Encrypted File System 6.858 Final Project Cheng Chen & Osama Badar
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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 -
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 . -
11.7 the Windows 2000 File System
830 CASE STUDY 2: WINDOWS 2000 CHAP. 11 11.7 THE WINDOWS 2000 FILE SYSTEM Windows 2000 supports several file systems, the most important of which are FAT-16, FAT-32, and NTFS (NT File System). FAT-16 is the old MS-DOS file system. It uses 16-bit disk addresses, which limits it to disk partitions no larger than 2 GB. FAT-32 uses 32-bit disk addresses and supports disk partitions up to 2 TB. NTFS is a new file system developed specifically for Windows NT and car- ried over to Windows 2000. It uses 64-bit disk addresses and can (theoretically) support disk partitions up to 264 bytes, although other considerations limit it to smaller sizes. Windows 2000 also supports read-only file systems for CD-ROMs and DVDs. It is possible (even common) to have the same running system have access to multiple file system types available at the same time. In this chapter we will treat the NTFS file system because it is a modern file system unencumbered by the need to be fully compatible with the MS-DOS file system, which was based on the CP/M file system designed for 8-inch floppy disks more than 20 years ago. Times have changed and 8-inch floppy disks are not quite state of the art any more. Neither are their file systems. Also, NTFS differs both in user interface and implementation in a number of ways from the UNIX file system, which makes it a good second example to study. NTFS is a large and complex system and space limitations prevent us from covering all of its features, but the material presented below should give a reasonable impression of it. -
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 .............................................................................................................................. -
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. -
Secure Untrusted Data Repository (SUNDR)
Secure Untrusted Data Repository (SUNDR) Jinyuan Li, Maxwell Krohn,∗ David Mazieres,` and Dennis Shasha NYU Department of Computer Science Abstract for over 20,000 different software packages. Many of these packages are bundled with various operating sys- SUNDR is a network file system designed to store data tem distributions, often without a meaningful audit. By securely on untrusted servers. SUNDR lets clients de- compromising sourceforge, an attacker can therefore in- tect any attempts at unauthorized file modification by troduce subtle vulnerabilities in software that may even- malicious server operators or users. SUNDR’s protocol tually run on thousands or even millions of machines. achieves a property called fork consistency, which guar- Such concerns are no mere academic exercise. For ex- antees that clients can detect any integrity or consistency ample, the Debian GNU/Linux development cluster was failures as long as they see each other’s file modifications. compromised in 2003 [2]. An unauthorized attacker used An implementation is described that performs compara- a sniffed password and a kernel vulnerability to gain su- bly with NFS (sometimes better and sometimes worse), peruser access to Debian’s primary CVS and Web servers. while offering significantly stronger security. After detecting the break-in, administrators were forced to freeze development for several days, as they employed manual and ad-hoc sanity checks to assess the extent of 1 Introduction the damage. Similar attacks have also succeeded against Apache [1], Gnome [32], and other popular projects. SUNDR is a network file system that addresses a long- Rather than hope for invulnerable servers, we have de- standing tension between data integrity and accessibility. -
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. -
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.