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Re: [Condor-users] bash script



Hi again Laouch, correct me if I'm wrong:
You want to run this:
recon-all -i database/tcpr/tcpr1/t1_3d/tcpr1.nii.gz  -subjid tcpr1
recon-all -i database/tcpr/tcpr2/t1_3d/tcpr2.nii.gz  -subjid tcpr2
.
.
.
recon-all -i database/tcpr/tcpr26/t1_3d/tcpr26.nii.gz  -subjid tcpr26
recon-all -i database/tcpr/tcpr27/t1_3d/tcpr27.nii.gz  -subjid tcpr27

If that's is right,  think you can use a submit like this:

Universe    = vanilla
Getenv        = True
Requirements    = Arch =="X86_64"
Priority    = 0
Executable    = recon-all
Arguments    = -i
database/tcpr/tcpr$(process)/t1_3d/tcpr$(process).nii.gz  -subjid
tcpr$(process)

Output        = job-$(process).out
Error        = job-$(process).err
Log        = job-$(process).log

Queue 27

Hope this help you.
Bye
On 12/27/11, LAOUCHEDI MAKHLOUF <laoumakhl@xxxxxxxx> wrote:
> hi Edier the file content is (a freesurfer command) :
> #!/bin/sh
> i=1
> j=1
> k=1
> for l in /home/mlaouche/database/tcpr/tcpr*
> do
> recon-all -i database/tcpr/tcpr$((i++))/t1_3d/tcpr$((j++)).nii.gz  -subjid
> tcpr$((k++))
> done
>
> and there is 27 datasets named tcpr1.niingz ...tcpr27.nii.gz
>
> thank you
> --- En date de : Mar 27.12.11, Edier Zapata <edalzap@xxxxxxxxx> a écrit :
>
> De: Edier Zapata <edalzap@xxxxxxxxx>
> Objet: Re: [Condor-users] bash script
> À: "Condor-Users Mail List" <condor-users@xxxxxxxxxxx>
> Date: Mardi 27 décembre 2011, 17h27
>
> Hi Lauoched,
>  you are only submitting 1 job (the Queue line mean how many jobs).
>
> What exactly you are trying to do?
>
> Bye
> On 12/27/11, LAOUCHEDI MAKHLOUF <laoumakhl@xxxxxxxx> wrote:
>> hi everyone
>>                   i wrote a for loop shell script and i submitted it to
>> condor, with changing the excutable and arguments (for the executable i
>> put
>> "/bin/bash" instead of "for" and for the argument i put "myfile.sh" like
>> advised by Dimitri Maziuk), and it worked well but it works only on one
>> nod
>> (when i check with condor_q only one job is generated and running)
>>
>> the content of my .job.submit file after modification :
>>
>> Universe    = vanilla
>> Requirements    = Arch =="X86_64"
>> Priority    = 0
>> Executable    = /bin/sh
>> Output        = .MC_recon_all_tout_gd.sh.job.out
>> Error        = .MC_recon_all_tout_gd.sh.job.err
>> Log        = .MC_recon_all_tout_gd.sh.job.log
>> Getenv        = True
>> Arguments    = "MC_recon_all_tout_gd.sh"
>> Queue
>>
>>
>> thanks for help
>>
>
>
> --
> Edier Alberto Zapata Hernández
> Ingeniero de Sistemas
> Universidad de Valle
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-- 
Edier Alberto Zapata Hernández
Ingeniero de Sistemas
Universidad de Valle