Introduction to Unix
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At—At, Batch—Execute Commands at a Later Time
at—at, batch—execute commands at a later time at [–csm] [–f script] [–qqueue] time [date] [+ increment] at –l [ job...] at –r job... batch at and batch read commands from standard input to be executed at a later time. at allows you to specify when the commands should be executed, while jobs queued with batch will execute when system load level permits. Executes commands read from stdin or a file at some later time. Unless redirected, the output is mailed to the user. Example A.1 1 at 6:30am Dec 12 < program 2 at noon tomorrow < program 3 at 1945 pm August 9 < program 4 at now + 3 hours < program 5 at 8:30am Jan 4 < program 6 at -r 83883555320.a EXPLANATION 1. At 6:30 in the morning on December 12th, start the job. 2. At noon tomorrow start the job. 3. At 7:45 in the evening on August 9th, start the job. 4. In three hours start the job. 5. At 8:30 in the morning of January 4th, start the job. 6. Removes previously scheduled job 83883555320.a. awk—pattern scanning and processing language awk [ –fprogram–file ] [ –Fc ] [ prog ] [ parameters ] [ filename...] awk scans each input filename for lines that match any of a set of patterns specified in prog. Example A.2 1 awk '{print $1, $2}' file 2 awk '/John/{print $3, $4}' file 3 awk -F: '{print $3}' /etc/passwd 4 date | awk '{print $6}' EXPLANATION 1. Prints the first two fields of file where fields are separated by whitespace. 2. Prints fields 3 and 4 if the pattern John is found. -
Unix Introduction
Unix introduction Mikhail Dozmorov Summer 2018 Mikhail Dozmorov Unix introduction Summer 2018 1 / 37 What is Unix Unix is a family of operating systems and environments that exploits the power of linguistic abstractions to perform tasks Unix is not an acronym; it is a pun on “Multics”. Multics was a large multi-user operating system that was being developed at Bell Labs shortly before Unix was created in the early ’70s. Brian Kernighan is credited with the name. All computational genomics is done in Unix http://www.read.seas.harvard.edu/~kohler/class/aosref/ritchie84evolution.pdfMikhail Dozmorov Unix introduction Summer 2018 2 / 37 History of Unix Initial file system, command interpreter (shell), and process management started by Ken Thompson File system and further development from Dennis Ritchie, as well as Doug McIlroy and Joe Ossanna Vast array of simple, dependable tools that each do one simple task Ken Thompson (sitting) and Dennis Ritchie working together at a PDP-11 Mikhail Dozmorov Unix introduction Summer 2018 3 / 37 Philosophy of Unix Vast array of simple, dependable tools Each do one simple task, and do it really well By combining these tools, one can conduct rather sophisticated analyses The Linux help philosophy: “RTFM” (Read the Fine Manual) Mikhail Dozmorov Unix introduction Summer 2018 4 / 37 Know your Unix Unix users spend a lot of time at the command line In Unix, a word is worth a thousand mouse clicks Mikhail Dozmorov Unix introduction Summer 2018 5 / 37 Unix systems Three common types of laptop/desktop operating systems: Windows, Mac, Linux. Mac and Linux are both Unix-like! What that means for us: Unix-like operating systems are equipped with “shells”" that provide a command line user interface. -
A Microkernel API for Fine-Grained Decomposition
A Microkernel API for Fine-Grained Decomposition Sebastian Reichelt Jan Stoess Frank Bellosa System Architecture Group, University of Karlsruhe, Germany freichelt,stoess,[email protected] ABSTRACT from the microkernel APIs in existence. The need, for in- Microkernel-based operating systems typically require spe- stance, to explicitly pass messages between servers, or the cial attention to issues that otherwise arise only in dis- need to set up threads and address spaces in every server for tributed systems. The resulting extra code degrades per- parallelism or protection require OS developers to adopt the formance and increases development effort, severely limiting mindset of a distributed-system programmer rather than to decomposition granularity. take advantage of their knowledge on traditional OS design. We present a new microkernel design that enables OS devel- Distributed-system paradigms, though well-understood and opers to decompose systems into very fine-grained servers. suited for physically (and, thus, coarsely) partitioned sys- We avoid the typical obstacles by defining servers as light- tems, present obstacles to the fine-grained decomposition weight, passive objects. We replace complex IPC mecha- required to exploit the benefits of microkernels: First, a nisms by a simple function-call approach, and our passive, lot of development effort must be spent into matching the module-like server model obviates the need to create threads OS structure to the architecture of the selected microkernel, in every server. Server code is compiled into small self- which also hinders porting existing code from monolithic sys- contained files, which can be loaded into the same address tems. Second, the more servers exist | a desired property space (for speed) or different address spaces (for safety). -
Oracle Solaris: the Carrier-Grade Operating System Technical Brief
