Tomography reconstruction multinode optimization - #111

Merged

davramov merged 72 commits into

als-computing:mainfrom

davramov:recon-optimization

Apr 6, 2026

Commits on Jan 28, 2026

initial commit with multinode support
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e09c193
adding logic for determining qos based on number of nodes requested
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21244e5
Adding specific tag for microct image (for more efficient caching on NERSC). Also switching from podman to shifter for better overhead performance
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77d15cc
Adding reconstruct_multinode() method
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9e90a26
Making the cancel_sfapi_job.py script more useful
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31ed453
in setup.cfg, adding a new section for flake8 to ignore the reconstruction codes in scripts/perlmutter/* and scripts/polaris/*, since they are a linting nightmare but work
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a88fd45
Adding nersc_recon_num_nodes = 4 to Config832, which is used in bl832/nersc.py to set the number of nodes to use for reconstruction
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3691601
separating single node (production) nersc reconstruction flow from the multinode reconstruction flow
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1f48743
Making a spearate deployment for the nersc multinode reconstruction flow
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8ad972f
Creating option to turn on/off the nersc multinode reconstruction flow for the dispatcher
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81dd6c9

Commits on Feb 9, 2026

Updating segmentation to use inference_v4.
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141a5a6
removing comments. segmentation still isn't working
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b4cab67

Commits on Feb 11, 2026

Configuring to use all the nodes in the reservation
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340fcb2
num_nodes fix
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f2f8806
changing segmentation confidence from 0.5 to 0.2
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347816d

Commits on Feb 12, 2026

Setting patch-size=400 and confidence=0.5
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dd07993
confidence=0.2
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54d832c
Adding prefect variable to override defaults for segmentation
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e9336dc
updating segmentation to v5
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567899e

Commits on Feb 13, 2026

new checkpoint
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68490df
adding checkpoint as part of the segmentation variable
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290a983
adding support for a list of confidence scores that map to the prompt list
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1d5b8b4

Commits on Feb 20, 2026

updaing nersc flows with multisegmentation flows
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b8d6cee
updaing nersc recon reservation name
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9ae81fc
updating reservation name
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5532d12
adjusting node numbers
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4dea9a7
adjusting path for combine step scripts
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d37213f
Update prompt list for latest sam3 version
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e88ad2d
transferring segmented results to data832 as they complete rather than waiting
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7e1562c
making sam3 results go into its own folder so its not messy
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cd239b3
using the latest segmentation versions
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0b4c709

Commits on Feb 21, 2026

using combine_sam_dino_v2
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3461d17
removing cellpose from the multiseg workflow and increasing the number of nodes for dino/sam
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a869d02
updating default number of num nodes for sam3 segmenation
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790e1e0
adding extract_regions task to the multiseg flow
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a5d92c8
removing some commented code
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f0a91fd
copy recon/segment results from prscratch to cfs when the flow is done
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ba6dd58
using new code
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8e588de
shortened prompt list
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42dce23
fixing combine step
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0a1682f

Commits on Feb 24, 2026

reservation
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51c85f9
fixing combine step reservation (CPU)
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2aebe99

Commits on Mar 13, 2026

linting
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5e1778c
removing cellpose
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dd78a6e
removing extract_regions flow (replaced by the combine step)
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b73bfe5
renaming segmantion flows/tasks to segmentation_sam3 to differentiate from dino
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58fe7c5
removing commented code
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827d7c7
removing multiresolution multinode optimization efforts from this PR
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6e03983
Adding pytests for bl832/nersc.py: reconstruction, segmentation, multiresolution
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eee3733
Adding pytests for bl832/nersc.py: reconstruction, segmentation, multiresolution
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87e107d

Commits on Mar 18, 2026

Commits on Mar 20, 2026

Updating pytests
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0e66b2f

Commits on Mar 23, 2026

Commits on Apr 1, 2026

renaming DINO references to DINOv3
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0be1eeb
Updating pytest for nersc bc of the DINO -> DINOv3 naming changes
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d696931