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

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.

. /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?


Cituji Labounek Renà <xlabou01@xxxxxxxxxxxxxxxxxx>:


you are right in error file is written something like that:

/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

/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?

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

Kind Regards,

Cituji Ben Cotton <ben.cotton@xxxxxxxxxxxxxxxxxx>:


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.


Ben Cotton

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