[Neuroimaging] Slow node starts with nipype

[Ian Malone]

Hi,

I've been given some nipype workflows to run, and I find that they
seem to go very slowly in between execution steps. For example, I'm
currently looking at the message:

161031-15:42:50,278 workflow INFO:
     Running: pm_scale -i
/var/lib/midas/data/lha1946/images/nii/original/7938.nii.gz -o
/var/drc/scratch1/malone/dti-test-masks-20161031/outgif/13839424_01_PETMR_20161019-wd/dmri_workflow/susceptibility_correction_with_fm/pm_scale/7938_scaled.nii.gz

But the command in question doesn't seem to be running (this is a
fairly quick command if executed directly). There's a similar hold-up
for other steps and, with quite a long multi-step pipeline, a lot of
time seems to be spent doing nothing (watching top, similarly a list
of fslmath nodes all launches, the fslmaths processes show up briefly
in top, then there's a delay before anything more happens).

Does anyone have suggestions for what might be happening? This is
using the MultiProc engine, storage is NFS.

-- 
imalone