Dear all,
Currently, I am in the process of porting and optimising FSL for use with our new supercomputer which uses Easy build for software installation and SLURM as the resource manager.
I was able to install FSL 5.0.9 using easy build and added the new bedpostx patch (http://fsl.fmrib.ox.ac.uk/fsldownloads/patches/bedpostx-patch-fsl-5.0.9.tar.gz).
I came across some issues when customising the bedpostx_gpu script.
1. in the following code (line number:251), the preprocessing job name is bedpostx_preproc_gpu. But I could see only bedpostx_postproc_gpu under the ..../FSL/5.0.9/fsl/bin/ directory. Where can I find this script?
torque_command="qsub -V $queue -l nodes=1:ppn=1:gpus=1,walltime=00:40:00 -N bedpostx_prepr\
oc_gpu -o ${subjdir}.bedpostX/logs -e ${subjdir}.bedpostX/logs"
Following post processing code looks good in terms of the job name.
torque_command="qsub -V $queue -l nodes=1:ppn=1:gpus=1,walltime=00:40:00 -N bedpostx_postproc_g\
pu -o ${subjdir}.bedpostX/logs -e ${subjdir}.bedpostX/logs -W depend=afterokarray:$bedpostid"
2. #280
echo "${FSLDIR}/bin/xfibres_gpu --data=${subjdir}.bedpostX/data_$part --mask=$subjdir.bedp\
ostX/nodif_brain_mask -b ${subjdir}.bedpostX/bvals -r ${subjdir}.bedpostX/bvecs --forcedir --logdi\
r=$subjdir.bedpostX/diff_parts/data_part_$partzp $gopts ${subjdir} $part $njobs $nvox" >> ${subjdi\
r}.bedpostX/commands.txt
Here there is a reference to ${FSLDIR}/bin/xfibres_gpu. But I have only ${FSLDIR}/bin/xfibres
3. Hope I need to do the changes only in bedpostx_gpu script for optimising it for SLURM. I got confused after seeing the reference to fsl_sub in the following line:
#SGE
bedpostid=`${FSLDIR}/bin/fsl_sub $queue -l ${subjdir}.bedpostX/logs -N bedpostx_gpu -j $splitID\
-t ${subjdir}.bedpostX/commands.txt`
Could some one explain to me which all scripts needs to be changed for SLURM?
Many thanks in advance,
Lekshmi