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bids-apps / freesurfer

BIDS app wrapping recon-all from FreeSurfer
Apache License 2.0
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question about running in parallel #48

Open ajdneuro12 opened 4 years ago

ajdneuro12 commented 4 years ago

Hi all,

Thanks for the great app! I am trying to run a large number of participants but I am having trouble running in parallel. I am running it on an hpc with singularity. I have tried specifying multiple participants with the participant label and changing the number of cpus but it is not running in parallel. Thanks for your help!

Best, Alex

Shotgunosine commented 4 years ago

Hi @ajdneuro12, sorry for the incredibly delayed response. I would suggest running one subject per job on the HPC. Will that work for you? I'm not sure if this is still an issue or not, but in some cases running multiple subjects on the same node along with using openmp parallelization for some steps can result in more CPUs than available being requested.

alexlicohen commented 4 years ago

I agree with this, submit one job per subject, then you can go a group level analysis later if needed.

-Alex

On Jun 30, 2020, at 11:42 AM, Dylan Nielson notifications@github.com wrote:

Hi @ajdneuro12 https://github.com/ajdneuro12, sorry for the incredibly delayed response. I would suggest running one subject per job on the HPC. Will that work for you? I'm not sure if this is still an issue or not, but in some cases running multiple subjects on the same node along with using openmp parallelization for some steps can result in more CPUs than available being requested.

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