PrepareJob

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Lines starting not with "#" are commands to execute programs in this job.
 
Lines starting not with "#" are commands to execute programs in this job.
 
  
 
== Example (Beast) ==
 
== Example (Beast) ==

Revision as of 15:47, 27 April 2015

To run your job on the cluster, prepare it on your local machine, then copy it to the cluster. Beside the datafiles you will need a jobfile containing all you setting.

Name your job file and your data files in a consistent way:

  • Job file: myjobfile.sh
  • User: Mustermann
  • Email: max@mustermann.de

These jobfiles are written in a sort of "shell" command syntax of Linux systems.

Lines starting with "##" or "# " are comment lines to document some stuff for better reading afterwards.

Lines starting with "#$" are commands for the job scheduler "qsub".

Lines starting not with "#" are commands to execute programs in this job.

Example (Beast)

you may use this as a template for Beast simply change all occurrences of "myjobfile" to your actual project name. also change User and email to your settings.

  1. #!/bin/csh
  2. #
  3. # Username (Which account to be charged cpu time)
  4. #$ -A Mustermann
  5. #
  6. #
  7. # If you want to make it queue now, get rid of the -a option by adding ## before $
  8. # If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS]
  9. ##$ -a 201407300600
  10. #
  11. #
  12. # Send mail to these users
  13. #$ -M max@mustermann.de
  14. #
  15. # Mail at beginning/end/on suspension
  16. #$ -m bes
  17. #
  18. # Export these environmental variables
  19. #$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
  20. #
  21. # The job is located in the current
  22. # working directory.
  23. #$ -cwd
  24. #$ -o myjobfile.out
  25. #$ -e myjobfile.err
  26. #
  27. env >./xenv
  28. /share/apps/beast180/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out
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