Dear Roberto,
The easiest way to stop queuing is just to unset your SGE_ROOT
environment variable in a terminal and then run things in that
terminal. That is: unset SGE_ROOT
This way you don't need to modify any scripts.
All the best,
Mark
On 13 Jul 2011, at 08:20, roberto toro wrote:
> Hello!
>
> I would like to use bedpostX without SGE (it is configured in our system, but I don't want to use it).
> So I made a version of bedpostx where I deleted everything SGE related. I got this (plus all the directory verification/creation):
>
> echo Queuing preprocessing stages
> ${FSLDIR}/bin/bpx_preproc -l ${subjdir}.bedpostX/logs
> ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}
>
> echo Queuing parallel processing stage
> ${FSLDIR}/bin/fslval ${subjdir}/data dim3
> slice=0
> while [ $slice -lt $nslices ]
> do
> $FSLDIR/bin/zeropad $slice 4
> ${FSLDIR}/bin/bedpostx_single_slice.sh $subjdir $nfibres $fudge $burnin $njumps $sampleevery $model $slice
> slice=$(($slice + 1))
> done
>
> echo Queuing post processing stage
> ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir
>
>
> Is it ok? I'm I missing something?
>
> thank you!
> roberto
>
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