Basic Unix Commands
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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. -
Copy — Copy file from Disk Or URL
Title stata.com copy — Copy file from disk or URL Syntax Description Options Remarks and examples Also see Syntax copy filename1 filename2 , options filename1 may be a filename or a URL. filename2 may be the name of a file or a directory. If filename2 is a directory name, filename1 will be copied to that directory. filename2 may not be a URL. Note: Double quotes may be used to enclose the filenames, and the quotes must be used if the filename contains embedded blanks. options Description public make filename2 readable by all text interpret filename1 as text file and translate to native text format replace may overwrite filename2 replace does not appear in the dialog box. Description copy copies filename1 to filename2. Options public specifies that filename2 be readable by everyone; otherwise, the file will be created according to the default permissions of your operating system. text specifies that filename1 be interpreted as a text file and be translated to the native form of text files on your computer. Computers differ on how end-of-line is recorded: Unix systems record one line-feed character, Windows computers record a carriage-return/line-feed combination, and Mac computers record just a carriage return. text specifies that filename1 be examined to determine how it has end-of-line recorded and that the line-end characters be switched to whatever is appropriate for your computer when the copy is made. There is no reason to specify text when copying a file already on your computer to a different location because the file would already be in your computer’s format. -
Attachment D to Adm. Memo No. 004 INSTRUCTIONS FOR
Attachment D to Adm. Memo No. 004 INSTRUCTIONS FOR FORMATTING A DISKETTE Formatting is the preparation of diskettes for storage of information. There are several different versions of the format command that can be used. The version that you use depends upon the type of diskette and the type of disk drive in which the diskette is being formatted. In order for us to be able to read the Tuition Grant diskettes you send, the diskettes should be properly formatted. Below is a table that identifies the more commonly used diskette types and disk drive specifications. The correct version of the format command will appear in the row for your diskette type and drive type. The format command uses the parameter “d:” to indicate the disk drive designation. For example, your 5 ¼ drive may be the “A:” drive. Instead of typing “FORMAT D:”, replace the drive designation with “A:” and type “FORMAT A:”. To verify that the disks were formatted correctly, perform the CHKDSK command on the newly formatted diskette. The format for the CHKDSK command is “CHKDSK d:”. When the command returns the disk information, compare it to the information in the fourth column of the table that corresponds to your diskette type and disk drive.. If the “total disk space” numbers are the same, the diskette is formatted correctly. DISK TYPE DRIVE TYPE FORMAT COMMAND SPACE INFO. 5 ¼” DSDD DSDD FORMAT d: 362,496 bytes total disk space 5 ¼” DSDD HD FORMAT d: /T:40 /N:9 362,496 bytes total disk space 5 ¼” HD DSDD Cannot be formatted 5 ¼” HD HD FORMAT d: 1,213,952 bytes total disk space 3 ½” DSDD DSDD FORMAT d: 730,112 bytes total disk space 3 ½” DSDD HD FORMAT d: /T:80 /N:9 730,112 bytes total disk space 3 ½” HD DSDD Cannot be formatted 3 ½” HD HD FORMAT d: 1,457,664 bytes total disk space 3 ½” DSHD FORMAT d: 1,457,664 bytes total disk space. -
UNIX Cheat Sheet – Sarah Medland Help on Any Unix Command List a Directory Change to Directory Make a New Directory Remove A
