Bug report

[iffthomas]

Hi all, I'm rather new to github and couldn't submit it as a bug, I've got a problem with 2 commands:

Will work

"python -m monai.apps.nnunet nnUNetV2Runner train --input_config "./input.yaml" --configs "2d" --trainer_class_name 'nnUNetTrainer_1epoch'"

Will not work

python -m monai.apps.nnunet nnUNetV2Runner train --input_config "./input.yaml" --configs "2d" --trainer_class_name 'nnUNetTrainer_250epoch'"

What I'm aimiing at is to run this command to save time, however it's not working as indended, I can let it train for 1000 epochs but not for 250

python -m monai.apps.nnunet nnUNetV2Runner run --input_config "./input.yaml" --configs "2d" --trainer_class_name 'nnUNetTrainer_250epoch'"

2023-11-03 09:13:00,858 - INFO - number of GPUs is 1, device ids are (0,)
Traceback (most recent call last):
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/monai/apps/nnunet/main.py", line 20, in
fire.Fire({"nnUNetV2Runner": nnUNetV2Runner})
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/fire/core.py", line 475, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/fire/core.py", line 691, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/monai/apps/nnunet/nnunetv2_runner.py", line 589, in train
self.train_single_model(config=cfg, fold=_fold, gpu_id=gpu_id_for_all, **kwargs)
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/monai/apps/nnunet/nnunetv2_runner.py", line 538, in train_single_model
run_training(
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/nnunetv2/run/run_training.py", line 189, in run_training
nnunet_trainer = get_trainer_from_args(dataset_name_or_id, configuration, fold, trainer_class_name,
File "/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/nnunetv2/run/run_training.py", line 42, in get_trainer_from_args
raise RuntimeError(f'Could not find requested nnunet trainer {trainer_name} in '
RuntimeError: Could not find requested nnunet trainer nnUNetTrainer_250epoch in nnunetv2.training.nnUNetTrainer (/cluster/home/ifft/miniconda3/envs/venv-spine/lib/python3.10/site-packages/nnunetv2/training/nnUNetTrainer). If it is located somewhere else, please move it there.

Expected behavior
Both command should work, one training only 1 epoch, the other one 250 epochs but for only the 2d configuration (also doesn't work with nnUNetV2Runner run command

Environment

python -c 'import monai; monai.config.print_debug_info()'

================================
Printing MONAI config...

MONAI version: 1.3.0
Numpy version: 1.26.0
Pytorch version: 2.0.1
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 865972f
MONAI file: /cluster/home//miniconda3/envs/venv-spine/lib/python3.10/site-packages/monai/init.py

Optional dependencies:
Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.
ITK version: 5.3.0
Nibabel version: 5.1.0
scikit-image version: 0.20.0
scipy version: 1.11.3
Pillow version: 10.0.1
Tensorboard version: NOT INSTALLED or UNKNOWN VERSION.
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: 0.15.2
tqdm version: 4.66.1
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: 5.9.6
pandas version: 2.1.1
einops version: NOT INSTALLED or UNKNOWN VERSION.
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
pynrrd version: NOT INSTALLED or UNKNOWN VERSION.
clearml version: NOT INSTALLED or UNKNOWN VERSION.

For details about installing the optional dependencies, please visit:
https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

================================
Printing system config...

System: Linux
Linux version: CentOS Linux 7 (Core)
Processor:
Machine: x86_64
Python version: 3.10.13
Process name: python
Command: ['python', '-c', 'import monai; monai.config.print_debug_info()']
Num physical CPUs: 20
Num logical CPUs: 40
Num usable CPUs: 2
CPU usage (%): [9.1, 3.5, 2.8, 3.7, 7.1, 4.7, 0.2, 0.2, 0.2, 0.0, 1.2, 0.5, 0.4, 0.3, 0.2, 0.0, 100.0, 100.0, 0.1, 0.5, 80.3, 1.4, 0.4, 0.0, 0.0, 0.0, 0.1, 5.6, 0.0, 0.0, 100.0, 0.1, 0.0, 0.0, 0.0, 100.0, 0.0, 0.0, 100.0, 5.8]
CPU freq. (MHz): 1763
Load avg. in last 1, 5, 15 mins (%): [20.2, 18.6, 18.2]
Disk usage (%): 4.9
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 249.6
Available memory (GB): 214.4
Used memory (GB): 30.7

================================
Printing GPU config...

Num GPUs: 1
Has CUDA: True
CUDA version: 11.8
cuDNN enabled: True
NVIDIA_TF32_OVERRIDE: None
TORCH_ALLOW_TF32_CUBLAS_OVERRIDE: None
cuDNN version: 8700
Current device: 0
Library compiled for CUDA architectures: ['sm_37', 'sm_50', 'sm_60', 'sm_61', 'sm_70', 'sm_75', 'sm_80', 'sm_86', 'sm_90', 'compute_37']
GPU 0 Name: NVIDIA GeForce GTX 1080 Ti
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 28
GPU 0 Total memory (GB): 10.9
GPU 0 CUDA capability (maj.min): 6.1

[iffthomas]

Okay sooo what the problem was, was that the ReadMe was missleading: to specify
some were

nnUNetTrainer_250epochs

An s is missing in the tutorial here:
https://github.com/Project-MONAI/tutorials/tree/main/nnunet