ECC Linux workshop (intro course)

WHAT WILL BE COVERED UNIX/Linux Overview Red Hat Enterprise Linux ECC-UNIX accounts How to Login GUI Navigation Applications Command Line Shell Commands and Create Text Files File Permissions Remote Access & File Transfer X Window + PUTTY Security & ECC Policies Help Requests

UNIX overview UNIX was developed in 1969 at Bell Labs. Originally used as a workbench for programmers to develop new software for testing. Main Functions of UNIX: - High performance Computing (Clustering, job scheduling) - Resource Sharing (File and sharing) - Multi-User Access - Programming and Software Development

LINUX Linus Torvalds developed the Linux kernel in 1991. Collaborated with the GNU Project in 1992, to create the first free operating system for the public. Many distributions of Linux include Debian, Fedora, Mandriva, SUSE, Slackware, and Android Most distributions are free for use, some are NOT

RED HAT ENTERPRISE LINUX Enterprise level operating system Trademark and Support are NOT free CentOS and Scientific Linux are free “rebuild”versions of Red Hat Enterprise Linux

Centos 6 and 7 http://www.centos.org/ A free, community supported enterprise OS. Exact replica of Red Hat Enterprise Linux 6 and 7

ECC-UNIX ACCOUNT ALL ENGINEERING STUDENTS, USING LINUX SYSTEMS OR APPLICATIONS WILL NEED A ECC-UNIX ACCOUNT NEW USERS WILL NEED TO APPLY FOR ECC-UNIX ACCOUNTS AT THE ECC LAB FRONT DESK COUGAR ID CARD MUST BE PRESENT WHEN APPLYING FOR AN ECC-UNIX ACCOUNT ONLY ENGINEERING AFFILIATED STUDENTS AND FACULTY ARE ALLOWED TO CREATE A ECC-UNIX ACCOUNT ANY NON ENGINEERING STUDENTS OR FACULTY MUST OBTAIN SPONSORSHIP TO CREATE AN ACCOUNT ECC UNIX ACCOUNTS NOW USE COUGARNET PASSWORD AUTHENTICATION.

Switch to cougarnet authentication Starting Fall 2014 COUGARNET ACCOUNT PASSWORDS WILL BE USED TO LOGIN TO ALL ENGINEERING LINUX SYSTEMS NEW USERS WILL STILL NEED TO CREATE A ECC-UNIX ACCOUNT USERNAME ALL ACCOUNT PASSWORDS WILL HAVE TO BE RESET BY UofH CENTRAL IT.

RESET PASSWORD (online) GO TO: http://www.uh.edu/infotech/ Click “Password Reset” Enter security information On CougarNet Click “Reset”

HOW TO LOGIN Open Remote Desktop Connection from the Windows Start menu and enter the hostname – HOSTS: tuxedo.egr.uh.edu, linus.egr.uh.edu USE ECC UNIX/CougarNet ACCOUNT TO LOGIN

RDP LOGIN

NAGIVATE THE GUI (GRAPHICAL USER INTERFACE) Applications Accessories word processing System tools Command line (terminal) Places Home folder Subdirectories Search for files System Preferences Administration Utilities System Documentation

APPLICATIONS Firefox LibreOffice Terminal Text Editors Web Browser Open source version of Microsoft Word, Excel, and PowerPoint Terminal Command line shell prompt Faster than GUI Text Editors EMACS Gedit VI/ VIM/ NANO (command line)

Class software location Location: /usr/local Software: MATLAB, Abacus, Fluent, Cadence, Comsol, etc…

MATLAB Location of MATLAB Software folder: /usr/local/MATLAB Current licensed versions: R2012a and R2013a To run application using GUI Click “Computer” -> “Filesystem” -> “usr” -> “local” -> “MATLAB” -> “R2013a” -> “bin” -> “matlab” Easy way! on CLI Matlab 2012a Type: $ matlab Matlab R2013a Type: $ matlab2013

