OpenFE

PaperCodeNeed >5GB

Run different free energy protocols

Readiness

Readiness: Need >5GB
Smoke: not_tested
Artifacts: not_applicable
Production: needs_materialized_openfe_apptainer_sif
Storage: >5
Strategy: Materialize official OpenFE Apptainer SIF externally or add conda/oras/docker/skopeo tooling, then run OpenFE/OpenMM/RDKit Slurm smoke.
Next: Process in the >5GB container lane: materialize official OpenFE SIF externally or provision docker/oras/skopeo/conda fallback, then run OpenFE/OpenMM/RDKit smoke.

OpenFE source/package verified: OpenFreeEnergy/openfe MIT; latest observed v1.12.0 commit 97bef39 released 2026-06-29, conda-forge 1.12.0 updated 2026-06-30. Official HPC install path recommends Apptainer/Singularity image oras://ghcr.io/openfreeenergy/openfe:<version>-apptainer. Singularity/Slurm/GPU available, but python312_slim lacks openfe/openmm/rdkit. Official Apptainer pull for 1.11.1-apptainer failed once with network reset and retry was interrupted/killed; no image acquired and no Slurm smoke. 2026-07-05 SOP recheck: shared python312_slim lacks openfe/openmm/rdkit; official OpenFE Apptainer pull previously failed/interrupted; no image, runner, or Slurm smoke exists. Kept Smoke Pending. 2026-07-05 SOP batch recheck: shared python312_slim lacks openfe/openmm/rdkit; official OpenFE Apptainer pull previously failed/interrupted; no image, runner, or Slurm smoke exists. Kept Smoke Pending. 2026-07-05 18:19 +08:00 backend re-audit: OpenFE evidence/cache/smoke folders exist (~4.8 MB) but no OpenFE/OpenMM/RDKit SIF or direct Slurm smoke exists; shared python312_slim remains insufficient. Agents agreed Smoke Pending remains correct. 2026-07-06 21:34 +08:00 continuation: official OpenFE Apptainer pull for tag 1.12.0-apptainer failed with MANIFEST_UNKNOWN. Anonymous GHCR tag listing requires auth. A guarded latest-apptainer pull began downloading but did not complete within the timeout and left no SIF; no OpenFE/OpenMM smoke submitted. 2026-07-06 23:06 +08:00 continuation: retried official OpenFE `latest-apptainer` ORAS pull from ghcr.io/openfreeenergy/openfe for 600 seconds; tag exists and download began, but layer transfer reset with `connection reset by peer` before a SIF was written. No OpenFE/OpenMM smoke submitted. 2026-07-07 00:58 +08:00 continuation: retried official OpenFE `latest-apptainer` ORAS pull for a bounded 12 minutes; GHCR transfer again failed before SIF materialization with HTTP/2 PROTOCOL_ERROR. No OpenFE/OpenMM/RDKit smoke submitted. 2026-07-07 01:16 +08:00 continuation: reviewed in 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 03:24 +08:00 continuation: retried official GHCR `latest-apptainer` ORAS pull for 900 seconds. Transfer again failed before SIF materialization with connection reset while writing layer; no OpenFE/OpenMM/RDKit smoke submitted. Kept Smoke Pending. 2026-07-07 04:32 +08:00 continuation: official GHCR/latest-apptainer SIF still absent after repeated transfer failures; primary OpenFE docs recommend Apptainer/Singularity for HPC, so promotion still requires a materialized OpenFE SIF plus OpenFE/OpenMM/RDKit Slurm smoke. Kept Smoke Pending. 2026-07-07 15:26 +08:00 implementation attempt: bounded implementation retry tested exact official tags 1.11.1-apptainer and latest-apptainer with isolated APPTAINER_CACHEDIR/APPTAINER_TMPDIR. Both Singularity pulls failed before SIF materialization with GHCR HTTP/2 PROTOCOL_ERROR while writing image layers. Backend has no micromamba/conda/oras/skopeo/docker fallback, so no OpenFE/OpenMM/RDKit Slurm smoke was possible. Kept Smoke Pending. 2026-07-07 15:32 +08:00 final Smoke Pending triage: reclassified from Smoke Pending to Production Blocked. Official OpenFE source/install path is known, but exact backend blocker is persistent: official 1.11.1-apptainer and latest-apptainer pulls fail before SIF materialization with GHCR HTTP/2 transfer errors, and backend lacks micromamba/conda/oras/skopeo/docker/podman fallback. No OpenFE/OpenMM/RDKit Slurm smoke can be submitted until image/tooling is available. 2026-07-10T22:37:32+08:00 continuation recheck: no materialized OpenFE SIF or fallback docker/oras/skopeo/conda path is available; official GHCR transfers remain the blocker before OpenFE/OpenMM/RDKit smoke can run. 2026-07-10T22:55:53+08:00 SOP reclassification: moved from Production Blocked to Need >5GB because blocked on large official Apptainer image/container acquisition, not code wiring.