[GE users] -sync y option for SGE 6 / 5.3

Patrice Seyed apseyed at bu.edu
Thu May 18 19:05:44 BST 2006


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Hi Andreas,

I appreciate your neuronal activity today.

so are you saying (for returning after a job is complete),

instead of :

JOBID=`qsub $1 | awk '{print $3}'`
 qevent -j $JOBID ###(after Ron's patch)

or

qrsh $1

another option would:

JOBID=`qsub $1 | awk '{print $3 }'`
qrsh -hold_jid $JOBID sleep 0


if so, looks good.  -Patrice



Andreas Haas wrote:
> On Thu, 18 May 2006, Patrice Seyed wrote:
>
>   
>> Hi,
>>
>> I'm not sure what you mean by last one in a series of jobs.
>>     
>
> Well, if you got only a single job, the above sentence is
> somewhat pointless. My assumption was, you have a job workflow
> and look for a means to wait for an entire workflow.
>
> As a matter of course you could also submit any job with
> qrsh. However, if you don't need to wait for a job run,
> the use of
>
>    qrsh <command> &
>
> is a waste of resources due to the rsh/rshd etc. overhead.
>
> Possibly best would be use of normal qsub as used for the
> actual job workload and then send a dummy job such as
>
>    qrsh -hold_jid <list_of_qsub_job_names> sleep 0
>
> then you mis-use interdependent job capability and qrsh wait
> capability as workaround for -sync yes 8-}
>
> Andreas
>
>   
>> maybe i can in fact use qrsh for this purpose, I tested this out:
>>     
>
>   
>> $ cat test1.sh
>> sleep 10
>> date
>> $ qrsh test1.sh
>> Thu May 18 12:27:18 EDT 2006
>>
>> qrsh returns when the script is finished, which is the behavior i needed.
>>
>>  i can just redirect the stdout somewhere else. any objections?
>>     
>
> Sure.
>   
>> Patrice
>>
>>
>> Andreas Haas wrote:
>>     
>>> Can you use qrsh for the last one in a series of jobs?
>>> Though 5.3 qrsh had not the capability to run non-binary
>>> jobs, but you might work around this.
>>>
>>> Andreas
>>>
>>> On Tue, 16 May 2006, Patrice Seyed wrote:
>>>
>>>
>>>       
>>>> Hi,
>>>>
>>>> Is there a clean way to emulate the '-sync y' option available under SGE
>>>> 6 in SGE 5.3?
>>>>
>>>> There is a tool we are using that requires this option, i.e. requires
>>>> qsub to return only after the job is done.
>>>>
>>>> I may try to script a wrapper to do this. If anyone has pointed advice
>>>> on this I would greatly appreciate it.
>>>>
>>>> Cheers,
>>>> Patrice
>>>>
>>>>
>>>> --
>>>> Patrice Seyed
>>>> Linux System Administrator - LinGA
>>>> RHCE, SCSA
>>>> Boston University Medical Campus
>>>>
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>>>>
>>>>
>>>>
>>>>         
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>>>       
>> --
>> Patrice Seyed
>> Linux System Administrator - LinGA
>> RHCE, SCSA
>> Boston University Medical Campus
>>
>> ---------------------------------------------------------------------
>> To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
>> For additional commands, e-mail: users-help at gridengine.sunsource.net
>>
>>
>>     
>
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>   


-- 
Patrice Seyed
Linux System Administrator - LinGA
RHCE, SCSA
Boston University Medical Campus 

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