Log index — Hugging Face, Zenodo, MD production, automation
All paths below are relative to the tubulin-cppf-md repository root unless noted. Logs are append-only operational records (upload progress, gmx/mdrun launches, polling scripts). They may contain local paths and timestamps from the HPC; they should not contain secrets if you followed docs/HUGGINGFACE_DATASET.md (never paste tokens into logs or chat).
Mirror upload (revision_exec tree, minus prod trajectories)
Script: revision_exec/scripts/huggingface_upload_revision_exec_mirror.sh — uploads revision_exec/** to the dataset with preserved structure, but excludes **/prod/**/*.xtc so files already published via huggingface_upload_trajectories.sh are not duplicated. Log your run to a new revision_exec/logs/hf_mirror_revision_exec_YYYYMMDD.nohup.log and add a one-line note below.
Revision export (run_export_all.sh, Step 2 xvg)
Live logs live under revision_exec/analysis_revision/work/, which is gitignored (large/clean tree). To preserve progress in git, periodically copy the main log into revision_exec/logs/:
TS=$(date +%Y%m%d_%H%M%S)
cp -a revision_exec/analysis_revision/work/export_all_9sys.log \
"revision_exec/logs/analysis_revision_export_all_9sys_SNAPSHOT_${TS}.log"
| File | Notes |
|---|---|
revision_exec/logs/analysis_revision_export_all_9sys_SNAPSHOT_20260504_215951.log |
In-progress nine-system export (includes dimer_rep1 complete, dimer_rep2 hbond running as of snapshot time). |
revision_exec/logs/analysis_revision_dimer_rep1_export_SNAPSHOT_20260504_215951.log |
Earlier rep1-only export attempt log. |
revision_exec/logs/analysis_revision_dimer_rep1_rerun_SNAPSHOT_20260504_215951.log |
Rep1 rerun log. |
After the job finishes, take one final snapshot with the same cp -a command and commit. For Hub archival of the same files without committing huge history, use huggingface_upload_revision_exec_mirror.sh (the work/ tree uploads under revision_exec/analysis_revision/work/ on the dataset).
Hugging Face Hub (hf_*)
| File | Approx. size (order of magnitude) | Contents |
|---|---|---|
revision_exec/logs/hf_upload_nohup.log |
Large (~10 MB+) | Main batch upload under nohup; commits per file, retries, hub API chatter. |
revision_exec/logs/hf_upload_dimer_extensions_20260504.nohup.log |
~1–2 MB | Dimer extension segments upload session. |
revision_exec/logs/hf_upload_dimer_rep2_part0003_20260502.nohup.log |
sub‑MB | Rep2 part file upload slice. |
revision_exec/logs/hf_upload_monomer_beta_rep2_20260501.nohup.log |
sub‑MB | Monomer beta rep2 upload. |
revision_exec/logs/hf_poll_upload_incremental_monomers.nohup.log |
~1–2 MB | Incremental monomer polling / upload helper (hf_poll_upload_incremental_monomers workflow). |
Related repo artefacts (not in this folder)
revision_exec/scripts/huggingface_upload_trajectories.sh— canonical upload driver (--dry-run,--bundle,--create-repo).revision_exec/scripts/HF_DATASET_REPO.env.example— template forHF_DATASET_REPO.revision_exec/HF_UPLOAD_SHA256SUMS_*.txt— checksum manifests to ship alongside the Hub dataset and for Zenodo cross-reference.
Zenodo
| File | Contents |
|---|---|
revision_exec/logs/zenodo_upload_nohup.log |
Zenodo-related upload or staging log (smaller subset / metadata strategy per project policy). |
See docs/ZENODO_UPLOAD_SERVER.md when using Zenodo in parallel with Hugging Face.
MD production and GPU queue (rep*, monomer_*, auto_*, dimer_queue_*)
These logs capture mdrun / extension jobs and small shell wrappers that chain jobs after checkpoints:
rep{1,2,3}_gpu*_extend*.nohup.log— extension runs per replicate and GPU slot.monomer_*_gpu*_200ns.nohup.log— monomer 200 ns production windows.auto_start_*.log/auto_start_*.sh— automated starters after a stage completes.auto_after_*.log/auto_after_*.sh— chained “next segment” automation.dimer_queue_*.log— dimer job queue coordinator.*.pid— process id sidecars for the corresponding nohup jobs.
Use them to answer “which GPU / which day / which extension part produced this xtc?” without inferring from file dates alone.
Other
| File | Contents |
|---|---|
revision_exec/logs/complex_validation_report.txt |
Validation report (full). |
revision_exec/logs/complex_validation_report_clean.txt |
Cleaned / filtered variant for sharing. |
revision_exec/logs/gpuooo_6000q3.nohup.log |
Node- or queue-specific session. |
Maintenance
- When starting a new long upload:
nohup bash revision_exec/scripts/huggingface_upload_trajectories.sh ... > revision_exec/logs/hf_upload_YYYYMMDD_description.nohup.log 2>&1 & - Add a one-line row to the Hugging Face table above so future readers find the new file quickly.