The Applied Mathematics Research Lab Located in CAS 240 (330) (x6776 on campus) Administrator: Zach Tocchi Website:

-One of the first networks on campus, if not the first network -Run and maintained independently from the rest of UA campus -Topology of the AMRL network: Internet Firewall Remote (Fourier) GibbsFaculty & Lab Machines

AMRL features: -Dell Optiplex Workstations (6 Linux and 2 Windows) -w/ dual monitors -HP LaserJet 4300n printer (please keep on economy setting) -HP ScanJet 4200c flatbed scanner -HP ScanJet 7800 form-feed scanner -Whiteboard -Refrigerator, Microwave, Coffee Maker -Note: No cleaning crew, so try to keep things clean

AMRL software: -Most machines run linux (CentOS 5) -LaTeX -Matlab -Maple -Gnuplot -Compilers -etc -2 Windows machines (WinXP Pro) -Adobe Acrobat Pro (for use with scanners) -(also have matlab, maple, TeX, etc. for use in a pinch)

-Everyone should already have an account created -First log in with username and given password (pay close attention to 0 vs o vs O) -Passwords should be changed immediately -For linux, log in and open a terminal (right-click desktop area, select ‘open terminal’) -Type passwd, hit enter, follow instructions -Windows and Linux passwords are independent, so passwords will need to be changed on the Windows machines as well -Note: domain is MATHSCI -Easiest way to change password is to hit Ctrl-Alt-Del after logging in and select change password -(Can also change passwords using AMRL Login) -PASSWORDS SHOULD BE STRONG! -Use upper and lower case, numerals, special characters -Think of ‘gamer’ friends, ‘133t’-speak, etc (ex:

Introduction to Linux: -Linux is a free OS whose kernel was original designed by Linus Torvalds based on the Unix kernel -In an office environment, unix-based systems are ideal as they are stable and secure -Linux is open-source (meaning the source code is freely available to anyone) -A downside is that Linux is so customizable that it now comes in literally hundreds of flavors, the most popular being Fedora Core, Redhat, Ubuntu, SuSE, Slackware, Arch, Debbian, Gentoo, Knoppix, CentOS

Linux Software: -Terminal (or shell): Command-line interface -Office packages: Similar in use to MS Office -OpenOffice (Writer  Word), (Impress  PowerPoint), (Calc  Excel) -Internet packages: Web-browsing, -Several options, but most common are: -Mozilla Firefox web browser -Mozilla Thunderbird client -Compilers: For C++, Java, fortran, etc (run through the terminal) -Text editors: For writing code (for LaTeX, C++, fortran, etc) -Emacs, Vi, Pico -Graphics packages -The GIMP (like Photoshop), gnuplot, xfig Additional software in the AMRL: -Matlab -Maple

Linux file system: -Unlike Windows, Linux does not base its structure on drives -Rather the highest level directory is ‘/’ (the root directory) -The most important directory for a user is /home/‘username’ -/mnt, /media also important

Linux file permissions: -Similar to the Windows environment, only certain users can access certain files, but unlike windows, only one user in Linux has access to all files -Root user: has full system access -Non-root user: limited system access -Access to home directory -Access to user-mounted devices (flash drives, CDs, etc) -Cannot install software, cannot access other users’ files, cannot change system files -Users are also members of groups, and users with similar groups can access each other’s files. Talk to an admin if you wish to change permissions on files for some reason or wish to add a group so that a particular user can view your files.

Basic Unix/ Linux Commands: -Linux commands are entered into a shell -Most actions today can be performed using either commands or ‘point- and-click’ -Command syntax - -Command: name of command (ex: ls, for ‘list’) -Flags are options for the program -Common flag to know is ‘--help’ -Arguments are additional inputs (filenames, etc) -Examples: ls -l /home/jadams/ (list (long) the contents of /home/jadams) g77 -o hw4.exe hw4.f (g77 fortran compiler, output to hw4.exe, use hw4.f as input)

Basic Unix/ Linux Commands: -ls: list contents of directory -cd: change directory -./ = current directory -../ = parent directory - ~/ = user’s home directory - Thus if I am in /home/jadams/temp, the following all have the same result: - cd../ - cd /home/jadams - cd ~/ -pwd: present working directory (in case you are ‘lost’) -whoami: (in case you are really lost)

Basic Unix/ Linux Commands: -mkdir: make a directory -rmdir: remove a directory (only works if directory is empty) -cp: copy a given file or directory -Use: cp file1 file2 (copies file1 to file2) -mv: move a given file or directory (same use as above) -rm: remove file or directory -cat: print contents of a file (without ‘opening’ it… similar to quick look with Mac OS X Leopard) -less/ more: prints file with scrollable option (less has more features) -head/ tail: prints first/ last 10 lines of file (can print more with -n option) -grep: (get regular expression pattern) search a file for a ‘pattern’ -man: manual (help file for other commands) -who: shows who is logged on -top: process list that is continually refreshed -ssh: used to connect remotely from home or between machines

Basic Unix/ Linux Commands: -tar: similar to zip files. 2 good versions to know: -tar -czvf file1.tgz dir1/ (creates file1.tgz by tarring and zipping./dir1/) -tar –zxvf file1.tar.gz (extracts file1.tar.gz) -lp: print file (use for text files) -convert: converts image files -Compilers: -g77: fortan compiler -gcc: gnu c/c++ compiler -icc: intel c/c++ compiler -latex: compiles tex documents, but more commonly, the programs kile or texmaker are used

Redirection and piping: -Might be useful: -> directs output to a file -Example: ls > list.txt (takes output from list and puts it in a text file) -| pipes output from one command into another -Example: ls | grep myfile (lists the current directory and then searches that list for ‘myfile’) -Example2: cat temp.txt | grep hello (takes contents of file temp.txt and searches for hello) Local software: -matlab, maple (xmaple), kile, etc.

Notes/ Reminders: -Login, change passwords -Ssh only through remote -File extensions don’t matter much in linux -Send a test so we have your -Please keep printer on economy mode -New setup for windows machines allows full access -This is my chair (do not use!) 