Yup you are doing things perfectly.. GetOpt::Tabular is an argument
parsing thing, instead of getting you to install this via CPAN I have
just rewritten that part of the code to use the standard library for
doing this meaning you won't have to do anything to make it work now.
:)
Just re-download from here:
http://mavis.anu.edu.au/scripts/qbatch
And it should just work now. Also there is no need to add the .pl
extension if you dont want to.
a
2008/11/13 Markus Gschwind <[log in to unmask]>:
> Hi Andrew!
>
> 1)
> I thus copied the qbatch into my batch directory, called it "qbatch.pl" and
> tried to run it on my script myaddROI.sh (which has at first a subjectloop).
>
> Is that correct?
>
> I got the error below:
> (I am running a SLES 10.2 on a x86_64
>
> gschwind@server:/local/DATA/gschwind/batches/mybatches> ../qbatch.pl
> myaddROI.sh
> Can't locate Getopt/Tabular.pm in @INC (@INC contains:
> /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl .) at
> ../qbatch.pl line 10.
> BEGIN failed--compilation aborted at ../qbatch.pl line 10.
> gschwind@server:/local/DATA/gschwind/batches/mybatches>
>
>
> Where do I get the Getopt Tabular from? In the system add-software it is not
> available.
>
> 2)
> When trying
> qsub myaddROI.sh
> it says:
> Your job 349 ("myaddROI.sh") has been submitted
> but there is nothing going in "top".
> What is the problem?
>
> Could you please give me a hint?
>
> Thanks a lot and all the best!
> Markus
>
>
>
>
>
> 2008/11/12 Andrew Janke <[log in to unmask]>
>>
>> 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
>
>
>
> --
> 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
|