THE 2013 INTERNATIONAL WORKSHOP ON STATISTICAL METHODOLOGY FOR HUMAN GENOMIC STUDIES UNIX cheat sheet – Sarah Medland Help on any Unix command man {command} Type man ls to read the manual for the ls command. which {command} Find out where a program is installed whatis {command} Give short description of command. List a directory ls {path} ls -l {path} Long listing, with date, size and permisions. ls -R {path} Recursive listing, with all subdirs. Change to directory cd {dirname} There must be a space between. cd ~ Go back to home directory, useful if you're lost. cd .. Go back one directory. Make a new directory mkdir {dirname} Remove a directory/file rmdir {dirname} Only works if {dirname} is empty. rm {filespec} ? and * wildcards work like DOS should. "?" is any character; "*" is any string of characters. Print working directory pwd Show where you are as full path. Copy a file or directory cp {file1} {file2} cp -r {dir1} {dir2} Recursive, copy directory and all subdirs. cat {newfile} >> {oldfile} Append newfile to end of oldfile. Move (or rename) a file mv {oldfile} {newfile} Moving a file and renaming it are the same thing. View a text file more {filename} View file one screen at a time. less {filename} Like more , with extra features. cat {filename} View file, but it scrolls. page {filename} Very handy with ncftp . nano {filename} Use text editor. head {filename} show first 10 lines tail {filename} show last 10 lines Compare two files diff {file1} {file2} Show the differences. sdiff {file1} {file2} Show files side by side. Other text commands grep '{pattern}' {file} Find regular expression in file. -
Introduction to Linux – Part 1
Introduction to Linux – Part 1 Brett Milash and Wim Cardoen Center for High Performance Computing May 22, 2018 ssh Login or Interactive Node kingspeak.chpc.utah.edu Batch queue system … kp001 kp002 …. kpxxx FastX ● https://www.chpc.utah.edu/documentation/software/fastx2.php ● Remote graphical sessions in much more efficient and effective way than simple X forwarding ● Persistence - can be disconnected from without closing the session, allowing users to resume their sessions from other devices. ● Licensed by CHPC ● Desktop clients exist for windows, mac, and linux ● Web based client option ● Server installed on all CHPC interactive nodes and the frisco nodes. Windows – alternatives to FastX ● Need ssh client - PuTTY ● http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html - XShell ● http://www.netsarang.com/download/down_xsh.html ● For X applications also need X-forwarding tool - Xming (use Mesa version as needed for some apps) ● http://www.straightrunning.com/XmingNotes/ - Make sure X forwarding enabled in your ssh client Linux or Mac Desktop ● Just need to open up a terminal or console ● When running applications with graphical interfaces, use ssh –Y or ssh –X Getting Started - Login ● Download and install FastX if you like (required on windows unless you already have PuTTY or Xshell installed) ● If you have a CHPC account: - ssh [email protected] ● If not get a username and password: - ssh [email protected] Shell Basics q A Shell is a program that is the interface between you and the operating system -
The Microsoft Compound Document File Format"
OpenOffice.org's Documentation of the Microsoft Compound Document File Format Author Daniel Rentz ✉ mailto:[email protected] http://sc.openoffice.org License Public Documentation License Contributors Other sources Hyperlinks to Wikipedia ( http://www.wikipedia.org) for various extended information Mailing list ✉ mailto:[email protected] Subscription ✉ mailto:[email protected] Download PDF http://sc.openoffice.org/compdocfileformat.pdf XML http://sc.openoffice.org/compdocfileformat.odt Project started 2004-Aug-30 Last change 2007-Aug-07 Revision 1.5 Contents 1 Introduction ......................................................................................................... 3 1.1 License Notices 3 1.2 Abstract 3 1.3 Used Terms, Symbols, and Formatting 4 2 Storages and Streams ........................................................................................... 5 3 Sectors and Sector Chains ................................................................................... 6 3.1 Sectors and Sector Identifiers 6 3.2 Sector Chains and SecID Chains 7 4 Compound Document Header ............................................................................. 8 4.1 Compound Document Header Contents 8 4.2 Byte Order 9 4.3 Sector File Offsets 9 5 Sector Allocation ............................................................................................... 10 5.1 Master Sector Allocation Table 10 5.2 Sector Allocation Table 11 6 Short-Streams ................................................................................................... -
