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Cluster Computing: Program Execution and Security Tips

Learn about cluster computing on Lisa system, how to run programs, and important security measures. Includes details on job submission, password changes, and job status monitoring.

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Cluster Computing: Program Execution and Security Tips

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  1. Contents What is a cluster? Why do you need a cluster? How to run a program on Lisa? Security Special buttons Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  2. What is a cluster? Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  3. The Lisa system Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  4. The people in the cluster group Jaap Dijkshoorn Walter de Jong Bas van der Vlies Maarten van Ingen Ramon Bastiaans Willem Vermin Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  5. Why do you need a cluster? Run the same program 1000 times 1 processor available Several processors run the program at the same time Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  6. How to run a program on Lisa? • Available software • Genehunter, MeV, Mendel, Mx, R, SimWalk, QTDT, Solar, Twinsim, Allegro, GASP, GASSOC, LOKI, Mapmaker, MEGA2, PEDIG, SAGE, TRANSMIT, UNPHASED, Vitesse, Linbugs • Other software: e-mail danielle@psy.vu.nl • How to run program ‘mx’ with input file ‘mxinput’ on Lisa? • WinSCP • cd command • create a file • start mx • submit mx to Lisa Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  7. WinSCP Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  8. WinSCP Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  9. cd – change directory Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  10. cd – change directory Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  11. cd – change directory Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  12. cd – change directory Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  13. Copy, create or edit a file • Copy - Copy / Paste as usual in windows • Create: Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  14. Copy, create or edit a file • File names in Unix • case sensitive • advise: no special characters like !@#$%^& • advise: no spaces Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  15. Copy, create or edit a file Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  16. Copy, create or edit a file Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  17. Copy, create or edit a file • Edit: Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  18. Start mx Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  19. Start mx Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  20. Start mx • module command Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  21. Start mx Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  22. Submit a job • Why not use the interactive node? • Not allowed • system managers will kill your job • Independency • Jobs are not dependent of startup terminal • shut down PC no problem • 1 jobs each time • Not possible to run a lot of jobs at ones Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  23. Submit a job • jobscript Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  24. Submit a job Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  25. Submit a job Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  26. Submit a job Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  27. Submit two jobs at one node • Why? • Each node contains two processors • A job gets exclusive access to a node • Even a serial job gets a whole node with two processors Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  28. Submit two jobs at one node Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  29. Submit two jobs at one node Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  30. Jobstatus Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  31. Jobstatus Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  32. Remove a job Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  33. Security • Do not share logins • Maintain your workstation/pc • Notify SARA in case of troubles • Password • Change it at least every year • Use capitals and special characters • Not easy to guess Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  34. Change password Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  35. Change password Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  36. Change password Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  37. Change password Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  38. Submit job button Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  39. Job status button Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  40. Submit job and status button output Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

  41. Lisa • Questions? Laura Leistikowhic@sara.nl http://www.sara.nl click userinfo

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