Empty output after program kill #8
Description
Hey, I tried using this software, but after running, I see a Kill event and the output segmented.mrc file is empty. Do you have any advice or troubleshooting I should try to get this working?
Thanks,
[etidwell@xxx ~]$ membrain segment --tomogram-path /data_path/full_rec.mrc --ckpt-path /data_path/membrain-seg/MemBrain_seg_v10_alpha.ckpt --out-folder /data_path/predictions_min_4 --segmentation-threshold -4
Segmenting tomogram /data_path/full_rec.mrc
This can take several minutes. If you are bored, why not learn about what's happening under the hood by reading the MemBrain v2 preprint?
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography
https://www.biorxiv.org/content/10.1101/2024.01.05.574336v1
INFO:root:Performing 8-fold test-time augmentation. I.e. the following bar will run 8 times.
/programs/x86_64-linux/membrain-seg/0.0.8/membrain-seg/src/membrain_seg/segmentation/segment.py:160: FutureWarning: torch.cuda.amp.autocast(args...) is deprecated. Please use torch.amp.autocast('cuda', args...) instead.
with torch.cuda.amp.autocast():
100%|█████████████████████████████████████████████████████████████| 1224/1224 [02:02<00:00, 9.98it/s]
100%|█████████████████████████████████████████████████████████████| 1224/1224 [01:57<00:00, 10.37it/s]
100%|█████████████████████████████████████████████████████████████| 1224/1224 [01:57<00:00, 10.39it/s]
100%|█████████████████████████████████████████████████████████████| 1224/1224 [01:58<00:00, 10.35it/s]
100%|█████████████████████████████████████████████████████████████| 1224/1224 [01:58<00:00, 10.36it/s]
100%|█████████████████████████████████████████████████████████████| 1224/1224 [01:58<00:00, 10.35it/s]
100%|█████████████████████████████████████████████████████████████| 1224/1224 [01:58<00:00, 10.34it/s]
100%|█████████████████████████████████████████████████████████████| 1224/1224 [01:58<00:00, 10.37it/s]
/programs/x86_64-linux/membrain-seg/0.0.8/bin.capsules/membrain-seg.aliases/membrain: line 2: 3392411 Killed "${SB_BASE}"/x86_64-linux//membrain-seg/0.0.8/bin/membrain "$@"