Comsol Location of Comsol software executable $ /usr/local/comsol40a_Wosik/bin/comsol Create a command path in your home .bashrc file export PATH=$PATH:/usr/local/comsol40a_Wosik/bin/ Save .bashrc file Type $ source .bashrc TO CHECK YOUR CONFIGURATION: Check you path with $ echo $PATH Also check the path location of a shell command using which Ex. $ which comsol

Cadence Software Location: /usr/local/Cadence Please check the ECE webpage for Cadence setup to ECC- UNIX account profiles IE. http://www.ee.uh.edu/research/cadence-university-program Click the “Getting started in Cadence” link to open a profile configuration document. Skip steps 1 – 7 (new configuration next slide)

Cadence (Continued) Using your favorite text editor… Edit ~/.login Add lines: #Cadence Calp path set path=($path /usr/local/bin /usr/local/calp) source /usr/local/calp/nlogin Save file Edit ~/.cshrc #Cadence Virtuoso Path alias virtuoso "/usr/local/Cadence/ic/tools/dfII/bin/virtuoso &" setenv PATH ${PATH}:/usr/local/Cadence/ic/tools/dfII/bin setenv PATH ${PATH}:/usr/local/Cadence/tools/bin source /usr/local/calp/ncshrc Run virtuoso: in the shell Type: $ tcsh $ source ~/.login $ virtuoso & MUST BE IN A X11 (remote graphical) SESSION TO RUN THIS PROGRAM

silvaco Location of program is located in /usr/local/SILVACO.x64 Users can set the path to run the program in there home directory. Set your path in your home folder .bashrc file. Using (vim,nano) text editor, enter the following line in your profile: export PATH=$PATH:/usr/local/SILVACO.x64/bin/ Save .bashrc file Type $ source .bashrc TO CHECK YOUR CONFIGURATION: Check you path with $ echo $PATH Also check the path location of a shell command using which Ex. $ which deckbuild

fluent Location: : /usr/local/ANSYS-15/v150/fluent/bin/fluent Run Fluent from the CLI (easy way) In home .bashrc file, add ##Fluent Path export PATH=$PATH:/usr/local/ANSYS-15/v150/fluent/bin/ Save… Type: $ fluent

ACCESS THE COMMAND LINE PROMPT Applications  System tools  Terminal Fully text based command prompt Shell prompt [ username@<hostname> <current working directory>] $

Shell command syntax Example: [user@host ~]$ ls –al [file] Command syntax and arguements are DIFFERENT for each and every shell command [user@host ~]$ command [OPTIONS] …[file] [file2] Example: [user@host ~]$ ls –al [file] - Will display all files in the current working directory with a “long listing format”

USING SIMPLE SHELL COMMANDS Navigation: ls – list directory contents ls –l - view files and permissions pwd – print, current working directory cd – change directory cd <directory path> Ex. (to go to user home directory) [user]$ cd /home/user or cd ~ Copying, Moving, and Deleting cp – copy files and directories cp <file source> <file destination> mv – move or rename file mv <file source> <file destination> touch – make basic text files touch <file name> mkdir – create a directory mkdir <directory file path> rm – delete a file (can be destructive) rm <file path> rmdir – delete directory (empty directory) rmdir <file path>

SHELL COMMANDS (continued) Search commands: find – search for files Find <sourse directory> -name <name of file or directory> -print Documentation: man – manual pages man <command or application> Change File Permissions: chown – change file owner and group chown owner:group <file path> chgrp <groupname> <file path> System commands: top – show current processes that are running df –h: show the file system disk space usage w : show users currently logged on to the system uptime : show date, load average, and # of users uname –a : show current OS version and computer hostname Network Statistics Ifconfig : show IP address information netstat –rn : show IP routing information

More commands Wget: network downloader du: -estimate file space usage Ex: $ du –sh [file/directory] diff or cmp: Diff: compare files line by line Ex. $ diff [file1] [file2] Tar: create archive of files also with compression Create tar archive file $ tar –cvf [archive.tar] [files or directory] Extract tar achive file $ tar –xvf [tar_file.tar] You can compress using the –z option and syntax as follows $ tar –czvf [archive.tar.gz] [files and or directory] Wget: network downloader Extract files from http links directly to your current working directory $ wget [options] [URL]

