[GE users] How to get variable SGE parameters?

Michael James Michael.James at csiro.au
Wed Oct 4 08:43:16 BST 2006

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On Wed, 4 Oct 2006 05:26 pm, Reuti wrote:
> 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.

> 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.

Hang on, you're writing on the  "qsub"  command line, I'm putting
 #$ -o no-need-for-the-quotes_but-it-still-does-me-no-good
 in a comment in the qsub-ed script.
Either way, the joblet's script hasn't run yet,
 so it can't do any manipulation besides concatenate.

Michael James                         michael.james at csiro.au
System Administrator                    voice:  02 6246 5040
CSIRO Bioinformatics Facility             fax:  02 6246 5166

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