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38 changes: 19 additions & 19 deletions docs/models/run-a-model/build_a_model.md
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ The instructions below outline how to build an ACCESS model using the build-from
This build workflow is specifically designed to run on the [National Computating Infrastructure (NCI)](https://nci.org.au/about-us/who-we-are) supercomputer [_Gadi_][gadi].


As an example, in the following instrutions we will show how to build a modified [mom5 component](/models/model_components/ocean/#mom5) for [ACCESS-ESM1.5](/models/configurations/access-esm/#access-esm15). All other components and packages (i.e., dependencies) will remain the same as the official [ACCESS-ESM1.5 release]({{esm1_5_build_config}}).
As an example, in the following instructions we will show how to build a modified [mom5 component](/models/model_components/ocean/#mom5) for [ACCESS-ESM1.5](/models/configurations/access-esm/#access-esm15). All other components and packages (i.e., dependencies) will remain the same as the official [ACCESS-ESM1.5 release]({{esm1_5_build_config}}).

!!! tip
The instructions below remain valid (with simple tweaks) for any model or package.
Expand All @@ -30,7 +30,7 @@ If you are looking for information on how to run a model, refer to the [Run a Mo
To set up _Spack_ on _Gadi_, refer to [Set up Spack for building ACCESS models]({{spack_setup}}).

## Navigate into your Spack directory
Navigate into the directory where you cloned the _Spack_ repositories during [Spack's setup]({{spack_setup}}#create-a-directory-for-spack).<br>
Navigate into the directory where you cloned the _Spack_ repositories during the [Spack setup]({{spack_setup}}#create-a-directory-for-spack).<br>
The suggested directory is `/g/data/$PROJECT/$USER/spack/0.22`:
```
cd /g/data/$PROJECT/$USER/spack/0.22
Expand All @@ -39,7 +39,7 @@ cd /g/data/$PROJECT/$USER/spack/0.22
## Enable spack

!!! warning
This step needs to be carried out for any new login or new shell
This step needs to be carried out for any new login or new shell environment

To add the `spack` command to your shell, as well as other settings, run:
```
Expand All @@ -51,13 +51,13 @@ To add the `spack` command to your shell, as well as other settings, run:

## Create a Spack development environment

_Spack_ has [environments](https://spack.readthedocs.io/en/latest/environments.html) that, in some ways, are similar to _Conda_ environments or _Python_ virtual environments: they create an isolated operating environment where _Spack_ can only see and access specific packages. This allows to build and deploy new packages in a coherent fashion.
_Spack_ has [environments](https://spack.readthedocs.io/en/latest/environments.html) that are, in some ways, similar to _Conda_ environments or _Python_ virtual environments: they create an isolated operating environment where _Spack_ can only see and access specific packages. This allows the build and deployment of new packages in a coherent fashion.

_Spack_ environments are located inside `/g/data/$PROJECT/$USER/spack/0.22/environments`, each in a separate directory. Each environment configuration is defined within its directory using the [`spack.yaml`](https://spack.readthedocs.io/en/latest/config_yaml.html#config-yaml) file.
{: id="spack-environment-folder"}

!!! warning
_Spack_ environments' location can be changed within _Spack_ configuration files and the directory specified above represents the default location for a _Spack_ instance that has been set up following [Spack's setup instructions]({{spack_setup}}).
_Spack_ environments' location can be changed within _Spack_ configuration files and the directory specified above represents the default location for a _Spack_ instance that has been set up following the [Spack setup instructions]({{spack_setup}}).

### Create the environment

Expand Down Expand Up @@ -86,7 +86,7 @@ spack env create mom5_dev ACCESS-ESM1.5/spack.yaml
The newly-created `mom5_dev` _Spack_ <b>environment folder</b> is `/g/data/$PROJECT/$USER/spack/0.22/environments/mom5_dev`.

### Activate the environment
To activate the `mom5_dev` _Spack_ environment run:
To activate the `mom5_dev` _Spack_ environment, run:
```
spack env activate -p mom5_dev
```
Expand All @@ -97,14 +97,14 @@ spack env activate -p mom5_dev

## Compile Spack environment packages (optional)

It is always good to first compile all the packages in the newly created _Spack_ environment as is (without changing).
It is recommended to first compile all the packages in the newly created _Spack_ environment as is without making any changes.

Compiling all the packages present in a _Spack_ environment is referred to as [installing the environment](https://spack.readthedocs.io/en/latest/environments.html#installing-an-environment).

### Concretize the Spack environment
[Concretizing](https://spack.readthedocs.io/en/latest/environments.html#concretizing) the _Spack_ environment is necessary to force _Spack_ to update its knowledge of all the packages (their specs) within the environment.

To concretize the `mom5_dev` environment run:
To concretize the `mom5_dev` environment, run:
```
spack concretize -f --fresh
```
Expand Down Expand Up @@ -174,14 +174,14 @@ spack concretize -f --fresh

### Install the Spack environment

To compile the packages in the `mom5_dev` environment run:
To compile the packages in the `mom5_dev` environment, run:
```
spack install
```

!!! tip
It takes 30-40 mins to compile all the packages for the first time.<br>
However, subsequent installations will re-use the built dependencies, therefore the total compilation time will be reduced.
It takes 30-40 minutes to compile all the packages for the first time.<br>
Subsequent installations, however, will compile quicker as the built dependencies are reused.

