[GE users] Sequential array jobs
andy.schwierskott at sun.com
Wed Sep 22 08:34:33 BST 2004
job dependencies on job names are a 6.0 feature.
On Tue, 21 Sep 2004, Charu Chaubal wrote:
> Orion Poplawski wrote:
>> Charu Chaubal wrote:
>>> Orion Poplawski wrote:
>>> > Is it possible to submit an array job where the tasks execute
>>> Array jobs are intended to be mutually independent, so you can't have
>>> dependency on sequence among them.
>>> Why not just submit jobs one by one with -hold_jid?
>>> If you find that submit time is long for submitting many jobs at once,
>>> have you tried using GE 6? Submit times for GE 6 can be quicker than
>>> for SGE 5.3.
>> I guess I was just looking for a built in counter with the task ID
>> providing step of the job to complete. Also, with -hold_jid I need to
>> determine the job ID of the previous qsub somehow, right? Is there an
>> easy way to do this or do I need to parse the output from qsub?
> Parsing is not necessary --- you can use -hold_jid with job names.
> So, you could do something like
> qsub -N $name.1 -v COUNT=1 job.sh
> while [ $x -lt $END ]
> qsub -hold_jid $prev -N $name.$x -v COUNT=$x job.sh
> (you could probably make this into a generic wrapper script, so you could
> have your users do something like 'qsub_seq <name> <start> <end> <step>
>> I think something like:
>> qsub -t 1-10:sequential job
>> would be simpler than something like (excuse the shell mishmash):
>> jid=`qsub job $x | <parse job id>`
>> while [ $x -lt 11 ]
>> jid=`qsub -hold_jid $jid job $x | <parse job id>`
>> I am using GE 6.
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