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Applicable to participants in the Early Access Program (EAP) only!

The instructions below assume that you already have an user account in AgResearch Active Directory and your password is not temporar. Also, that you are on the AgResearch local network (LAN) when attempting to connect. Further, one would need to be a member of project in order to have access to both a project folder as well as a scratch folder.

To connect your local machine to the eRI cluster a Secure Shell (SSH) connection needs to be established. If you are using a Unix-like operating system like MacOS or Linux this can be achieved simply using the inbuilt terminal. Windows users must make use of an SSH client (e.g. WSL, PuTTY, MobaXterm).

\uD83D\uDCD8 Instructions

  1. 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)

  2. 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

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

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

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

  6. Run export PATH=/agr/persist/apps/miniconda/bin:$PATH

  7. Run conda init bash

  8. Run source ~/.bashrc

  9. Start working…

While other datasets or projects might be visible, please do not attempt to modify them during this phase of data staging/migration.

Copying data

scp can be used to copy data to/from the login node.

Copy from eRI login node to Inscrutable

Login to Inscrutable and then, for example:
copy a file from the user home on the eRI login node to the user home on Inscrutable.

scp username@agresearch.co.nz@login-0.eri.agresearch.co.nz:/home/agresearch.co.nz/username/slurm-94.out /home/username/slurm-94.out

Copy from Inscrutable to eRI login node

scp -r /home/username/my-data username@agresearch.co.nz@login-0.eri.agresearch.co.nz:/home/agresearch.co.nz/username/my-data

Accessing other data

Datasets are located at /agr/persist/datasets/

Most datasets are still being actively copied! Please let support know if you need access to a specific dataset.

See also https://nznesi.atlassian.net/wiki/spaces/eRI/pages/2712272946/Accessing+eRI+storage#Locating-legacy-data

Troubleshooting

Login from Inscrutable

The default authentication method is set to Kerberos authentication. If it doesn’t work you will be prompted to authenticate using a password.

Expired Kerberos ticket session

In case of an expired or no valid Kerberos authentication session, running klist will output something like:

inscrutable$ klist
klist: No credentials cache found (filename: /tmp/krb5cc_1292_D5QPAU)

The solution is to refresh the session using kinit

inscrutable$ kinit

enter your password when prompted and verify with klist that there is a krbtgt with expiration date in the future listed.

Support

How do I get help? lists the various options to contact the help desk for the AgResearch eRI.

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