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FSL  November 2008

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Subject:

Re: fsl_sub in onw scripts?

From:

Andrew Janke <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 12 Nov 2008 22:35:16 +1100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (87 lines)

Hi Markus,

At the risk of invoking the wrath of the authors of fsl_sub, I should
mention that if you have a working SGE setup it also means that you
can just use SGE by itself.  So you can either just submit your jobs
via qsub (if it is a script) or you can use some of the various handy
dandy interfaces to it such as this one:

   http://mavis.anu.edu.au/scripts/qbatch

Now I might have written it but it cannot be proven... :)

Use it by simply inserting qbatch in front of any command that you
would like to be "Batchified".

for subject in 1 2 3 4 5 etc
do
    fslxxxx  freddy-${subject}.nii ...
done

becomes

for subject in 1 2 3 4 5 etc
do
    qbatch fslxxxx  freddy-${subject}.nii ...
done

Or if you want a bit more control

for subject in 1 2 3 4 5 etc
do
    qbatch -q long.q -N myjob-$subject -logfile logs/$subject.log
fslxxxx  freddy-${subject}.nii ...
done

Then do something like this to watch your exceptional brilliance at
scripting working:

   $ watch qstat -f

have fun.


a

On Wed, Nov 12, 2008 at 10:11 PM, Markus Gschwind
<[log in to unmask]> wrote:
> Hello experts!
>
> I'd like to know if there is an easy way of submitting the processes in home
> made scripts to fsl_sub and how the syntax would be.
>
> I am thinkin of parallelising multiple subject's probtrackx tasks. So at the
> beginning there is the subject loop
>
> for subject in 1 2 3 4 5 etc
> do
> ...etc
> which I would like to send to the SGE-cluster.
>
> How would I need to do this?
>
>
> Thanks a lot!
> Markus
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>



-- 
Andrew Janke - [log in to unmask]
Department of Geriatric Medicine, ANU
([log in to unmask] || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

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