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 | + | # @ arguments = -mode VN -np 1024 -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 | + | # @ arguments = -mode VN -np 1024 -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 | + | # @ arguments = -mode VN -np 1024 -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 14:56, 26 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 = $(job_name)_01
- @ executable = mpirun32
- @ bg_size = 512
- @ arguments = -mode VN -np 1024 -exe path/namd2 -cwd "path" -args "01mi.in"
- @ input = /dev/null
- @ output = mi.$(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 = -mode VN -np 1024 -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 = -mode VN -np 1024 -exe path/namd2 -cwd "path" -args "03mi.in"
- @ input = /dev/null
- @ output = mi.$(step_name).out
- @ error = mi.err.$(step_name)
- @ notification = complete
- @ queue
