[GE users] How do I know when an array has finished?

Michael James Michael.James at csiro.au
Wed Oct 4 09:08:05 BST 2006


Does SGE provide a way to know when an array of jobs has finished?

That is, apart from polling  "qstat"  repeatedly.
Or building the joblets to empty the input directory.

What I think I'm asking for, would be a call,

qcheck  -N Job-name  -w time-to-wait-before-returning)

It can return 3 values:
	0  finished
	1  running
	2  ?Que?  (never seen it)

So it could be polled by setting  "time-to-wait" to 0.

Or it could be added to a mother-script to collate results.

qsub -N $jobname  -t 1-$jobcount
if    qcheck -N $jobname  -w 604800
then
	collate-results
else
	echo "It didn't finish in a week"
fi

Perl and java wrappers would be good too.

michaelj

PS: We eventually managed to wrap  "qstat"  to sort of do this,
 qstat ? sleep...  qstat ?  sleep...  etc.
 but had some ugliness when the machine filled up with  qstat  jobs
 that refused to finish, waiting on some other mythical grid... ?

-- 
Michael James                         michael.james at csiro.au
System Administrator                    voice:  02 6246 5040
CSIRO Bioinformatics Facility             fax:  02 6246 5166

No matter how much you pay for software,
 you always get less than you hoped.
Unless you pay nothing, then you get more.

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