Re: [Condor-users] bash script

[Edier Zapata <edalzap@xxxxxxxxx>]

Glad it worked.
 You're welcome

On 12/27/11, LAOUCHEDI MAKHLOUF <laoumakhl@xxxxxxxx> wrote:
> hi Edier
>               thank you very much; it's ok
>
> --- 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>
> Cc: "LAOUCHEDI MAKHLOUF" <laoumakhl@xxxxxxxx>
> Date: Mardi 27 décembre 2011, 18h40
>
> 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
>


-- 
Edier Alberto Zapata Hernández
Ingeniero de Sistemas
Universidad de Valle