Linux Fundamentals (L-120)
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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 :::::::::::::::::::::::::::::::::::::::: -
Cygwin User's Guide
Cygwin User’s Guide Cygwin User’s Guide ii Copyright © Cygwin authors Permission is granted to make and distribute verbatim copies of this documentation provided the copyright notice and this per- mission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this documentation under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this documentation into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the Free Software Foundation. Cygwin User’s Guide iii Contents 1 Cygwin Overview 1 1.1 What is it? . .1 1.2 Quick Start Guide for those more experienced with Windows . .1 1.3 Quick Start Guide for those more experienced with UNIX . .1 1.4 Are the Cygwin tools free software? . .2 1.5 A brief history of the Cygwin project . .2 1.6 Highlights of Cygwin Functionality . .3 1.6.1 Introduction . .3 1.6.2 Permissions and Security . .3 1.6.3 File Access . .3 1.6.4 Text Mode vs. Binary Mode . .4 1.6.5 ANSI C Library . .4 1.6.6 Process Creation . .5 1.6.6.1 Problems with process creation . .5 1.6.7 Signals . .6 1.6.8 Sockets . .6 1.6.9 Select . .7 1.7 What’s new and what changed in Cygwin . .7 1.7.1 What’s new and what changed in 3.2 . -
Scons API Docs Version 4.2
SCons API Docs version 4.2 SCons Project July 31, 2021 Contents SCons Project API Documentation 1 SCons package 1 Module contents 1 Subpackages 1 SCons.Node package 1 Submodules 1 SCons.Node.Alias module 1 SCons.Node.FS module 9 SCons.Node.Python module 68 Module contents 76 SCons.Platform package 85 Submodules 85 SCons.Platform.aix module 85 SCons.Platform.cygwin module 85 SCons.Platform.darwin module 86 SCons.Platform.hpux module 86 SCons.Platform.irix module 86 SCons.Platform.mingw module 86 SCons.Platform.os2 module 86 SCons.Platform.posix module 86 SCons.Platform.sunos module 86 SCons.Platform.virtualenv module 87 SCons.Platform.win32 module 87 Module contents 87 SCons.Scanner package 89 Submodules 89 SCons.Scanner.C module 89 SCons.Scanner.D module 93 SCons.Scanner.Dir module 93 SCons.Scanner.Fortran module 94 SCons.Scanner.IDL module 94 SCons.Scanner.LaTeX module 94 SCons.Scanner.Prog module 96 SCons.Scanner.RC module 96 SCons.Scanner.SWIG module 96 Module contents 96 SCons.Script package 99 Submodules 99 SCons.Script.Interactive module 99 SCons.Script.Main module 101 SCons.Script.SConsOptions module 108 SCons.Script.SConscript module 115 Module contents 122 SCons.Tool package 123 Module contents 123 SCons.Variables package 125 Submodules 125 SCons.Variables.BoolVariable module 125 SCons.Variables.EnumVariable module 125 SCons.Variables.ListVariable module 126 SCons.Variables.PackageVariable module 126 SCons.Variables.PathVariable module 127 Module contents 127 SCons.compat package 129 Module contents 129 Submodules 129 SCons.Action -
File Transfer
File Transfer Joon Kim PICSciE Research Computing Workshop Department of Chemistry 10/30/2017 Introduction Hyojoon (Joon) Kim. Ph.D. Cyber Infrastructure Engineer Role: Design & build a campus network and infrastructure that will better support our researchers 2 Our goal today • Overview of widely used tools • Learn about data transfer basics • Pick the right tool for your job • Know what to expect • Learn about Globus • Q&A 3 Data transfer Data Data source destination This part is our topic! 4 Why do we care? Without good practice, you will waste time and effort 1. Start data transfer using SCP at 10pm. Usually takes 10 hours. 2. At 2am, there was a brief 1-minute network outage. Transfer job aborted. 3. Arrive 8am in the morning. See the damage. Start again, which will take 10 hours. 4. Lost a day of work. Time Effort 5 Why do we care? Without good practice, you will waste time and effort 1. Start data transfer using SCP at 10pm. Usually takes 10 hours. Really? Are you SURE that’s the best? Time Effort 6 We want you to Focus on your research, not on transferring data around Time Effort 7 Data Transfer Tools 8 Transfer tools What transfer tool do you use? 9 What we normally see 10 Secure Copy (SCP) • Secure Copy (SCP) • Uses SSH for authentication and data transfer (TCP port 22) • Unix-based systems (including Mac OS X): Should have it by default • Windows: WinSCP (https://winscp.net/eng/download.php) 11 Secure Copy (SCP) • Secure Copy (SCP) • Uses SSH for authentication and data transfer (TCP port 22) • Unix-based systems (including Mac OS X): Should have it by default • Windows: WinSCP (https://winscp.net/eng/download.php) 12 rsync • rsync (rsync over SSH) • Sync files and directories between two endpoints. -
