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Hi, I'm having some trouble running nnUNet on the Synapse BCV dataset. I run it on a anaconda powershell prompt, and this error occurs the same for both 2D and 3D training. The version I am currently using is 2.2.1, I tried the latest version too and it reported the very same error. I noticed that there are multiple different processes and AttributeErrors, which are a bit different from what I saw in previous issues, and that's why I raised a separate one. The outputs are as follows:
2024-05-08 06:03:36.244731: unpacking dataset...
2024-05-08 06:04:31.883632: unpacking done...
2024-05-08 06:04:31.889076: do_dummy_2d_data_aug: False
2024-05-08 06:04:31.893605: Creating new 5-fold cross-validation split...
2024-05-08 06:04:31.899590: Desired fold for training: 0
2024-05-08 06:04:31.905573: This split has 24 training and 6 validation cases.
D:\conda\lib\site-packages\torch\onnx\symbolic_helper.py:1466: UserWarning: ONNX export mode is set to TrainingMode.EVAL, but operator 'instance_norm' is set to train=True. Exporting with train=True.
warnings.warn(
2024-05-08 06:04:38.226775: Unable to plot network architecture:
2024-05-08 06:04:38.230765: failed to execute WindowsPath('dot'), make sure the Graphviz executables are on your systems' PATH
2024-05-08 06:04:38.259687:
2024-05-08 06:04:38.264674: Epoch 0
2024-05-08 06:04:38.269661: Current learning rate: 0.01
using pin_memory on device 0
Process Process-5:
Traceback (most recent call last):
File "D:\conda\lib\multiprocessing\process.py", line 315, in _bootstrap
self.run()
File "D:\conda\lib\multiprocessing\process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 41, in producer
with threadpool_limits(1, None):
File "D:\conda\lib\site-packages\threadpoolctl.py", line 171, in __init__
self._original_info = self._set_threadpool_limits()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 268, in _set_threadpool_limits
modules = _ThreadpoolInfo(prefixes=self._prefixes,
File "D:\conda\lib\site-packages\threadpoolctl.py", line 340, in __init__
self._load_modules()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 373, in _load_modules
self._find_modules_with_enum_process_module_ex()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 485, in _find_modules_with_enum_process_module_ex
self._make_module_from_path(filepath)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 515, in _make_module_from_path
module = module_class(filepath, prefix, user_api, internal_api)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 606, in __init__
self.version = self.get_version()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 646, in get_version
config = get_config().split()
AttributeError: 'NoneType' object has no attribute 'split'
Process Process-6:
Traceback (most recent call last):
File "D:\conda\lib\multiprocessing\process.py", line 315, in _bootstrap
self.run()
File "D:\conda\lib\multiprocessing\process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 41, in producer
with threadpool_limits(1, None):
File "D:\conda\lib\site-packages\threadpoolctl.py", line 171, in __init__
self._original_info = self._set_threadpool_limits()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 268, in _set_threadpool_limits
modules = _ThreadpoolInfo(prefixes=self._prefixes,
File "D:\conda\lib\site-packages\threadpoolctl.py", line 340, in __init__
self._load_modules()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 373, in _load_modules
self._find_modules_with_enum_process_module_ex()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 485, in _find_modules_with_enum_process_module_ex
self._make_module_from_path(filepath)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 515, in _make_module_from_path
module = module_class(filepath, prefix, user_api, internal_api)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 606, in __init__
self.version = self.get_version()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 646, in get_version
config = get_config().split()
AttributeError: 'NoneType' object has no attribute 'split'
Process Process-7:
Traceback (most recent call last):
File "D:\conda\lib\multiprocessing\process.py", line 315, in _bootstrap
self.run()
File "D:\conda\lib\multiprocessing\process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 41, in producer
with threadpool_limits(1, None):
File "D:\conda\lib\site-packages\threadpoolctl.py", line 171, in __init__
self._original_info = self._set_threadpool_limits()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 268, in _set_threadpool_limits
modules = _ThreadpoolInfo(prefixes=self._prefixes,
File "D:\conda\lib\site-packages\threadpoolctl.py", line 340, in __init__
self._load_modules()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 373, in _load_modules
self._find_modules_with_enum_process_module_ex()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 485, in _find_modules_with_enum_process_module_ex
self._make_module_from_path(filepath)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 515, in _make_module_from_path
module = module_class(filepath, prefix, user_api, internal_api)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 606, in __init__
self.version = self.get_version()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 646, in get_version
config = get_config().split()
