Release 2.5.0: AlphaFold3 v3.0.3 (RTX/Blackwell Tokamax stack)#626
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Update alphafold3 submodule to official AF3 v3.0.3 (KosinskiLab fork main 86b9ea3) and alphafold submodule to 5bf5b9f. This brings the JAX 0.9.1 / tokamax 0.0.11 stack required for RTX PRO 6000 (Blackwell, CC 12.0) GPUs, resolving the silent ptxas failures on gpu50-53. Preserves gapped/discontinuous residue ID support and keeps the AF2 backend on numpy<2 / jax 0.5.3. Validated: full unit/integration suites, RTX PRO 6000 GPU smoke (alphafold3==3.0.3, jax 0.9.1, tokamax 0.0.11), and AF2 monomer GPU inference. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Bumps
alphapulldown.__version__to 2.5.0 for the AlphaFold3 v3.0.3 release.The AF3 content (submodule -> official v3.0.3 / KosinskiLab fork main 86b9ea3, alphafold submodule -> 5bf5b9f, container version override, smoke-test fix) merged in #625 (855fc0b).
This release brings the JAX 0.9.1 / tokamax 0.0.11 stack required for RTX PRO 6000 (Blackwell, CC 12.0) GPUs, fixing the silent ptxas failures on gpu50-53.
Validation
alphafold3==3.0.3,jax==0.9.1,tokamax==0.0.11,rtx_smoke=ok.TestRunModes::test__monomer) PASSED on gpu32 under numpy<2 / jax 0.5.3, confirming the AF2 backend remains runnable after the NumPy 2 chain-feature fix.🤖 Generated with Claude Code