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Low cpu usage?

See original GitHub issue

Hello!

I am running TractSeg with --nr_cpus 8. I’ve noticed that TractSeg doesn’t even pass 200% cpu usage while it runs.

The following is the typical resource usage graph for app-tractseg

screenshot from 2018-12-06 18-59-32

I am wondering if --nr_cpus is not properly applied, or maybe we are not using this option right?

	TractSeg -i dwi.nii.gz --raw_diffusion_input \
		--csd_type $(jq -r .csd config.json) \
		--output_type tract_segmentation \
		--keep_intermediate_files \
		--postprocess \
		--nr_cpus 8 \
		-o . \
		$opts

https://github.com/brainlife/app-tractseg/blob/1.7.1/run.sh#L35

Please comment!

Issue Analytics

State:
Created 5 years ago
Comments:20 (5 by maintainers)

Top GitHub Comments

1reaction

wasserthcommented, Jan 21, 2019

I seems like using python 3 + pytorch 1.0 (instead of python 2.7 + pytorch 0.4) increases the CPU usage significantly. Runtime therefore decreases by a factor of at least 3x.

0reactions

wasserthcommented, Dec 21, 2018

I tried it with a higher batch size. This increased the runtime by around 30% but CPU usage is still way below 100%. The downside of increasing the batch size is higher memory usage (around 30GB of RAM).