Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- verified
- Production
- production_validated_runner_api_slurm_antiberty
- Storage
- <5
- Strategy
- shared Python 3.10 SIF plus clean CPU torch/transformers target
- Next
- Production ready; monitor user-submitted antibody sequences and consider adding optional batched FASTA input examples in the UI.
AntiBERTy source/PyPI verified (jeffreyruffolo/AntiBERTy rev fd8b42271d1710a16e7fb4c55da3f027d947d177, antiberty 0.1.3). Direct Python 3.12 pip target pulled ~12 GB CUDA/PyTorch stack and incompatible transformers 5.x; import smoke failed; no Slurm benchmark run. 2026-07-05 SOP triage: AntiBERTy source/PyPI are verified, but Python 3.12 installation pulled an unsuitable large CUDA/PyTorch stack and incompatible transformers 5.x; upstream requires an older pinned torch/transformers runtime. No validated shared backend SIF exists. Reclassified from Smoke Pending to Production Blocked until a compatible pinned container is built. 2026-07-09T14:28:56+08:00 SOP blocked recheck: live backend import probe using /media/nik/seagate_nik/bio_server/tools/antifold/container/python310.sif found /media/nik/seagate_nik/bio_server/tools/antiberty/py310deps effectively empty and pydeps containing a partial CUDA-heavy Torch tree. torch import fails with 'Failed to load PyTorch C extensions', transformers is missing, and AntiBERTyRunner cannot import. No Slurm/API benchmark submitted; remains Production Blocked until a pinned Python 3.10/3.11 container or clean target with compatible torch/transformers is built. 2026-07-09T17:22:25+08:00 SOP production validation: promoted from Production Blocked to Production Ready. Built a clean pinned CPU runtime at /home/nik/bio_server_venvs/antiberty_py310_cpu_site with antiberty 0.1.3, torch 1.13.1+cpu, transformers 4.30.2, and numpy 1.26.4, executed inside /media/nik/seagate_nik/bio_server/tools/antifold/container/python310.sif. Direct Slurm benchmark job 602 completed exit 0 on validated heavy/light antibody chains. Implemented the production runner adapter and validated through Ubuntu runner API remote job 906d8bc141e7 / Slurm job 624. The API run completed in 10.155 s and produced embeddings of shapes 124x512 and 114x512, species predictions Human and Mouse, chain predictions Heavy and Light, pseudo-log-likelihoods -0.41638609766960144 and -0.09879834204912186, filled-mask sequences, FASTA, per-sequence CSV, summary JSON, and runner artifacts. Artifacts verified: summary.json, results.csv, antiberty_sequences.fasta, antiberty_results.csv, antiberty_summary.json, antiberty_result.json, antiberty_stdout.txt, antiberty_stderr.txt, run_antiberty.py, slurm.out, and slurm.err.