Hoffman2:Job Array: Difference between revisions
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===Example=== | ===Example=== | ||
====Lots of numbers====--> | ====Lots of numbers====--> | ||
Let's | Let's see how job array can replace a loop which can run only in one node | ||
#!/bin/bash | #!/bin/bash | ||
# myFuncSlowWrapper.sh | # myFuncSlowWrapper.sh |
Revision as of 21:30, 19 December 2019
Job Array or Array jobs make it possible to process different subjects/files using the same script on multiple Hoffman2 working nodes at the same time.
Here, we use the this template code to show how it can be done Submit job
#!/bin/bash #$ -cwd # error = Merged with joblog #$ -o joblog.$JOB_ID #$ -j y #$ -pe shared 2 #$ -l h_rt=8:00:00,h_data=4G # Email address to notify #$ -M $USER@mail # Notify when #$ -m bea #$ -t 1-50:1
The only difference comparing with the single subject version is this part
#$ -t 1-50:1
The -t option should be followed by a number range together with the step interval in the following format:
-t lower-upper:interval
where
lower
- is replaced with the starting number
upper
- is replaced with the ending number
interval
- is replaced with the step interval
So adding the argument
-t 10-100:5
will step through the numbers 10, 15, 20, 25, ..., 100 submitting a job for each one.
There will be an environment variable called SGE_TASK_ID
whose value will be incremented over the range you specified. Hoffman2 job scheduler will submit one job for each SGE_TASK_ID, so your work will be parallelized.
Example
====Lots of numbers====--> Let's see how job array can replace a loop which can run only in one node
#!/bin/bash # myFuncSlowWrapper.sh for i in {1..100}; do myFunc.sh $i; done
The only drawback is that this will take quite a while since all 100 iterations will be done on a single processor. With job arrays, the computations will be split among many processors and can finish much more quickly. You would instead write a wrapper script called myFuncFastWrapper.sh as
#!/bin/bash # myFuncFastWrapper.sh echo $SGE_TASK_ID myFunc.sh $SGE_TASK_ID
And submit it with
qsub -cwd -V -N PJ -l h_data=1024M,h_rt=01:00:00 -M $HOME -m bea -t 1-100:1 myFuncWrapper.sh