Skip to content

Commit

Permalink
Changed filepath 'first_steps.md' to 'set_up_nci_account.md' and all …
Browse files Browse the repository at this point in the history
…references in the other files.
  • Loading branch information
atteggiani committed Aug 26, 2024
1 parent b64c95c commit 73fb5e9
Show file tree
Hide file tree
Showing 16 changed files with 24 additions and 24 deletions.
2 changes: 1 addition & 1 deletion docs/about/user_support/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ Click on the questions to unfold the answers.

Go to our [**Model Data**](/model_evaluation/data/model_catalogs) section on the ACCESS-Hive to learn how to find and access model data.

In both cases, you need to have access to the specific projects at NCI in order to read the data. For more information, check how to [**Set Up your NCI Account**](/getting_started/first_steps).
In both cases, you need to have access to the specific projects at NCI in order to read the data. For more information, check how to [**Set Up your NCI Account**](/getting_started/set_up_nci_account).

??? question "What is the difference between _teams_ and _working groups_?"

Expand Down
File renamed without changes
4 changes: 2 additions & 2 deletions docs/getting_started/are.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ ARE gives you access to NCI’s _Gadi_ supercomputer and data collections.
There are multiple applications included in ARE, but the two most used for ACCESS-related activities are [Virtual Desktop (VDI)](#vdi) and [JupyterLab](#jupyterlab).

## Prerequisites
To use ARE, you must have an NCI account and be a member of a project with computing resources (known as Service Units, or SU). For instructions on how to set up an account and join projects, see <a href="/getting_started/first_steps">Set Up and Customize your NCI Account</a>.
To use ARE, you must have an NCI account and be a member of a project with computing resources (known as Service Units, or SU). For instructions on how to set up an account and join projects, see <a href="/getting_started/set_up_nci_account">Set Up and Customize your NCI Account</a>.

## Start an ARE session
<!-- Tab labels -->
Expand Down Expand Up @@ -51,7 +51,7 @@ Hence, there are multiple [PBS directives](https://opus.nci.org.au/display/Help/

!!! warning
The specified project must have allocated _Service Units (SU)_.<br>
For more information, check [how to join relevant NCI projects](/getting_started/first_steps#join-relevant-nci-projects).
For more information, check [how to join relevant NCI projects](/getting_started/set_up_nci_account#join-relevant-nci-projects).

- **<span markdown id="storage-option">Storage</span>**<br>
`/g/data` (inserted as _gdata/&lt;project-ID&gt;_) `/scratch` (inserted as _scratch/&lt;project-ID&gt;_) data storage projects that will be available to the session.<br>
Expand Down
4 changes: 2 additions & 2 deletions docs/getting_started/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@
If you have never used NCI Gadi for ACCESS models, run through these two pages to get set up. If you already have an NCI account but have never used ARE, it is a web-based interface to Gadi that is useful for many ACCESS-related activities.

<div class="card-container">
<a href="/getting_started/first_steps" class="vertical-card aspect-ratio1to1">
<a href="/getting_started/set_up_nci_account" class="vertical-card aspect-ratio1to1">
<div class="card-image-container">
<img class="img-contain with-padding white-background" src="/assets/first_steps_logo.png" alt="Set up NCI account">
<img class="img-contain with-padding white-background" src="/assets/set_up_nci_account_logo.png" alt="Set up NCI account">
</div>
<div class="card-text-container bold">
Set Up your NCI Account
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ To run models on _Gadi_ instead, you need to join a project with computing resou
To join a project, search for it on [NCI website](https://my.nci.org.au/mancini/project-search) and request membership.

!!! tip
The first project you join will become your default one. If you would like to change this, check out [how to change your default project on Gadi](/getting_started/first_steps#change-default-project-on-gadi).
The first project you join will become your default one. If you would like to change this, check out [how to change your default project on Gadi](/getting_started/set_up_nci_account#change-default-project-on-gadi).

