Cannot run auto3dseg_hello_world.ipynb in Google Colab

[stang29]

Hi there,
I was trying to run the simple MONAI Auto3DSeg "Hello World" Example from (https://github.com/Project-MONAI/tutorials/blob/main/auto3dseg/notebooks/auto3dseg_hello_world.ipynb) and I keep getting this error after the runner.run() command:

2025-04-02 05:20:53,077 - INFO - Running data analysis...
2025-04-02 05:20:53,079 - INFO - Found 1 GPUs for data analyzing!
/usr/local/lib/python3.11/dist-packages/monai/apps/auto3dseg/data_analyzer.py:132: UserWarning: File /content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/datastats.yaml already exists and will be overwritten.
  warnings.warn(f"File {output_path} already exists and will be overwritten.")
100%|██████████| 12/12 [00:00<00:00, 23.03it/s]2025-04-02 05:20:53,629 - INFO - Writing data stats to /content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/datastats.yaml.
2025-04-02 05:20:53,645 - INFO - Writing by-case data stats to /content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/datastats_by_case.yaml, this may take a while.

2025-04-02 05:20:53,713 - INFO - BundleGen from https://github.com/Project-MONAI/research-contributions/releases/download/algo_templates/e4cf5a1.tar.gz
algo_templates.tar.gz: 104kB [00:00, 557kB/s]                              2025-04-02 05:20:53,908 - INFO - Downloaded: /tmp/tmp_6rhtgkb/algo_templates.tar.gz
2025-04-02 05:20:53,908 - INFO - Expected md5 is None, skip md5 check for file /tmp/tmp_6rhtgkb/algo_templates.tar.gz.
2025-04-02 05:20:53,909 - INFO - Writing into directory: /content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d.

2025-04-02 05:20:54,767 - INFO - Generated:/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0
2025-04-02 05:20:54,968 - INFO - Generated:/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/segresnet_0
2025-04-02 05:20:55,014 - INFO - segresnet2d_0 is skipped! SegresNet2D is skipped due to median spacing of [1.0, 1.0, 1.0],  which means the dataset is not highly anisotropic, e.g. spacing[2] < 3*(spacing[0] + spacing[1])/2) .
2025-04-02 05:20:55,247 - INFO - Generated:/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/swinunetr_0
2025-04-02 05:20:55,332 - INFO - The keys num_warmup_epochs cannot be found in the /content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/hyper_parameters.yaml for training. Skipped overriding key num_warmup_epochs.
2025-04-02 05:20:55,334 - INFO - ['python', '/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/scripts/train.py', 'run', "--config_file='/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/hyper_parameters.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/hyper_parameters_search.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/network.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/network_search.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/transforms_infer.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/transforms_train.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/transforms_validate.yaml'", '--training#num_epochs_per_validation=1', '--training#num_images_per_batch=2', '--training#num_epochs=2']
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
[<ipython-input-12-1c41d1ce6924>](https://localhost:8080/#) in <cell line: 0>()
----> 1 runner.run()

5 frames
[/usr/lib/python3.11/subprocess.py](https://localhost:8080/#) in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    569         retcode = process.poll()
    570         if check and retcode:
--> 571             raise CalledProcessError(retcode, process.args,
    572                                      output=stdout, stderr=stderr)
    573     return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '['python', '/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/scripts/train.py', 'run', "--config_file='/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/hyper_parameters.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/hyper_parameters_search.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/network.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/network_search.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/transforms_infer.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/transforms_train.yaml,/content/drive/MyDrive/Colab_Notebooks/pvs_models/Monai_auto3d/dints_0/configs/transforms_validate.yaml'", '--training#num_epochs_per_validation=1', '--training#num_images_per_batch=2', '--training#num_epochs=2']' returned non-zero exit status 1.

This also happens when I try to run the MONAI Auto3DSeg AutoRunner (https://github.com/Project-MONAI/tutorials/blob/main/auto3dseg/notebooks/auto_runner.ipynb).

Environment:
Python version: Python 3.11.11
GPU: A100 (from google colab)
(Running in jupyter notebook in google colab)
print_config() output:

MONAI version: 1.4.0
Numpy version: 1.26.0
Pytorch version: 2.6.0+cu124
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 46a5272196a6c2590ca2589029eed8e4d56ff008
MONAI __file__: /usr/local/lib/python3.11/dist-packages/monai/__init__.py

Optional dependencies:
Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.
ITK version: NOT INSTALLED or UNKNOWN VERSION.
Nibabel version: 5.3.2
scikit-image version: 0.25.2
scipy version: 1.14.1
Pillow version: 11.1.0
Tensorboard version: 2.18.0
gdown version: 5.2.0
TorchVision version: 0.21.0+cu124
tqdm version: 4.67.1
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: 5.9.5
pandas version: 2.2.2
einops version: 0.8.1
transformers version: 4.50.2
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
pynrrd version: NOT INSTALLED or UNKNOWN VERSION.
clearml version: NOT INSTALLED or UNKNOWN VERSION.

In one of the many iterations of trying to debug, I had all the optional dependencies also installed but I still got the error, so I don't think it's related to that. I've also triple checked my pathnames, I'm wondering if it has something to do with the fact that it's trying to access google drive, but I'm not sure. Thank you in advance!

[KumoLiu]

Hi @stang29, could you please try the latest version of MONAI-weekly or consider downgrading your PyTorch version to below 2.6? There are some issues introduced in version 2.6 that have been addressed in the latest release. Thank you!

[stang29]

Thanks for the quick reply! I'm not sure either of those worked for me. I first tried downgrading my pytorch version to 2.5 (should it be lower?) (command: !pip uninstall torch torchvision torchaudio -y; !pip install torch==2.5.0) and then installing regular monai and the command following the tutorial (command: !pip install monai; !python -c "import monai" || pip install -U "monai-weekly[fire, nibabel, yaml, tqdm, einops]") . Then I tried keeping pytorch 2.6 and installing monai weekly (command; !pip install monai-weekly !python -c "import monai" || pip install -U "monai-weekly[fire, nibabel, yaml, tqdm, einops]"). I also made sure to uninstall monai / monai-weekly before installing either.