No Slide Title
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
The Design of the EMPS Multiprocessor Executive for Distributed Computing
The design of the EMPS multiprocessor executive for distributed computing Citation for published version (APA): van Dijk, G. J. W. (1993). The design of the EMPS multiprocessor executive for distributed computing. Technische Universiteit Eindhoven. https://doi.org/10.6100/IR393185 DOI: 10.6100/IR393185 Document status and date: Published: 01/01/1993 Document Version: Publisher’s PDF, also known as Version of Record (includes final page, issue and volume numbers) Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. -
Using NROFF and TROFF
Using NROFF and TROFF Part Number: 800-1755-10 Revision A, of 9 May 1988 UNIX is a registered trademark of AT&T. SunOS is a trademark of Sun Microsystems, Inc. Sun Workstation is a registered trademark of Sun Microsystems, Inc. Material in this manual comes from a number of sources: NrofflTroff User's Manual, Joseph F. Ossanna, Bell Laboratories, Murray Hill, New Jersey; A Troff Tutorial, Brian W. Kernighan, Bell Laboratories, Murray Hill, New Jersey; Typ ing Documents on the UNIXSystem: Using the -ms Macros with Troff and Nroff, M. E. Lesk, Bell Laboratories, Murray Hill, New Jersey; A Guide to Preparing Documents with -ms, M. E. Lesk, Bell Laboratories, Murray Hill, New Jersey; Document Formatting on UNIXUsing the -ms Macros, Joel Kies, University of California, Berkeley, California; Writing Papers with Nroff Using -me, Eric P. Allman, University of California, Berkeley; and Introducing the UNIXSystem, Henry McGilton, Rachel Morgan, McGraw-Hill Book Company, 1983. These materials are gratefully acknowledged. Copyright © 1987, 1988 by Sun Microsystems, Inc. This publication is protected by Federal Copyright Law, with all rights reserved. No part of this publication may be reproduced, stored in a retrieval system, translated, transcribed, or transmitted, in any form, or by any means manual, electric, electronic, electro-magnetic, mechanical, chemical, optical, or other wise, without prior explicit written permission from Sun Microsystems. Contents Chapter 1 Introduction . 1.1. nrof f andtrof f . Text Formatting Versus Word Processing TheEvolutionof nr of f andt ro f f Preprocessors and Postprocessors 1.2. tr of f, Typesetters, and Special-Purpose Formatters ............ 1.3. -
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 . -
Introduction to Unix
Introduction to Unix Rob Funk <[email protected]> University Technology Services Workstation Support http://wks.uts.ohio-state.edu/ University Technology Services Course Objectives • basic background in Unix structure • knowledge of getting started • directory navigation and control • file maintenance and display commands • shells • Unix features • text processing University Technology Services Course Objectives Useful commands • working with files • system resources • printing • vi editor University Technology Services In the Introduction to UNIX document 3 • shell programming • Unix command summary tables • short Unix bibliography (also see web site) We will not, however, be covering these topics in the lecture. Numbers on slides indicate page number in book. University Technology Services History of Unix 7–8 1960s multics project (MIT, GE, AT&T) 1970s AT&T Bell Labs 1970s/80s UC Berkeley 1980s DOS imitated many Unix ideas Commercial Unix fragmentation GNU Project 1990s Linux now Unix is widespread and available from many sources, both free and commercial University Technology Services Unix Systems 7–8 SunOS/Solaris Sun Microsystems Digital Unix (Tru64) Digital/Compaq HP-UX Hewlett Packard Irix SGI UNICOS Cray NetBSD, FreeBSD UC Berkeley / the Net Linux Linus Torvalds / the Net University Technology Services Unix Philosophy • Multiuser / Multitasking • Toolbox approach • Flexibility / Freedom • Conciseness • Everything is a file • File system has places, processes have life • Designed by programmers for programmers University Technology Services -
The Strange Birth and Long Life of Unix - IEEE Spectrum Page 1 of 6
The Strange Birth and Long Life of Unix - IEEE Spectrum Page 1 of 6 COMPUTING / SOFTWARE FEATURE The Strange Birth and Long Life of Unix The classic operating system turns 40, and its progeny abound By WARREN TOOMEY / DECEMBER 2011 They say that when one door closes on you, another opens. People generally offer this bit of wisdom just to lend some solace after a misfortune. But sometimes it's actually true. It certainly was for Ken Thompson and the late Dennis Ritchie, two of the greats of 20th-century information technology, when they created the Unix operating system, now considered one of the most inspiring and influential pieces of software ever written. A door had slammed shut for Thompson and Ritchie in March of 1969, when their employer, the American Telephone & Telegraph Co., withdrew from a collaborative project with the Photo: Alcatel-Lucent Massachusetts Institute of KEY FIGURES: Ken Thompson [seated] types as Dennis Ritchie looks on in 1972, shortly Technology and General Electric after they and their Bell Labs colleagues invented Unix. to create an interactive time- sharing system called Multics, which stood for "Multiplexed Information and Computing Service." Time-sharing, a technique that lets multiple people use a single computer simultaneously, had been invented only a decade earlier. Multics was to combine time-sharing with other technological advances of the era, allowing users to phone a computer from remote terminals and then read e -mail, edit documents, run calculations, and so forth. It was to be a great leap forward from the way computers were mostly being used, with people tediously preparing and submitting batch jobs on punch cards to be run one by one. -
The Strange Birth and Long Life of Unix - IEEE Spectrum