There are several NCI projects that may be relevant to you, depending on the tasks you want to carry out.<br>
For tasks supported by ACCESS-NRI (e.g., running a supported model configuration, using a supported model evaluation tool, etc.), you will find a list of relevant projects to join in the pages relative to each respective task.
Expand Down
2 changes: 1 addition & 1 deletion docs/model_evaluation/evaluation_on_gadi/cosima.md
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ COSIMA is the Consortium for Ocean-Sea Ice Modelling in Australia, which brings
## Getting Started

The easiest way to use the _COSIMA Cookbook_ is through the [Australian Research Environment (ARE)](https://are.nci.org.au)" on _Gadi_.<br>
To be able to access _Gadi_ you need to have an NCI account. For more information, check how to [Set Up your NCI Account](/getting_started/first_steps).
To be able to access _Gadi_ you need to have an NCI account. For more information, check how to [Set Up your NCI Account](/getting_started/set_up_nci_account).

To use the <i>COSIMA Cookbook</i> that is pre-installed in the `conda/analysis3` environment of *hh5*, you need to <a href="https://my.nci.org.au/mancini/project/hh5" target="_blank">join NCI project *hh5*</a>.

Expand Down
2 changes: 1 addition & 1 deletion docs/model_evaluation/evaluation_on_gadi/ilamb_workflow.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ ACCESS-NRI is releasing an NCI configuration of ILAMB under the name **ILAMB-wor
### Pre-requisites

<i>ILAMB</i> is provided through the `xp65` NCI projects on <i>Gadi</i>, so you need to have an NCI account and be a member of this projects to use it.<br>
To obtain an NCI account and join NCI projects, refer to how to [Set Up your NCI Account](/getting_started/first_steps).
To obtain an NCI account and join NCI projects, refer to how to [Set Up your NCI Account](/getting_started/set_up_nci_account).

Depending on your needs, you may want to also join the following supported data collections:

Expand Down
2 changes: 1 addition & 1 deletion docs/model_evaluation/index.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# Data and Model Evaluation


In this section you will find some collated information on data in the context of climate modelling which is important for model evaluation. Then there is also a collation of model evaluation tools available on *Gadi*. If you are new to using the Gadi supercomputer, visit the [Set Up your NCI Account](/getting_started/first_steps) section for instructions on how to get an account, log in, and get set up to access climate data on Gadi.
In this section you will find some collated information on data in the context of climate modelling which is important for model evaluation. Then there is also a collation of model evaluation tools available on *Gadi*. If you are new to using the Gadi supercomputer, visit the [Set Up your NCI Account](/getting_started/set_up_nci_account) section for instructions on how to get an account, log in, and get set up to access climate data on Gadi.
<!--## Prerequisites
If you are new to MED and are wondering [*"What is Model Evaluation and Diagnostics about?"*](./model_evaluation_getting_started/index.md), we recommend you read our [Getting Started with MED page](./model_evaluation_getting_started/index.md): -->
Expand Down
2 changes: 1 addition & 1 deletion docs/models/run-a-model/index.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Run a Model
If you are a new user of ACCESS climate models, please refer to how to [Set Up your NCI Account](/getting_started/first_steps).
If you are a new user of ACCESS climate models, please refer to how to [Set Up your NCI Account](/getting_started/set_up_nci_account).

If you are unsure which ACCESS model is the right choice for your experiment, take a look at the overview of [ACCESS Models](/models).

Expand Down
10 changes: 5 additions & 5 deletions docs/models/run-a-model/run-access-cm.md
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@

### General prerequisites

Before running {{ model }}, you need to [Set Up your NCI Account](/getting_started/first_steps).
Before running {{ model }}, you need to [Set Up your NCI Account](/getting_started/set_up_nci_account).

If you are unsure whether {{ model }} is the right choice for your experiment, take a look at the overview of [ACCESS Models](/models).

Expand Down Expand Up @@ -52,7 +52,7 @@ Go to the [ARE VDI](https://are.nci.org.au/pun/sys/dashboard/batch_connect/sys/d

- **Project** &rarr; a project of which you are a member.<br>
The project must have allocated _Service Units (SU)_ to run your simulation. Usually, but not always, this corresponds to your `$PROJECT`.<br>
For more information, refer to how to [Join relevant NCI projects](/getting_started/first_steps#join-relevant-nci-projects).
For more information, refer to how to [Join relevant NCI projects](/getting_started/set_up_nci_account#join-relevant-nci-projects).

