RPL Quick Start Guide
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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 -
Powerview Command Reference
PowerView Command Reference TRACE32 Online Help TRACE32 Directory TRACE32 Index TRACE32 Documents ...................................................................................................................... PowerView User Interface ............................................................................................................ PowerView Command Reference .............................................................................................1 History ...................................................................................................................................... 12 ABORT ...................................................................................................................................... 13 ABORT Abort driver program 13 AREA ........................................................................................................................................ 14 AREA Message windows 14 AREA.CLEAR Clear area 15 AREA.CLOSE Close output file 15 AREA.Create Create or modify message area 16 AREA.Delete Delete message area 17 AREA.List Display a detailed list off all message areas 18 AREA.OPEN Open output file 20 AREA.PIPE Redirect area to stdout 21 AREA.RESet Reset areas 21 AREA.SAVE Save AREA window contents to file 21 AREA.Select Select area 22 AREA.STDERR Redirect area to stderr 23 AREA.STDOUT Redirect area to stdout 23 AREA.view Display message area in AREA window 24 AutoSTOre .............................................................................................................................. -
Surviving the TEX Font Encoding Mess Understanding The
Surviving the TEX font encoding mess Understanding the world of TEX fonts and mastering the basics of fontinst Ulrik Vieth Taco Hoekwater · EuroT X ’99 Heidelberg E · FAMOUS QUOTE: English is useful because it is a mess. Since English is a mess, it maps well onto the problem space, which is also a mess, which we call reality. Similary, Perl was designed to be a mess, though in the nicests of all possible ways. | LARRY WALL COROLLARY: TEX fonts are mess, as they are a product of reality. Similary, fontinst is a mess, not necessarily by design, but because it has to cope with the mess we call reality. Contents I Overview of TEX font technology II Installation TEX fonts with fontinst III Overview of math fonts EuroT X ’99 Heidelberg 24. September 1999 3 E · · I Overview of TEX font technology What is a font? What is a virtual font? • Font file formats and conversion utilities • Font attributes and classifications • Font selection schemes • Font naming schemes • Font encodings • What’s in a standard font? What’s in an expert font? • Font installation considerations • Why the need for reencoding? • Which raw font encoding to use? • What’s needed to set up fonts for use with T X? • E EuroT X ’99 Heidelberg 24. September 1999 4 E · · What is a font? in technical terms: • – fonts have many different representations depending on the point of view – TEX typesetter: fonts metrics (TFM) and nothing else – DVI driver: virtual fonts (VF), bitmaps fonts(PK), outline fonts (PFA/PFB or TTF) – PostScript: Type 1 (outlines), Type 3 (anything), Type 42 fonts (embedded TTF) in general terms: • – fonts are collections of glyphs (characters, symbols) of a particular design – fonts are organized into families, series and individual shapes – glyphs may be accessed either by character code or by symbolic names – encoding of glyphs may be fixed or controllable by encoding vectors font information consists of: • – metric information (glyph metrics and global parameters) – some representation of glyph shapes (bitmaps or outlines) EuroT X ’99 Heidelberg 24. -
Database Globalization Support Guide
Oracle® Database Database Globalization Support Guide 19c E96349-05 May 2021 Oracle Database Database Globalization Support Guide, 19c E96349-05 Copyright © 2007, 2021, Oracle and/or its affiliates. Primary Author: Rajesh Bhatiya Contributors: Dan Chiba, Winson Chu, Claire Ho, Gary Hua, Simon Law, Geoff Lee, Peter Linsley, Qianrong Ma, Keni Matsuda, Meghna Mehta, Valarie Moore, Cathy Shea, Shige Takeda, Linus Tanaka, Makoto Tozawa, Barry Trute, Ying Wu, Peter Wallack, Chao Wang, Huaqing Wang, Sergiusz Wolicki, Simon Wong, Michael Yau, Jianping Yang, Qin Yu, Tim Yu, Weiran Zhang, Yan Zhu This software and related documentation are provided under a license agreement containing restrictions on use and disclosure and are protected by intellectual property laws. Except as expressly permitted in your license agreement or allowed by law, you may not use, copy, reproduce, translate, broadcast, modify, license, transmit, distribute, exhibit, perform, publish, or display any part, in any form, or by any means. Reverse engineering, disassembly, or decompilation of this software, unless required by law for interoperability, is prohibited. The information contained herein is subject to change without notice and is not warranted to be error-free. If you find any errors, please report them to us in writing. If this is software or related documentation that is delivered to the U.S. Government or anyone licensing it on behalf of the U.S. Government, then the following notice is applicable: U.S. GOVERNMENT END USERS: Oracle programs (including any operating system, integrated software, any programs embedded, installed or activated on delivered hardware, and modifications of such programs) and Oracle computer documentation or other Oracle data delivered to or accessed by U.S. -
An Empirical Comparison of Widely Adopted Hash Functions in Digital Forensics: Does the Programming Language and Operating System Make a Difference?
