Auto3Dseg cuda OOM during Ensembling

[udiram]

Describe the bug Models have all finished training, and during the ensembling process, cuda runs out of memory.

Reproduce Steps to reproduce the behavior: Run Autorunner on AMOS22 dataset

manually resetting cuda cache, restarting kernel and instance all come back to this error.

Expected behavior training proceeds without error MONAI version: 1.2.0 Numpy version: 1.25.2 Pytorch version: 2.0.1+cu117 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False MONAI rev id: c33f1ba588ee00229a309000e888f9817b4f1934 MONAI file: /home/exouser/.local/lib/python3.10/site-packages/monai/init.py

Optional dependencies: Pytorch Ignite version: 0.4.11 ITK version: 5.3.0 Nibabel version: 5.1.0 scikit-image version: 0.21.0 Pillow version: 9.0.1 Tensorboard version: 2.14.0 gdown version: 4.7.1 TorchVision version: 0.15.2+cu117 tqdm version: 4.66.1 lmdb version: 1.4.1 psutil version: 5.9.0 pandas version: 2.0.3 einops version: 0.6.1 transformers version: 4.21.3 mlflow version: 2.6.0 pynrrd version: 1.0.0

Environment (please complete the following information): OS: ubuntu 22.04 Python 3.10.12 Driver Version: 525.85.05 CUDA Version: 12.0 GRID A100X-40C - 125GB RAM

I'm happy to provide any other logs to help, this is the second time I've run into this issue, the issue persists after a full kernel restart and RAM clearing.

[KumoLiu]

Hi @dongyang0122, could you please share some comments here? Thanks in advance!

[udiram]

hi @KumoLiu just following up on this, are there any other similar issues I could reference to trouble shoot? thanks!

[KumoLiu]

Hi @udiram, here are some similar issues you could refer to: https://github.com/Project-MONAI/tutorials/discussions/1089 https://github.com/Project-MONAI/tutorials/discussions/975 Thanks!

[udiram]

hi Kumo, #1089 worked for me to get training going, and like I mentioned in that issue, the same fixes (i.e. setting the spacing in swinunetr to 1.5, 1.5, 1.5), so thanks for this!

I am, however, still running into the ensembling issue that doesn't seem to be addressed in #975 specifically. The good thing about the crash happening so late is that the inferences from the test images are indeed saved, but what I am missing is a model.pth to run the model on some ground truth images as I had hoped to do. Do you know if there is a way to extract this? similar to a model trained with the https://github.com/Project-MONAI/tutorials/blob/main/3d_segmentation/swin_unetr_btcv_segmentation_3d.ipynb routine. Once I have that model file, I shouldn't necessarily need to go through the rest of the auto3dseg pipeline.

All of this with the caveat that Auto3dseg doing this automatically without GPU issues would be great!

[KumoLiu]

Hi @udiram, I looked at the source code, and found that the model is saved under "bundle_root/models". https://github.com/Project-MONAI/research-contributions/blob/0cd69f2a64b727ab8103d30512b39a7eb6a09ed3/auto3dseg/algorithm_templates/segresnet/scripts/segmenter.py#L1136 https://github.com/Project-MONAI/research-contributions/blob/0cd69f2a64b727ab8103d30512b39a7eb6a09ed3/auto3dseg/algorithm_templates/segresnet/configs/hyper_parameters.yaml#L2

Thanks!

[udiram]

Thanks @KumoLiu! I'll give it a go!

[udiram]

hi @KumoLiu is there anywhere for me to see which model performed best during training? so I can run inference using that model, I notice that every fold for every model has an associated .pt file but I'm not seeing a global best model/fold.

thanks

[KumoLiu]

Hi @udiram, I think "model.pt" is the best model for each fold. There is also a final model has been saved. You may need to ensemble to get the final result. https://github.com/Project-MONAI/research-contributions/blob/0cd69f2a64b727ab8103d30512b39a7eb6a09ed3/auto3dseg/algorithm_templates/segresnet/scripts/segmenter.py#L1288-L1295 https://github.com/Project-MONAI/research-contributions/blob/0cd69f2a64b727ab8103d30512b39a7eb6a09ed3/auto3dseg/algorithm_templates/segresnet/scripts/segmenter.py#L1136-L1137

[udiram]

Hi @KumoLiu , thanks for the info, so I guess I'm a bit stuck until this ensembling issue is figured out, is there anything else, debugging or log wise, that you or @dongyang0122 need in order to figure it out?

thanks!

[KumoLiu]

Hi @udiram, for how to ensemble, you can refer to: https://github.com/Project-MONAI/tutorials/blob/main/modules/cross_validation_models_ensemble.ipynb https://github.com/Project-MONAI/MONAI/blob/281cb0119c01eaa8e6c841880b91f92f45e8d7f7/monai/apps/auto3dseg/ensemble_builder.py#L404

Thanks!

[udiram]

Hi @KumoLiu

Thanks for the resources, does this integrate into the Auto3dseg pipeline in any way? Is there any ways to point the ensembler at the files generated by auto3dseg?

Thanks

[KumoLiu]

Hi @udiram, yes, it has already been integrated into the AutoRunner. https://github.com/Project-MONAI/MONAI/blob/281cb0119c01eaa8e6c841880b91f92f45e8d7f7/monai/apps/auto3dseg/auto_runner.py#L815

You can also override it by:

runner = AutoRunner(input=input)
runner.set_ensemble_method(ensemble_method_name="AlgoEnsembleBestByFold")

Just FYI: https://github.com/Project-MONAI/tutorials/tree/main/auto3dseg/notebooks

Thanks!

[udiram]

sure, I'll give the over ride a try, do you have any ideas on how to run ensembling with less gpu usage, similar to the fix during validation for #1089 ?

thanks!

[udiram]

Hi @KumoLiu, just following up on this issue!