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Note

Applicable to participants in the Early Access Program (EAP) only!In order to use the compute resources you need an account. Please request an account before connecting https://nznesi.atlassian.net/wiki/spaces/eRI/pages/2715779396/How+do+I+get+help#Via-the-support-portal.

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.

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Instruction for NeSI staff access

See NeSI internal documentation

\uD83D\uDCD8 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 connect

  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…

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

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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 https://bioconda.github.io/ Usage — Bioconda documentation (very important - unless you setup the channel priorities as described there, installations from BioConda won’t work reliably)

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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.

Code Block
breakoutModewide
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 (project folder)

Code Block
breakoutModewide
scp -r /home/username/my-data username@agresearch.co.nz@login-0.eri.agresearch.co.nz:/home/agresearch.co.nz/username/my-dataagr/persist/projects/XXXX-abc_defghijklm

Copy from NeSI Mahuika to eRI login node

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