2015 Annual ADFSL Conference on Digital Forensics, Security and Law Proceedings May 19th, 11:45 AM An Empirical Comparison of Widely Adopted Hash Functions in Digital Forensics: Does the Programming Language and Operating System Make a Difference? Satyendra Gurjar Cyber Forensics Research and Education Group (UNHcFREG), Tagliatela College of Engineering, ECECS Department, University of New Haven, [email protected] Ibrahim Baggili Cyber Forensics Research and Education Group (UNHcFREG), Tagliatela College of Engineering, ECECS Department, University of New Haven Frank Breitinger CyberFollow F thisorensics and additional Research worksand Education at: https:/ Gr/commons.eroup (UNHcFREG),au.edu/adfsl Tagliatela College of Engineering, ECECS Depar Partment,t of the Univ Aviationersity ofSaf Newety and Hav Securityen Commons, Computer Law Commons, Defense and Security AliceStudies Fischer Commons , Forensic Science and Technology Commons, Information Security Commons, CyberNational For Securityensics Resear Law Commonsch and Education, OS and GrNetworksoup (UNHcFREG), Commons T, Otheragliatela Computer College Sciences of Engineering, Commons ECECS, and theDepar Socialtment, Contr Univol,ersity Law , ofCrime, New andHav enDe,viance AFischer@newha Commons ven.edu Scholarly Commons Citation Gurjar, Satyendra; Baggili, Ibrahim; Breitinger, Frank; and Fischer, Alice, "An Empirical Comparison of Widely Adopted Hash Functions in Digital Forensics: Does the Programming Language and Operating System Make a Difference?" (2015). Annual ADFSL Conference on Digital Forensics, Security and Law. 6. https://commons.erau.edu/adfsl/2015/tuesday/6 This Peer Reviewed Paper is brought to you for free and open access by the Conferences at Scholarly Commons. It has been accepted for inclusion in Annual ADFSL Conference on Digital Forensics, Security and Law by an (c)ADFSL authorized administrator of Scholarly Commons. -
Lecture 17 the Shell and Shell Scripting Simple Shell Scripts
Lecture 17 The Shell and Shell Scripting In this lecture • The UNIX shell • Simple Shell Scripts • Shell variables • File System commands, IO commands, IO redirection • Command Line Arguments • Evaluating Expr in Shell • Predicates, operators for testing strings, ints and files • If-then-else in Shell • The for, while and do loop in Shell • Writing Shell scripts • Exercises In this course, we need to be familiar with the "UNIX shell". We use it, whether bash, csh, tcsh, zsh, or other variants, to start and stop processes, control the terminal, and to otherwise interact with the system. Many of you have heard of, or made use of "shell scripting", that is the process of providing instructions to shell in a simple, interpreted programming language . To see what shell we are working on, first SSH into unix.andrew.cmu.edu and type echo $SHELL ---- to see the working shell in SSH We will be writing our shell scripts for this particular shell (csh). The shell scripting language does not fit the classic definition of a useful language. It does not have many of the features such as portability, facilities for resource intensive tasks such as recursion or hashing or sorting. It does not have data structures like arrays and hash tables. It does not have facilities for direct access to hardware or good security features. But in many other ways the language of the shell is very powerful -- it has functions, conditionals, loops. It does not support strong data typing -- it is completely untyped (everything is a string). But, the real power of shell program doesn't come from the language itself, but from the diverse library that it can call upon -- any program. -
CMSC 426/626 - Computer Security Fall 2014
Authentication and Passwords CMSC 426/626 - Computer Security Fall 2014 Outline • Types of authentication • Vulnerabilities of password authentication • Linux password authentication • Windows Password authentication • Cracking techniques Goals of Authentication • Identification - provide a claimed identity to the system. • Verification - establish validity of the provided identity. We’re not talking about message authentication, e.g. the use of digital signatures. Means of Authentication • Something you know, e.g. password • Something you have, e.g. USB dongle or Common Access Card (CAC) • Something you are, e.g. fingerprint • Something you do, e.g. hand writing Password-Based Authentication • User provides identity and password; system verifies that the password is correct for the given identity. • Identity determines access and privileges. • Identity can be used for Discretionary Access Control, e.g. to give another user access to a file. Password Hashing Password • System stores hash of the user password, not