An Oracle White Paper February 2011 Oracle Solaris: The Carrier-Grade Operating System Oracle White Paper—Oracle Solaris: The Carrier-Grade OS Executive Summary.............................................................................1 ® Powering Communication—The Oracle Solaris Ecosystem..............3 Integrated and Optimized Stack ......................................................5 End-to-End Security ........................................................................5 Unparalleled Performance and Scalability.......................................6 Increased Reliability ........................................................................7 Unmatched Flexibility ......................................................................7 SCOPE Alliance ..............................................................................7 Security................................................................................................8 Security Hardening and Monitoring .................................................8 Process and User Rights Management...........................................9 Network Security and Encrypted Communications .......................10 Virtualization ......................................................................................13 Oracle VM Server for SPARC .......................................................13 Oracle Solaris Zones .....................................................................14 Virtualized Networking...................................................................15 -
Openvms Record Management Services Reference Manual
OpenVMS Record Management Services Reference Manual Order Number: AA-PV6RD-TK April 2001 This reference manual contains general information intended for use in any OpenVMS programming language, as well as specific information on writing programs that use OpenVMS Record Management Services (OpenVMS RMS). Revision/Update Information: This manual supersedes the OpenVMS Record Management Services Reference Manual, OpenVMS Alpha Version 7.2 and OpenVMS VAX Version 7.2 Software Version: OpenVMS Alpha Version 7.3 OpenVMS VAX Version 7.3 Compaq Computer Corporation Houston, Texas © 2001 Compaq Computer Corporation Compaq, AlphaServer, VAX, VMS, the Compaq logo Registered in U.S. Patent and Trademark Office. Alpha, PATHWORKS, DECnet, DEC, and OpenVMS are trademarks of Compaq Information Technologies Group, L.P. in the United States and other countries. UNIX and X/Open are trademarks of The Open Group in the United States and other countries. All other product names mentioned herein may be the trademarks of their respective companies. Confidential computer software. Valid license from Compaq required for possession, use, or copying. Consistent with FAR 12.211 and 12.212, Commercial Computer Software, Computer Software Documentation, and Technical Data for Commercial Items are licensed to the U.S. Government under vendor’s standard commercial license. Compaq shall not be liable for technical or editorial errors or omissions contained herein. The information in this document is provided "as is" without warranty of any kind and is subject to change without notice. The warranties for Compaq products are set forth in the express limited warranty statements accompanying such products. Nothing herein should be construed as constituting an additional warranty. -
Beginning Portable Shell Scripting from Novice to Professional
Beginning Portable Shell Scripting From Novice to Professional Peter Seebach 10436fmfinal 1 10/23/08 10:40:24 PM Beginning Portable Shell Scripting: From Novice to Professional Copyright © 2008 by Peter Seebach All rights reserved. No part of this work may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage or retrieval system, without the prior written permission of the copyright owner and the publisher. ISBN-13 (pbk): 978-1-4302-1043-6 ISBN-10 (pbk): 1-4302-1043-5 ISBN-13 (electronic): 978-1-4302-1044-3 ISBN-10 (electronic): 1-4302-1044-3 Printed and bound in the United States of America 9 8 7 6 5 4 3 2 1 Trademarked names may appear in this book. Rather than use a trademark symbol with every occurrence of a trademarked name, we use the names only in an editorial fashion and to the benefit of the trademark owner, with no intention of infringement of the trademark. Lead Editor: Frank Pohlmann Technical Reviewer: Gary V. Vaughan Editorial Board: Clay Andres, Steve Anglin, Ewan Buckingham, Tony Campbell, Gary Cornell, Jonathan Gennick, Michelle Lowman, Matthew Moodie, Jeffrey Pepper, Frank Pohlmann, Ben Renow-Clarke, Dominic Shakeshaft, Matt Wade, Tom Welsh Project Manager: Richard Dal Porto Copy Editor: Kim Benbow Associate Production Director: Kari Brooks-Copony Production Editor: Katie Stence Compositor: Linda Weidemann, Wolf Creek Press Proofreader: Dan Shaw Indexer: Broccoli Information Management Cover Designer: Kurt Krames Manufacturing Director: Tom Debolski Distributed to the book trade worldwide by Springer-Verlag New York, Inc., 233 Spring Street, 6th Floor, New York, NY 10013. -
CSE 220: Systems Programming Input and Output
CSE 220: Systems Programming Input and Output Ethan Blanton Department of Computer Science and Engineering University at Buffalo Introduction Unix I/O Standard I/O Buffering Summary References I/O Kernel Services We have seen some text I/O using the C Standard Library. printf() fgetc() … However, all I/O is built on kernel system calls. In this lecture, we’ll look at those services vs. standard I/O. © 2020 Ethan Blanton / CSE 220: Systems Programming Introduction Unix I/O Standard I/O Buffering Summary References Everything is a File These services are particularly important on Unix systems. On Unix, “everything is a file”. Many devices and services are accessed by opening device nodes. Device nodes behave like (but are not) files. Examples: /dev/null: Always readable, contains no data. Always writable, discards anything written to it. /dev/urandom: Always readable, reads a cryptographically secure stream of random data. © 2020 Ethan Blanton / CSE 220: Systems Programming Introduction Unix I/O Standard I/O Buffering Summary References File Descriptors All access to files is through file descriptors. A file descriptor is a small integer representing an open file in a particular process. There are three “standard” file descriptors: 0: standard input 1: standard output 2: standard error …sound familiar? (stdin, stdout, stderr) © 2020 Ethan Blanton / CSE 220: Systems Programming Introduction Unix I/O Standard I/O Buffering Summary References System Call Failures Kernel I/O (and most other) system calls return -1 on failure. When this happens, the global variable errno is set to a reason. Include errno.h to define errno in your code. -
