• In progress

    • Getting started on AgResearch eRI

    Owned by Rina
    Last updated: 22-08-2024 by Matt Bixley
    3 min read

    Work in Progress: active data transfer/staging is still happening in the background. Hence, not all of your datasets will have read/write access at this point in time.
    We are referring to this process as the “cutover process”. Please raise a request to clarify the status for your dataset.

    Getting started

    When making the move over to eRI, there is some information you can provide or have thought about to help smooth the process.

    • New AgResearch staff (or those who have not used the existing, legacy HPC) planning to utilise the compute resources, will need a username created and home directory (/home/agresearch.co.nz/username) provisioned.

    • Do you have legacy data that needs to move (be cutover)? this could take some time and requires activation by AgResearch.

      • Background: Most data has been transferred from the legacy HPC to the new eRI HPC already. Any data that has not been migrated will not readable/writeable until it has been cut over. This ensures both data sets remain in sync.

      • Please make a request to support@cloud.nesi.org.nz

    • Do you need a new dataset/project (with compute allocation) created or will you be accessing another workspace?

      • If you are unsure what the difference between a dataset and a project is, check out the frequently asked questions page for more information.

      • Go to ColdFront at https://coldfront.eri.agresearch.co.nz/, a self-service tool that allows you to set up a project, apply for a share of compute resources and perform administrative tasks such as managing other project members and checking the progress of the project all in one place. For more information about this tool and how to connect to it, click here.

      • Important: when setting up a new project, you need to give it a title following the format yyyy-nameofproject, for example, 2077-micetrial.

      • If you experience difficulty getting set up with ColdFront, you can reach out for more support by emailing NeSI’s support desk.

    • How do I know if there is already data or a project?

    • What software/version might you need?

    • Finally, NeSI also offers regular online office hour sessions, hosted via Zoom. These sessions are open to anyone - you don't need to be an existing NeSI user. Information on when the next office hour will be hosted is here.

    Logging in

    • OPTIONAL: If working from outside the AgResearch local network, connect to AgR VPN
      (or Inscrutable or Iramohio first: e.g. connect via a Terminal application:
      ssh inscrutable.agresearch.co.nz)
      See also Connecting to the eRI compute cluster from Windows
      Once logged on, continue to

    • Connect to an eRI login node:
      ssh username@agresearch.co.nz@login-0.eri.agresearch.co.nz
      (or login-1) enter your password if prompted

    • List the contents of your sandbox project folder:
      ls -la /agr/persist/projects/XXXX-abc_defghijklm

    • List the contents of your scratch folder:
      ls -la /agr/scratch/projects/XXXX-abc_defghijklm

    • Change into the scratch location:
      cd /agr/scratch/projects/XXXX-abc_defghijklm

    • More technical details are given here on how to connect to the AgResearch HPC from your computer.

    Accessing storage resources

    Every AgResearch user can access the storage. Some datasets have tighter access restrictions.
    Please raise a request to clarify the access permissions for your dataset.

    See https://nznesi.atlassian.net/wiki/spaces/eRI/pages/2712272946

    Accessing compute resources

    Compute access is currently handled via a service request.

    https://nznesi.atlassian.net/wiki/spaces/eRI/pages/2789834787

    Accessing Open Ondemand (OOD)

    Browser Access - https://ondemand.eri.agresearch.co.nz/

    Login - one of several formats will work for the login

    first.last@agresearch.co.nz

    userid@agresearch.co.nz THIS IS MOST LIKELY TO WORK

    agresearch\userid

    Password - your AgResearch password

    Authentication

    How to get help?

    https://nznesi.atlassian.net/wiki/spaces/eRI/pages/2715779396