Plans were saved to /home/work/nnUNet/nnUNetFrame/DATASET/nnUNet_preprocessed/Dataset006_Lung/nnUNetPlans.json
Preprocessing...
Preprocessing dataset Dataset006_Lung
Configuration: 2d...
0%| | 0/63 [00:13<?, ?it/s]
Traceback (most recent call last):
File "/home/work/anaconda3/envs/python3.9_torch1.10_cuda11.3/bin/nnUNetv2_plan_and_preprocess", line 8, in
sys.exit(plan_and_preprocess_entry())
File "/home/work/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_entrypoints.py", line 197, in plan_and_preprocess_entry
preprocess(args.d, args.overwrite_plans_name, args.c, np, args.verbose)
File "/home/work/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 138, in preprocess
preprocess_dataset(d, plans_identifier, configurations, num_processes, verbose)
File "/home/work/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 116, in preprocess_dataset
preprocessor.run(dataset_id, c, plans_identifier, num_processes=n)
File "/home/work/nnUNet/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 246, in run
raise RuntimeError('Some background worker is 6 feet under. Yuck. \n'
RuntimeError: Some background worker is 6 feet under. Yuck.
OK jokes aside.
One of your background processes is missing. This could be because of an error (look for an error message) or because it was killed by your OS due to running out of RAM. If you don't see an error message, out of RAM is likely the problem. In that case reducing the number of workers might help
Plans were saved to /home/work/nnUNet/nnUNetFrame/DATASET/nnUNet_preprocessed/Dataset006_Lung/nnUNetPlans.json Preprocessing... Preprocessing dataset Dataset006_Lung Configuration: 2d... 0%| | 0/63 [00:13<?, ?it/s] Traceback (most recent call last): File "/home/work/anaconda3/envs/python3.9_torch1.10_cuda11.3/bin/nnUNetv2_plan_and_preprocess", line 8, in
sys.exit(plan_and_preprocess_entry())
File "/home/work/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_entrypoints.py", line 197, in plan_and_preprocess_entry
preprocess(args.d, args.overwrite_plans_name, args.c, np, args.verbose)
File "/home/work/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 138, in preprocess
preprocess_dataset(d, plans_identifier, configurations, num_processes, verbose)
File "/home/work/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 116, in preprocess_dataset
preprocessor.run(dataset_id, c, plans_identifier, num_processes=n)
File "/home/work/nnUNet/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 246, in run
raise RuntimeError('Some background worker is 6 feet under. Yuck. \n'
RuntimeError: Some background worker is 6 feet under. Yuck.
OK jokes aside.
One of your background processes is missing. This could be because of an error (look for an error message) or because it was killed by your OS due to running out of RAM. If you don't see an error message, out of RAM is likely the problem. In that case reducing the number of workers might help