[GE users] Controlling multiple jobs

seandavi seandavi at gmail.com
Tue Apr 20 17:20:43 BST 2010


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On Tue, Apr 20, 2010 at 10:20 AM, dr_st <stephane.teletchea at univ-nantes.fr<mailto:stephane.teletchea at univ-nantes.fr>> wrote:
Dear colleagues,

I've searched though the manual, tried to get the answers from the
mailing list archive, but not found yet the anwser.

I have a working shell script launching hundreds of jobs, and i would
like to trigger an action (e-mail notification for instance + shell
script for filtering results) when all of them have finished.

So far i thought of putting in one qsub file the commands for the
hundreds of jobs, but i'm not sure this solution will be what i'm searching.

Each job can take from 20 minutes to 4 hours to complete, and the
cluster is not at my own disposal (of course!), so a solution for
triggering the check_them_all command after all jobs are finished is
probably something others have done already.

I found the "status" script at
http://gridengine.sunsource.net/ds/viewMessage.do?dsForumId=38&dsMessageId=252554

But i do not want to monitor regularly the job queue.

I'm using SGE 1.6.1u5


You could submit a final job that just does the email and make it depend on the jobs you just submitted.

qsub --hold_jid <<job_id_list>> emailscript.sh

Where job_id_list is a list of the job ids that you submitted.  Alternatively, you could give each job the same name and do a hold based on the job name.  When all the jobs in the dependency list are completed, emailscipt.sh will execute on the cluster.

Sean




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