Re: [HTCondor-users] submitted jobs are not running

[Labounek Renà <xlabou01@xxxxxxxxxxxxxxxxxx>]

I apologize for the last spam. Finally, I have soluted it with very  
simple way of cahnging slice_0033.sh file into next form. And it works  
now.

slice_0033.sh
#!/bin/sh
. /etc/fsl/5.0/fsl.sh
/usr/share/fsl/5.0/bin/bedpostx_single_slice.sh  
/home/labounek/test/dti 33 --nf=3 --fudge=1 --bi=1000 --nj=1250  
--se=25 --model=2 --cnonlinear

I would like to thank to everebody here for help. I really approciate it.

Kind regrads,
Rene Labounek

Cituji Labounek Renà <xlabou01@xxxxxxxxxxxxxxxxxx>:

> In terminal opened by condor_submit, the variable $FSLDIR and I  
> suppose also other fsl-based variables are not known.
>
> I have tried to copy my .bashrc file to /home/condor folder which I  
> have created, but it did not help. Of course, I have changed owner  
> of the folder and files inside at condor:mri (condor belongs to mri  
> group).
>
> Any other ideas why terminal opened by condor does not know  
> variables defined by my .bashrc file? And how to fix it?
>
> Rene
>
>
>
> Cituji Labounek Renà <xlabou01@xxxxxxxxxxxxxxxxxx>:
>
> > Ben,
> >
> > you are right in error file is written something like that:
> >
> > slice_0033.error:
> > /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh: 1:  
> > /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh: /bin/zeropad: not  
> > found
> > /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh: 76:  
> > /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh: /bin/xfibres: not  
> > found
> >
> > I undertand it can not find two other libraries zeropad and  
> > xfibres, but when I am running the slice_0033.sh script (Executable  
> > in condor_submit) directly in terminal, the script works well.
> >
> > labounek@emperor:~/test/dti.bedpostX/condor_logs$ ./slice_0033.sh
> > labounek@emperor:~/test/dti.bedpostX/condor_logs$
> >
> > slice_0033.sh:
> > #!/bin/sh
> > /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh  
> > /home/labounek/test/dti 33 --nf=3 --fudge=1 --bi=1000 --nj=1250  
> > --se=25 --model=2 --cnonlinear
> >
> > So unfortunately, I am still lost :-( Could the problem be e.g. the  
> > Universe? Or should I set something more in slice_0033.condor file?
> >
> > slice_0033.condor:
> > Executable = /home/labounek/test/dti.bedpostX/condor_logs/slice_0033.sh
> > Universe = vanilla
> > Output = /home/labounek/test/dti.bedpostX/condor_logs/slice_0033.out
> > Error = /home/labounek/test/dti.bedpostX/condor_logs/slice_0033.error
> > Log   = /home/labounek/test/dti.bedpostX/condor_logs/slice_0033.log
> > Queue
> >
> > Kind Regards,
> > Rene
> >
> > Cituji Ben Cotton <ben.cotton@xxxxxxxxxxxxxxxxxx>:
> >
> > > Rene,
> > >
> > > The output suggests that your jobs ran and completed very quickly. If
> > > you have Output and Error defined in your submit file, I'd look in
> > > those locations to see what output your job produced. That may give
> > > you an indication of why it completed so quickly.
> > >
> > >
> > > Thanks,
> > > BC
> > >
> > > --
> > > Ben Cotton
>
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