Acute: High-Level Programming Language Design for Distributed Computation
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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 -
Types and Programming Languages by Benjamin C
< Free Open Study > . .Types and Programming Languages by Benjamin C. Pierce ISBN:0262162091 The MIT Press © 2002 (623 pages) This thorough type-systems reference examines theory, pragmatics, implementation, and more Table of Contents Types and Programming Languages Preface Chapter 1 - Introduction Chapter 2 - Mathematical Preliminaries Part I - Untyped Systems Chapter 3 - Untyped Arithmetic Expressions Chapter 4 - An ML Implementation of Arithmetic Expressions Chapter 5 - The Untyped Lambda-Calculus Chapter 6 - Nameless Representation of Terms Chapter 7 - An ML Implementation of the Lambda-Calculus Part II - Simple Types Chapter 8 - Typed Arithmetic Expressions Chapter 9 - Simply Typed Lambda-Calculus Chapter 10 - An ML Implementation of Simple Types Chapter 11 - Simple Extensions Chapter 12 - Normalization Chapter 13 - References Chapter 14 - Exceptions Part III - Subtyping Chapter 15 - Subtyping Chapter 16 - Metatheory of Subtyping Chapter 17 - An ML Implementation of Subtyping Chapter 18 - Case Study: Imperative Objects Chapter 19 - Case Study: Featherweight Java Part IV - Recursive Types Chapter 20 - Recursive Types Chapter 21 - Metatheory of Recursive Types Part V - Polymorphism Chapter 22 - Type Reconstruction Chapter 23 - Universal Types Chapter 24 - Existential Types Chapter 25 - An ML Implementation of System F Chapter 26 - Bounded Quantification Chapter 27 - Case Study: Imperative Objects, Redux Chapter 28 - Metatheory of Bounded Quantification Part VI - Higher-Order Systems Chapter 29 - Type Operators and Kinding Chapter 30 - Higher-Order Polymorphism Chapter 31 - Higher-Order Subtyping Chapter 32 - Case Study: Purely Functional Objects Part VII - Appendices Appendix A - Solutions to Selected Exercises Appendix B - Notational Conventions References Index List of Figures < Free Open Study > < Free Open Study > Back Cover A type system is a syntactic method for automatically checking the absence of certain erroneous behaviors by classifying program phrases according to the kinds of values they compute. -
The Gnu Binary Utilities
The gnu Binary Utilities Version cygnus-2.7.1-96q4 May 1993 Roland H. Pesch Jeffrey M. Osier Cygnus Support Cygnus Support TEXinfo 2.122 (Cygnus+WRS) Copyright c 1991, 92, 93, 94, 95, 1996 Free Software Foundation, Inc. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modi®ed versions of this manual under the conditions for verbatim copying, provided also 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 manual into another language, under the above conditions for modi®ed versions. The GNU Binary Utilities Introduction ..................................... 467 1ar.............................................. 469 1.1 Controlling ar on the command line ................... 470 1.2 Controlling ar with a script ............................ 472 2ld.............................................. 477 3nm............................................ 479 4 objcopy ....................................... 483 5 objdump ...................................... 489 6 ranlib ......................................... 493 7 size............................................ 495 8 strings ........................................ 497 9 strip........................................... 499 Utilities 10 c++®lt ........................................ 501 11 nlmconv .................................... -
Computer Matching Agreement
COMPUTER MATCHING AGREEMENT BETWEEN NEW tvIEXICO HUMAN SERVICES DEPARTMENT AND UNIVERSAL SERVICE ADMINISTRATIVE COMPANY AND THE FEDERAL COMMUNICATIONS COMMISSION INTRODUCTION This document constitutes an agreement between the Universal Service Administrative Company (USAC), the Federal Communications Commission (FCC or Commission), and the New Mexico Human Services Department (Department) (collectively, Parties). The purpose of this Agreement is to improve the efficiency and effectiveness of the Universal Service Fund (U SF’) Lifeline program, which provides support for discounted broadband and voice services to low-income consumers. Because the Parties intend to share information about individuals who are applying for or currently receive Lifeline benefits in order to verify the individuals’ eligibility for the program, the Parties have determined that they must execute a written agreement that complies with the Computer Matching and Privacy Protection Act of 1988 (CMPPA), Public Law 100-503, 102 Stat. 2507 (1988), which was enacted as an amendment to the Privacy Act of 1974 (Privacy Act), 5 U.S.C. § 552a. By agreeing to the terms and conditions of this Agreement, the Parties intend to comply with the requirements of the CMPPA that are codified in subsection (o) of the Privacy Act. 5 U.S.C. § 552a(o). As discussed in section 11.B. below, U$AC has been designated by the FCC as the permanent federal Administrator of the Universal Service funds programs, including the Lifeline program that is the subject of this Agreement. A. Title of Matching Program The title of this matching program as it will be reported by the FCC and the Office of Management and Budget (0MB) is as follows: “Computer Matching Agreement with the New Mexico Human Services Department.” B. -
