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Uploading from cnt1 to Pennsieve

Shared with the CNT

This procedure runs on infrastructure the lab and the CNT operate together. The CNT manual keeps its own copy; changes to the shared steps are agreed with the CNT.

What this page tells you

To upload from CNT1: ssh to bscsub then CNT1, run 'module load pennsieve', complete the config wizard with your API token/secret, verify with whoami, 'pennsieve dataset use N', create a manifest for the CNT1 folder, and upload it. Page contains an API token/secret.

Credential removed

A password or key that appeared in the original text has been removed. Get it from the lab password manager, never from a wiki page.

Uploading from CNT1 to Pennsieve

  1. Open Terminal
  2. SSH into the BSC cluster
    • Command: ssh USER@bscsub.pmacs.upenn.edu
    • Example: ssh <pennkey>@bscsub.pmacs.upenn.edu
  3. SSH into CNT1
    • Once on BSC, log in to CNT1 with ssh USER@CNT1
  4. Load and configure the Pennsieve agent, or run the ./pennsieve_setup.sh script to do it (the setup script's companion page was not migrated)
    • Load the module: module load pennsieve
    • Start the config wizard: pennsieve config wizard
    • In a separate terminal, get your secret and token with this command: cat .pennsieve/config.ini
    • Enter the api_token and api_secret from your own .pennsieve/config.ini (they are personal; never paste them into a wiki page)
    • Create a new profile and name it as you wish
    • Confirm with 'Y'
  5. Verify the Pennsieve login
    • Command: pennsieve whoami
    • Make sure it returns your Pennsieve username
  6. Identify the dataset number
    • Log in to Pennsieve and find the dataset node ID (N) you want to use
  7. Select the dataset
    • Command: pennsieve dataset use N
  8. Create a manifest for your folder
    • Command: pennsieve manifest create "cnt1 folder name"
    • Example: pennsieve manifest create "/project/rns/NYU_Neuropace/"
  9. Upload the manifest
    • Command: pennsieve upload manifest # (replace # with the manifest ID)
  10. (Optional) View the command history
    • Command: history