[GE users] Submit problems

craffi dag at sonsorol.org
Wed Aug 5 14:35:36 BST 2009

Suggest you back up a step and confirm that SGE can run simple jobs as  
your non-root user. This will help determine if you have a SGE  
configuration issue or not.

Try something like:

qsub -cwd $SGE_ROOT/$SGE_CELL/examples/jobs/sleeper.sh

and see if that happens and if you get output. You can also copy that  
sleeper.sh script into your own home directory and do a "qsub -cwd ./ 
sleeper.sh" on it.

While the job is pending or running you can do a "qstat -j <jobID>" on  
it to see more information. The command "qstat -f" is also great as it  
will show you if any queues, jobs or machines are in error states.

Remember that your user needs to exist on all the remote nodes and the  
directory from where you are submitting the job should be shared out  
to all those worker nodes.


On Aug 4, 2009, at 1:56 PM, zzachariah wrote:

> When I submit a job as non-root user, I login as the non-root user  
> and use qsub to submit.
> zkzac at z22 3 >> qsub m2a
> Your job 25 ("m2a") has been submitted
> zkzac at z22 4 >>
> zkzac at z22 4 >>
> zkzac at z22 4 >> qstat
> job-ID  prior   name       user         state submit/start at      
> queue                          slots ja-task-ID
> -----------------------------------------------------------------------------------------------------------------
>     25 0.00000 m2a        zkzac        qw    08/04/2009  
> 09:38:47                                    1
> obviously it is trying to submit. But this job actually take about 2  
> hours to complete and qstat returns nothing after about 30 seconds.  
> Something is wrong somewhere and I am not able to trace it. The job  
> does not even start as I can see no output. I am not seeing any  
> relevant log entries also.
> --Zac
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