Unix Essentials (Pdf)
Unix Essentials Bingbing Yuan Next Hot Topics: Unix – Beyond Basics (Mon Oct 20th at 1pm) 1 Objectives • Unix Overview • Whitehead Resources • Unix Commands • BaRC Resources • LSF 2 Objectives: Hands-on • Parsing Human Body Index (HBI) array data Goal: Process a large data file to get important information such as genes of interest, sorting expression values, and subset the data for further investigation. 3 Advantages of Unix • Processing files with thousands, or millions, of lines How many reads are in my fastq file? Sort by gene name or expression values • Many programs run on Unix only Command-line tools • Automate repetitive tasks or commands Scripting • Other software, such as Excel, are not able to handle large files efficiently • Open Source 4 Scientific computing resources 5 Shared packages/programs https://tak.wi.mit.edu Request new packages/programs Installed packages/programs 6 Login • Requesting a tak account http://iona.wi.mit.edu/bio/software/unix/bioinfoaccount.php • Windows PuTTY or Cygwin Xming: setup X-windows for graphical display • Macs Access through Terminal 7 Connecting to tak for Windows Command Prompt user@tak ~$ 8 Log in to tak for Mac ssh –Y [email protected] 9 Unix Commands • General syntax Command Options or switches (zero or more) Arguments (zero or more) Example: uniq –c myFile.txt command options arguments Options can be combined ls –l –a or ls –la • Manual (man) page man uniq • One line description whatis ls 10 Unix Directory Structure root / home dev bin nfs lab . jdoe BaRC_Public solexa_public -
ECOGEO Workshop 2: Introduction to Env 'Omics
ECOGEO Workshop 2: Introduction to Env ‘Omics Unix and Bioinformatics Ben Tully (USC); Ken Youens-Clark (UA) Unix Commands pwd rm grep tail install ls ‘>’ sed cut cd cat nano top mkdir ‘<’ history screen touch ‘|’ $PATH ssh cp sort less df mv uniq head rsync/scp Unix Command Line 1. Open Terminal window Unix Command Line 2. Open Chrome and navigate to Unix tutorial at Protocols.io 3. Group: ECOGEO 4. Protocol: ECOGEO Workshop 2: Unix Module ! This will allow you to copy, paste Unix scripts into terminal window ! ECOGEO Protocols.io for making copy, paste easier Unix Command Line $ ls ls - lists items in the current directory Many commands have additional options that can be set by a ‘-’ $ ls -a Unix Command Line $ ls -a lists all files/directories, including hidden files ‘.’ $ ls -l lists the long format File Permissions | # Link | User | Group | Size | Last modified $ ls -lt lists the long format, but ordered by date last modified Unix Command Line Unix Command Line $ cd ecogeo/ cd - change directory List the contents of the current directory Move into the directory called unix List contents $ pwd pwd - present working directory Unix Command Line /home/c-debi/ecogeo/unix When were we in the directory home? Or c-debi? Or ecogeo? $ cd / Navigates to root directory List contents of root directory This where everything is stored in the computer All the commands we are running live in /bin Unix Command Line / root bin sys home mnt usr c-debi BioinfPrograms cdebi Desktop Downloads ecogeo unix assembly annotation etc Typical Unix Layout Unix Command Line Change directory to home Change directory to c-debi Change directory to ecogeo Change directory to unix List contents Change directory to data Change directory to root Unix Command Line Change directory to unix/data in one step $ cd /home/c-debi/ecogeo/unix/data Tab can be used to auto complete names $ cd . -
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. -
“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. -
Unix/Linux Command Reference
Unix/Linux Command Reference .com File Commands System Info ls – directory listing date – show the current date and time ls -al – formatted listing with hidden files cal – show this month's calendar cd dir - change directory to dir uptime – show current uptime cd – change to home w – display who is online pwd – show current directory whoami – who you are logged in as mkdir dir – create a directory dir finger user – display information about user rm file – delete file uname -a – show kernel information rm -r dir – delete directory dir cat /proc/cpuinfo – cpu information rm -f file – force remove file cat /proc/meminfo – memory information rm -rf dir – force remove directory dir * man command – show the manual for command cp file1 file2 – copy file1 to file2 df – show disk usage cp -r dir1 dir2 – copy dir1 to dir2; create dir2 if it du – show directory space usage doesn't exist free – show memory and swap usage mv file1 file2 – rename or move file1 to file2 whereis app – show possible locations of app if file2 is an existing directory, moves file1 into which app – show which app will be run by default directory file2 ln -s file link – create symbolic link link to file Compression touch file – create or update file tar cf file.tar files – create a tar named cat > file – places standard input into file file.tar containing files more file – output the contents of file tar xf file.tar – extract the files from file.tar head file – output the first 10 lines of file tar czf file.tar.gz files – create a tar with tail file – output the last 10 lines