Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- ready
- Storage
- <5
- Strategy
- shared python312_slim.sif + cluster_pdbs_mdtraj_py312_site + MDTraj/scikit-learn CA RMSD clustering adapter
- Next
- Production Ready for scoped MDTraj CA-RMSD agglomerative clustering of PDB inputs. Optional expansion: GUI upload mapping for trajectory files and additional clustering methods.
No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged MDTraj runtime/fixture/artifacts/runner. Cluster PDBs is a small utility candidate using MDTraj, but no direct Slurm clustering smoke has run. Kept Smoke Pending. 2026-07-05 18:21 +08:00 backend re-audit: no staged MDTraj runtime, fixture, artifacts, or runner found under shared backend root; no object-store smoke evidence. Kept Smoke Pending. 2026-07-05 23:25 +08:00 implementation pass: staged MDTraj CPU Python target at /media/nik/seagate_nik/bio_server/envs/cluster_pdbs_mdtraj_py312_site with mdtraj 1.11.0, NumPy 1.26.4, SciPy 1.17.1, scikit-learn 1.9.0, and pandas 3.0.3. Direct Slurm job 433 ran under /media/nik/seagate_nik/bio_server/runs/cluster-pdbs/smoke_20260705_232550 using shared python312_slim.sif and explicit /media/nik/seagate_nik bind. The smoke generated three tiny PDB conformers, loaded them with MDTraj, computed a CA RMSD matrix, clustered them into two clusters, and emitted summary.json, results.csv, rmsd_matrix.csv, input PDBs, job.log, slurm.out, and slurm.err. 2026-07-08T00:21:35+08:00 SOP runner-adapter pass: added real backend adapter using shared python312_slim.sif and cluster_pdbs_mdtraj_py312_site. Ubuntu runner API job 69f2c6c1080a / Slurm job 523 passed MDTraj 1.11.0 clustering with 3 PDB conformers, 2 clusters, max_rmsd_nm=0.0564276, results.csv, rmsd_matrix.csv, cluster_pdbs_runtime.json, job.log, slurm.out, and zero-byte slurm.err.