Readiness
- Readiness
- Need >5GB
- Smoke
- not_tested
- Artifacts
- not_applicable
- Production
- needs_atomsurf_builder_sif_with_deltaconv
- Storage
- >5
- Strategy
- shared python312_slim.sif + tool ext3 overlay
- Next
- Process in the >5GB builder/runtime lane: build/transfer AtomSurf SIF with CMake/compiler/libcurl, complete deltaconv submodules, compile deltaconv, then rerun Slurm smoke.
AtomSurf source staged from Vincentx15/atomsurf rev e4ba27616f80fcd6a2b5a62dc160d67daa548fc4; MIT license; size ~59 MB. Existing python312_slim plus shared site-packages can import torch 2.12.1+cu130, torch_geometric 2.8.0, esm 2.0.0, and top-level atomsurf, but functional imports fail due missing compiled torch_sparse and NumPy ABI warnings. No Slurm smoke submitted; no heavy install duplicated. 2026-07-05 SOP triage: AtomSurf source is staged and small, but current shared Python/Torch/PyG path only reaches partial imports; functional imports fail due missing compatible compiled torch_sparse and NumPy ABI warnings. No direct Slurm smoke or runner exists. Reclassified from Smoke Pending to Production Blocked until compatible compiled runtime is built. 2026-07-09T17:42:30+08:00 SOP blocked implementation attempt: partially unblocked the Python/Torch/PyG stack by staging /media/nik/seagate_nik/bio_server/tools/atomsurf/py312_pyg_site with torch_sparse 0.6.18+pt24cpu, torch_scatter 2.1.2+pt24cpu, torch_cluster 1.6.3+pt24cpu, torch_spline_conv 1.2.2+pt24cpu, pyg_lib 0.4.0+pt24cpu, fair-esm 2.0.0, libigl 2.5.1, robust-laplacian 1.1.0, potpourri3d 1.4.0, plyfile, trimesh, pdb2pqr, hydra-core 1.3.2, and omegaconf 2.3.0. Import probes now load torch, torch_geometric, torch_sparse, torch_scatter, torch_cluster, pyg_lib, and atomsurf under python312_slim.sif. Direct Slurm attempts 635-638 progressed from missing esm to missing igl to missing deltaconv. deltaconv 1.0.2 is source-only and failed to build in the slim SIF because a builder-capable CMake/setuptools/compiler environment is not available inside the runtime. Keep Production Blocked until a Python 3.8/3.10 or builder-capable AtomSurf SIF with deltaconv is built, then rerun the bounded surface/graph/model benchmark. 2026-07-10T17:43:52+08:00 SOP blocked build recheck: retried deltaconv 1.0.2 build for AtomSurf under shared python312_slim.sif with staged py312_pyg_site. Binding host cmake failed inside the slim container because libcurl.so.4 was missing; using the staged Python cmake package did not expose a cmake executable on PATH, and deltaconv still failed at build_ext with 'CMake must be installed'. Logs: /media/nik/seagate_nik/bio_server/tools/atomsurf/artifacts/deltaconv_build_probe_20260710_174228.log and deltaconv_build_probe_20260710_174256_wheelcmake.log. Keep Production Blocked pending a builder-capable AtomSurf SIF/container with CMake/compiler/runtime libraries. 2026-07-10T22:37:32+08:00 continuation attempt: retried AtomSurf deltaconv from recursive git source to resolve prior missing Eigen/CMake issues. Clone reached deltaconv submodules but stalled during Eigen/geometry-central submodule acquisition, and no compiled deltaconv wheel/import was produced. Remaining blocker is still a builder-capable AtomSurf SIF/container with CMake/compiler/runtime libs and vendored/available deltaconv submodules. 2026-07-10T22:55:53+08:00 SOP reclassification: moved from Production Blocked to Need >5GB because needs dedicated builder-capable PyTorch/PyG/deltaconv container rather than small runner wiring.