NeMo2 to Megatron Bridge Checkpoint Conversion and Fine-tuning

[jstjohn]

Description

Example scripts demonstrating fine-tuning from a starting checkpoint, and a checkpoint conversion script for migrating nemo2 checkpoints to megatron bridge.

Usage

See README.md in evo2_megatron recipe in this PR for usage.

Type of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Refactor
• Documentation update
• Other (please describe):

CI Pipeline Configuration

Configure CI behavior by applying the relevant labels. By default, only basic unit tests are run.

• ciflow:skip - Skip all CI tests for this PR
• ciflow:notebooks - Run Jupyter notebooks execution tests for bionemo2
• ciflow:slow - Run slow single GPU integration tests marked as @pytest.mark.slow for bionemo2
• ciflow:all - Run all tests (unit tests, slow tests, and notebooks) for bionemo2. This label can be used to enforce running tests for all bionemo2.
• ciflow:all-recipes - Run tests for all recipes (under bionemo-recipes). This label can be used to enforce running tests for all recipes.

Unit tests marked as @pytest.mark.multi_gpu or @pytest.mark.distributed are not run in the PR pipeline.

For more details, see CONTRIBUTING

Note

By default, only basic unit tests are run. Add appropriate labels to enable an additional test coverage.

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Pre-submit Checklist

• I have tested these changes locally
• I have updated the documentation accordingly
• I have added/updated tests as needed
• All existing tests pass successfully

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[jstjohn]

Will mark ready once #1403 merges. Until then the new tests will not work.

[jstjohn]

Pull in dataset bugfix from #1393

[jstjohn]

/ready to test 7567299

[jstjohn]

/ok to test 7567299

[jstjohn]

/ok to test cf65fd7

[jstjohn]

/ok to test 86c2d06