[GE users] job dependency question

Daniel Templeton Dan.Templeton at Sun.COM
Wed Oct 8 03:44:30 BST 2008


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Close.  The second command would be "qsub -hold_jid pre commandB.sh".

Daniel

Mag Gam wrote:
> As usualy, thanks Rayson.
>
> So, I have these 2 commands.
>
> I suppose I can do:
>
> qsub -N pre commandA.sh
> qsub -hold_pre commandB.sh
>
>
>  commandA.sh
>  #!/bin/bash
>  #$ -o output
> #$ -S /bin/bash
> #$ -S -V
> tar -cvf file.tar /large_directory
>
> CommandB.sh
> #!/bin/bash
>  #$ -o output
>  #$ -S /bin/bash
> #$ -S -V
> gzip file.tar
>
> Does this sound right?
>
> TIA
>
>
> On Tue, Oct 7, 2008 at 10:38 PM, Rayson Ho <rayrayson at gmail.com> wrote:
>   
>> Basically, you submit the first job, and qsub will return its job id.
>> You then pass first job's job id to -hold_jid when you submit the 2nd
>> job.
>>
>> A more advanced way is to use job names, by using -N.
>>
>> Anyway, play with a few dummy jobs and you will get the concept.
>>
>> Rayson
>>
>>
>>
>> On 10/7/08, Mag Gam <magawake at gmail.com> wrote:
>>     
>>> Thanks for the quick reponse.
>>>
>>> I believe I have tried this too, but I am still confused with the job
>>> name and job id.
>>>
>>> I looked at https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2007-June/025538.html,
>>>  and http://gridengine.sunsource.net/servlets/ReadMsg?list=users&msgNo=447
>>>
>>> Do I need another script to check for jobs? Sorry for such a newbie question
>>>
>>>
>>> TIA
>>>
>>>
>>>
>>> On Tue, Oct 7, 2008 at 10:25 PM, Rayson Ho <rayrayson at gmail.com> wrote:
>>>       
>>>> The link in your email is for job arrays.
>>>>
>>>> You should read the qsub manpage instead, and look up the "hold_jid"
>>>> option. If you google "qsub" and "hold_jid", the results should at
>>>> least include a few examples.
>>>>
>>>> Rayson
>>>>
>>>>
>>>>
>>>> On 10/7/08, Mag Gam <magawake at gmail.com> wrote:
>>>>         
>>>>> I have been reading many SGE job dependency pages online (such as
>>>>> http://open.rsp.com.au/?page_id=11) but I am still not able to do the
>>>>> task I wanted to do. Or perhaps I may be looking at the wrong thing.
>>>>> Here is what I am looking for:
>>>>>
>>>>> I have 2 commands. Command A and Command B. Command A needs to run
>>>>> first and then execute Command B once Command A is completed. In other
>>>>> words Command B depends on Command A.
>>>>>
>>>>> commandA.sh
>>>>>
>>>>> #!/bin/bash
>>>>> #$ -o output
>>>>> #$ -S /bin/bash
>>>>> #$ -S -V
>>>>> tar -cvf file.tar /large_directory
>>>>>
>>>>>
>>>>> CommandB.sh
>>>>> #!/bin/bash
>>>>> #$ -o output
>>>>> #$ -S /bin/bash
>>>>> #$ -S -V
>>>>> gzip file.tar
>>>>>
>>>>>
>>>>> Basically, I want to submit both of the jobs to our GRID but with
>>>>> commandB running after CommandA
>>>>>
>>>>> TIA
>>>>>
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>>>>>
>>>>>           
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>>>>
>>>>         
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>>>
>>>       
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>>     
>
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