The Strange Birth and Long Life of Unix - IEEE Spectrum http://spectrum.ieee.org/computing/software/the-strange-birth-and-long-li... COMPUTING / SOFTWARE FEATURE The Strange Birth and Long Life of Unix The classic operating system turns 40, and its progeny abound By WARREN TOOMEY / DECEMBER 2011 They say that when one door closes on you, another opens. People generally offer this bit of wisdom just to lend some solace after a misfortune. But sometimes it's actually true. It certainly was for Ken Thompson and the late Dennis Ritchie, two of the greats of 20th-century information technology, when they created the Unix operating system, now considered one of the most inspiring and influential pieces of software ever written. A door had slammed shut for Thompson and Ritchie in March of 1969, when their employer, the American Telephone & Telegraph Co., withdrew from a collaborative project with the Photo: Alcatel-Lucent Massachusetts Institute of KEY FIGURES: Ken Thompson [seated] types as Dennis Ritchie looks on in 1972, shortly Technology and General Electric after they and their Bell Labs colleagues invented Unix. to create an interactive time-sharing system called Multics, which stood for "Multiplexed Information and Computing Service." Time-sharing, a technique that lets multiple people use a single computer simultaneously, had been invented only a decade earlier. Multics was to combine time-sharing with other technological advances of the era, allowing users to phone a computer from remote terminals and then read e-mail, edit documents, run calculations, and so forth. It was to be a great leap forward from the way computers were mostly being used, with people tediously preparing and submitting batch jobs on punch cards to be run one by one. -
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 -
Install and Run External Command Line Softwares
job monitor and control top: similar to windows task manager (space to refresh, q to exit) w: who is there ps: all running processes, PID, status, type ps -ef | grep yyin bg: move current process to background fg: move current process to foreground jobs: list running and suspended processes kill: kill processes kill pid (could find out using top or ps) 1 sort, cut, uniq, join, paste, sed, grep, awk, wc, diff, comm, cat All types of bioinformatics sequence analyses are essentially text processing. Unix Shell has the above commands that are very useful for processing texts and also allows the output from one command to be passed to another command as input using pipe (“|”). less cosmicRaw.txt | cut -f2,3,4,5,8,13 | awk '$5==22' | cut -f1 | sort -u | wc This makes the processing of files using Shell very convenient and very powerful: you do not need to write output to intermediate files or load all data into the memory. For example, combining different Unix commands for text processing is like passing an item through a manufacturing pipeline when you only care about the final product 2 Hands on example 1: cosmic mutation data - Go to UCSC genome browser website: http://genome.ucsc.edu/ - On the left, find the Downloads link - Click on Human - Click on Annotation database - Ctrl+f and then search “cosmic” - On “cosmic.txt.gz” right-click -> copy link address - Go to the terminal and wget the above link (middle click or Shift+Insert to paste what you copied) - Similarly, download the “cosmicRaw.txt.gz” file - Under your home, create a folder -
The Evolution of the Unix Time-Sharing System*
The Evolution of the Unix Time-sharing System* Dennis M. Ritchie Bell Laboratories, Murray Hill, NJ, 07974 ABSTRACT This paper presents a brief history of the early development of the Unix operating system. It concentrates on the evolution of the file system, the process-control mechanism, and the idea of pipelined commands. Some attention is paid to social conditions during the development of the system. NOTE: *This paper was first presented at the Language Design and Programming Methodology conference at Sydney, Australia, September 1979. The conference proceedings were published as Lecture Notes in Computer Science #79: Language Design and Programming Methodology, Springer-Verlag, 1980. This rendition is based on a reprinted version appearing in AT&T Bell Laboratories Technical Journal 63 No. 6 Part 2, October 1984, pp. 1577-93. Introduction During the past few years, the Unix operating system has come into wide use, so wide that its very name has become a trademark of Bell Laboratories. Its important characteristics have become known to many people. It has suffered much rewriting and tinkering since the first publication describing it in 1974 [1], but few fundamental changes. However, Unix was born in 1969 not 1974, and the account of its development makes a little-known and perhaps instructive story. This paper presents a technical and social history of the evolution of the system. Origins For computer science at Bell Laboratories, the period 1968-1969 was somewhat unsettled. The main reason for this was the slow, though clearly inevitable, withdrawal of the Labs from the Multics project. To the Labs computing community as a whole, the problem was the increasing obviousness of the failure of Multics to deliver promptly any sort of usable system, let alone the panacea envisioned earlier. -
A Brief History of Unix
A Brief History of Unix Tom Ryder [email protected] https://sanctum.geek.nz/ I Love Unix ∴ I Love Linux ● When I started using Linux, I was impressed because of the ethics behind it. ● I loved the idea that an operating system could be both free to customise, and free of charge. – Being a cash-strapped student helped a lot, too. ● As my experience grew, I came to appreciate the design behind it. ● And the design is UNIX. ● Linux isn’t a perfect Unix, but it has all the really important bits. What do we actually mean? ● We’re referring to the Unix family of operating systems. – Unix from Bell Labs (Research Unix) – GNU/Linux – Berkeley Software Distribution (BSD) Unix – Mac OS X – Minix (Intel loves it) – ...and many more Warning signs: 1/2 If your operating system shows many of the following symptoms, it may be a Unix: – Multi-user, multi-tasking – Hierarchical filesystem, with a single root – Devices represented as files – Streams of text everywhere as a user interface – “Formatless” files ● Data is just data: streams of bytes saved in sequence ● There isn’t a “text file” attribute, for example Warning signs: 2/2 – Bourne-style shell with a “pipe”: ● $ program1 | program2 – “Shebangs” specifying file interpreters: ● #!/bin/sh – C programming language baked in everywhere – Classic programs: sh(1), awk(1), grep(1), sed(1) – Users with beards, long hair, glasses, and very strong opinions... Nobody saw it coming! “The number of Unix installations has grown to 10, with more expected.” — Ken Thompson and Dennis Ritchie (1972) ● Unix in some flavour is in servers, desktops, embedded software (including Intel’s management engine), mobile phones, network equipment, single-board computers..