, ksh, csh, tcsh and many more) is one such program ● Linux has a multiuser platform at its base which means permissions and security comes easy. Many Flavours Connect to UPPMAX ● (Download XQuartz or other X11 server for Mac OS ) ● Linux and MacOS: – start Terminal – $ ssh -X [email protected] Connect to UPPMAX for windows users ● Download a X-server such as GWSL or X-ming or VcXsrv or an other of your choosing ● Install WSL and a Distribution such as ubuntu or a ssh program such as MobaXTerm ● Connect to $ ssh -X [email protected] Windows links ● https://sourceforge.net/projects/vcxsrv/ ● https://mobaxterm.mobatek.net/ ● https://opticos.github.io/gwsl/ ● https://sourceforge.net/projects/xming/ ● https://docs.microsoft.com/en-us/windows/wsl/install-wi n10 ● Don’t forget to update to wsl2 X11-forwarding graphics from the command line ● Graphics can be sent through the SSH connection you’re using to connect - Use ssh -Y or ssh -X ● MacOS users will need to install XQuartz. ● When starting a graphical program, a new window will open, but your terminal will be “locked”. - Run using & at the end to run it as a background proccess e.g. “gedit &” - Alternatively, use ctrl-z to put gedit to sleep and -
C Shell Scripts File Permissions a Simple Spelling Checker Command
Cshell scripts Asimple spelling checker mylatex1.csh #!/bin/csh #!/bin/csh tr -cs "[:alpha:]" "[\n*]" < $1 \ latex file.tex |tr"[:upper:]" "[:lower:]" \ dvips -f file.dvi > file.ps |sort -u > tempfile rm file.aux file.dvi file.log comm -23 tempfile /usr/share/dict/words rm tempfile mylatex2.csh #!/bin/csh Put one word per line \ |convert everything to lowercase \ latex $1.tex |sor t the words,remove duplicates and write the result to ’tempfile’. dvips -f $1.dvi > $1.ps rm $1.aux $1.dvi $1.log Pr int those words in ’tempfile’ that are not in the dictionary. Remove the temporar y file. Graham Kemp,Chalmers University of Technology Graham Kemp,Chalmers University of Technology File permissions Command substitution in a script ls -l To include the output from one command within the command line for another command, enclose the command whose output is to be included rwxrwx rwx within ‘backquotes‘. For example: rwxr -xr -x #!/bin/csh 111101101 echo Date and time is: date echo 1111 011 012 = 7558 echo "Your username is:" ‘whoami‘ echo "Your current directory is:" ‘pwd‘ chmod 755 file.sh chmod u+x file.sh chmod -R a+rX . Graham Kemp,Chalmers University of Technology Graham Kemp,Chalmers University of Technology Editing several files at once (1) sed scripts Suppose wewant to change ‘‘cie’’to‘‘cei’’inall files in the current grep href publications.html \ director y whose name ends with ‘‘.tex’’. |sed ’s/[ˆ"]*"//’ \ |sed ’s/".*//’ #!/bin/csh Instead of giving a single editing command on the command line,wecan ls *.tex | sed ’s/.*/sed s\/cie\/cei\/g & > &tmp/’ > s1 create a script file containing a sequence of editing commands. -
Shell Script & Advance Features of Shell Programming
Kirti Kaushik et al, International Journal of Computer Science and Mobile Computing, Vol.4 Issue.4, April- 2015, pg. 458-462 Available Online at www.ijcsmc.com International Journal of Computer Science and Mobile Computing A Monthly Journal of Computer Science and Information Technology ISSN 2320–088X IJCSMC, Vol. 4, Issue. 4, April 2015, pg.458 – 462 RESEARCH ARTICLE Shell Script & Advance Features of Shell Programming Kirti Kaushik* Roll No.15903, CS, Department of Computer science, Dronacharya College of Engineering, Gurgaon-123506, India Email: [email protected] Jyoti Yadav Roll No. 15040, CS, Department of Applied Computer science, Dronacharya College of Engineering, Gurgaon-123506, India Email: [email protected] Kriti Bhatia Roll No. 15048, CS, Department of Applied Computer science, Dronacharya College of Engineering, Gurgaon-123506, India Email: [email protected] Abstract-- In this research paper, the idea of shell scripting and writing computer programs is examined and different parts of shell programming are likewise contemplated. A shell script is a PC system intended to be controlled by the UNIX shell which is a charge line translator. The different tongues of shell scripts are thought to be scripting dialects. Regular operations performed by shell scripts incorporate document control, program execution, and printing content. A shell script can give an advantageous variety ofa framework order where unique environment settings, charge alternatives, or post-transforming apply naturally, yet in a manner that permits the new script to still go about as a completely typical UNIX summon. The real ideas like Programming in the Borne and C-shell, in which it would be clarified that how shell programming could be possible in Borne and C-shell. -
Use Perl Regular Expressions in SAS® Shuguang Zhang, WRDS, Philadelphia, PA
NESUG 2007 Programming Beyond the Basics Use Perl Regular Expressions in SAS® Shuguang Zhang, WRDS, Philadelphia, PA ABSTRACT Regular Expression (Regexp) enhance search and replace operations on text. In SAS®, the INDEX, SCAN and SUBSTR functions along with concatenation (||) can be used for simple search and replace operations on static text. These functions lack flexibility and make searching dynamic text difficult, and involve more function calls. Regexp combines most, if not all, of these steps into one expression. This makes code less error prone, easier to maintain, clearer, and can improve performance. This paper will discuss three ways to use Perl Regular Expression in SAS: 1. Use SAS PRX functions; 2. Use Perl Regular Expression with filename statement through a PIPE such as ‘Filename fileref PIPE 'Perl programm'; 3. Use an X command such as ‘X Perl_program’; Three typical uses of regular expressions will also be discussed and example(s) will be presented for each: 1. Test for a pattern of characters within a string; 2. Replace text; 3. Extract a substring. INTRODUCTION Perl is short for “Practical Extraction and Report Language". Larry Wall Created Perl in mid-1980s when he was trying to produce some reports from a Usenet-Nes-like hierarchy of files. Perl tries to fill the gap between low-level programming and high-level programming and it is easy, nearly unlimited, and fast. A regular expression, often called a pattern in Perl, is a template that either matches or does not match a given string. That is, there are an infinite number of possible text strings. -
