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CCPR Workshop Introduction to the Cluster

CCPR Workshop Introduction to the Cluster. July 13, 2006. Outline. What is a cluster? How can CCPR’s cluster help you? Using the cluster Connecting from Windows Unix commands Submitting jobs Managing jobs. What is a cluster?. Think of a cluster as having two parts :

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CCPR Workshop Introduction to the Cluster

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  1. CCPR WorkshopIntroduction to the Cluster July 13, 2006

  2. Outline • What is a cluster? • How can CCPR’s cluster help you? • Using the cluster • Connecting from Windows • Unix commands • Submitting jobs • Managing jobs

  3. What is a cluster? • Think of a cluster as having two parts: • Hardware: a collection of computers • Cluster management system: software for coordinating hardware with a collection of computational tasks (batch jobs)

  4. CCPR’s Cluster: Management System • Jobs are submitted to the cluster via the cluster management system • An advanced batch system • Efficiently allocates resources to jobs • Remembers job requirements • Remembers node specs and availability • Schedules jobs according to requested resources and priority • Users can easily view jobs

  5. How does this help your research? • Easy access to software and data • Faster processors • More RAM • Easy to share data, programs, etc. with colleagues via the cluster • More advanced users: parallel processing, compilers, etc. • Your pc is available for other work when you submit a job to the cluster • Submit a job and forget about it

  6. Using the Cluster • Connecting from Windows • Unix Commands • Submitting jobs • Managing jobs

  7. Secure Shell • Secure Shell software (2 pieces) • SSH Secure Shell Client (Telnet) • SSH Secure File Transfer Client (FTP). • Download software from www.ssc.ucla.edu Computing  Security

  8. Secure Shell: Connecting to lexis from Windows • Connect to lexis via SSH Secure Shell Client • Startup SSH Secure Shell/File Transfer • Click Quick Connect • Enter: • Host Name: lexis.ccpr.ucla.edu • User Name: your lexis account name • Port Number: 22 • Click connect and enter password • Can add “profile” for repeated use • Same process for SSH Secure File Transfer Client

  9. Samba: Transferring files from pc to lexis • Analagous to “mapping a drive” • Allows user to view lexis files via Windows Explorer interface • Must use vpn when you’re off campus. Download from • http://www.bol.ucla.edu/services/vpn/ • Step-by-step instructions: • http://lexis.ccpr.ucla.edu/using/samba/

  10. Samba: Transferring files from pc to lexis • Open Windows Explorer on the local machine. • Select Tools->Map Network Drive • In the "Folder" text box enter: \\lexis.ccpr.ucla.edu\your-user-name • Click "Reconnect at login" if you want the drive to be mounted each time the computer starts up. • Click the "different user name" link to enter your user name and password for the connection. • Click "OK" then click the "Finish" button on the Map Network Drive window.

  11. Unix commands

  12. More Unix Commands

  13. More Unix commands

  14. Getting help in Unix

  15. Unix Commands: Using Aliases • Alias • Create an alias for commonly used commands • Example: alias ls=“ls –lah” • Anytime you type ls, you will see the ls command with options lah (l=long, a=all, h=human-readable) • Edit .aliases file to create and remove aliases

  16. Unix commands: Pipes and grep

  17. Editing Files on Lexis • Pico – easiest editor. Open and type. Commands listed at bottom of editor. • Vi – more advanced. You can move around quickly, do copy/paste, search, etc, but keystrokes required for everything. • Emacs – most advanced

  18. Submitting Stata and SAS jobs • Submit jobs by typing qjob, qstata, qsas, qmatlab at Unix prompt • You will then be prompted for: • filename • memory (number in megs, ex. 1050) • if memory > 1 gig -> Over 2 hours (y/n), • job type (for qjob only) • submit (y/n) • Alternatively, submit all options without being prompted: • qstata sample.do 500 y

  19. Files produced by qstata • filename.log - This is the log file from Stata. The output of your entire Stata job is caputured in this file. • filename.do.cmd - This is the Command file that is submitted to the cluster. • filename.do.joblog - This file will capture the output of your CMD file and any errors that may occur (Stata output is not captured by this log.)

  20. Job Management

  21. Job Management • qstat or qstatus to view overall cluster usage • qstat –jjobnumber for information particular to your job • qdel jobnumber to kill your job

  22. Working interactively - qinteractive • To work interactively, type “qinteractive” at prompt • Default RAM allotted is 256 • Request x megs by typing “qinteractive x” • Please use interactive nodes responsibly • Limited number of spaces • Testing only • Logoff promptly

  23. Questions/Comments

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