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ALCF Reconstruction and Segmentation for bl832#114

Open

davramov wants to merge 55 commits into

als-computing:mainals-computing/splash_flows:mainfrom

davramov:alcf_recon_segmentationdavramov/splash_flows:alcf_recon_segmentationCopy head branch name to clipboard

Conversation Commits55 (55)Checks Files changed

Open

ALCF Reconstruction and Segmentation for bl832#114
davramov wants to merge 55 commits into
als-computing:mainfrom
davramov:alcf_recon_segmentation

Commits

Commits on Jun 17, 2026

Updating ALCF endpoints to include the synaps-i allocation (to be set up)
davramov
committed
Updating bl832 config.py to distinguish IRI and SYNAPS-I ALCF endpoints
davramov
committed
Adding the config.yaml file for setting up the globus compute endpoint for reconstruction on ALCF
davramov
committed
Adding the config.yaml file for setting up the globus compute endpoint for segmentation on ALCF. Still needs to be configured for GPU and the environment with dependencies
davramov
committed
Adding segmentation Prefect task, and segmentation globus compute code for the TomographyController. Turning off TIFF to ZARR on ALCF for the demo
davramov
committed
Making separate ALCF SYNAPS-I endpoint configs for raw, reconstructed, and segmented data
davramov
committed
Refactoring ALCF reconstruction flow to use the prune_controller class
davramov
committed
Removing old commented out prune code
davramov
committed
linting and docstrings
davramov
committed
Docstrings, linting, and type hints
davramov
committed
Updating globus compute config for segmentation
davramov
committed
turning ALCF recon+segmentation into a separate flow from recon+zarr conversion
davramov
committed
updating pytest for alcf reconstruction
davramov
committed
Adjusting endpoint names for synaps
davramov
committed
adding the alcf_forge_recon_segment flow to prefect.yaml as a separate deployment
davramov
committed
updating bl832 dispatcher to include alcf_forge_recon_segment as a separate option
davramov
committed
adding transfer client uuid for ALCF SYNAPS-I
davramov
committed
this configuration worked for launching segmentation on 1 GPU
davramov
committed
Updating segmentation compute endpoint config
davramov
committed
Adding a separate wrapper for segmentation v2. At some point we may want to collapse these into the final version, but for testing purposes I'm leaving both codes
davramov
committed
adding globus compute configs for segmentation (single and multinode)
davramov
committed
removing old segment config
davramov
committed
Segmentation wrapper v2 calls the segmentation inference version on polaris that scales well to multiple gpu nodes
davramov
committed
removing stale comments
davramov
committed
removing stale comments
davramov
committed
Cleaning, adding helpful comments
davramov
committed
typo, and cleaning file paths
davramov
committed
Adding ALCF recon multinode
davramov
committed
More optimization. Went from 284s on 8 nodes to 77s
davramov
committed
docstring
davramov
committed
fixing typo
davramov
committed
Segmentation with inference_v4 working
davramov
committed
Adding checkpoint v2
davramov
committed
adding tasks/flows for segmentation with dino and cellpose on ALCF
davramov
committed
Adding combine segmentation results function to the ALCF controller
davramov
committed
Updating segmentation directory paths to put each models outputs into its own subfolder
davramov
committed
Adding combine_segmentations to the multiseg flow
davramov
committed
updating ALCF conda env for dino/cellpose
davramov
committed
Updating the combine step to use the dino/cellpose env
davramov
committed
Adding globus compute configs for dino, cellpose, and combine steps
davramov
committed
linting
davramov
committed
Adding globus compute endpoint uuids
davramov
committed
updating globus compute endpoint uuid and adding integration test functions for each segmentation step
davramov
committed
linting
davramov
committed
adding new flow to prefect.yaml for deployment
davramov
committed
updaing dispatcher flow to handle the multisegment option
davramov
committed
Updating to match NERSC deployment
davramov
committed
removing commented code
davramov
committed
removing cellpose flows/tasks
davramov
committed
renaming segmentation flow/tasks to segmentation_sam3 so it is obviously separated from dino segmentation
davramov
committed
Docstrings
davramov
committed
Adding _tests/bl832/test_alcf.py to test: reconstruction, segmentation, multiresolution flows
davramov
committed
Adding script used to generate latex segmentation timing table in the nature comms paper
davramov
committed
linting
davramov
committed
globus compute config
davramov
committed

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