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Operational Guidance

Session Requirement

Run all operations in resilient sessions:

tmux new -s parkit
# or
screen -S parkit

Open OnDemand graphical sessions are also accepted. projark enforces this for both deposit and retrieve. Disclaimer: Open OnDemand is currently available only on Biowulf compute nodes, not directly on Helix. Since projark is Helix-only today, use tmux/screen on Helix; Open OnDemand support is future-facing until Helix access is available.

Scratch Paths

Default staging/retrieval base:

/scratch/$USER/CCBR-<projectnumber>/

Datatype subfolders (Analysis/Rawdata) are managed automatically.

Split Threshold

projark deposit supports configurable split threshold/chunk size:

projark deposit ... --split-size-gb 500

Default is 500 GB.

Cleanup Policy

  • Default: cleanup enabled after successful deposit.
  • To retain artifacts: --no-cleanup.

Logging and Notifications

  • projark logs include ISO 8601 timestamps.
  • On completion/failure, projark deposit and projark retrieve send email to $USER@nih.gov.
  • Notification sender is NCICCBR@mail.nih.gov.
  • projark ls and parkit ls do not send email and require no session/gate checks.

HPC-DME Configuration

  • Proxy settings (hpc.server.proxy.url, hpc.server.proxy.port) must be commented out in $HPC_DM_UTILS/hpcdme.properties. projark deposit checks this and aborts with an error if active proxy lines are found.
  • After the preflight checks, projark deposit prints the active lines from hpcdme.properties so you can verify configuration before the transfer begins.

Dot-File Exclusion

Hidden files (filenames starting with .) are automatically excluded from dm_register_directory during deposit. This prevents shell per-directory history files and other hidden files from being registered to HPC-DME.

Temp File Isolation

dm_* CLI commands produce response files (e.g. *.tmp) that are now isolated inside a per-call temporary directory and automatically deleted after each command. No temp files accumulate in your working directory.

DME Search Index Lag

The HPC-DME search index used by projark ls and parkit ls can lag up to 60 minutes behind a recent deposit. If newly deposited files do not appear in ls output, wait and retry.