Aspera CLI User Guide
Aspera Command- Line Interface Guide 3.7.7 Mac OS X Revision: 74 Generated: 09/25/2018 16:52 Contents Introduction............................................................................................................... 3 System Requirements............................................................................................... 3 Installation................................................................................................................. 3 Installing the Aspera CLI.....................................................................................................................................3 Configuring for Faspex.........................................................................................................................................4 Configuring for Aspera on Cloud........................................................................................................................ 4 Uninstalling........................................................................................................................................................... 5 aspera: The Command-Line Transfer Client........................................................ 5 About the Command-Line Client.........................................................................................................................5 Prerequisites.......................................................................................................................................................... 6 aspera Command Reference................................................................................................................................ -
Bash Guide for Beginners
Bash Guide for Beginners Machtelt Garrels Garrels BVBA <tille wants no spam _at_ garrels dot be> Version 1.11 Last updated 20081227 Edition Bash Guide for Beginners Table of Contents Introduction.........................................................................................................................................................1 1. Why this guide?...................................................................................................................................1 2. Who should read this book?.................................................................................................................1 3. New versions, translations and availability.........................................................................................2 4. Revision History..................................................................................................................................2 5. Contributions.......................................................................................................................................3 6. Feedback..............................................................................................................................................3 7. Copyright information.........................................................................................................................3 8. What do you need?...............................................................................................................................4 9. Conventions used in this -
Lab Work 06. Linux Shell. Files Globbing & Streams Redirection