<terminal-window>
<terminal-line data="input" directory="[mom5_dev]">spack install</terminal-line>
Expand Down Expand Up @@ -302,10 +302,10 @@ This is done through the [`spack develop`](https://spack.readthedocs.io/en/lates

### Mark package as a development package

There are in general two cases that influence the command to run to mark a package as "in development", depending on the state of the package's source code:
There are, in general, two cases that influence the command to run to mark a package as "in development", depending on the state of the package's source code:

1. [The new source code already exists](#case1)
2. [The new source code does not exist yet](#case2)
2. [The new source code does not yet exist](#case2)

#### Case 1. The new source code already exists {: id='case1'}
If the new source code for the development package already exists in the filesystem (this also includes cases when the new source code is in a `git` repo that can be cloned), to mark a package as "in development" we will need two things:
Expand Down Expand Up @@ -364,7 +364,7 @@ develop:
The source code is automatically copied inside the [environment's folder](#spack-environment-folder).

!!! warning
As you might notice, differently from [Case 1](#case1), there is no `path` specification inside the `develop` portion of the `spack.yaml` environment configuration file.<br>
As opposed to [Case 1](#case1), there is no `path` specification inside the `develop` portion of the `spack.yaml` environment configuration file.<br>
This means that _Spack_ automatically expects to find the source code inside the [environment's folder](#spack-environment-folder).

## Compile modified Spack environment packages
Expand All @@ -376,7 +376,7 @@ spack concretize -f --fresh
spack install
```
!!! warning
Even though the `spack install` command this time will only build the development package, it might still take a long time to complete, depending on the specific package.
Although this time the `spack install` command will only build the development package, it might still take a long time to complete, depending on the specific package.

<terminal-window lineDelay=0>
<terminal-line data="input" lineDelay=200 directory="[mom5_dev]">
Expand Down Expand Up @@ -511,7 +511,7 @@ All compiled packages will be placed in directories having the following format:
For instances of _Spack_ on _Gadi_ you should ignore the **system** scope.

!!! tip
For the _Spack_ instance obtained through the [Spack's setup instructions]({{spack_setup}}), `$(prefix)` corresponds to the `/g/data/$PROJECT/$USER/spack/0.22/spack` directory.
For the _Spack_ instance obtained through the [Spack setup instructions]({{spack_setup}}), `$(prefix)` corresponds to the `/g/data/$PROJECT/$USER/spack/0.22/spack` directory.

For the example above, `mom5_dev` _Spack_ environment's configuration file (`spack.yaml`) contains the following lines that fall in the **environment** scope:
```yaml
Expand All @@ -522,11 +522,11 @@ config:
!!! tip
`$spack` refers to the `$(prefix)` directory above.

This means the packages that we just built in this example can be found under `/g/data/$PROJECT/$USER/spack/0.22/spack/../restricted/ukmo/release/<architecture>/<compiler>/<package-name>`.
This means the packages built in this example can be found in `/g/data/$PROJECT/$USER/spack/0.22/spack/../restricted/ukmo/release/<architecture>/<compiler>/<package-name>`.

## Troubleshooting build errors

Sometimes you might get errors while compiling the packages.<br>
Sometimes you might encounter errors while compiling the packages.<br>
_Spack_ prints out the error message and generates a full build log that can be viewed by the user. The location of the build log is shown at the end of the error message.

For example, if we try to install the `mom5_dev` environment with an error in the new `mom5` source code (in this example a `use` statement in the `<new-mom5-source-code-folder>/src/accessom_coupler/ocean_solo.F90` file has been purposely commented out to force an error in compilation), we might get an output error similar to the following:
Expand All @@ -541,7 +541,7 @@ See build log for details:
<span class="red">==></span> Error: access-esm1p5-git.2024.05.1=2024.05.1-aysea5r7rbwy22lluvl64baperlokktv: Package was not installed
<span class="red">==></span> Error: Installation request failed. Refer to reported errors for failing package(s).</code></pre>

In this case the error might be obvious already from the error message but, for more information, the build log can be examined.
If the error is not obvious from the error message, see the build log for more information.

<custom-references>
- [https://spack.readthedocs.io/en/latest/](https://spack.readthedocs.io/en/latest/)
Expand Down
2 changes: 1 addition & 1 deletion docs/models/run-a-model/run-access-cm.md
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Expand Up @@ -6,7 +6,7 @@
!!! warning
**Important for _accessdev_ users!**<br>
If you were an _accessdev_ user, make sure you are a member of [hr22](https://my.nci.org.au/mancini/project/hr22/join) and [ki32](https://my.nci.org.au/mancini/project/ki32/join) projects.<br>
Then, refer to instructions on how to [Set up persistent session worflow for {{ model }}]({{ '#set-up-%s-persistent-session'%model.lower() }}), and how to [port suites from accessdev](#port-suites-from-accessdev).
Then, refer to instructions on how to [Set up persistent session workflow for {{ model }}]({{ '#set-up-%s-persistent-session'%model.lower() }}), and how to [port suites from accessdev](#port-suites-from-accessdev).

## Prerequisites

Expand Down

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