[GE users] job dependency question

Mag Gam magawake at gmail.com
Wed Oct 8 03:50:58 BST 2008


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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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