Many Slides Borrowed from Ben Zhao, Christo Wilson, & Others
12. Network Attacks Blase Ur and David Cash (many slides borrowed from Ben Zhao, Christo Wilson, & others) February 7th, 2020 CMSC 23200 / 33250 Network threat model • Network scanning • Attacks on confidentiality (e.g., eavesdropping) • Attacks on integrity (e.g., spoofing, packet injection) • Attacks on availability (e.g., denial of service (DoS)) Scanning and observing networks Network Scanning: Ping • Essential, low-level network utility • Sends a “ping” ICMP message to a host on the internet $ ping 66.66.0.255 PING 66.66.0.255 (66.66.0.255) 56(84) bytes of data. 64 bytes from 66.66.0.255: icmp_seq=1 ttl=58 time=41.2 ms • Destination host is supposed to respond with a “pong” – Indicating that it can receive packets • By default, ping messages are 56 bytes long (+ some header bytes) – Maximum size 65535 bytes • What if you send a ping that is >65535 bytes long? Ping of Death • $ ping –s 65535 66.66.0.255 – Attack identified in 1997 – IPv6 version identified/fixed in 2013 Network Scanning: Traceroute • traceroute — hops between me and host – Sends repeated ICMP reqs w/ increasing TTL Port Scanning • What services are running on a server? Nmap • 5 seconds to scan a single machine!! SYN scan Only send SYN Responses: • SYN-ACK — port open • RST — port closed • Nothing — filtered (e.g., firewall) Port Scanning on Steroids • How do you speed up scans for all IPv4? – Don’t wait for responses; pipeline – Parallelize: divide & conquer IPv4 ranges – Randomize permutations w/o collisions • Result: the zmap tool – Scan all of IPv4 in 45mins (w/ GigE cxn) – IPv4 in 5 mins w/ 10GigE Eavesdropping Tools: Wireshark, tcpdump, Bro, … Steps: 1. -
Lecture 7 Network Management and Debugging
SYSTEM ADMINISTRATION MTAT.08.021 LECTURE 7 NETWORK MANAGEMENT AND DEBUGGING Prepared By: Amnir Hadachi and Artjom Lind University of Tartu, Institute of Computer Science [email protected] / [email protected] 1 LECTURE 7: NETWORK MGT AND DEBUGGING OUTLINE 1.Intro 2.Network Troubleshooting 3.Ping 4.SmokePing 5.Trace route 6.Network statistics 7.Inspection of live interface activity 8.Packet sniffers 9.Network management protocols 10.Network mapper 2 1. INTRO 3 LECTURE 7: NETWORK MGT AND DEBUGGING INTRO QUOTE: Networks has tendency to increase the number of interdependencies among machine; therefore, they tend to magnify problems. • Network management tasks: ✴ Fault detection for networks, gateways, and critical servers ✴ Schemes for notifying an administrator of problems ✴ General network monitoring, to balance load and plan expansion ✴ Documentation and visualization of the network ✴ Administration of network devices from a central site 4 LECTURE 7: NETWORK MGT AND DEBUGGING INTRO Network Size 160 120 80 40 Management Procedures 0 AUTOMATION ILLUSTRATION OF NETWORK GROWTH VS MGT PROCEDURES AUTOMATION 5 LECTURE 7: NETWORK MGT AND DEBUGGING INTRO • Network: • Subnets + Routers / switches Time to consider • Automating mgt tasks: • shell scripting source: http://www.eventhelix.com/RealtimeMantra/Networking/ip_routing.htm#.VvjkA2MQhIY • network mgt station 6 2. NETWORK TROUBLES HOOTING 7 LECTURE 7: NETWORK MGT AND DEBUGGING NETWORK TROUBLESHOOTING • Many tools are available for debugging • Debugging: • Low-level (e.g. TCP/IP layer) • high-level (e.g. DNS, NFS, and HTTP) • This section progress: ping trace route GENERAL ESSENTIAL TROUBLESHOOTING netstat TOOLS STRATEGY nmap tcpdump … 8 LECTURE 7: NETWORK MGT AND DEBUGGING NETWORK TROUBLESHOOTING • Before action, principle to consider: ✴ Make one change at a time ✴ Document the situation as it was before you got involved. -
Why Is C. Diff So Hard to Culture and Kill?
