Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- production_pass
- Storage
- <5
- Strategy
- shared python312_slim.sif + dynamicmpnn_py312_site overlay with Torch/PyG/Graphein runtime, staged DynamicMPNN checkpoints, and bundled benchmark PDB fixtures
- Next
- Production Ready. Optional hardening: expose custom state PDB upload mode and larger sample/batch presets after validating runtime limits.
No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged DynamicMPNN source/test data/checkpoints/artifacts/runner. Upstream full training data is >5GB, but scoped evaluation can use small test archives with shared PyTorch SIF plus overlay. Kept Smoke Pending. 2026-07-05 18:24 +08:00 backend re-audit: no staged DynamicMPNN source/test data/checkpoint/artifacts/runner found. Kept Smoke Pending. 2026-07-06 implementation attempt: cloned Alex-Abrudan/DynamicMPNN at /media/nik/seagate_nik/bio_server/tools/dynamicmpnn/source/DynamicMPNN rev 1f3e326c0f4d275ee8b3918e4726e19d3eef6c3f. Repo includes checkpoints and packaged benchmark PDB resources. Shared python312_slim.sif with existing sequence_design/proteus overlays has torch_geometric and torch_scatter but import still lacks graphein, torch_cluster, python-dotenv, beartype, einops, and loguru. No Slurm evaluation smoke submitted; kept Smoke Pending. 2026-07-06 19:30 +08:00 direct Slurm smoke passed. Job 469, run /media/nik/seagate_nik/bio_server/runs/dynamicmpnn/smoke_20260706_193000, source rev 1f3e326c0f4d275ee8b3918e4726e19d3eef6c3f. Installed missing runtime overlay pieces including torch_cluster, pyg_lib, Torch Geometric 2.6.1, Graphein runtime deps, and host-built cpdb-protein. Ran official dynamicmpnn.evaluate on bundled 1BDT/1QTG benchmark PDBs with checkpoints/multi_chain_reload.ckpt, AF3 evaluation disabled, num_samples=2, device=cpu. Artifacts: summary.json, results.csv, eval_output/samples/samples.csv, eval_output/samples/samples.fasta, manifest.json, job.log, Slurm logs. Sanity: 2 sample rows, 2 FASTA sequences, sequence length 52. Promote to Runner Adapter Pending; API/runner wiring remains next. 2026-07-08T02:10:18+08:00: Production Ready promotion: backend runner API job 4734a8e20a4d / Slurm job 535 completed cleanly using shared python312_slim.sif, dynamicmpnn_py312_site/proteusai/palm overlays, official dynamicmpnn.evaluate, bundled 1BDT/1QTG benchmark, AF3 evaluation disabled, and multi_chain_reload checkpoint. Produced zero-byte slurm.out/slurm.err, summary.json, samples.csv, samples.fasta, dynamicmpnn_manifest.json, and two 52-aa sampled sequences.