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

Robert Griffiths Robert.Griffiths at int.sc.mufg.jp
Wed Oct 4 09:12:46 BST 2006


Hi Michael,

Why don't you just write another job and submit it contingent on your array
job? Then, when that finishes, it can e-mail you.

Something like

Qsub MYARRAYJOB
QSUB MYCLEANUPJOB -hold_jid MYARRAYJOB -m e

(With whichever other options you normally submit)

Your contingent job will only run when all of the tasks in your arrayjob
have finished running.

Not as fully-functional as you'd like, perhaps, but it's quick & dirty and
it works!

Regards,

Rob Griffiths

-----Original Message-----
From: Michael James [mailto:Michael.James at csiro.au] 
Sent: 04 October 2006 09:08
To: users at gridengine.sunsource.net
Subject: [GE users] How do I know when an array has finished?


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.

---------------------------------------------------------------------
To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
For additional commands, e-mail: users-help at gridengine.sunsource.net


**********************************************************
IMPORTANT NOTICE - CHANGE OF NAME

Please note that Mitsubishi Securities International plc has changed its name to Mitsubishi UFJ Securities International plc. All MUSI e-mail addresses have now changed from firstname.lastname at mitsubishi-sec-intl.com to firstname.lastname at int.sc.mufg.jp (please note that the domain name ends in ".jp", not ".com"). 

Mitsubishi UFJ Securities International plc ("MUSI") is registered in England, company number 1698498 and registered office at 6 Broadgate, London EC2M 2AA.   MUSI is part of the Mitsubishi UFJ Financial Group and is authorised and regulated by The Financial Services Authority. This message is intended solely for the individual addressee named above. The information contained in this e-mail is confidential and may be legally privileged.  If you are not the intended recipient please delete in its entirety.  Messages sent via this medium may be subject to delays, non-delivery and unauthorised alteration.  The information contained herein or attached hereto has been obtained from sources we believe to be reliable but we do not represent that it is accurate or complete.  Any reference to past performance should not be taken as an indication of future performance.

The information contained herein or attached hereto is not to be construed as an offer or solicitation to buy or sell any security, instrument or investment.  MUSI or any affiliated company, may have an interest, position, or effect transactions, in any investment mentioned herein.  Any opinions or recommendations expressed herein are solely those of the author or analyst and are subject to change without notice.

---------------------------------------------------------------------
To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
For additional commands, e-mail: users-help at gridengine.sunsource.net




More information about the gridengine-users mailing list