Why is C. diff so hard to culture and kill? Clostridium difficile, commonly referred to as C. diff, is the #1 nosocomial infection in hospitals (it actually kicked staph infections out of the top spot). At Assurance, we test for this organism as part of our Gastrointestinal (GI) panel. C. diff is a gram-positive anaerobe, meaning it does not like oxygen. Its defensive mechanism is sporulation – where it essentially surrounds itself with a tough outer layer of keratin and can live in water, soil, etc. for over a decade. For reference, anthrax is another organism that sporulates. Once C. diff sporulates, it is very hard to kill and in fact, bleach is one of the only disinfectants that work. Unfortunately, it can spread quickly throughout hospitals. Spores of C. diff are found all over hospital surfaces and even in some hospital water systems. It’s the most threatening for those who are immunocompromised or the elderly, who are the most likely to end up with C. diff infections. With our PCR testing, we’re looking for the C. diff organism itself but we’re also looking at the production of toxin. Unless it produces toxins A AND B together OR toxin B, C. diff doesn’t cause severe disease. Many babies are exposed to it during birth or in the hospitals and may test positive on our GI panel. Unless they are expressing those toxins (both toxin A&B or just toxin B) it is not considered a clinical infection. Studies show that toxins A&B together causes infection, as well as toxin B. -
GNU Grep: Print Lines That Match Patterns Version 3.7, 8 August 2021
GNU Grep: Print lines that match patterns version 3.7, 8 August 2021 Alain Magloire et al. This manual is for grep, a pattern matching engine. Copyright c 1999{2002, 2005, 2008{2021 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 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, with no Front-Cover Texts, and with no Back-Cover Texts. A copy of the license is included in the section entitled \GNU Free Documentation License". i Table of Contents 1 Introduction ::::::::::::::::::::::::::::::::::::: 1 2 Invoking grep :::::::::::::::::::::::::::::::::::: 2 2.1 Command-line Options ::::::::::::::::::::::::::::::::::::::::: 2 2.1.1 Generic Program Information :::::::::::::::::::::::::::::: 2 2.1.2 Matching Control :::::::::::::::::::::::::::::::::::::::::: 2 2.1.3 General Output Control ::::::::::::::::::::::::::::::::::: 3 2.1.4 Output Line Prefix Control :::::::::::::::::::::::::::::::: 5 2.1.5 Context Line Control :::::::::::::::::::::::::::::::::::::: 6 2.1.6 File and Directory Selection:::::::::::::::::::::::::::::::: 7 2.1.7 Other Options ::::::::::::::::::::::::::::::::::::::::::::: 9 2.2 Environment Variables:::::::::::::::::::::::::::::::::::::::::: 9 2.3 Exit Status :::::::::::::::::::::::::::::::::::::::::::::::::::: 12 2.4 grep Programs :::::::::::::::::::::::::::::::::::::::::::::::: 13 3 Regular Expressions ::::::::::::::::::::::::::: 14 3.1 Fundamental Structure :::::::::::::::::::::::::::::::::::::::: -
Mac OS X Server Administrator's Guide
034-9285.S4AdminPDF 6/27/02 2:07 PM Page 1 Mac OS X Server Administrator’s Guide K Apple Computer, Inc. © 2002 Apple Computer, Inc. All rights reserved. Under the copyright laws, this publication may not be copied, in whole or in part, without the written consent of Apple. The Apple logo is a trademark of Apple Computer, Inc., registered in the U.S. and other countries. Use of the “keyboard” Apple logo (Option-Shift-K) for commercial purposes without the prior written consent of Apple may constitute trademark infringement and unfair competition in violation of federal and state laws. Apple, the Apple logo, AppleScript, AppleShare, AppleTalk, ColorSync, FireWire, Keychain, Mac, Macintosh, Power Macintosh, QuickTime, Sherlock, and WebObjects are trademarks of Apple Computer, Inc., registered in the U.S. and other countries. AirPort, Extensions Manager, Finder, iMac, and Power Mac are trademarks of Apple Computer, Inc. Adobe and PostScript are trademarks of Adobe Systems Incorporated. Java and all Java-based trademarks and logos are trademarks or registered trademarks of Sun Microsystems, Inc. in the U.S. and other countries. Netscape Navigator is a trademark of Netscape Communications Corporation. RealAudio is a trademark of Progressive Networks, Inc. © 1995–2001 The Apache Group. All rights reserved. UNIX is a registered trademark in the United States and other countries, licensed exclusively through X/Open Company, Ltd. 062-9285/7-26-02 LL9285.Book Page 3 Tuesday, June 25, 2002 3:59 PM Contents Preface How to Use This Guide 39 What’s Included