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6 changes: 3 additions & 3 deletions README.md
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@@ -1,10 +1,10 @@
# NeSI support documentation
# Mahuika support documentation

[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nesi/support-docs?quickstart=1)

[![Deploy to gh-pages](https://github.com/nesi/support-docs/actions/workflows/deploy.yml/badge.svg?branch=main&event=deployment_status)](https://github.com/nesi/support-docs/actions/workflows/deploy.yml)

This repository contains the sources files for the NeSI support documentation.
This repository contains the sources files for the Mahuika support documentation.

Rendered pages are visible at [https://docs.nesi.org.nz](http://docs.nesi.org.nz).

Expand Down Expand Up @@ -64,6 +64,6 @@ mkdocs serve -c

## Migration

Migration of the Zendesk documentation is done using our [migration pipeline (NeSI internal GitLab](https://git.hpcf.nesi.org.nz/cwal219/migratedocs).
Migration of the Zendesk documentation is done using our [migration pipeline (NeSI internal GitLab)](https://git.hpcf.nesi.org.nz/cwal219/migratedocs).

Any one off filters (e.g. don't need to be checked every time, just when converting from ZD) should go there.
2 changes: 1 addition & 1 deletion docs/Announcements/Release_Notes/index.md
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Expand Up @@ -26,4 +26,4 @@ a reference to the vendor release notes or documentation.
## REANNZ HPC services

OpenOnDemand is a recent example of a service composed of multiple
components and dependencies that NeSI maintains.
components and dependencies that REANNZ maintains.
4 changes: 2 additions & 2 deletions docs/CONTRIBUTING.md
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Expand Up @@ -19,7 +19,7 @@ tags: []
- [How to make small contributions and an introduction to pull requests](https://www.youtube.com/watch?v=ltgpwHSO2NM)
- [How to use CodeSpace for bigger changes](https://www.youtube.com/watch?v=2bHOLf2hxaA)

The primary target audience is the NeSI team.
The primary target audience is the Mahuika team.

Any changes made should be merged via a pull request.

Expand Down Expand Up @@ -252,7 +252,7 @@ Most of these are collected together in the [modules list repo](https://github.c

Fix the information in the module file.

#### NeSI Documentation Link
#### Documentation Link

Is there a child page with the same title as the module? This is case sensitive, specifically in the front matter YAML:

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4 changes: 2 additions & 2 deletions docs/Data_Transfer/Globus/Data_Transfer_using_Globus.md
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Expand Up @@ -87,12 +87,12 @@ any person who has a Globus account.

| Endpoint Name | Description | Recommended Use | Apply for Use | Contact |
| ------------- | ----------- | --------------- | ------------- | ------- |
|[NeSI HPC storage]| NeSI Globus Endpoint, located at Tamaki Data Centre | File-sharing and transferring files to/from NESI HPC and storage facilities. | [First Time Setup](./First_Time_Setup.md) | {% include "partials/support_request.html" %} |
|[NeSI HPC storage]| NeSI Globus Endpoint, located at Tamaki Data Centre | File-sharing and transferring files to/from Mahuika HPC and storage facilities. | [First Time Setup](./First_Time_Setup.md) | {% include "partials/support_request.html" %} |
| [University of Otago - HCS](https://app.globus.org/file-manager?origin_id=108e72ac-c509-4cd0-940f-b7e3aa543007), [University of Otago - CHC HCS](https://app.globus.org/file-manager?origin_id=eeb5308a-2471-4696-9571-dd2092e041f9) | Endpoint for the High Capacity Research Storage Cluster, Dunedin Campus, University of Otago and Endpoint for the High Capacity Research Storage Cluster, Christchurch Campus, University of Otago | Primary endpoint for Otago Dunedin; uses local service accounts or Globus sharing. | [Access Form](https://www.otago.ac.nz/its/forms/hcs-high-speed-data-transfer-service-access-form) | [university@otago.ac.nz](mailto:university@otago.ac.nz) |
| University of Auckland Research Data Collection | Endpoint provides access to UoA research data. | Transferring files between UoA research drives and Mahuika | Apply by email | [researchdata@auckland.ac.nz](mailto:researchdata@auckland.ac.nz) |
| AgResearch DTN01 | A Globus endpoint attached to AgResearch's institutional Linux storage platform | Sharing large datasets with external collaborators and moving large datasets between NeSI's facility and AgResearch's internal storage platform | Apply by email | [servicedesk@agresearch.co.nz](mailto:servicedesk@agresearch.co.nz) |
| PFR Globus Connect Server | Endpoint provides access to Plant Food Research data | Generally for internal users, but also for sharing large datasets with collaborators | Contact the Plant and Food person you are wanting to share data with. | |
| MWLR PN-DTN-username | Customised endpoints for users to transfer data between MWLR and NeSI, or to share data with third-party collaborators | Generally for internal users, but also for sharing large datasets with collaborators | Contact the MWLR person you are wanting to share data with. | [IToperations@landcareresearch.co.nz](mailto:IToperations@landcareresearch.co.nz) |
| MWLR PN-DTN-username | Customised endpoints for users to transfer data between MWLR and Mahuika, or to share data with third-party collaborators | Generally for internal users, but also for sharing large datasets with collaborators | Contact the MWLR person you are wanting to share data with. | [IToperations@landcareresearch.co.nz](mailto:IToperations@landcareresearch.co.nz) |
| Scion Data | Endpoint provides access to Scion research data | Sharing large datasets with external collaborators and moving large datasets between NeSI's facility and Scion's internal storage platform | Contact the Scion person you are wanting to share data with. | |
| ESR Endpoint | Endpoint provides access to ESR data | Generally for internal users, but also for sharing large datasets with collaborators | Contact the ESR person you are wanting to share data with. | |

