[GE users] Parameter sweep application

Andreas Haas Andreas.Haas at Sun.COM
Thu Apr 20 12:19:43 BST 2006


As explained you submit it with qsub as an "-t 1-100" array
job. For this you need a single shell script. Note you
will get scambled output if you use -o <output_path>
in a way that only a single output file is being used.
So you better use a per array task output file and
join these outputs into a single output file once all
array tasks are done. Synchronization can be done
with "-sync yes".

Alternatively all of the above could be done with DRMAA e.g.
with Python DRMAA binding.

   http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz

Regards,
Andreas


On Thu, 20 Apr 2006, Massimo Canonico wrote:

> Hi,
> I'm newbie in GE.
>
> If I must run 100 experiments where the executable, the output path and
> the input path are always the same,  is there a way to specify all jobs
> in one bash file?
>
> something like this:
> ------------
> !#/bin/bash
>
> $exepath = /home/mex/sig
> $outpath = /mayhem/sealion/mex
>
> $executable      = $(exepath)/Negative
>
> $argExp1 = -par1
> $argExp2 = -par2
> ...
> $argExp100 = -par100
>
>  for ((i=1; i < 100; i++)) do $executable $argExp$i > $outpath$i; done
>
> ----------------------------------
>
> Must I write a script that generates 100 bash files or is there a smart
> solution?
>
> I know that in other batch schedulers like condor it is possible using
> just one file.
>
> Cheers,
>  Massimo
>
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