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arrayszshhpcqsubsungridengine

$SGE_TASK_ID not getting set with qsub array grid job

With a very simple zsh script:

#!/bin/zsh

nums=(1 2 3)
num=$nums[$SGE_TASK_ID]

$SGE_TASK_ID is the sun-grid engine task id. I'm using qsub to submit an array of jobs.

I am following what is advised in the qsub manpage (http://www.clusterresources.com/torquedocs/commands/qsub.shtml#t) and submitting my array job as 

#script name: job_script.sh
qsub job_script.sh -t 1-3

$SGE_TASK_ID is not being set for this array job... does anyone have any ideas why?

Thanks!

Solution

  • thanks everyone for the answers. I found a solution that works:

    Depending on how the cluster is set up, the Sun Grid Engine might be configured to use another variable name for array ids.. This was the case for me. I found out the variable to use by doing the following:

    // job_script.sh

    #!/bin/zsh
env >> ~/job_env
set >> ~/job_env

    This dumps all environment variables set by the script into a file called job_env. Just simply look in the file and look for a variable array ID that is incremented for each job. Should not be that hard to find.

    Remember to submit the job_script.sh with qsub as follows:

    qsub -t 1-3 job_script.sh

    In my case, the ID that was set was $PBS_ARRAYID. I don't think that's the default so $SGE_TASK_ID should work for standard SGE setups on clusters.

    Cheers!