AttributeError: 'NoneType' object has no attribute 'split'

[jiaomei222]

(nnU-Net) [xwwang@localhost nnUNet-master]$ nnUNet_train 3d_fullres nnUNetTrainerV2 4 0

Please cite the following paper when using nnUNet:

Isensee, F., Jaeger, P.F., Kohl, S.A.A. et al. "nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation." Nat Methods (2020). https://doi.org/10.1038/s41592-020-01008-z

If you have questions or suggestions, feel free to open an issue at https://github.com/MIC-DKFZ/nnUNet

############################################### I am running the following nnUNet: 3d_fullres My trainer class is: <class 'nnunet.training.network_training.nnUNetTrainerV2.nnUNetTrainerV2'> For that I will be using the following configuration: num_classes: 2 modalities: {0: 'MRI'} use_mask_for_norm OrderedDict([(0, False)]) keep_only_largest_region None min_region_size_per_class None min_size_per_class None normalization_schemes OrderedDict([(0, 'nonCT')]) stages...

stage: 0 {'batch_size': 9, 'num_pool_per_axis': [3, 3, 3], 'patch_size': array([40, 56, 40]), 'median_patient_size_in_voxels': array([36, 50, 35]), 'current_spacing': array([1., 1., 1.]), 'original_spacing': array([1., 1., 1.]), 'do_dummy_2D_data_aug': False, 'pool_op_kernel_sizes': [[2, 2, 2], [2, 2, 2], [2, 2, 2]], 'conv_kernel_sizes': [[3, 3, 3], [3, 3, 3], [3, 3, 3], [3, 3, 3]]}

I am using stage 0 from these plans I am using sample dice + CE loss

I am using data from this folder: /home/xwwang/nnUNet-master/nnUNet_preprocessed/Task004_Hippocampus/nnUNetData_plans_v2.1 ############################################### loading dataset loading all case properties 2022-07-10 00:02:50.282663: Creating new 5-fold cross-validation split... 2022-07-10 00:02:50.283967: Desired fold for training: 0 2022-07-10 00:02:50.284058: This split has 208 training and 52 validation cases. unpacking dataset done 2022-07-10 00:02:57.099654: lr: 0.01 Traceback (most recent call last): File "_ctypes/callbacks.c", line 237, in 'calling callback function' File "/opt/Anaconda/lib/python3.8/site-packages/threadpoolctl.py", line 400, in match_module_callback self._make_module_from_path(filepath) File "/opt/Anaconda/lib/python3.8/site-packages/threadpoolctl.py", line 515, in _make_module_from_path module = module_class(filepath, prefix, user_api, internal_api) File "/opt/Anaconda/lib/python3.8/site-packages/threadpoolctl.py", line 606, in init self.version = self.get_version() File "/opt/Anaconda/lib/python3.8/site-packages/threadpoolctl.py", line 646, in get_version config = get_config().split() AttributeError: 'NoneType' object has no attribute 'split' using pin_memory on device 0 Traceback (most recent call last): File "_ctypes/callbacks.c", line 237, in 'calling callback function' File "/opt/Anaconda/lib/python3.8/site-packages/threadpoolctl.py", line 400, in match_module_callback self._make_module_from_path(filepath) File "/opt/Anaconda/lib/python3.8/site-packages/threadpoolctl.py", line 515, in _make_module_from_path module = module_class(filepath, prefix, user_api, internal_api) File "/opt/Anaconda/lib/python3.8/site-packages/threadpoolctl.py", line 606, in init self.version = self.get_version() File "/opt/Anaconda/lib/python3.8/site-packages/threadpoolctl.py", line 646, in get_version config = get_config().split() AttributeError: 'NoneType' object has no attribute 'split'

[jiaomei222]

And the final Traceback is, Traceback (most recent call last): File "/opt/Anaconda/lib/python3.8/threading.py", line 932, in _bootstrap_inner self.run() File "/opt/Anaconda/lib/python3.8/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "/home/xwwang/.local/lib/python3.8/site-packages/batchgenerators/dataloading/multi_threaded_augmenter.py", line 92, in results_loop raise RuntimeError("Abort event was set. So someone died and we should end this madness. \nIMPORTANT: " RuntimeError: Abort event was set. So someone died and we should end this madness. IMPORTANT: This is not the actual error message! Look further up to see what caused the error. Please also check whether your RAM was full Exception in thread Thread-5: Traceback (most recent call last): File "/opt/Anaconda/lib/python3.8/threading.py", line 932, in _bootstrap_inner self.run() File "/opt/Anaconda/lib/python3.8/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "/home/xwwang/.local/lib/python3.8/site-packages/batchgenerators/dataloading/multi_threaded_augmenter.py", line 92, in results_loop raise RuntimeError("Abort event was set. So someone died and we should end this madness. \nIMPORTANT: " RuntimeError: Abort event was set. So someone died and we should end this madness. IMPORTANT: This is not the actual error message! Look further up to see what caused the error. Please also check whether your RAM was full

[FabianIsensee]

your threadpoolctl seems to be broken. Have you tried reinstalling it?

[GregorKoehler]

Hi @jiaomei222, Were you able to resolve this issue back then? If you still encounter problems, please let us know! Otherwise, we'll close this issue in roughly 2 weeks.