[GE users] How to get variable SGE parameters?

Reuti reuti at staff.uni-marburg.de
Wed Oct 4 08:01:46 BST 2006


Am 04.10.2006 um 08:42 schrieb Michael James:

> 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?

Yes.

>
>> 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!

-o '$JOB_NAME.o$JOB_ID.$TASK_ID'

is working fine for me, for each array task I get a new file.

-- Reuti

> 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.
>
> michaelj
>
> -- 
> 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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