Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- production_pass
- Storage
- <5
- Strategy
- shared python312_slim.sif plus staged aev_plig_py312_site/palm_py312_site runtime and RCSB/PDBBind-style structure fixture extraction
- Next
- Production Ready. Optional hardening: expose uploaded PDB/SDF mode in UI and add cleanup for per-job source-tree intermediate graph files.
No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged AEV-PLIG source/runtime/artifacts/runner. Upstream needs Python 3.8 with CUDA PyTorch/PyG/RDKit/TorchANI/qcelemental, so a dedicated SIF is preferred over python312_slim. Code link corrected to current upstream repository. Kept Smoke Pending. 2026-07-05 18:24 +08:00 backend re-audit: no staged AEV-PLIG source/runtime/SIF/artifacts/runner found; code link remains corrected to isakvals/AEV-PLIG; dependency stack is heavy but not yet a proven storage blocker. Kept Smoke Pending. 2026-07-06 21:01 +08:00 implementation attempt: cloned isakvals/AEV-PLIG to /media/nik/seagate_nik/bio_server/tools/aev-plig/source/AEV-PLIG rev 98a28c5; source is about 725 MB and includes data/example_dataset.csv plus processed CSV assets. Upstream demo needs Python 3.8 with torch/torch-scatter/torch_geometric/RDKit/TorchANI/qcelemental and trained model name; no compatible chemistry/GNN SIF or Slurm prediction smoke exists yet. 2026-07-06 21:34 +08:00 recheck: staged source remains present, but no Python 3.8 chemistry/GNN SIF or confirmed trained model artifact path was completed; no Slurm smoke submitted. 2026-07-07 00:14 +08:00 continuation: included in next-10 Smoke Pending review; no SOP-valid direct Slurm smoke completed in this pass. Status unchanged pending the previously identified runtime/model/container blocker. 2026-07-07 00:58 +08:00 continuation: reviewed in the remaining Smoke Pending batch; no SOP-valid direct Slurm smoke completed and status remains unchanged pending the established runtime/model/container blocker. 2026-07-07 01:16 +08:00 continuation: confirmed bundled trained ensemble files model_GATv2Net_ligsim90_fep_benchmark_0..9.model (each 30,303,716 bytes) and staged a small aev_plig_py312_site layer with torch-geometric 2.5.3, torchani 2.2.4, qcelemental 0.28.0, biopandas 0.4.1, and setuptools, reusing shared palm_py312_site torch 2.4.1+cpu and RDKit 2026.03.3. Source imports pass. Direct Slurm job 483 reached RDKit processing but failed because the staged clone lacks upstream example_database SDF/PDB files referenced by data/example_dataset.csv (e.g. data/example_database/3ao4.sdf). Kept Smoke Pending. 2026-07-07 03:24 +08:00 continuation: backend recheck confirmed source rev 98a28c515be6df63a7a7bc7c3a84ea0de5904599, data/example_dataset.csv, trained ensemble files, and staged runtime remain present, but data/example_database is still absent; no real SDF/PDB benchmark structures available to rerun process_and_predict.py. Kept Smoke Pending. 2026-07-07 04:31 +08:00 promotion: built a real one-row RCSB-derived smoke fixture from AEV-PLIG's example PDB ID 3ao4 by downloading the RCSB PDB, extracting bound ligand residue 833 chain A with coordinates into data/sop_smoke_database/3ao4.sdf, and writing data/sop_smoke_3ao4.csv. Direct Slurm job 492 passed using shared python312_slim.sif plus aev_plig_py312_site and palm_py312_site, source rev 98a28c515be6df63a7a7bc7c3a84ea0de5904599, and ten bundled trained model_GATv2Net_ligsim90_fep_benchmark ensemble files (30,303,716 bytes each). Run /media/nik/seagate_nik/bio_server/runs/aev-plig/smoke_20260707_043032 produced summary.json, results.csv, input_dataset.csv, fixture.json, job.log, and Slurm logs. Prediction sanity: finite ensemble preds mean 4.745427072727273, min 3.7371862, max 5.9523234 for 3ao4_rcsb_833. Runner/API adapter remains pending. 2026-07-08T11:35:13+08:00: Production Ready promotion: backend runner API job b26cc11354fd / Slurm job 539 completed cleanly using shared python312_slim.sif, aev_plig_py312_site/palm overlays, AEV-PLIG source rev 98a28c515be6df63a7a7bc7c3a84ea0de5904599, ten bundled model_GATv2Net_ligsim90_fep_benchmark ensemble models, and the validated 3ao4 RCSB fixture. Produced zero-byte slurm.out/slurm.err, results.csv, input_dataset.csv, fixture.json, and finite preds mean 4.7454270727.