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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).

NeSI staff access

  1. First copy the following SSH host configs. You can rename the login nodes I named them eri-X as their true hostnames are generic login-X:

Host bastion
   User nesi-support
   Hostname 163.7.177.182
   ServerAliveInterval 300
   ServerAliveCountMax 2

Host eri-0
   User USER
   Hostname 10.29.107.20
   ProxyCommand ssh -W %h:%p bastion
   ServerAliveInterval 300
   ServerAliveCountMax 2
   #ForwardX11 yes
   #ForwardX11Trusted yes

Host eri-1
   User USER
   Hostname 10.1.112.21
   ProxyCommand ssh -W %h:%p bastion
   ServerAliveInterval 300
   ServerAliveCountMax 2

  1. Second, send one of your public keys to someone that already has access so they can add it to: 

/home/nesi-support/.ssh/authorized_keys

  1. Login to one of the eri login nodes with passwd provided by platforms and I recommend adding your personal pubkey auth to avoid passwords altoghether, eg from Mahuika:

$ ssh-copy-id -i ~/.ssh/mypubkey.pub eri-0

\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)
    See also Connecting to the eRI compute cluster from Windows

  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. Start working…

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

Installed Applications

Modules

module spider to list the available applications as module.

Conda

Conda is installed but needs to be enabled:

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

  2. Run conda init bash

  3. Run source ~/.bashrc

Singularity

Available as Apptainer and aliasing enabled, meaning both apptainer --version and singularity --version will work.

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 how to locate legacy (migrated) data: 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 utilise Kerberos authentication using your AgResearch domain credentials from the login session of the workstation/laptop.
If it doesn’t work you will be prompted to authenticate using your AgResearch AD password.

SSH Key-Based Authentication

Key-based authentication is supported as well. Make sure to use the supported format:
username@agresearch.co.nz@login-0.eri.agresearch.co.nz for the username@host part.

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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