How to access the AgResearch eRI compute cluster

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

 Instructions for AgR staff access

1. 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

2. 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…

Available Applications

Modules

module spider to list the available applications as module. See also How to find and load software (aka modules)

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

4. See also Usage — Bioconda documentation (very important - unless you setup the channel priorities as described there, installations from BioConda won’t work reliably)

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.

(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.

Copy from Inscrutable to eRI login node (project folder)

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/

See also how to locate legacy (migrated) data: Accessing eRI storage | Locating legacy data

Troubleshooting

Login from Inscrutable

Expired Kerberos ticket session

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

The solution is to refresh the session using 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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