[GE users] Putting e-mail address in a variable inside script

kasper_fischer kasper.fischer at ruhr-uni-bochum.de
Thu May 28 09:14:07 BST 2009


Hello,

you can try to use qalter in your qsub script, e. g.:
    qalter $JOB_ID -M $EMAIL_ADDRESS

Greetings

Kasper

sanfermines schrieb:
> We are using SGE 6.1 right now, so that feature is not included in it.
>
> We may upgrade the version, but not yet.
>
> Any other ideas or suggestions?
>
> I have tried to do a qalter after the job was started but it seems to ignore it.
>
> Thank you very much.
>
> On Sun, May 24, 2009 at 6:33 AM, Rayson Ho <rayrayson at gmail.com> wrote:
>   
>> Not exactly a hack, but a nice new feature in SGE 6.2update2 called
>> "Job Submission Verifiers" (JSV).
>>
>> You can use a client-side JSV to process the job script during job
>> submission. What you need is to get the job script via CMDNAME inside
>> your JSV, and then parse the job script line-by-line to extract the
>> email address needed. The JSV can be written in any programming
>> language, and you can invoke other binaries or scripts to further
>> lookup your mapping file.
>>
>> Once you have the correct email address, the JSV can then add it as
>> additional parameters.
>>
>> See the admin guide and also the manpage for further details.
>>
>> http://gridengine.sunsource.net/nonav/source/browse/~checkout~/gridengine/doc/htmlman/htmlman1/jsv.html?pathrev=V62u2_TAG
>>
>> Rayson
>>
>>
>>
>> On 5/23/09, sanfermines <sanfermines at gmail.com> wrote:
>>     
>>> Michael, I have a text file like this:
>>>
>>> linux_username  --> email_address
>>>
>>> Inside every script I would like to search in that file for $USER and
>>> grep his e-mail address which I storage in $EMAIL_ADDRESS, but as
>>> Daniel told, #$ variables are not interpretated.
>>>
>>> So... there isn't any "hack" to accomplish that?
>>>
>>> Thank you very much.
>>>
>>> On Fri, May 22, 2009 at 4:29 PM, templedf <dan.templeton at sun.com> wrote:
>>>       
>>>> Actually, that shouldn't work. The #$ line isn't interpreted by the
>>>> shell. It's interpreted by qsub, and qsub doesn't do variable
>>>> interpolation on the #$ lines.
>>>>
>>>> Daniel
>>>>
>>>> pollinger wrote:
>>>>         
>>>>> sanfermines wrote:
>>>>>
>>>>>           
>>>>>> Hello Everybody,
>>>>>>
>>>>>> I would like to put in a script a line as follows:
>>>>>>
>>>>>>             
>>>>>  >
>>>>>
>>>>>           
>>>>>> #$ -M $EMAIL_ADDRESS
>>>>>>
>>>>>> where $EMAIL_ADDRESS is a variable with the real e-mail address
>>>>>>
>>>>>>             
>>>>> This should work if $EMAIL_ADDRESS is defined on the execution host when
>>>>> the job script is executed.
>>>>>
>>>>>
>>>>>           
>>>>>> But this way, SGE doesn't process properly the variable.
>>>>>>
>>>>>>             
>>>>> What exactly does SGE wrong?
>>>>>
>>>>> Regards,
>>>>> Harald
>>>>>
>>>>>
>>>>>           
>>>>>> Any ideas?
>>>>>>
>>>>>> Thank you very much.
>>>>>>
>>>>>>             
>>>>>
>>>>>           
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>>>       
>
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