Project-MONAI / Project-MONAI/tutorials
fork vs spawn on MacOS Python 3.9 error
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Description
Hi all,
I'm running macos conda-forge on the M1 architecture and testing the mednist_tutorial.ipynb and other jupyter notebooks. I get the following error
File "/opt/homebrew/Caskroom/miniforge/base/envs/pytorch_env/lib/python3.9/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/opt/homebrew/Caskroom/miniforge/base/envs/pytorch_env/lib/python3.9/multiprocessing/spawn.py", line 126, in _main
self = reduction.pickle.load(from_parent)
AttributeError: Can't get attribute 'MedNISTDataset' on <module '__main__' (built-in)>
This seems to be caused by spawn which apparently became default by Python 3.8 and later. It is fixed by adding the argument multiprocessing_context="fork" to calls of torch.utils.data.DataLoader, however, I suggest that a deeper fixed is made for non-experts.
Steps to reproduce the behavior
On MacOS/python-forge
2. jupyter lab mednist_tutorial.ipynb
3. press the clear kernel and run all button
Expected behavior
A demo network should be set up and trained
Environment
% python --version
Python 3.9.10
% python -c 'import monai; monai.config.print_debug_info()'
================================
Printing MONAI config...
================================
MONAI version: 0.9.dev2210
Numpy version: 1.22.3
Pytorch version: 1.10.2
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: 1a660e6a7a50e985af5ff76b559baab44175438c
MONAI __file__: /opt/homebrew/Caskroom/miniforge/base/envs/pytorch_env/lib/python3.9/site-packages/monai/__init__.py
Optional dependencies:
Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.
Nibabel version: NOT INSTALLED or UNKNOWN VERSION.
scikit-image version: NOT INSTALLED or UNKNOWN VERSION.
Pillow version: 9.0.1
Tensorboard version: 2.8.0
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: NOT INSTALLED or UNKNOWN VERSION.
tqdm version: 4.63.0
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: NOT INSTALLED or UNKNOWN VERSION.
pandas version: NOT INSTALLED or UNKNOWN VERSION.
einops version: 0.4.1
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow 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...
================================
`psutil` required for `print_system_info`
================================
Printing GPU config...
================================
Num GPUs: 0
Has CUDA: False
cuDNN enabled: False
Thank you for a nice package, Jon
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with mednist_tutorial.ipynb in Jupyter Lab on macOS with Python 3.9, reproduce the error by clearing the kernel and running all, then inspect the notebook's torch.utils.data.DataLoader calls. Done means the demo network can be set up and trained without the MedNISTDataset multiprocessing error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python, pytorch
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100