LAB WORK 06. LINUX SHELL. FILES GLOBBING & STREAMS REDIRECTION. 1. PURPOSE OF WORK • Learn to use shell file globbing (wildcard); • Learn basic concepts about standard UNIX/Linux streams redirections; • Acquire skills of working with filter-programs. • Get experience in creating composite commands that have a different functional purpose than the original commands. 2. TASKS FOR WORK NOTE. Start Your UbuntuMini Virtual Machine on your VirtualBox. You need only Linux Terminal to complete the lab tasks. Before completing the tasks, make a Snapshot of your Virtual Linux. If there are problems, you can easily go back to working condition! 2.0. Create new User account for this Lab Work. • Login as student account (user with sudo permissions). • Create new user account, example stud. Use adduser command. (NOTE. You can use the command “userdel –rf stud” to delete stud account from your Linux.) $ sudo adduser stud • Logout from student account (logout) and login as stud. 2.1. Shell File Globbing Study. 2.2. File Globbing Practice. (Fill in a Table 1 and Table 2) 2.3. Command I/O Redirection Study. 2.4. Redirection Practice. (Fill in a Table 3 and Table 4) © Yuriy Shamshin, 2021 1/20 3. REPORT Make a report about this work and send it to the teacher’s email (use a docx Report Blank). REPORT FOR LAB WORK 06: LINUX SHELL. FILES GLOBBING & STREAMS REDIRECTION Student Name Surname Student ID (nV) Date 3.1. Insert Completing Table 1. File globbing understanding. 3.2. Insert Completing Table 2. File globbing creation. 3.3. Insert Completing Table 3. Command I/O redirection understanding. -
Cygwin User's Guide
Cygwin User’s Guide i Cygwin User’s Guide Cygwin User’s Guide ii Copyright © 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012 Red Hat, Inc. Permission is granted to make and distribute verbatim copies of this documentation provided the copyright notice and this per- mission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this documentation under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this documentation into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the Free Software Foundation. Cygwin User’s Guide iii Contents 1 Cygwin Overview 1 1.1 What is it? . .1 1.2 Quick Start Guide for those more experienced with Windows . .1 1.3 Quick Start Guide for those more experienced with UNIX . .1 1.4 Are the Cygwin tools free software? . .2 1.5 A brief history of the Cygwin project . .2 1.6 Highlights of Cygwin Functionality . .3 1.6.1 Introduction . .3 1.6.2 Permissions and Security . .3 1.6.3 File Access . .3 1.6.4 Text Mode vs. Binary Mode . .4 1.6.5 ANSI C Library . .5 1.6.6 Process Creation . .5 1.6.6.1 Problems with process creation . .5 1.6.7 Signals . .6 1.6.8 Sockets . .6 1.6.9 Select . -
File Transfer: Basics and Best Practices
File Transfer: Basics and Best Practices Joon Kim. Ph.D. PICSciE Research Computing Workshop @Chemistry 09/07/2018 Our goal today • Learn about data transfer basics • Pick the right tool for your job • Know what to expect • Overview of widely used tools • Learn about RC’s resources • Globus and Data Transfer Nodes • Q&A 2 Why do we care? Without good practice, you will waste time and effort 1. Start data transfer using SCP at 10pm. Usually takes 10 hours. 2. At 2am, there was a brief 1-minute network outage. Transfer job aborted. 3. Arrive 8am in the morning. See the damage. Start again, which will take 10 hours. Time 4. Lost a day of work. Effort 3 Why do we care? Without good practice, you will waste time and effort 1. Start data transfer using SCP at 10pm. Usually takes 10 hours. Is that really the best? Time Effort 4 We want you to Focus on your research, not on transferring data X X Time Effort 5 Use case 1 • I have data at Argonne National Lab that I want to process & analyze at Princeton HPC clusters Argonne’s Chemical Sciences and Engineering (CSE) division Princeton HPC Clusters 6 Use case 2 • I have data on my workstation/laptop that I want to process & analyze at Princeton HPC clusters workstation/laptop Princeton HPC Clusters 7 Data Transfer Basics 8 Data transfer: Overview Three key elements • Endpoints 1/10/100 Gbps • Network Source Destination SCP • Transfer tool FTP SFTP rsync rsync over ssh These will determine how you transfer data and how fast it will be 9 Why is my data transfer slow? Where are the bottlenecks? scp scp ftp ftp Source Destination 10 1. -
Command Line Interface (Shell)
