[Neuroimaging] Slow node starts with nipype

[JB Poline]

Hi Satra

I'm just curious: What was the rationale for increasing this time from
2 to 30s ?

cheers
JB

On 31 October 2016 at 09:02, Satrajit Ghosh <satra at mit.edu> wrote:
> 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.
>
> poll_sleep_duration
>
> http://nipype.readthedocs.io/en/latest/users/config_file.html
>
> you can set this to:
>
> wf_variable.config['execution']['poll_sleep_duraion'] = 2
>
> cheers,
>
> satra
>
> 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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>
>
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