[GE users] Upper bound for array jobs?

Reuti reuti at staff.uni-marburg.de
Fri Aug 27 20:47:19 BST 2004


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Hi Bernard,

>Finally mqsub executes the qsub command:
>
>qsub -t 1-100 test_array.sh

although your job should work this way, it's not necessary to create all the 
individual job scripts for each task (which will result in 26,000 scripts in 
/scratch).

If the scripts runtest1.sh...runtest100.sh can't be made unique (and decide 
with a given parameter what to do), I would suggest first to avoid the creation 
of the all the job script files. I think you could skip the "mqsub" step, if 
you adjust the test_array.sh script like:

#!/bin/sh

exec `awk ' (NR==myline) { print $0 } ' myline=$SGE_TASK_ID 
/scratch/test.batch`

This will handle all lines in the test.batch according to the given line number 
and execute one script file. Can you use this in your environment? (Ignore the 
line break, it's just one long line).

Greetings - Reuti

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