AttributeError: 'NoneType' object has no attribute 'split'
Process Process-8:
Traceback (most recent call last):
File "D:\conda\lib\multiprocessing\process.py", line 315, in _bootstrap
self.run()
File "D:\conda\lib\multiprocessing\process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 41, in producer
with threadpool_limits(1, None):
File "D:\conda\lib\site-packages\threadpoolctl.py", line 171, in __init__
self._original_info = self._set_threadpool_limits()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 268, in _set_threadpool_limits
modules = _ThreadpoolInfo(prefixes=self._prefixes,
File "D:\conda\lib\site-packages\threadpoolctl.py", line 340, in __init__
self._load_modules()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 373, in _load_modules
self._find_modules_with_enum_process_module_ex()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 485, in _find_modules_with_enum_process_module_ex
self._make_module_from_path(filepath)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 515, in _make_module_from_path
module = module_class(filepath, prefix, user_api, internal_api)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 606, in __init__
self.version = self.get_version()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 646, in get_version
config = get_config().split()
AttributeError: 'NoneType' object has no attribute 'split'
Process Process-9:
Exception in thread Traceback (most recent call last):
Thread-4 File "D:\conda\lib\multiprocessing\process.py", line 315, in _bootstrap
self.run()
File "D:\conda\lib\multiprocessing\process.py", line 108, in run
self._target(*self._args, **self._kwargs)
:
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 41, in producer
with threadpool_limits(1, None):
Traceback (most recent call last):
File "D:\conda\lib\site-packages\threadpoolctl.py", line 171, in __init__
self._original_info = self._set_threadpool_limits()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 268, in _set_threadpool_limits
modules = _ThreadpoolInfo(prefixes=self._prefixes,
File "D:\conda\lib\site-packages\threadpoolctl.py", line 340, in __init__
self._load_modules()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 373, in _load_modules
self._find_modules_with_enum_process_module_ex()
File "D:\conda\lib\threading.py", line 980, in _bootstrap_inner
File "D:\conda\lib\site-packages\threadpoolctl.py", line 485, in _find_modules_with_enum_process_module_ex
self._make_module_from_path(filepath)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 515, in _make_module_from_path
module = module_class(filepath, prefix, user_api, internal_api)
File "D:\conda\lib\site-packages\threadpoolctl.py", line 606, in __init__
self.version = self.get_version()
File "D:\conda\lib\site-packages\threadpoolctl.py", line 646, in get_version
config = get_config().split()
self.run()
File "D:\conda\lib\threading.py", line 917, in run
AttributeError: 'NoneType' object has no attribute 'split'
self._target(*self._args, **self._kwargs)
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 125, in results_loop
raise e
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 103, in results_loop
raise RuntimeError("One or more background workers are no longer alive. Exiting. Please check the "
RuntimeError: One or more background workers are no longer alive. Exiting. Please check the print statements above for the actual error message
Traceback (most recent call last):
File "D:\conda\lib\runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "D:\conda\lib\runpy.py", line 87, in _run_code
exec(code, run_globals)
File "C:\Users\user\AppData\Roaming\Python\Python39\Scripts\nnUNetv2_train.exe\__main__.py", line 7, in <module>
File "f:\ldl\nnunet\nnunetv2\run\run_training.py", line 268, in run_training_entry
run_training(args.dataset_name_or_id, args.configuration, args.fold, args.tr, args.p, args.pretrained_weights,
File "f:\ldl\nnunet\nnunetv2\run\run_training.py", line 204, in run_training
nnunet_trainer.run_training()
File "f:\ldl\nnunet\nnunetv2\training\nnUNetTrainer\nnUNetTrainer.py", line 1279, in run_training
train_outputs.append(self.train_step(next(self.dataloader_train)))
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 196, in __next__
item = self.__get_next_item()
File "C:\Users\user\AppData\Roaming\Python\Python39\site-packages\batchgenerators\dataloading\nondet_multi_threaded_augmenter.py", line 181, in __get_next_item
raise RuntimeError("One or more background workers are no longer alive. Exiting. Please check the "
RuntimeError: One or more background workers are no longer alive. Exiting. Please check the print statements above for the actual error message
I would appreciate it if you help :-)
The text was updated successfully, but these errors were encountered:
Hi, I'm having some trouble running nnUNet on the Synapse BCV dataset. I run it on a anaconda powershell prompt, and this error occurs the same for both 2D and 3D training. The version I am currently using is 2.2.1, I tried the latest version too and it reported the very same error. I noticed that there are multiple different processes and AttributeErrors, which are a bit different from what I saw in previous issues, and that's why I raised a separate one. The outputs are as follows:
I would appreciate it if you help :-)
The text was updated successfully, but these errors were encountered: