Test include-markdown in Run CM2

docs/models/run_a_model/rose_cylc.md → docs/includes/rose_cylc.md

@@ -8,14 +8,19 @@
 ## About
 The _Rose/Cylc_ workflow management tool consists of two components:
 
-* The [_Cylc_](https://niwa.co.nz/environmental-information/cylc-suite-engine) (pronounced ‘silk’) task engine, developed by the New Zealand National Institute of Water and Atmospheric Research (NIWA). Cylc is a workflow manager that automatically executes tasks according to the model's configuration. It also monitors all tasks, reporting any errors that may occur.
-* The [_Rose_](https://www.metoffice.gov.uk/research/approach/modelling-systems/rose) framework developed by the UKMO which configures tasks for the _Cylc_ engine. Rose is a toolkit that can be used to view, edit and run some of the [ACCESS models](/models/access_models).
+<!--about-rose-cylc-start-->
+
+* The [_Cylc_](https://cylc.github.io/cylc-doc/7.8.8/html/index.html) (pronounced ‘silk’) task engine, developed by the New Zealand National Institute of Water and Atmospheric Research - NIWA (now Earth Sciences NZ). Cylc is a workflow manager that automatically executes tasks according to the model's configuration. _Cylc_ controls how the job will be run and manages the time steps of each model component. It also monitors all tasks, reporting any errors that may occur.
+* The [_Rose_](https://metomi.github.io/rose/doc/html/index.html) framework, developed by the UKMO which configures tasks for the _Cylc_ engine. Rose is a toolkit that can be used to view, edit and run some of the [ACCESS models](/models/access_models).
 
 A set of tasks configured by _Rose_ to run with the _Cylc7_ engine is called a _suite_. Every _suite_ has a unique identifier called `suite-ID` in the form `u-LLNNN`, where `L` is a letter and `N` is a number (e.g., u-ab123).
 
+<!--about-rose-cylc-end-->
 
 ## Prerequisites
 
+<!--nci-and-mosrs-account-start-->
+
 - **NCI account**<br>
     Before running an ACCESS model, you need to [Set Up your NCI Account](/getting_started/set_up_nci_account).
 
@@ -27,6 +32,8 @@ A set of tasks configured by _Rose_ to run with the _Cylc7_ engine is called a _
     !!! warning
         The waiting time to obtain a MOSRS account can be up to 3 weeks.
 
+<!--nci-and-mosrs-account-end-->
+
 - **Join NCI projects**<br>
     Join the following projects by requesting membership on their respective NCI project pages:
 
@@ -36,6 +43,8 @@ A set of tasks configured by _Rose_ to run with the _Cylc7_ engine is called a _
 
 ## Connecting to Gadi
 
+<!--connecting-to-gadi-until-vdi-storage-start-->
+
 You can run _Rose/Cylc_ either from a [_Gadi_ login node](#connect-via-gadi-login-node) or via an [ARE VDI session](#launch-are-vdi-desktop). 
 
 ### Connect via Gadi login node
@@ -65,9 +74,13 @@ 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 [_SU_](https://opus.nci.org.au/spaces/Help/pages/236881132/Allocations...). By default, this will be set to your default project `$PROJECT`.
 
+<!--connecting-to-gadi-until-vdi-storage-end-->
+
 - **Storage** &rarr; `gdata/hr22+scratch/$PROJECT` (minimum)<br>
     The storage folders listed above are the minimum required to run _Rose/Cylc_.
 
+<!--connecting-to-gadi-after-vdi-storage-start-->
+
 Launch the ARE session and, once it starts, click on _Launch VDI Desktop_.
 
 ![Launch ARE VDI session example](/assets/run_access_cm/launch_are_vdi.gif){: class="example-img" loading="lazy"}
@@ -78,11 +91,17 @@ Once the new tab opens, you will see a Desktop with a few folders on the left. C
 
 ![Open ARE VDI terminal example](/assets/run_access_cm/open_are_vdi_terminal.gif){: class="example-img" loading="lazy"}
 
+<!--connecting-to-gadi-after-vdi-storage-end-->
+
 
 ## Set up a persistent session
 
+<!--persistent-session-start-->
+
 NCI provides a service called [_persistent sessions_](https://opus.nci.org.au/spaces/Help/pages/241926895/Persistent+Sessions) to enable long running processes, like _Cylc_, to stay active even when the user disconnects from _Gadi_.
 
+You will need to start a persistent session in order to run {{ model }}.
+
 It is recommended to have only one active persistent session at any given time, as multiple _Cylc_ sessions can use the same persistent session.
 
 Note that persistent sessions are terminated during the quarterly maintenance at NCI and will need to be restarted afterwards. The new persistent session can be given the same name as used previously.
@@ -163,19 +182,38 @@ persistent-sessions kill <persistent-session-uuid>
 !!! warning
     When you terminate a _persistent session_, any model running on that session will stop. Therefore, you should check whether you have any active model runs before terminating a _persistent session_.
 
+<!--persistent-session-end-->
+
 ## Set up Rose/Cylc
 
+
+
 ### Rose and Cylc executables
 
+<!--rose-cylc-executables-start-->
+
 Make the `rose` and `cylc` executables available by loading the _Cylc_ module:
 
 ```
 module use /g/data/hr22/modulefiles
 module load cylc7
 ```
 
+<terminal-window data="input">
+    <terminal-line>module use /g/data/hr22/modulefiles</terminal-line>
+    <terminal-line>module load cylc7</terminal-line>
+    <terminal-line data="output">Using the cylc session &lt;name&gt;.&lt;$USER&gt;.&lt;project&gt;.ps.gadi.nci.org.au</terminal-line>
+    <terminal-line data="output"></terminal-line>
+    <terminal-line data="output">Loading cylc7/24.03</terminal-line>
+    <terminal-line data="output">&emsp;Loading requirement: mosrs-setup/2.0.1</terminal-line>
+</terminal-window>
+
+<!--rose-cylc-executables-end-->
+
 ### MOSRS Authentication
 
+<!--mosrs-auth-start-->
+
 The ACCESS models which use _Cylc_ require a connection to the MOSRS mirror on _Gadi_. To connect to this mirror, you must first authenticate your MOSRS credentials with:
 
 ```
@@ -196,6 +234,8 @@ This will request the username and password you received when you created your M
 
 After the first authentication, you will need to run `mosrs-auth` every 24 hours and for every new connection to _Gadi_ (e.g., new terminal) to verify your password against the saved credentials.
 
+<!--mosrs-auth-end-->
+
 ## Get the model configuration
 
 Depending on the specific model, its configuration will be hosted either on _GitHub_ or MOSRS. The [Run a Model](/models/run_a_model/) documentation for the respective model will specify where the configuration is stored.<br>

docs/models/access_models/access-cm.md

@@ -2,9 +2,13 @@
 
 ![ACCESS CM model](/assets/model-config-logos/configurations-without-titles/access-cm.png){: class="img-contain white-background round-edges with-padding intro-img" loading="lazy"}
 
+<!--cm2-description-start-->
+
 The ACCESS Coupled Model (ACCESS-CM) is a fully-coupled global climate model that includes [atmosphere](/models/model_components/atmosphere), [aerosols and atmospheric chemistry](/models/model_components/aerosols_atmospheric_chemistry), [land](/models/model_components/land), [ocean](/models/model_components/ocean) and [sea ice](/models/model_components/sea-ice) components, linked together by a [coupler](/models/model_components/coupler).<br>
 It produces physical climate simulations.
 
+<!--cm2-description-end-->
+
 {% set model = "ACCESS-CM2" %}
 
 ## {{ model }}