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Add MONAI quickstart example #2773

Merged
merged 29 commits into from
Feb 28, 2024
Merged

Add MONAI quickstart example #2773

merged 29 commits into from
Feb 28, 2024

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charlesbvll
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@charlesbvll charlesbvll commented Jan 4, 2024 •
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Issue

Description

MONAI (Medical Open Network for AI) is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of the PyTorch Ecosystem and we don't yet have an example for it.

Related issues/PRs

N/A

Proposal

Explanation

Add a quickstart example using Flower and MONAI.

Checklist

  • Implement proposed change
  • Update the changelog entry below
  • Make CI checks pass
  • Ping maintainers on Slack (channel #contributions)

Changelog entry

MONAI (Medical Open Network for AI) is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of the PyTorch Ecosystem. You can find the example at https://github.com/adap/flower/tree/main/examples/quickstart-monai.

Any other comments?

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@charlesbvll charlesbvll marked this pull request as ready for review January 4, 2024 21:16
jafermarq
jafermarq reviewed Jan 4, 2024
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@jafermarq jafermarq left a comment •
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Hi @charlesbvll, some minor comments below. More concerning is the fact that I'm getting segmentation faults when running this on Ubuntu x64 (no matter if I use or don't use GPU) (but no issues on mac arm64). Seems to be related to the dataloaders...

Update: setting num_workers=0 in the dataloaders seems to fix the issue in Ubuntu. But this slows down training so I don't think it's an ideal solution

@jafermarq jafermarq added the part: examples Add or update a Flower example label Jan 4, 2024
@charlesbvll
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Hi @charlesbvll, some minor comments below. More concerning is the fact that I'm getting segmentation faults when running this on Ubuntu x64 (no matter if I use or don't use GPU) (but no issues on mac arm64). Seems to be related to the dataloaders...

Update: setting num_workers=0 in the dataloaders seems to fix the issue in Ubuntu. But this slows down training so I don't think it's an ideal solution

@jafermarq I don't know of any other solutions to fix num_workers > 0 related errors, even if the training is slower, I think it's better to set num_workers=0 for stability.

jafermarq
jafermarq reviewed Jan 5, 2024
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Let's keep the default num_workers

jafermarq
jafermarq previously approved these changes Jan 17, 2024
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jafermarq commented Jan 17, 2024 •
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@charlesbvll, I added a link to this example in the top-level readme. Also, adding MONAI to the list of supported frameworks. Looks good?

@danieljanes danieljanes enabled auto-merge (squash) February 28, 2024 19:13
@danieljanes danieljanes merged commit 42f13ad into main Feb 28, 2024
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@danieljanes danieljanes deleted the add-monai-quickstart branch February 28, 2024 19:23
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@danieljanes danieljanes danieljanes approved these changes

@jafermarq jafermarq jafermarq left review comments

@tanertopal tanertopal Awaiting requested review from tanertopal tanertopal is a code owner

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@charlesbvll @jafermarq @danieljanes