ROSHAMBO

5-30 minutesPaperCodeNeed >5GB

Molecular shape comparison and similarity scoring

Readiness

Readiness: Need >5GB
Smoke: not_tested
Artifacts: not_applicable
Production: needs_cuda_rdkit_inchi_builder_sif
Storage: >5
Strategy: Build ROSHAMBO CUDA/RDKit/INCHI SIF on a machine with privileged/fakeroot Singularity or Docker, then transfer SIF for Slurm tiny-SDF smoke.
Next: Process in the >5GB CUDA/container lane: build/transfer roshambo_cuda_rdkit.sif with nvcc and RDKit C++/INCHI, then run tiny SDF similarity smoke.

No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged ROSHAMBO source/RDKit/CUDA SIF/artifacts/runner. Upstream requires compiled RDKit with INCHI and CUDA, so python312_slim is not the right base; still a bounded tiny-SDF smoke candidate after dedicated SIF staging. Kept Smoke Pending. 2026-07-05 18:24 +08:00 backend re-audit: no staged ROSHAMBO source, RDKit/CUDA SIF, artifacts, or runner found; no object-store smoke evidence. Kept Smoke Pending. 2026-07-06 21:01 +08:00 implementation attempt: cloned molecularinformatics/roshambo to /media/nik/seagate_nik/bio_server/tools/roshambo/source/roshambo rev 916fe97. Upstream setup.py requires RDBASE/RDKIT_INCLUDE_DIR/RDKIT_LIB_DIR/RDKIT_DATA_DIR and CUDA_HOME, RDKit built with INCHI, and CUDA compilation for PAPER kernels; shared python312_slim.sif has no such RDKit/CUDA build, so no Slurm similarity smoke was submitted. 2026-07-06 21:34 +08:00 recheck: staged source remains present, but no CUDA/RDKit 2023.03.1 + INCHI compiled SIF exists; no similarity 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: 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: backend inventory still lacks a dedicated roshambo_cuda_rdkit.sif with CUDA and RDKit INCHI build/runtime; no tiny SDF similarity Slurm smoke could be run. Kept Smoke Pending. 2026-07-07 04:32 +08:00 continuation: source remains staged but no roshambo_cuda_rdkit.sif exists; primary ROSHAMBO README requires compiled RDKit with INCHI enabled and matching Python plus CUDA build before a valid similarity smoke. Kept Smoke Pending. 2026-07-07 15:26 +08:00 implementation attempt: source rev 916fe97f81a3fdb48e7bb85384eb597836d2b01e was rechecked. setup.py hard-fails without RDBASE, RDKIT_INCLUDE_DIR, RDKIT_LIB_DIR, RDKIT_DATA_DIR, and CUDA_HOME, and compiles CUDA/C++ PAPER extension sources. Existing palm/chembl Python RDKit wheels include rdinchi for Python use but do not provide the required RDKit C++ header/lib build plus CUDA_HOME/nvcc SIF. No SOP-valid similarity smoke was possible. Kept Smoke Pending. 2026-07-07 15:32 +08:00 final Smoke Pending triage: reclassified from Smoke Pending to Production Blocked. Source rev 916fe97f81a3fdb48e7bb85384eb597836d2b01e is staged and Python RDKit/rdinchi imports work, but upstream setup.py requires RDKit C++ headers/libs and CUDA_HOME/nvcc to compile CUDA/C++ extensions. Singularity fakeroot/mount namespace is unavailable on backend, so the required SIF cannot be built in-place; no valid similarity smoke can run until a dedicated SIF is built/transferred. 2026-07-10T22:37:32+08:00 continuation recheck: still lacks CUDA_HOME/nvcc plus RDKit C++ headers/libs with INCHI in a buildable SIF. Python RDKit wheels remain insufficient for upstream CUDA/C++ extension build. 2026-07-10T22:55:53+08:00 SOP reclassification: moved from Production Blocked to Need >5GB because requires CUDA/RDKit C++/INCHI build container; Python wheels are insufficient.