Command Line Interface (Shell) 1 Organization of a computer system users applications graphical user shell interface (GUI) operating system hardware (or software acting like hardware: “virtual machine”) 2 Organization of a computer system Easier to use; users applications Not so easy to program with, interactive actions automate (click, drag, tap, …) graphical user shell interface (GUI) system calls operating system hardware (or software acting like hardware: “virtual machine”) 3 Organization of a computer system Easier to program users applications with and automate; Not so convenient to use (maybe) typed commands graphical user shell interface (GUI) system calls operating system hardware (or software acting like hardware: “virtual machine”) 4 Organization of a computer system users applications this class graphical user shell interface (GUI) operating system hardware (or software acting like hardware: “virtual machine”) 5 What is a Command Line Interface? • Interface: Means it is a way to interact with the Operating System. 6 What is a Command Line Interface? • Interface: Means it is a way to interact with the Operating System. • Command Line: Means you interact with it through typing commands at the keyboard. 7 What is a Command Line Interface? • Interface: Means it is a way to interact with the Operating System. • Command Line: Means you interact with it through typing commands at the keyboard. So a Command Line Interface (or a shell) is a program that lets you interact with the Operating System via the keyboard. 8 Why Use a Command Line Interface? A. In the old days, there was no choice 9 Why Use a Command Line Interface? A. -
Name Synopsis Description
Perl version 5.8.7 documentation - find2perl NAME find2perl - translate find command lines to Perl code SYNOPSIS find2perl [paths] [predicates] | perl DESCRIPTION find2perl is a little translator to convert find command lines to equivalent Perl code. The resulting code is typically faster than running find itself. "paths" are a set of paths where find2perl will start its searches and "predicates" are taken from the following list. ! PREDICATE Negate the sense of the following predicate. The ! must be passed as a distinct argument, so it may need to be surrounded by whitespace and/or quoted from interpretation by the shell using a backslash (just as with using find(1)). ( PREDICATES ) Group the given PREDICATES. The parentheses must be passed as distinct arguments, so they may need to be surrounded by whitespace and/or quoted from interpretation by the shell using a backslash (just as with using find(1)). PREDICATE1 PREDICATE2 True if _both_ PREDICATE1 and PREDICATE2 are true; PREDICATE2 is not evaluated if PREDICATE1 is false. PREDICATE1 -o PREDICATE2 True if either one of PREDICATE1 or PREDICATE2 is true; PREDICATE2 is not evaluated if PREDICATE1 is true. -follow Follow (dereference) symlinks. The checking of file attributes depends on the position of the -follow option. If it precedes the file check option, an stat is done which means the file check applies to the file the symbolic link is pointing to. If -follow option follows the file check option, this now applies to the symbolic link itself, i.e. an lstat is done. -depth Change directory traversal algorithm from breadth-first to depth-first. -
Dhavide Aruliah Director of Training, Anaconda Sequences to Bags
Building Dask Bags & Globbing PA R A L L E L P R O G R A M M I N G W I T H DA S K I N P Y T H O N Dhavide Aruliah Director of Training, Anaconda Sequences to bags nested_containers = [[0, 1, 2, 3],{}, [6.5, 3.14], 'Python', {'version':3}, '' ] import dask.bag as db the_bag = db.from_sequence(nested_containers) the_bag.count() 6 the_bag.any(), the_bag.all() True, False PARALLEL PROGRAMMING WITH DASK IN PYTHON Reading text files import dask.bag as db zen = db.read_text('zen') taken = zen.take(1) type(taken) tuple PARALLEL PROGRAMMING WITH DASK IN PYTHON Reading text files taken ('The Zen of Python, by Tim Peters\n',) zen.take(3) ('The Zen of Python, by Tim Peters\n', '\n', 'Beautiful is better than ugly.\n') PARALLEL PROGRAMMING WITH DASK IN PYTHON Glob expressions import dask.dataframe as dd df = dd.read_csv('taxi/*.csv', assume_missing=True) taxi/*.csv is a glob expression taxi/*.csv matches: taxi/yellow_tripdata_2015-01.csv taxi/yellow_tripdata_2015-02.csv taxi/yellow_tripdata_2015-03.csv ... taxi/yellow_tripdata_2015-10.csv taxi/yellow_tripdata_2015-11.csv taxi/yellow_tripdata_2015-12.csv PARALLEL PROGRAMMING WITH DASK IN PYTHON Using Python's glob module %ls Alice Dave README a02.txt a04.txt b05.txt b07.txt b09.txt b11.txt Bob Lisa a01.txt a03.txt a05.txt b06.txt b08.txt b10.txt taxi import glob txt_files = glob.glob('*.txt') txt_files ['a01.txt', 'a02.txt', ... 'b10.txt', 'b11.txt'] PARALLEL PROGRAMMING WITH DASK IN PYTHON More glob patterns glob.glob('b*.txt') glob.glob('?0[1-6].txt') ['b05.txt', ['a01.txt', 'b06.txt', 'a02.txt',