PSC Student Technology Orientation

Social Sciences Computing9/16/2011

Introductions

• Social Sciences Computing– Jim Kane – Manager, SSC Network and Helpdesk

– Kyle Small – Linux Systems Administrator

– Chris Mustazza – Director, Student Technology & Social Sciences Computing

the plan

• Introduce ourselves

• Tell you about the resources available to you as PSC students, and, more generally, as SAS students

• Give you a crash course on the amazing things possible in the wonderful world of Linux

• Give some brief advice on data security and backups

• Let you know where to find computing help for any questions you may have

You have a bunch of accounts…

• …and they can by difficult to keep straight. • Here’s a quick review of accounts you

(should) have:– PennKey – access to most University-wide

resources– Email – your SAS email address– SAS Domain account – for logging into lab

computers and accessing Windows file servers– Linux account – for accessing SSC Linux resources

Requesting server accounts

• It’s highly likely that you already have a PennKey and email address.

• But perhaps you haven’t yet requested your domain and Linux accounts. If not, you can find the request form here:

https://www.ssc.upenn.edu/web_account_services/acct_request.html

Computer Labs

Computer Labs

• Log in with either PennKey or SAS domain account– PennKey gives you a generic experience– SAS domain account gives you a more personalized experience

• You can find a listing of available computer labs here:http://www.sas.upenn.edu/computing/rds/labs

• Labs include:– UDAL (104 and 108 McNeil)– GDAL (303 McNeil)– PSC Lab (223 McNeil)

• The Weigle Information Commons is also a great resource for all Penn students:http://wic.library.upenn.edu/

Software in the labs

• Highlights – most labs have Stata, SAS, SPSS(now PASW), R, MS Office.

• Others have more nonstandard software for specific purposes, e.g. GDAL has Gauss, Scientific Word, etc.

• See: http://www.sas.upenn.edu/computing/teaching_resources/computer_labs for details.

Running jobs in the labs

N.B: Lab computers are good for running small jobs; the machines do not lock, so you’d need to be present the whole

time the job is running, unlike with Linux.

Windows File Servers

• Your SAS domain account allows you access to shares on SSC Windows files servers

• Storage space on server may be requested for specific projects.

Printing

• Printing is available in all of our labs

• SAS provides the ability to print to several lab printers from your own computer. More information is available here:

http://www.sas.upenn.edu/computing/printing

• There is also wireless printing available in the Library:

http://www.library.upenn.edu/computing/printing/Personal.html

How it works

•Student installs driver package for location he/she wishes to print

•Student prints document from any location – dorm room, library, etc.

•Print job gets queued at release station(jobs are queued for finite amounts of time, usually 120 minutes – then flushed).

•Student swipes ID card to release job and pay for printing

•Document prints

Linux

What is Linux?

• An operating system for computers – analogous to Windows or MacOs.• It’s just another way to manage your documents, run programs, etc.

• Linux is the generic name for the operating system – specific flavors include:• RedHat/CentOS• Ubuntu

What’s the point?

Benefits of using Linux for PSC students:

• Run long jobs from anywhere without the need to sit at a lab computer• Let’s say you need to run a Stata job with a runtime of 30 hours – you could

log into Linux, start the job, and go about other tasks. You can connect to Linux from anywhere to check on your job or view the results after completion.

• Store your files/jobs in a safe place• Writing code can be frustrating, and the worst thing ever is losing data –

especially code that you’ve labored over for hours. The Linux server is regularly backed up, so you won’t have to worry about losing your work.

Linux Resources

lambic.ssc.upenn.edu

porter.ssc.upenn.edu pils.ssc.upenn.edu

Lambic:• File Server• Holds /home and /work directories.• Shares data between porter/pils.

Porter:• Webserver• Serves /home/PENNKEY/public_html pages.

Pils:• Statistics Server• R• SAS• STATA• Matlab

Software you’ll need to get started

• Connecting and running jobs – SecureCRT • http://www.upenn.edu/computing/product

• Transferring files to your Linux account – FileZilla• http://www.upenn.edu/computing/product

• Graphical interface – Xming • http://sourceforge.net/projects/xming/

Windows

MacOS• Connecting and running jobs – Terminal• Built into Mac OS

• Transferring files to your Linux account – Fetch• http://www.upenn.edu/computing/product

• Graphical interface – X11• Built into Mac OS

Connecting to Linux from Windows

1. Open SecureCRT2. Click the quick connect icon ( )3. Protocol: SSH24. Hostname: pils.ssc.upenn.edu5. Port: 226. Username: your PennKey username7. Click Connect

