Using GNU or Slurm for atlas building

[helena.g...@googlemail.com]

Dear Paul,

I am hoping to use ASHS to build my own atlas from my manual segmentations but our university does not have Sun Grid Engine. In a previous post, you mentioned something about GNU processing being an alternative to SGE but it's not clear to me how I would implement that within the framework of the atlas building code. It would be great if you could provide some pointers on how to go about that.

Thanks so much for any help with this.

Best wishes,

Helena

[Paul Yushkevich]

Hi Helena,

The most recent ASHS code on GitHub also has SLURM support.

Please let me know if that works for you

Paul

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Paul A. Yushkevich, Ph.D.
Professor of Radiology
Penn Image Computing and Science Laboratory
University of Pennsylvania Perelman School of Medicine

[helena.g...@googlemail.com]

Hi Paul,

Thanks for the info. That's very helpful. I have now run fast ashs with the -P flag and the first four stages ran without error. Now in the fifth stage, the process gets stuck with the last lines in the nohup.out file being:

+ local GRAYLIST=

+ [[ usegray = \u\s\e\g\r\a\y ]]

+ GRAYLIST='-g /lustre/scratch/wbic-beta/hg424/ashs_atlas/train/main_left/bl_lists/usegray_0/graylist.txt'

+ [[ -n '' ]]

+ local DRYFRAC=0.01

++ bl /lustre/scratch/wbic-beta/hg424/ashs_atlas/train/main_left/bl_lists/usegray_0/truthlist.txt /lustre/scratch/wbic-beta/hg424/ashs_atlas/train/main_left/bl_lists/usegray_0/autolist.txt 0 1 6x6x0 0.01 0 /lustre/scratch/wbic-beta/hg424/ashs_atlas/train/main_left/adaboost_dryrun -g /lustre/scratch/wbic-beta/hg424/ashs_atlas/train/main_left/bl_lists/usegray_0/graylist.txt -p /lustre/scratch/wbic-beta/hg424/ashs_atlas/train/main_left/bl_lists/usegray_0/postlist.txt

++ grep 'of training data'

++ awk -F '[: ]' '{print $13}'

++ tail -n 1

Do you have an idea why ASHS gets stuck there?

I can also attach the nohup.out file if that helps but it is rather large and takes a very long time to load.

Thanks so much for any help!

Best,

Helena

[Paul Yushkevich]

Hi Helena,

It might be that the command bl needs more memory and is crashing because it is not getting enough. Please try providing it more memory, 8GB perhaps.

That's my best guess,

Thanks!
Paul

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