the plain text password. Hash Algorithm • Commonly used technique, e.g. UNIX password hashing. Password Hash Password Vulnerabilities Assume the authentication system stores hashed passwords. There are eight attack strategies. • Off-line Dictionary Attack - get hold of the password file, test a collection (dictionary) of possible passwords. ‣ Most systems protect the password file, but attackers sometimes get hold of one. • Specific Account Attack - given a specific user account, try popular passwords. ‣ Most systems use lockout mechanisms to make these attacks difficult. • Popular Password Attack - given a popular password, try it on multiple accounts. ‣ Harder to defend against - have to look for patterns in failed access attempts. • Targeted Password Guessing - use what you know about a user to intelligently guess their password. -
Jellyfish Count -M 21 -S 100M -T 10 -C Reads.Fasta
Jellysh 2 User Guide December 13, 2013 Contents 1 Getting started 2 1.1 Counting all k-mers . .2 1.1.1 Counting k-mers in sequencing reads . .3 1.1.2 Counting k-mers in a genome . .3 1.2 Counting high-frequency k-mers . .3 1.2.1 One pass method . .3 1.2.2 Two pass method . .4 2 FAQ 5 2.1 How to read compressed les (or other format)?newmacroname . .5 2.2 How to read multiple les at once? . .5 2.3 How to reduce the output size? . .6 3 Subcommands 7 3.1 histo .............................................7 3.2 dump .............................................7 3.3 query .............................................7 3.4 info ..............................................8 3.5 merge ............................................8 3.6 cite . .8 1 Chapter 1 Getting started 1.1 Counting all k-mers The basic command to count all k-mers is as follows: jellyfish count -m 21 -s 100M -t 10 -C reads.fasta This will count canonical (-C) 21-mers (-m 21), using a hash with 100 million elements (-s 100 M) and 10 threads (-t 10) in the sequences in the le reads.fasta. The output is written in the le 'mer_counts.jf' by default (change with -o switch). To compute the histogram of the k-mer occurrences, use the histo subcommand (see section 3.1): jellyfish histo mer_counts.jf To query the counts of a particular k-mer, use the query subcommand (see section 3.3): jellyfish query mer_counts.jf AACGTTG To output all the counts for all the k-mers in the le, use the dump subcommand (see section 3.2): jellyfish dump mer_counts.jf > mer_counts_dumps.fa To get some information on how, when and where this jellysh le was generated, use the info subcommand (see section 3.4): jellyfish info mer_counts.jf For more detail information, see the relevant sections in this document. -
Using International Characters in Bartender How to Read Data and Print Characters from Almost Every Language and Writing System in the World
Using International Characters in BarTender How to Read Data and Print Characters from Almost Every Language and Writing System in the World Supports the following BarTender software versions: BarTender 2016, BarTender 2019 WHITE PAPER Contents Overview 3 BarTender's Unicode Support 3 Understanding International Character Support 4 Fonts 4 Scripts 4 Asian Characters 5 Writing Systems that Read Right to Left 5 Entering International Text Into Text Objects 7 Using the Insert Symbols or Special Characters Dialog 7 Using the Windows Character Map 7 Using the Keyboard 8 Reading International Characters from a Database 9 Encoding International Characters in Barcodes 10 Using Unicode Data 10 ECI Protocol 11 Formatting According to Locale 12 About Data Types 12 Example 12 Appendix A: Languages, Encodings and Scripts 13 Appendix B: Configuring Windows 14 Installing Windows Input Support for International Languages 14 Windows Support for Additional Display Languages 15 Related Documentation 16 Overview With the built-in international character support that BarTender provides, you can add international characters to your design and encode them into barcodes or RFID tags on your template. When you design items for a single locale, you can configure the format (or appearance) of information that may vary between regions, such as date and time, currency, numbering, and so on. By using BarTender, you can also globalize your design and print international materials by inserting text in multiple languages. For example, the following item illustrates how BarTender can be used with many locales with its built-in Unicode support. BarTender's Unicode Support Unicode is a universal character encoding standard that defines the basis for the processing, storage and interchange of text data in any language. -
Husky: Towards a More Efficient and Expressive Distributed Computing Framework
