fsl_sub has to be used if using feat? about fsl_sub HOT 6 CLOSED

Any FSL tool that uses fsl_sub will be accelerated. This typically means any tool the FSL group has designed to run in parallel. This page lists cluster-aware tools, which suggests FEAT will have accelerated statistics (FLAME). I have included a sample dataset to the repository so you can test out that fsl_sub is correctly installed on your machine.

from fsl_sub.

Thanks

from fsl_sub.

To be clear, you only have to replace fsl_sub. Any fsl script that is designed to run in parallel (including those in FEAT) will take advantage of this modification. The standard fsl_sub is designed to run on a cluster in parallel if you have sun grid engine installed and in serial otherwise. The version I distribute here is designed to run on a cluster in parallel if you have sun grid engine installed and in parallel locally otherwise. Other groups have developed variations of fsl_sub that exploit different cluster methods (e.g. SLURM).

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Yeah, all clear thanks. By the way, I tried to run the example script you added (uncommented the first time bedpostx $BEDPOSTDIR line). All cores were being used - so looks like it's working in principle, although this also happened for FSLPARALLEL=0 - not sure why, but it's not that important for me.

Was also getting errors about popd and pushd not being available - didn't seem to matter though.

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OK, and can you confirm that the runtime is faster with my fsl_sub than with the default fsl_sub (which should only use one core). I only use pushd and popd in the test script. Maybe when I get time I will think of a solution that works on all systems.

from fsl_sub.

Yeah, I didn't do a very carefully test but your fsl_sub was clearly faster (15 minutes) and used all cores in the VM vs the original function only using one (40 minutes).

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