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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
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 connectConnect 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…
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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. |
Available Applications
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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:
Run
export PATH=/agr/persist/apps/miniconda/bin:$PATHRun
conda init bashRun
source ~/.bashrcSee 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.
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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.
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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)
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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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