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 .............................................................................................................................. -
Project1: Build a Small Scanner/Parser
Project1: Build A Small Scanner/Parser Introducing Lex, Yacc, and POET cs5363 1 Project1: Building A Scanner/Parser Parse a subset of the C language Support two types of atomic values: int float Support one type of compound values: arrays Support a basic set of language concepts Variable declarations (int, float, and array variables) Expressions (arithmetic and boolean operations) Statements (assignments, conditionals, and loops) You can choose a different but equivalent language Need to make your own test cases Options of implementation (links available at class web site) Manual in C/C++/Java (or whatever other lang.) Lex and Yacc (together with C/C++) POET: a scripting compiler writing language Or any other approach you choose --- must document how to download/use any tools involved cs5363 2 This is just starting… There will be two other sub-projects Type checking Check the types of expressions in the input program Optimization/analysis/translation Do something with the input code, output the result The starting project is important because it determines which language you can use for the other projects Lex+Yacc ===> can work only with C/C++ POET ==> work with POET Manual ==> stick to whatever language you pick This class: introduce Lex/Yacc/POET to you cs5363 3 Using Lex to build scanners lex.yy.c MyLex.l lex/flex lex.yy.c a.out gcc/cc Input stream a.out tokens Write a lex specification Save it in a file (MyLex.l) Compile the lex specification file by invoking lex/flex lex MyLex.l A lex.yy.c file is generated -
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. -
File Management Tools
File Management Tools ● gzip and gunzip ● tar ● find ● df and du ● od ● nm and strip ● sftp and scp Gzip and Gunzip ● The gzip utility compresses a specified list of files. After compressing each specified file, it renames it to have a “.gz” extension. ● General form. gzip [filename]* ● The gunzip utility uncompresses a specified list of files that had been previously compressed with gzip. ● General form. gunzip [filename]* Tar (38.2) ● Tar is a utility for creating and extracting archives. It was originally setup for archives on tape, but it now is mostly used for archives on disk. It is very useful for sending a set of files to someone over the network. Tar is also useful for making backups. ● General form. tar options filenames Commonly Used Tar Options c # insert files into a tar file f # use the name of the tar file that is specified v # output the name of each file as it is inserted into or # extracted from a tar file x # extract the files from a tar file Creating an Archive with Tar ● Below is the typical tar command used to create an archive from a set of files. Note that each specified filename can also be a directory. Tar will insert all files in that directory and any subdirectories. tar cvf tarfilename filenames ● Examples: tar cvf proj.tar proj # insert proj directory # files into proj.tar tar cvf code.tar *.c *.h # insert *.c and *.h files # into code.tar Extracting Files from a Tar Archive ● Below is the typical tar command used to extract the files from a tar archive. -
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. -
A DENOTATIONAL ENGINEERING of PROGRAMMING LANGUAGES to Make Software Systems Reliable and User Manuals Clear, Complete and Unambiguous
A DENOTATIONAL ENGINEERING OF PROGRAMMING LANGUAGES to make software systems reliable and user manuals clear, complete and unambiguous A book in statu nascendi Andrzej Jacek Blikle in cooperation with Piotr Chrząstowski-Wachtel It always seems impossible until it's done. Nelson Mandela Warsaw, March 22nd, 2019 „A Denotational Engineering of Programming Languages” by Andrzej Blikle in cooperation with Piotr Chrząstowski-Wachtel has been licensed under a Creative Commons: Attribution — NonCommercial — NoDerivatives 4.0 International. For details see: https://creativecommons.org/licenses/by-nc-nd/4.0/le- galcode Andrzej Blikle in cooperation with Piotr Chrząstowski-Wachtel, A Denotational Engineering of Programming Languages 2 About the current versions of the book Both versions ― Polish and English ― are in statu nascendi which means that they are both in the process of correction due to my readers’ remarks. Since December 2018 both versions, and currently also two related papers, are available in PDF format and can be downloaded from my website: http://www.moznainaczej.com.pl/what-has-been-done/the-book as well as from my accounts on ResearchGate, academia.edu and arXiv.org I very warmly invite all my readers to send their remarks and questions about all aspects of the book. I am certainly aware of the fact that my English requires a lot of improvements and therefore I shall very much appreciate all linguistic corrections and suggestions as well. You may write to me on [email protected]. All interested persons are also invited to join the project Denotational Engineering. For more details see: http://www.moznainaczej.com.pl/an-invitation-to-the-project Acknowledgements to the Polish version Since June 2018 a preliminary version of the Polish version has been made available to selected readers which resulted with a flow of remarks. -
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.