[Neuroimaging] Slow node starts with nipype

Satrajit Ghosh satra at mit.edu
Mon Oct 31 12:02:27 EDT 2016

dear ian,

there is a config option to sleep between nodes that was changed from 2s to
60s. you can reset that option to speed things up.



you can set this to:

wf_variable.config['execution']['poll_sleep_duraion'] = 2



On Mon, Oct 31, 2016 at 11:54 AM, Ian Malone <ibmalone at gmail.com> wrote:

> 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
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> Neuroimaging at python.org
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