Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- production_validated_runner_api_slurm_diffsbdd
- Storage
- <5
- Strategy
- shared python312_slim.sif + tool ext3 overlay
- Next
- Production Ready. Optional hardening: expose uploaded PDB/reference ligand inputs, tune n_samples/timesteps/num_nodes controls in the UI, add GPU validation when a CUDA DiffSBDD runtime is available, and reject runs with low sanitized molecule yield.
Production blocker evidence 2026-07-01: source https://github.com/arneschneuing/DiffSBDD revision 5d0d38d16c8932a0339fd2ce3f67ade98bbdff27 staged at /media/nik/seagate_nik/bio_server/tools/diffsbdd, install size 53M plus CPU env /home/nik/bio_server_venvs/diffsbdd_cpu size 2.2G and checkpoint crossdocked_fullatom_cond.ckpt 18M. Real Slurm smoke job 307 on cpu completed in about 6s and generated an SDF. RDKit parsed 1 molecule with 2 atoms, 1 bond, 1 conformer, SMILES FI. This proves code-path execution only; output is not scientifically meaningful because test used --timesteps 1 and tiny sampling. CUDA env unresolved; shared external-path micromamba extraction/linking failed. 2026-07-09T16:34:36+08:00 SOP promotion: DiffSBDD validated through Ubuntu runner API remote job 082562a128ab / Slurm job 596 using staged source /media/nik/seagate_nik/bio_server/tools/diffsbdd/DiffSBDD, Python runtime /home/nik/bio_server_venvs/diffsbdd_cpu/bin/python, and checkpoint /media/nik/seagate_nik/bio_server/tools/diffsbdd/DiffSBDD/checkpoints/crossdocked_fullatom_cond.ckpt. A direct preflight Slurm benchmark 595 used 5 samples, batch size 5, 18 ligand nodes, and 25 denoising timesteps, producing 5/5 sanitized molecules and 5 unique SMILES. The final API run completed in 9.069 s on the bundled 3RFM PDB/reference ligand with 5 samples, 25 denoising timesteps, and 18 ligand nodes; it produced 5 molecules, 5 unique SMILES, 4 RDKit-sanitized structures, 18 heavy atoms for every molecule, non-empty SDF output, per-molecule CSV, summary JSON, and runner artifacts. Artifacts verified: summary.json, results.csv, diffsbdd_generated.sdf, diffsbdd_molecule_metrics.csv, diffsbdd_molecule_summary.json, diffsbdd_result.json, diffsbdd_stdout.txt, diffsbdd_stderr.txt, 3rfm.pdb, 3rfm_B_CFF.sdf, slurm.out, and slurm.err.