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Expand Up @@ -6,11 +6,11 @@ tags:
title: Sync'ing with globus-automate
---

It is common to generate large amounts of simulation data on NeSI and
It is common to generate large amounts of simulation data on Mahuika and
then having to migrate the files to another computer for storage or
post-processing.

Here we show how to transfer data from NeSI to another computer
Here we show how to transfer data from Mahuika to another computer
***programmatically***, that is without using a web graphical user
interface and ***without typing your credentials each time you initiate
the transfer***.
Expand All @@ -28,7 +28,7 @@ A guest collection is directory whose content is shared via Globus.

## Step 1: Write a JSON file describing the transfer

On NeSI, create a file named `transfer_input.json` with the following
On Mahuika, create a file named `transfer_input.json` with the following
content:

``` sh
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Expand Up @@ -14,13 +14,13 @@ Before you can start submitting work you will need to connect to the cluster. Th

## Web Browser (Recommended)

### NeSI OnDemand
### Mahuika OnDemand

__OnDemand__ is a service providing access to Jupyter Notebooks, RStudio, VSCode, a Virtual Desktop, a terminal and other applications, allowing you to utilise cluster resources via the browser.

!!! tip "What next?"
- More info on
[NeSI OnDemand](../../Interactive_Computing/OnDemand/how_to_guide.md)
[Mahuika OnDemand](../../Interactive_Computing/OnDemand/how_to_guide.md)
- Visit [ondemand.nesi.org.nz](https://ondemand.nesi.org.nz/).

## Linux or MacOS
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Expand Up @@ -6,7 +6,7 @@ tags:
---

!!! prerequisite
Have your [connection to the NeSI cluster](Standard_Terminal_Setup.md) configured
Have your [connection to the Mahuika cluster](Standard_Terminal_Setup.md) configured

Some applications only accept connections from internal ports (i.e a
port on the same local network), if you are running one such application
Expand All @@ -27,10 +27,10 @@ cluster, `nesi` if you have set up your ssh config file as
described in [Standard Terminal Setup](Standard_Terminal_Setup.md).

**Remote Port:** The port number you will use on the remote machine (in
this case the NeSI cluster)
this case the Mahuika cluster)
!!! note
The following examples use aliases as set up in [standard terminal setup](Standard_Terminal_Setup.md).
This allows the forwarding from your local machine to the NeSI
This allows the forwarding from your local machine to the Mahuika
cluster, without having to re-tunnel through the lander node.

## Command line (OpenSSH)
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8 changes: 4 additions & 4 deletions docs/Getting_Started/Accessing_the_HPCs/VSCode.md
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---
created_at: 2024-08-05
description: How to set up Visual Studio Code to access the NeSI cluster
description: How to set up Visual Studio Code to access the Mahuika cluster
tags:
- ide
- vscode
- access
---

'Visual Studio Code' (not to be confused with 'Visual Studio') or 'VSCode', is a popular editor/IDE with many useful extensions.
The 'Remote' extension allows you to connect to a remote computer (like NeSI).
The 'Remote' extension allows you to connect to a remote computer (like Mahuika).

## Setup

Expand Down Expand Up @@ -67,7 +67,7 @@ The 'Remote' extension allows you to connect to a remote computer (like NeSI).

## Connecting

Under the 'Remote Explorer' Tab on the left, you should now see the NeSI machines (as well as any other machines configured in your `~/.ssh/config` file)
Under the 'Remote Explorer' Tab on the left, you should now see the Mahuika machines (as well as any other machines configured in your `~/.ssh/config` file)

![vscode explorer](../../assets/images/vscode-explorer.png)

Expand All @@ -83,7 +83,7 @@ Clicking on these will open a connection to that machine, you will then be promp

You may find that VSCode is not utilising your preferred versions of software (e.g. when debugging or linting your Python code).

As the NeSI cluster utilises [Environment Modules](../../Tutorials/Introduction_To_HPC/Environment_And_Modules.md), changing the executable used is not just a matter of changing the path in VSCode configuration, as the libraries required will not be loaded.
As the Mahuika cluster utilises [Environment Modules](../../Tutorials/Introduction_To_HPC/Environment_And_Modules.md), changing the executable used is not just a matter of changing the path in VSCode configuration, as the libraries required will not be loaded.

