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Getting Started

Platform Scope

  • Supported environment: Helix or Biowulf.
  • projark workflows are Helix-focused and enforce host checks.

Activate Environment

If mamba is already in your PATH, run:

mamba activate /vf/users/CCBR_Pipeliner/db/PipeDB/miniforge3/envs/parkit

If mamba is not already in your PATH, add the following block to your ~/.bashrc or ~/.zshrc:

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'mamba shell init' !!
export MAMBA_EXE='/vf/users/CCBR_Pipeliner/db/PipeDB/miniforge3/bin/mamba';
export MAMBA_ROOT_PREFIX='/vf/users/CCBR_Pipeliner/db/PipeDB/miniforge3';
__mamba_setup="$("$MAMBA_EXE" shell hook --shell zsh --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__mamba_setup"
else
    alias mamba="$MAMBA_EXE"  # Fallback on help from mamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<

Then run:

mamba activate /vf/users/CCBR_Pipeliner/db/PipeDB/miniforge3/envs/parkit

Required Environment

  • HPC_DME_APIs repository should be available locally. Follow this setup guide: https://ccbr.github.io/HowTos/docs/HPCDME/setup.html
  • HPC_DM_UTILS must resolve to <HPC_DME_APIs>/utils.
  • HPC_DM_JAVA_VERSION is auto-set on Helix/Biowulf if missing. Minimum required value is 23 (as of today).

Sync Preflight

Before archival/retrieval runs:

parkit checkapisync

If out of sync:

parkit syncapi

projark runs this check automatically and blocks if not synced.

Session Safety

Run all operations inside tmux, screen, or an Open OnDemand graphical session:

tmux new -s parkit
# or
screen -S parkit

projark deposit and projark retrieve enforce this check. 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.