A First Course to Openfoam
Basic Shell Scripting Slides from Wei Feinstein HPC User Services LSU HPC & LON [email protected] September 2018 Outline • Introduction to Linux Shell • Shell Scripting Basics • Variables/Special Characters • Arithmetic Operations • Arrays • Beyond Basic Shell Scripting – Flow Control – Functions • Advanced Text Processing Commands (grep, sed, awk) Basic Shell Scripting 2 Linux System Architecture Basic Shell Scripting 3 Linux Shell What is a Shell ▪ An application running on top of the kernel and provides a command line interface to the system ▪ Process user’s commands, gather input from user and execute programs ▪ Types of shell with varied features o sh o csh o ksh o bash o tcsh Basic Shell Scripting 4 Shell Comparison Software sh csh ksh bash tcsh Programming language y y y y y Shell variables y y y y y Command alias n y y y y Command history n y y y y Filename autocompletion n y* y* y y Command line editing n n y* y y Job control n y y y y *: not by default http://www.cis.rit.edu/class/simg211/unixintro/Shell.html Basic Shell Scripting 5 What can you do with a shell? ▪ Check the current shell ▪ echo $SHELL ▪ List available shells on the system ▪ cat /etc/shells ▪ Change to another shell ▪ csh ▪ Date ▪ date ▪ wget: get online files ▪ wget https://ftp.gnu.org/gnu/gcc/gcc-7.1.0/gcc-7.1.0.tar.gz ▪ Compile and run applications ▪ gcc hello.c –o hello ▪ ./hello ▪ What we need to learn today? o Automation of an entire script of commands! o Use the shell script to run jobs – Write job scripts Basic Shell Scripting 6 Shell Scripting ▪ Script: a program written for a software environment to automate execution of tasks ▪ A series of shell commands put together in a file ▪ When the script is executed, those commands will be executed one line at a time automatically ▪ Shell script is interpreted, not compiled. -
Examining the Hamilton C Shell
EXAMINING ROO M Examining the Hamilton C Shell Unix power for OS/2 Scott Richman tarting OS/2 for the first time was, file system), long filenames, and threads. in the background and the server will for me, like unlocking a Ferarri, Additionally, the Shell supports large be kept busy. sitting behind its wheel and find command lines and pipes (up to 64K) ing a Yugo's dash. What a disap and includes faster and more powerful Supporting Procedures pointment. Sure, the engine and utilities than those supplied with OS/2. Script programmers can create C Shell suspensionS were first rate, but the con This is more than Unix - this is a pow procedures, which are more like func trols were minimal, the clutch was stiff, erful requirement for development un tions: They accept a parameter list and and the pedals were nonresponsive! der OS/2. The ability to execute C shells return a value. These procedures are OS/2 comes with great stuff, but CMD simultaneously in different Presenta compiled into C Shell memory and are .EXE, the default command-line pro tion Manager (PM) text windows con then executed as new shell commands. cessor, is poor compared to the pow verts your PC into a flexible workstation. Procedures can greatly extend the erfuloperating system beneath. CMD.EXE The Hamilton C Shell comes with power and flexibility of your environ appears to be a port of the MS-DOS many programs and shell scripts. To ment. COMMAND.COM and lacks the major install the Shell, you simply copy the As an example, consider ZCW.CSH features of a serious front end. -
Shell Scripting, Scripting Examples
Last Time… on the website Lecture 6 Shell Scripting What is a shell? • The user interface to the operating system • Functionality: – Execute other programs – Manage files – Manage processes • Full programming language • A program like any other – This is why there are so many shells Shell History • There are many choices for shells • Shell features evolved as UNIX grew Most Commonly Used Shells – /bin/csh C shell – /bin/tcsh Enhanced C Shell – /bin/sh The Bourne Shell / POSIX shell – /bin/ksh Korn shell – /bin/bash Korn shell clone, from GNU Ways to use the shell • Interactively – When you log in, you interactively use the shell • Scripting – A set of shell commands that constitute an executable program Review: UNIX Programs • Means of input: – Program arguments [control information] – Environment variables [state information] – Standard input [data] • Means of output: – Return status code [control information] – Standard out [data] – Standard error [error messages] Shell Scripts • A shell script is a regular text file that contains shell or UNIX commands – Before running it, it must have execute permission: • chmod +x filename • A script can be invoked as: – ksh name [ arg … ] – ksh < name [ args … ] – name [ arg …] Shell Scripts • When a script is run, the kernel determines which shell it is written for by examining the first line of the script – If 1st line starts with #!pathname-of-shell, then it invokes pathname and sends the script as an argument to be interpreted – If #! is not specified, the current shell assumes it is a script in its own language • leads to problems Simple Example #!/bin/sh echo Hello World Scripting vs. -
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.