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AF3: --fast_kernels with fused triangle kernels; AlphaFold 3 v3.0.4 - #646

Merged

DimaMolod merged 11 commits into

mainfrom

Oct 7, 2026

Merged

AF3: --fast_kernels with fused triangle kernels; AlphaFold 3 v3.0.4#646
DimaMolod merged 11 commits into
mainfrom
exp/af3-v3.0.4

Commits on Oct 6, 2026
- Enable optional AF3 fused triangles with device checks and output provenance
  DimaMolod
  committed
  f76b072
- chore: alphafold3 submodule at the fork's renamed fused-triangle API
  
  DimaMolod
  and
  claude
  committed
  a2d47f1
- refactor: AF3 fused-triangle policy in its own module
  
  DimaMolod
  and
  claude
  committed
  e100030
- fix: AF3 kernel check runs on the GPU it checks; reason names the mode
  
  DimaMolod
  and
  claude
  committed
  4bed2a4
- fix: AF3 kernel record never fails a prediction, keyed seed-N
  
  DimaMolod
  and
  claude
  committed
  796fc70
- refactor: one FAST_KERNEL_FLAGS set for AlphaFold 2 and 3
  
  DimaMolod
  and
  claude
  committed
  2748c80
- docs: AF3 fused triangle kernels in sections, with terms and measurements
  
  DimaMolod
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  claude
  committed
  c235cd8
- chore: double-quoted fast_kernels default in AF3 setup
  
  DimaMolod
  and
  claude
  committed
  8f6c55e
- AF3: move the alphafold3 submodule to the fork's v3.0.4 update
  
  DimaMolod
  and
  claude
  committed
  d8b898c
- fix: run_multimer_jobs forwards --fast_kernels and the compile cache
  
  DimaMolod
  and
  claude
  committed
  18e5fcc
Commits on Oct 7, 2026
- chore: alphafold3 submodule at the merged fork (KosinskiLab/alphafold3#3, #4)
  
  DimaMolod
  and
  claude
  committed
  ef46bc2