The only way to make sure that VSCode has access to a suitable environment, is to load the required modules in your `~/.bashrc`

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Expand Up @@ -130,4 +130,4 @@ for a single transfer'.

!!! prerequisite "What Next?"
- [Moving files to and from the cluster](../../Data_Transfer/Data_Transfer_Overview.md)
- [X11 on NeSI](./X11.md)(optional).
- [X11 on Mahuika](./X11.md)(optional).
1 change: 1 addition & 0 deletions docs/Getting_Started/FAQs/Mahuika_HPC3_Differences.md
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Expand Up @@ -5,6 +5,7 @@ status:
tags:
- hpc3
- refresh
status: deprecated
Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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medium

Avast! Ye've scrawled the 'status' mark twice in yer header. One be empty as a ghost ship on line 4, and this new one says 'deprecated'. Pick one before the YAML parser throws ye overboard for yer sloppiness! We don't need two flags for the same mast.

---

This article presents an overview comparison of the differences between the NeSI Mahuika cluster and the new cluster (often referred to in documentation under the provisional name HPC3).
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Expand Up @@ -20,4 +20,4 @@ description: How to add a new member to your project.
![Adding_Members.png](../../assets/images/Adding_Members.png)

!!! prerequisite "What Next?"
- The new team member will now be able to access your project on NeSI, provided they have also set up their NeSI account.
- The new team member will now be able to access your project on Mahuika, provided they have also set up their [my.nesi.org.nz](https://my.nesi.org.nz/) account.
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Expand Up @@ -30,7 +30,7 @@ Profile](../Creating_an_Account.md)

In case your organisation is not part of the Tuakiri federated identity
management service, a user can still [request a REANNZ HPC Account
profile.](https://my.nesi.org.nz/html/request_nesi_account) NeSI will
profile.](https://my.nesi.org.nz/html/request_nesi_account) REANNZ will
(if approved) provision a so-called "virtual home account" on Tuakiri.

See also [Account Requests for non-Tuakiri
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Expand Up @@ -6,7 +6,7 @@ tags: []
See [Applying for a project](../Projects/Applying_for_a_New_Project.md) 
for how to access the form.

## Preparing a request to use NeSI resources
## Preparing a request to use Mahuika resources

The procedures for starting a request for a new NeSI project and editing
an in-progress request (draft) that you previously started are described
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Expand Up @@ -3,7 +3,7 @@ created_at: '2022-03-31T20:51:51Z'
tags:
- mynesi
- allocation
description: How to request a NeSI allocation renewal.
description: How to request a Mahuika allocation renewal.
---

## Types of Resource Requests
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2 changes: 1 addition & 1 deletion docs/Interactive_Computing/Jupyter_Interactive_Sessions.md
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Expand Up @@ -6,7 +6,7 @@ tags:
- notebook
- ipython
- python
description: How to run an JupyterLab interactive session on the NeSI cluster.
description: How to run an JupyterLab interactive session on the Mahuika cluster.
---

# JupyterLab interactive sessions
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2 changes: 1 addition & 1 deletion docs/Interactive_Computing/Marimo_Interactive_Sessions.md
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Expand Up @@ -5,7 +5,7 @@ tags:
- Marimo
- python
- notebook
description: How to run a Marimo interactive session on the NeSI cluster.
description: How to run a Marimo interactive session on the Mahuika cluster.
---

# Marimo interactive sessions
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---
created_at: 2025-01-24
description: How to set up your own custom kernals for use on NeSI JupyterHub
description: How to set up your own custom kernels for use on Mahuika JupyterHub
tags:
- JupyterHub
- Python
Expand All @@ -11,7 +11,7 @@ tags:

## Introduction

Jupyter kernels execute the code that you write. NeSI provides a number of
Jupyter kernels execute the code that you write. Mahuika provides a number of
Python and R kernels by default, which can be selected from the Launcher.

Many packages are preinstalled in our default Python and R environments
Expand Down Expand Up @@ -106,7 +106,7 @@ Fourth, create a Jupyter kernel based on your new conda environment:
python -m ipykernel install --user --name my-conda-env --display-name="My Conda Env"
```

