LoadLeveler Chain Jobs

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Now all the blocks on BlueGene are dynamic blocks. If you want to run jobs one after the other, you should use the following tricks.

Suppose you want to run 3 minimization steps which are dependent. For step 2 and 3, dependency command should be used. See the example.

  1. common
  2. @ job_type = bluegene
  3. @ job_name = min
  4. @ class = normaldyn
  5. @ initialdir = /gpfs/home2/yulinh/RCR/projects_BG/inactive_ERBB_lapatinib/inactive_HER2_temp1XKK_lapatinib/N003_mdwat_namd_run2
  6. @ wall_clock_limit = 00:20:00
  7. step 1
  8. @ step_name = $(job_name)_01
  9. @ executable = mpirun32
  10. @ bg_size = 512
  11. @ arguments = -mode VN -np 1024 -exe path/namd2 -cwd "path" -args "01mi.in"
  12. @ input = /dev/null
  13. @ output = mi.$(step_name).out
  14. @ error = mi.err.$(step_name)
  15. @ notification = complete
  16. @ queue
  17. step 2
  18. @ step_name = $(job_name)_02
  19. @ dependency = ($(job_name)_01 == 0)
  20. @ bg_size = 512
  21. @ arguments = -mode VN -np 1024 -exe path/namd2 -cwd "path" -args "02mi.in"
  22. @ input = /dev/null
  23. @ output = mi.$(step_name).out
  24. @ error = mi.err.$(step_name)
  25. @ notification = complete
  26. @ queue
  27. step 3
  28. @ step_name = $(job_name)_03
  29. @ dependency = ($(job_name)_02 == 0)
  30. @ bg_size = 512
  31. @ arguments = -mode VN -np 1024 -exe path/namd2 -cwd "path" -args "03mi.in"
  32. @ input = /dev/null
  33. @ output = mi.$(step_name).out
  34. @ error = mi.err.$(step_name)
  35. @ notification = complete
  36. @ queue