[GE users] How to get variable SGE parameters?

Reuti reuti at staff.uni-marburg.de
Wed Oct 4 08:26:58 BST 2006


Am 04.10.2006 um 09:17 schrieb Michael James:

> On Wed, 4 Oct 2006 05:01 pm, Reuti wrote:
>>> In any given script, -o and -e are inherently static!
>>
>> -o '$JOB_NAME.o$JOB_ID.$TASK_ID'
>>
>> is working fine for me, for each array task I get a new file.
>
> Isn't that what gridengine would have set output to without the -o ?

Yes, as written in issue 2102, this way users could (if it's  
implemented) get also a $TASK_ID for non array jobs. For now the  
$TASK_ID is interpreted only for array jobs, and you get the literal  
output $TASK_ID (for this variable, the others are working) for  
serial jobs.

> I tried it and got a file called the literal string  '$jobout'.
> Of course I thought, this is set up before shell has run,
>  it's just a string, not a variable.

The variables to -o / -e are special. They are not shell variables  
(therefore you need the ' around the expression, to avoid any  
interpretation by the shell), but only inside SGE's-internal-path- 
resolution. They are also different from the variables which are set  
by SGE inside the jobscript.

-- Reuti

> So I do have access to the SGE-defined variables.
> But still no manipulative power over them.
> Better than useless, but I want  printf.
>
> I used to cope letting gridengine call them what it wanted,
>  then renaming them to my convention.
> /dev/null  then  exec  is much cleaner IMHO.
> -- 
> Michael James                         michael.james at csiro.au
> System Administrator                    voice:  02 6246 5040
> CSIRO Bioinformatics Facility             fax:  02 6246 5166
>
> No matter how much you pay for software,
>  you always get less than you hoped.
> Unless you pay nothing, then you get more.
>
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