We must now edit the kernel to load the required NeSI environment
We must now edit the kernel to load the required environment
modules before the kernel is launched. Change to the directory the
kernelspec was installed to
`~/.local/share/jupyter/kernels/my-conda-env`, (assuming you kept
Expand Down Expand Up @@ -140,7 +140,7 @@ Launcher as "My Conda Env".
## Sharing your custom kernal with your project team members

You can also configure a shared Python kernel that others with access to
the same NeSI project will be able to load.
the same project will be able to load.

* To do this, you must make sure it also exists in a shared location
(other users cannot see your home directory).
Expand Down Expand Up @@ -169,7 +169,7 @@ python -m ipykernel install --user --name my-conda-env --display-name="My Conda
```

**Your project members** must now edit the kernel in their home directories
to load the required NeSI environment modules before the kernel is launched.
to load the required environment modules before the kernel is launched.
Change to the directory the kernelspec was installed to
`~/.local/share/jupyter/kernels/my-conda-env`, (assuming you kept
`--name my-conda-env` in the above command):
Expand Down Expand Up @@ -231,7 +231,7 @@ Now create an R Jupyter kernel based on your new conda environment:
R -e "IRkernel::installspec(name='myrwithmpfr', displayname = 'R with MPFR', user = TRUE)"
```

We must now to edit the kernel to load the required NeSI environment
We must now to edit the kernel to load the required environment
modules when the kernel is launched. Change to the directory the
kernelspec was installed to
(~/.local/share/jupyter/kernels/myrwithmpfr, assuming you kept `--name
Expand Down
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Expand Up @@ -17,13 +17,13 @@ module in your kernel or use a Conda environment.

To register a Jupyter kernel, you can follow the steps highlighted in
the [Jupyter kernels - Manual management](./Jupyter_kernels_Manual_management.md)
or use the `nesi-add-kernel` tool provided within the [Jupyter on NeSI service](https://jupyter.nesi.org.nz).
or use the `nesi-add-kernel` tool provided within the [Jupyter on Mahuika service](https://jupyter.nesi.org.nz).
This page details the latter option, which we recommend.

## Getting started

First you need to open a terminal. It can be from a session on Jupyter
on NeSI or from a regular ssh connection on Mahuika login node. If you
via OnDemand or from a regular ssh connection on Mahuika login node. If you
use the ssh option, make sure to load the JupyterLab module to have
access to the `nesi-add-kernel` tool:

Expand All @@ -39,7 +39,7 @@ follows:
nesi-add-kernel --help
```

Here is an example to add a TensorFlow kernel, using NeSI’s module:
Here is an example to add a TensorFlow kernel, using Mahuika’s module:

``` sh
nesi-add-kernel tf_kernel TensorFlow/2.8.2-gimkl-2022a-Python-3.10.5
Expand All @@ -48,7 +48,7 @@ nesi-add-kernel tf_kernel TensorFlow/2.8.2-gimkl-2022a-Python-3.10.5
!!! warning
The name given to your kernel in `nesi-add-kernel KERNEL_NAME MODULE` must only include lowercase letters, underscores, and dashes.

and to share the kernel with other members of your NeSI project:
and to share the kernel with other members of your project:

``` sh
nesi-add-kernel --shared tf_kernel_shared TensorFlow/2.8.2-gimkl-2022a-Python-3.10.5
Expand Down Expand Up @@ -117,7 +117,7 @@ nesi-add-kernel my_test_kernel Python/3.10.5-gimkl-2022a --venv my_test_venv

!!! danger

This section has not been tested on NeSI OnDemand
This section has not been tested on Mahuika OnDemand

To use a Singularity container, use the `-c` or `--container` options as
follows:
Expand Down
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