Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- production_pass
- Storage
- <5
- Strategy
- shared python312_slim.sif + RNA-FM PyTorch overlay and official checkpoint cache
- Next
- Production Ready. Optional hardening: add checkpoint selector for mRNA-FM and enforce UI length/batch limits.
No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged RNA-FM source/weights/SIF/artifacts/runner. RNA-FM/mRNA-FM public weights are small enough for a shared PyTorch SIF embedding smoke, but no direct Slurm smoke has run. Kept Smoke Pending. 2026-07-05 18:21 +08:00 backend re-audit: no staged RNA-FM source/weights/runtime/SIF/artifacts/runner found; only form spec exists locally. Kept Smoke Pending. 2026-07-06 implementation attempt: cloned ml4bio/RNA-FM at /media/nik/seagate_nik/bio_server/tools/rna-fm/source/RNA-FM rev 348951516e0963d22bbb33b3c9fc18c89081d38e and installed PyPI rna-fm 0.2.2 no-deps into /media/nik/seagate_nik/bio_server/envs/rna_fm_py312_site. Primary-source README says weights are downloaded from the cuhkaih/rnafm Hugging Face repo into pretrained/ and embedding extraction uses fm.pretrained.rna_fm_t12()/mrna_fm_t12(). Shared python312_slim.sif plus palm_py312_site currently fails import on missing ptflops, esm, and fairseq, and no official .pth/.pt weight cache was staged. No Slurm embedding smoke submitted; kept Smoke Pending. 2026-07-06 21:01 +08:00 recheck: staged ml4bio/RNA-FM source and PyPI rna-fm 0.2.2 no-deps overlay still cannot import under shared python312_slim because ptflops, esm, and fairseq are missing, and official cuhkaih/rnafm weights are not cached. No Slurm embedding smoke was submitted. 2026-07-06 21:34 +08:00 promotion: direct Slurm job 472 passed using shared python312_slim.sif, rna_fm_py312_site, palm_py312_site, and official cuhkaih/rnafm Hugging Face RNA-FM_pretrained.pth (1,194,424,423 bytes) cached at /media/nik/seagate_nik/bio_server/models/rna-fm/pretrained/RNA-FM_pretrained.pth. Run /media/nik/seagate_nik/bio_server/runs/rna-fm/smoke_20260706_213500 produced summary.json, results.csv, token_embeddings.pt, job.log, and Slurm logs. Two toy RNA sequences produced finite layer-12 embeddings with shape [2,58,640], per-sequence shapes [56,640] and [23,640], mean/std sanity values 0.0021/0.5240 and 0.0026/0.5159. Runner/API wiring remains pending. 2026-07-08T02:14:07+08:00: Production Ready promotion: backend runner API job c990fe4532ac / Slurm job 536 completed cleanly using shared python312_slim.sif, rna_fm_py312_site/palm overlays, and official RNA-FM_pretrained.pth. Produced zero-byte slurm.out/slurm.err, finite layer-12 embeddings shape [2,58,640], results.csv, token_embeddings.pt, and runtime summary.