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

sanfermines sanfermines at gmail.com
Tue May 26 12:27:27 BST 2009


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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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