This document provides an introduction to using the V4 Linux cluster at Cornell University. It explains how to connect to the login nodes, set up a home directory, transfer files, run programs interactively and in batch mode by submitting jobs to the scheduler. It also covers choosing queues, requesting resources like CPU time and disk space, managing jobs, and finding help resources. The goal is to help new users get started using the Linux cluster for their computational needs.

1. Introduction to Using theV4 Linux ClusterCornell Center for Advanced ComputingDrew DolgertJodie Sprousehttp://www.cac.cornell.edu/~ajd27/intro.html16 May 2011www.cac.cornell.edu1

2. 2.1 Connecthttp://www.cac.cornell.edu/~ajd27/intro.html

3. CAC

4. What is it?

8. SchedulerLogin Node

9. ajd27@linuxlogin1.cac.cornell.eduajd27@linuxlogin2.cac.cornell.edu

11. lsfirstrun/1469.OUpwd/home/ajd27

12. SSH ServerBASHWindowxclockX11 Server

13. SSH ServerBASHWindowxclockX11 Server

14. SSH ServerBASHWindowxclockX11 Server

15. SSH ServerBASHWindowxclockX11 Server

16. X11X11X11SSH

17. 3 Set Up Home DirectoryWeb sitehttp://www.cac.cornell.edu/~ajd27/intro.htmlDownload intro.tar.gzwith webbrowserYour computerlinuxlogin2Send with Secure Copy

18. http://www.cac.cornell.edu/~ajd27/intro.html3.1 Transfer Files3.2 cd and ls3.3 Getting Help

19. The Shell

20. lscdcatgrepfindlessechopwdexitrmlogoutmanmkdirfgbgsshifforexportcutsedawkmakexargsdifftouchchmodaliasumaskheadtailtoptarmvlnexprpushdpopdsourcesortsleeppushdpopdpsnohuptimedate

21. WorkingDirectoryVariablesNOW(other things)

22. /binhomeusrajd27srl6dev

23. /binhomeusr$HOME~ajd27~ajd27srl6dev

24. /binhomeusr..srl6relative../../srl6.

25. /binhomeusrajd27srl6rooted/home/ajd27/devdev

26. /binhomeusrajd27srl6${PATH}/bin:$HOME/binbin

27. 4.1 Starting: Read Examples of Sessions

29. DIRECTORY_WHERE_I_PUT_THE_GOOD_STUFF

30. Schedulerexport VARJob

31. echo *.txtYou type:Substitutionecho s0.txt s1.txt s2.txtecho hears:s0.txt s1.txt s2.txtecho answers:

32. process

33. sim<input.txtsim>output.txtsim 2>err.txtprocess

34. greplessgrep Mop *.txt | less

35. argumentspathgrep -C -i 2 mop <s0.txt >> mop.txtredirectsswitches

36. gediteclipsenanoemacsvisensibleprogrammerget-it-donedo-it-alldid what?

37. 5.1 Starting: Develop Commands to Run the Program5.2 Run a Simple Script

38. Run in batch!

39. SchedulerLogin Node

40. Choosing a Queuev4v4devv4-64g

41. Schedulinga Queue

42. -AAccount/project-N Job name-lNodes,walltime-jJoin out-error

43. #PBS For schedulerTODOFor compute node

44. Read 6.1 and 6.2Do 6.3 Submit a Script

45. batch fileinput filesSchedulerYourscriptjobWhat runs(and how you find out what ran)job outoutput files

46. blockedeligibleremovedrunningStates of a jobaccording to schedulercompleted

47. Shared Drives$TMPDIR$TMPDIR$TMPDIR$HOME$TMPDIR/v4scratch/$USER

48. Read 7.1Do 7.2 Use the local drive

49. Interactive #PBS -Ilinuxlogin2$ nsub local.shExecuting interactiveqsub: waiting for job 1085387.scheduler.v4linux to startqsub: job 1085387.scheduler.v4linux ready-bash-3.1$ hostnamecompute-3-48.v4linux

50. ControlPICPUprojectaccountdiskconsultingmembermemberCPUCPUdiskdisk

52. This talk http://slidesha.re/eAzPXhhelp@cac.cornell.eduhttp://www.cac.cornell.edu/help

53. Broader ViewCan’t finish on lab computer.Have to write more complex simulation.Need a research portal.

54. by Kman999 on Flickr: 225483156on Flickr by turbojoe/457215996on Flickr by vlashton/2103759668/anti_christa on Flickrantichrista/4499789643/eberg_canada on Flickreberg/555034750aitor_mac on Flickrmac_mania/3914910630/house-n-baby { Lea }'s house-n-baby/2669683890susanica/2702214137/Flickr by liewcf/268421712Rob Shenk on Flickrrcsj/2500928072/Mike Ross of corestore.org, wikipedia.