[GE users] job dependency question

Mag Gam magawake at gmail.com
Wed Oct 8 04:43:41 BST 2008


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Actually,

how would I get that JID? Since JIDs will be changing.



On Tue, Oct 7, 2008 at 10:50 PM, Mag Gam <magawake at gmail.com> wrote:
> Great Thankyou All.
>
> I will test it in my Lab tomorrow.
>
> Thanks everyone again!
>
> TIA
>
>
> On Tue, Oct 7, 2008 at 10:44 PM, Daniel Templeton <Dan.Templeton at sun.com> wrote:
>> 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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>>
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