- **Storage** &rarr; `gdata/access+gdata/hh5+gdata/hr22+gdata/ki32` (minimum)<br>
This is a list of all project data storage, joined by plus (`+`) signs, needed for the {{ model }} simulation. In ARE, storage locations need to be explicitly defined to access data from within a VDI instance.<br>
Expand Down Expand Up @@ -80,15 +80,15 @@ To start a new persistent session on _Gadi_, using either a login node or an ARE
persistent-sessions start <name>
```

This will start a persistent session with the given `name` that runs under your [default project](/getting_started/first_steps#change-default-project-on-gadi).<br>
This will start a persistent session with the given `name` that runs under your [default project](/getting_started/set_up_nci_account#change-default-project-on-gadi).<br>
If you want to assign a different project to the persistent session, use the option `-p`:
```
persistent-sessions start -p <project> <name>
```

!!! tip
While the project assigned to a persistent session does not have to be the same as the project used to run the {{ model }} configuration, it does need to have allocated _Service Units (SU)_.<br>
For more information, check how to [Join relevant NCI projects](/getting_started/first_steps#join-relevant-nci-projects).
For more information, check how to [Join relevant NCI projects](/getting_started/set_up_nci_account#join-relevant-nci-projects).

<terminal-window data="input">
<terminal-line>persistent-sessions start &lt;name&gt;</terminal-line>
Expand Down Expand Up @@ -262,7 +262,7 @@ For example, to run an {{ model }} suite under the `tm70` project (ACCESS-NRI),
![Rose change project example](/assets/run_access_cm/rose_change_project_are.gif){: class="example-img" loading="lazy"}

!!! warning
To run {{ model }}, you need to be a member of a project with allocated _Service Units (SU)_. For more information, check how to [Join relevant NCI projects](/getting_started/first_steps#join-relevant-nci-projects).
To run {{ model }}, you need to be a member of a project with allocated _Service Units (SU)_. For more information, check how to [Join relevant NCI projects](/getting_started/set_up_nci_account#join-relevant-nci-projects).

### Change run length and cycling frequency
{{ model }} suites are often run in multiple steps, each one constituting a cycle. The job scheduler resubmits the suite every chosen _Cycling frequency_ until the _Total Run length_ is reached.
Expand Down
4 changes: 2 additions & 2 deletions docs/models/run-a-model/run-access-esm.md
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ All {{model}} configurations are open source, licensed under [CC BY 4.0](https:/

### General prerequisites

Before running {{ model }}, you need to [Set Up your NCI Account](/getting_started/first_steps).
Before running {{ model }}, you need to [Set Up your NCI Account](/getting_started/set_up_nci_account).

### Model-specific prerequisites

Expand Down Expand Up @@ -408,7 +408,7 @@ project: lg87
If more than one project is used to run an {{ model }} configuration the `shortpath` option also needs to be uncommented and the path to the desired `/scratch/PROJECT_CODE` directory added.<br>
This ensures the same `/scratch` location is used for the _laboratory_, regardless of which project is used to run the experiment.
<br><br>
To run {{ model }}, you need to be a member of a project with allocated _Service Units (SU)_. For more information, check [how to join relevant NCI projects](/getting_started/first_steps#join-relevant-nci-projects).
To run {{ model }}, you need to be a member of a project with allocated _Service Units (SU)_. For more information, check [how to join relevant NCI projects](/getting_started/set_up_nci_account#join-relevant-nci-projects).

### Syncing output data

Expand Down
4 changes: 2 additions & 2 deletions docs/models/run-a-model/run-access-om.md
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ All {{model}} configurations are open source, licensed under [CC BY 4.0](https:/

### General prerequisites

Before running {{ model }}, you need to [Set Up your NCI Account](/getting_started/first_steps).
Before running {{ model }}, you need to [Set Up your NCI Account](/getting_started/set_up_nci_account).

### Model-specific prerequisites

Expand Down Expand Up @@ -372,7 +372,7 @@ project: ol01
If projects other than `ol01` are used to run {{ model }} configuration, then the `shortpath` field also needs to be uncommented and the path to the desired `/scratch/PROJECT_CODE` added.<br>