Create & EDITING TEXT FILES NANO ( simple cmd text editor) Nano <file> VIM (command line text editor) vim <edit file name or new file create> EMACS GUI(Graphical) text editor Located in Applications -> Accessories -> EMACS

FILE PERMISSIONS drwxrwxrwx First character: rwx permissions: d = directory (blue) l = symbolic link (cyan) ‘-’ = a file (white) rwx permissions: R = read W = write X = execute First set: owner Second set: group Third set: everyone

REMOTE ACCESS SSH – Secure Shell client A program used for “shell” access to a remote system. Login using UNIX/Linux terminal (shell), or through “PUTTY” Use ECC UNIX account info to login PUTTY (for Windows Users) Free application Allows shell logins from a windows desktop

Remote access (cont) SSH from PUTTY: Open PUTTY app from Windows Type the hostname or IP of destination Port is always 22 Enter ECC-UNIX user ID, and password If successful, user command prompt will be shown SSH from another terminal (shell): Type command: ssh <username>@<hostname>

Using x window in putty There are two methods for creating a graphic window display for an application using the PUTTY command line program on Windows, in conjuction with X-Win 32 (license required) or Xming (free). X-win 32: Start up x-win32 program, DO NOT login to server using the appliction. Instead, Start the PUTTY app (start -> all programs -> PUTTY) In “Connection” tab, click the ‘+’ for SSH, click on “X11”, click box for “Enable X11 forwarding” In dropdown box “Session”, type the hostname of the server you wish to connect to. Click “open” Run application of your choice (matlab,comsol,gedit,etc.)

Xming Free X-server application for windows Website: http://www.straightrunning.com/XmingNotes/ “Public Domain Releases” Download both “Xming” and “Xming-fonts”, install both apps. Run Xming, runs in the background. No initial setup is required. While Xming is running, start PUTTY session in X11 enabled mode ( previous slide)

file Transfer WinSCP: Transfer files from Windows to Linux and vice versa Download WinSCP from “software download” section on Access UH Login: Open WinSCP program Enter user credentials, click login

SECURTIY & ECC POLICIES ECC website http://ecc.egr.uh.edu/engineering- computing-center-policies ECC Usage Policy http://ecc.egr.uh.edu/sites/ecc.egr.uh.e du/files/files/cce_policy_computing.pdf

Security DO NOT, give anyone your password DO NOT, let anyone use your ECC-UNIX account Always properly logout of once you are finished with a session Remember, all activity on our Linux servers is being tracked and logged, including command history. Report any suspicious activity the following ECC IT administration below. Kiet Luong Manjunatha Shenoy Engineering IT Director / Systems Administrator 2 Information Security Officer Email:mshenoy@uh.edu Email: KietL@uh.edu

Security/Piracy DO NOT bring personal routers or switches and plug them into campus network wall ports. If a faculty member wants to connect routers or switches into network, notify the ECC IT administration BEFORE plugging anything onto our network. DO NOT bring personal desktops and plug into the campus network. Only laptops and tablets are allowed, which should only be using the UH wireless network. Desktops with wireless PCI or USB adapters are NOT permitted. DO NOT download and install any pirated or unlicensed software and or multimedia contents onto UH owned computers. This is against UH policy DO NOT use the UH network to conduct any illegal activity and or piracy. http://www.uh.edu/af/universityservices/policies/mapp/10mappit.htm

HELP REquest For help with your ECC-UNIX account profiles and or any issues related to our engineering Linux servers, please make requests to mshenoy@uh.edu Undergrad and or Graduate Students - If a change is needed on a faculty research server or computer. Please send an email to your faculty advisor/professor for approval. Always ask the faculty advisor to make technical request instead of going directly to the IT administration. Please follow this procedure so that your change request may be processed without delay.

WifI troubleshooting If there are WIFI problems with your laptop or other devices, please run the UH network test from your own devices connected to UH wireless network by going to: http://www.uh.edu/network-test/#0