Difference between revisions of "LoadLeveler Chain Jobs"
From Rizzo_Lab
| Line 14: | Line 14: | ||
# @ executable = mpirun32 | # @ executable = mpirun32 | ||
# @ bg_size = 512 | # @ bg_size = 512 | ||
| − | # @ arguments = -np 512 -exe namd2 -args "01mi.in" | + | # @ arguments = -np 512 -exe path/namd2 -cwd "path" -args "01mi.in" |
# @ input = /dev/null | # @ input = /dev/null | ||
# @ output = mi.$(step_name).out | # @ output = mi.$(step_name).out | ||
| Line 25: | Line 25: | ||
# @ dependency = ($(job_name)_01 == 0) | # @ dependency = ($(job_name)_01 == 0) | ||
# @ bg_size = 512 | # @ bg_size = 512 | ||
| − | # @ arguments = -np 512 -exe namd2 -args "02mi.in" | + | # @ arguments = -np 512 -exe path/namd2 -cwd "path" -args "02mi.in" |
# @ input = /dev/null | # @ input = /dev/null | ||
# @ output = mi.$(step_name).out | # @ output = mi.$(step_name).out | ||
| Line 36: | Line 36: | ||
# @ dependency = ($(job_name)_02 == 0) | # @ dependency = ($(job_name)_02 == 0) | ||
# @ bg_size = 512 | # @ bg_size = 512 | ||
| − | # @ arguments = -np 512 -exe namd2 -args "03mi.in" | + | # @ arguments = -np 512 -exe path/namd2 -cwd "path" -args "03mi.in" |
# @ input = /dev/null | # @ input = /dev/null | ||
# @ output = mi.$(step_name).out | # @ output = mi.$(step_name).out | ||
Revision as of 16:49, 20 October 2009
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.
- common
- @ job_type = bluegene
- @ job_name = min
- @ class = normaldyn
- @ initialdir = /gpfs/home2/yulinh/RCR/projects_BG/inactive_ERBB_lapatinib/inactive_HER2_temp1XKK_lapatinib/N003_mdwat_namd_run2
- @ wall_clock_limit = 00:20:00
- step 1
- @ step_name = $(job_name)_01
- @ executable = mpirun32
- @ bg_size = 512
- @ arguments = -np 512 -exe path/namd2 -cwd "path" -args "01mi.in"
- @ input = /dev/null
- @ output = mi.$(step_name).out
- @ error = mi.err.$(step_name)
- @ notification = complete
- @ queue
- step 2
- @ step_name = $(job_name)_02
- @ dependency = ($(job_name)_01 == 0)
- @ bg_size = 512
- @ arguments = -np 512 -exe path/namd2 -cwd "path" -args "02mi.in"
- @ input = /dev/null
- @ output = mi.$(step_name).out
- @ error = mi.err.$(step_name)
- @ notification = complete
- @ queue
- step 3
- @ step_name = $(job_name)_03
- @ dependency = ($(job_name)_02 == 0)
- @ bg_size = 512
- @ arguments = -np 512 -exe path/namd2 -cwd "path" -args "03mi.in"
- @ input = /dev/null
- @ output = mi.$(step_name).out
- @ error = mi.err.$(step_name)
- @ notification = complete
- @ queue