Husky: Towards a More Efficient and Expressive Distributed Computing Framework Fan Yang Jinfeng Li James Cheng Department of Computer Science and Engineering The Chinese University of Hong Kong ffyang,jfli,[email protected] ABSTRACT tends Spark, and Gelly [3] extends Flink, to expose to programmers Finding efficient, expressive and yet intuitive programming models fine-grained control over the access patterns on vertices and their for data-parallel computing system is an important and open prob- communication patterns. lem. Systems like Hadoop and Spark have been widely adopted Over-simplified functional or declarative programming interfaces for massive data processing, as coarse-grained primitives like map with only coarse-grained primitives also limit the flexibility in de- and reduce are succinct and easy to master. However, sometimes signing efficient distributed algorithms. For instance, there is re- over-simplified API hinders programmers from more fine-grained cent interest in machine learning algorithms that compute by fre- control and designing more efficient algorithms. Developers may quently and asynchronously accessing and mutating global states have to resort to sophisticated domain-specific languages (DSLs), (e.g., some entries in a large global key-value table) in a fine-grained or even low-level layers like MPI, but this raises development cost— manner [14, 19, 24, 30]. It is not clear how to program such algo- learning many mutually exclusive systems prolongs the develop- rithms using only synchronous and coarse-grained operators (e.g., ment schedule, and the use of low-level tools may result in bug- map, reduce, and join), and even with immutable data abstraction prone programming. -
Daniel Lyons [email protected] Why?
How to Hurt Your Friends with (loop) Daniel Lyons [email protected] Why? Fast Powerful Widely-used Like format you can probably do more with it than you realize. Even though you hate it, you may have to read it in someone else’s code. On my machine, 578 of 1068 library files contain at least one loop form (54.12%). It’s fast as hell. loop as List Comprehension Python: [ f(x) for x in L if p(x) ] Haskell: [ f(x) | x <- L, p(x) ] Erlang: [ f(X) || X <- L, p(X) ]. Loop: (loop for x in L when (p x) collect (f x)) Things You Can Do With loop Variable initialization and stepping Value accumulation Conditional and unconditional execution Pre- and post-loop operations Termination whenever and however you like This is taken from the list of kinds of loop clauses from CLtL Ch. 26 - variable initialization and stepping - value accumulation - termination conditions - unconditional execution - conditional execution - miscellaneous operations Initialization for/as with repeat for and as mean the same thing with is a single ‘let’ statement repeat runs the loop a specified number of times for Is Really Complicated for var from expr to expr for var in expr for var on expr Of course from can also be downfrom or upfrom, and to can also be downto, upto, below or above for var in expr: Loops over every item in the list Optionally by some stepping function for var on expr loops over the cdrs of a list, giving you each successive sublist Loops over each sublist of the list, e.g. -
Linux Command Line: Aliases, Prompts and Scripting
Linux Command Line: Aliases, Prompts and Scri... 1 Linux Command Line: Aliases, Prompts and Scripting By Steven Gordon on Wed, 23/07/2014 - 7:46am Here are a few notes on using the Bash shell that I have used as a demo to students. It covers man pages, aliases, shell prompts, paths and basics of shell scripting. For details, see the many free manuals of Bash shell scripting. 1. Man Pages Man pages are the reference manuals for commands. Reading the man pages is best when you know the command to use, but cannot remember the syntax or options. Simply type man cmd and then read the manual. E.g.: student@netlab01:~$ man ls If you don't know which command to use to perform some task, then there is a basic search feature called apropos which will do a keyword search through an index of man page names and short descriptions. You can run it using either the command apropos or using man -k. E.g.: student@netlab01:~$ man superuser No manual entry for superuser student@netlab01:~$ apropos superuser su (1) - change user ID or become superuser student@netlab01:~$ man -k "new user" newusers (8) - update and create new users in batch useradd (8) - create a new user or update default new user information Some common used commands are actually not standalone program, but commands built-in to the shell. For example, below demonstrates the creation of aliases using alias. But there is no man page for alias. Instead, alias is described as part of the bash shell man page.