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 temporary. Also, that you are on the AgResearch local network (LAN) when attempting to connect. Further, one would need to be a member of a project in order to have access to both a project (data/storage) folder as well as a scratch (compute) 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).
Instruction for NeSI staff access
See NeSI internal documentation
\uD83D\uDCD8 Instructions for AgR staff access
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 WindowsOnce logged on, continue to connect to an eRI login node:
ssh username@agresearch.co.nz@login-0.eri.agresearch.co.nz
(orlogin-1) enter your password if promptedList the contents of your sandbox project folder:
ls -la /agr/persist/projects/XXXX-abc_defghijklmList the contents of your scratch folder:
ls -la /agr/scratch/projects/XXXX-abc_defghijklmChange into the scratch location:
cd /agr/scratch/projects/XXXX-abc_defghijklmStart working…
While other datasets or projects might be visible, please do not attempt to modify them during this phase of data staging/migration.
Available Applications
Copying data
scp can be used to copy data to/from the login node.
(Before copying data, please check whether what you need is already there - all legacy HPC datasets should be accessible via the familiar /dataset paths, and legacy home directories under eRI home directories in legacy-hpc, which should be treated as readonly, since it will get overridden when changes are made on legacy home.)
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
Copy from NeSI Mahuika to eRI login node
How to copy data between NeSI Mahuika and AgR eRI
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.