[GE users] How to get variable SGE parameters?

Michael James Michael.James at csiro.au
Wed Oct 4 07:42:53 BST 2006

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On Tue, 26 Sep 2006 07:59 pm, Reuti wrote:
> > On Tue, 26 Sep 2006 05:37 pm, Olesen, Mark wrote:
> >> I would *definitely* second Reuti's RFE that
> >> the undefined value be changed (to the integer value 0).

> As you wish: I entered issue 2102 for it.
> But I'm not sure whether $SGE_TASK_ID
> should really be 0 in the job context.
By  "in the job context"  do you mean for non-array jobs?

> If you can assemble the output and error files
> with -o / -e    in a proper way already,

I don't understand "the proper way"? 
In any given script, -o and -e are inherently static!
So if all joblets in an array are executing the same script,
 (they have to be, don't they?)
 they will be fighting to overwrite the same file.
So for array jobs -o and -e  are useless,
 except to direct output to /dev/null.

To direct output and error dynamically use:
exec   1> $jobout   2> $joberr

In the bioinformatic context (embarrassingly parallel)
 single jobs don't count, all jobs are array jobs,
 the only time I submit a non-array job
 is when I'm testing, and forgot the  -t  parameter.

The whole point of a cluster is to do many jobs.
As an administrator, I encourage* my users to submit in arrays.
I get terse when I get the inevitable call,
 "Could you cancel my last batch, it was a mistake."
 and find some mother-script has queued 10,000 jobs.
1 array is much more manageable.
Also we calculate priority as -100 x number-of-digits-in-job-count.
It's cheating to say, "Here's one job, and here's another x 9,999.

> the current output of $SGE_TASK_ID could   
> stay this way as being "undefined".
My opinion stays as, "Oh Yuck!"; roll on issue 2102.


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

* A euphemism, ask the BOFH for the real meaning...

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