Doing this will make sure the same `/scratch` location is used for the _laboratory_, regardless of which project is used to run the experiment.
<br><br>
To run {{ model }}, you need to be a member of a project with allocated _Service Units (SU)_. For more information, check [how to join relevant NCI projects](/getting_started/first_steps#join-relevant-nci-projects).
To run {{ model }}, you need to be a member of a project with allocated _Service Units (SU)_. For more information, check [how to join relevant NCI projects](/getting_started/set_up_nci_account#join-relevant-nci-projects).

### Syncing output data

Expand Down
2 changes: 1 addition & 1 deletion drafts/med/model_evaluation_getting_started/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ Model Evaluation and Diagnostics (MED) of ACCESS models includes:
Here you can find information on how to access curated data stored at NCI and how to use it to evaluate specific models, such as comparing model output with observational data.

<div class="card-container">
<a href="../../getting_started/first_steps" class="vertical-card aspect-ratio1to1">
<a href="../../getting_started/set_up_nci_account" class="vertical-card aspect-ratio1to1">
<div class="card-image-container">
<img src="../../assets/model_evaluation/Gadi-19-2.jpg" alt="Computing Access" class="img-cover"></img>
</div>
Expand Down
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
# Conda Environment for Model Evaluation on Gadi

If you do not have `ssh` access to <i>Gadi</i>, refer to instructions on how to <a href="/getting_started/first_steps#login-to-gadi">login to Gadi</a>.
If you do not have `ssh` access to <i>Gadi</i>, refer to instructions on how to <a href="/getting_started/set_up_nci_account#login-to-gadi">login to Gadi</a>.

The following instructions explain how to load the curated python environment on NCI, which includes packages and scripts supported by ACCESS-NRI. Once loaded, these can be run directly on <i>Gadi</i> via `ssh`, Portable Batch System (PBS) scripts, or in JupyterLab.

???+ warning "ACCESS-NRI provides code and support, but not computing resources"
You do not automatically have access to all `/g/data/` storage on <i>Gadi</i>. You need to <a href="/getting_started/first_steps#join-relevant-nci-projects">join an NCI project</a> to view files on `/g/data/$PROJECT`.
You do not automatically have access to all `/g/data/` storage on <i>Gadi</i>. You need to <a href="/getting_started/set_up_nci_account#join-relevant-nci-projects">join an NCI project</a> to view files on `/g/data/$PROJECT`.
<br>
For model evaluation and diagnostics, you need to join projects `xp65` and `hh5` for code access and a `$PROJECT` with sufficient compute resources.

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

To have the huge amount of data from different experiments on the NCI storage at the palm of your hand, we provide a ("meta") catalog for you to query via python as part of the `#!python intake` package with our curated catalog plugin `#!python intake.cat.access_nri` .

To use this catalog, you need access to NCI's Gadi. Check out our [Getting Started with ACCESS at NCI](../model_evaluation_getting_started/first_steps.md) guide on how to get access.
To use this catalog, you need access to NCI's Gadi. Check out our [Getting Started with ACCESS at NCI](../model_evaluation_getting_started/set_up_nci_account.md) guide on how to get access.

Once logged in to Gadi, you will need to add the `#!python access-nri-catalog` to your `#!python conda` environments and start an [ARE JupyterLab Session](https://are.nci.org.au/pun/sys/dashboard). Check out our [ACCESS-NRI Intake Catalog](https://github.com/ACCESS-NRI/access-nri-intake-catalog/blob/main/docs/getting_started/index.rst) guide for the specific setup (note that you can only read in data from specific experiments if they are loaded through the *Storage* keyword).

Expand Down
2 changes: 1 addition & 1 deletion mkdocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ nav:

- Getting Started:
- getting_started/index.md
- Set Up your NCI Account: getting_started/first_steps.md
- Set Up your NCI Account: getting_started/set_up_nci_account.md
- Australian Research Environment (ARE): getting_started/are.md

- Models:
Expand Down

0 comments on commit 73fb5e9

Please sign in to comment.