Connecting to Linux

SecureCRT

Connecting to Linux from Mac OS

• Open the Terminal application – Click on Spotlight (magnifying glass in top-right corner of screen)– Type “Terminal” and select the top item return– At the prompt, type: ssh [your pennkey]@pils.ssc.upenn.edu– Type “yes” to accept the key (you’ll only be asked this the first time you log in)– Enter your password

Connecting to Linux

Copying files from windows1. Open FileZilla2. Enter pils.ssc.upenn.edu in the hostname box3. Enter username/password4. Set port to 22 (sftp)5. Click Quick Connect

Transferring Files from Windows to Linux

FileZilla

Transferring files from Mac to Linux

After you install and open Fetch:• Hostname: pils.ssc.upenn.edu• Username: your PennKey username• Password: you Linux password• Click “Connect”

Transferring files from Mac OS to Linux

• You can now open any folder on your computer and drag its contents into the Fetch window to transfer your files to Linux

Doing stuff in Linux

Basic Commandsks347@pils[~]$ lspublic_html dev work a_script.ploutput.log graph.jpg some_notes

ks347@pils[~]$ cd /dev

ks347@pils[~/dev]$ mkdir new_dir

ks347@pils[~/dev]$ cp ../a_script.pl new_dir

ks347@pils[~/dev]$ ls new_dira_script.pl

ks347@pils[~/dev]$ pwd/home/ks347/dev

• man - Display the manual page for a command• ls - List the contents of a directory• cd – Change to another directory• pwd – Print working (current) directory• mkdir – Make a directory• cp – Copy files • rm – Remove files• cat – Concatenate files and print their contents• tac – Same as cat but in reverse• more & less – Used to read through text 1 screen at a time• And many more….

Doing stuff in Linux

Launching appsks347@pils[~]$ stata

ks347@pils[~]$ xstata

ks347@pils[~]$ sas

ks347@pils[~]$ R

ks347@pils[~]$ matlab

stata – Launches the shell version of Stataxstata – launches the graphical version of Statsas – Launches the graphical version of SASR – Launches Rmatlab – Launches the graphical version of Matlab

Graphical interfaces from Windows

Setting up Xming with SecureCRT1. Start Xming2. Connect to a server3. Click Options->Session Options then navigate to Remote/X114. Check Forward X11 Packets if it is not already checked5. You can now go back to the shell and launch graphical apps (xstata, sas, etc.)

Graphical interfaces from Windows

Xming

Graphical interfaces from Mac OS

• Open the Terminal application, but this time use the following command to connect:ssh –X [your username]@pils.ssc.upenn.edu

Running jobs graphically from your Mac

• You can now launch Linux jobs in a graphical environment – e.g. xstata, sas.

Additional Linux Resources

• Linux Pocket Guide– Great reference for all Linux users– http://my.safaribooksonline.com/9780596806347

• Information on the “screen” command, for running jobs in the background in Linux– http://aperiodic.net/screen/quick_reference

Other Resources

PARC Terminal Servers

• PARC(Population Aging Research Center) has two terminal servers available for research use, at two different levels of security.

– PARC shared terminal server - Windows Terminal server that provides applications for use on datasets that require levels of security that are provided by normal network shares.

– PARC secure data enclave - Citrix server that provides an encrypted connection and isolation for datasets that require higher security.

See: http://parc.pop.upenn.edu/research-services

Web space

• Linux accountholders also get web space. When you connect to pils.ssc using SSH or SFTP, you’ll see a folder called “public_html.” Any files you put here will be accessible from:

http://www.ssc.upenn.edu/~username

AirPennNet Wireless Internet

• All SAS buildings, and most buildings on campus, provide wireless Internet through the AirPennNet* network

• The best way to configure your computer/device for APN is to join the AirPennNet-Help network.

• If you have any problems getting configured, we can help

*You will also see the “AirPennNet-Guest” network; this network is unencrypted, so we recommend using “AirPennNet.”

Data Backup and Security

Data backups

• In addition to providing convenient access to your files, storing your documents on the SSC servers provides a backup solution– We backup the servers regularly

• For documents that you may not be appropriate for the server, yet are still of the utmost importance (see: your collection of HD-quality episodes of The Daily Show), consider purchasing an external hard drive or USB key, or a cloud backup service.

Data security and privacy

• In you use files that contain sensitive data, consider encrypting/password-protecting them – Office provides this functionality.

• Consider the sensitivity of data before uploading documents to a cloud service (e.g. Google Docs). – For example, you should never upload personally

identifiable, evaluated student work to a third party (FERPA regulations require us to protect it.)

Getting Help

We’re always around to help…

• Please write, call, or drop by anytime:

McNeil 304215-898-6454

pops-lsp@ssc.upenn.edu

Or fill out our online form – we’ll get back to you ASAP:

http://www.sas.upenn.edu/computing/rds/ssc/request

Questions?