@@ -37,13 +37,13 @@ Numerous organisations and scientific groups worldwide have adopted a file forma
### NetCDF metadata
-
Metadata, which is typically described as
information about the data, enables users of data from different sources to decide which quantities are comparable. This facilitates building applications with powerful extraction, regridding and display capabilities.
+Metadata, which is typically described as information about the data, enables users of data from different sources to decide which quantities are comparable. This facilitates building applications with powerful extraction, regridding and display capabilities.
To facilitate this process, there are
conventions for Climate and Forecast metadata. These are designed to promote the processing and sharing of
NetCDF files. The conventions define metadata that provide a definitive description of what the data in each variable represents, and the spatial and temporal properties of the data.
### NetCDF data and variables
-Data in a
netCDF file is stored in the form of arrays, where each
netCDF dimension has a name and a length.
+Data in a
NetCDF file is stored in the form of arrays, where each
NetCDF dimension has a name and a length.
For example, temperature variation over time at a fixed location is stored as a one-dimensional array, whereas temperature over a region (i.e. varying location) at a fixed time is stored as a two-dimensional array. Thus, three-dimensional (3D) data would be temperature varying with time over a region, and four-dimensional (4D) data would be temperature varying with time over a region with varying altitude.
@@ -70,7 +70,7 @@ Our Model Evaluation and Diagnostics tools are based on the reading and storing
For more information, refer to a
quick overview of xarray and
xarray tutorials.
-`xarray` is a python package avaliable through the `conda` environment on NCI.
+`xarray` is a python package avaliable through the conda environment on NCI.
Hence, you can either use it directly (as shown below) or through the dataset capabilities of the [ACCESS-NRI Model Intake Catalog Tool](../../model_evaluation_model_catalogs/index.md).
diff --git a/docs/model_evaluation/model_evaluation_model_catalogs/index.md b/docs/model_evaluation/model_evaluation_model_catalogs/index.md
index 69a7efd0e..2f77a8691 100644
--- a/docs/model_evaluation/model_evaluation_model_catalogs/index.md
+++ b/docs/model_evaluation/model_evaluation_model_catalogs/index.md
@@ -24,21 +24,21 @@ The ACCESS-NRI Intake catalog enables users to find products that satisfy their
A simple use case of the ACCESS-NRI Intake catalog is a user wants to plot a timeseries of a variable from a specific data product.
-For example, the user is interested in plotting a scalar ocean variable called
temp_global_ave for an [ACCESS-ESM1-5](/models/configurations/access-esm) run called `HI_CN_05` (data product), which is an historical run using the same configuration as CMIP6 ACCESS-ESM1.5 historical `r1i1p1f1`, but with phosphorus limitation disabled within CASA-CNP.
+For example, the user is interested in plotting a scalar ocean variable called
temp_global_ave for an [ACCESS-ESM1.5](/models/configurations/access-esm) run called
HI_CN_05 (data product). This is an historical run using the same configuration as CMIP6 ACCESS-ESM1.5 historical
r1i1p1f1, except that the phosphorus limitation within
CASA-CNP is disabled.
-First we load the catalog using
+First, load the catalog as follows:
```python
import intake
catalog = intake.cat.access_nri
```
-To see all the available catalogs, simply prompt
+To see all available catalogs, run:
```
catalog
```
-Now we can load and plot available datasets of the variable "temp_global_ave" from the product "HI_CN_05" using
+Now you can load and plot available datasets for the
temp_global_ave variable of the
HI_CN_05 data product as follows:
```python
import matplotlib.pyplot as plt
diff --git a/docs/model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models.md b/docs/model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models.md
index bed729fd1..9029bd8bd 100644
--- a/docs/model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models.md
+++ b/docs/model_evaluation/model_evaluation_model_catalogs/model_evaluation_search_models.md
@@ -1,8 +1,8 @@
-# Search for a model in the ACCESS-NRI intake Catalog
+# Search for a model in the ACCESS-NRI Intake catalog
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/index.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/first_steps.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).
diff --git a/docs/model_evaluation/model_evaluation_on_gadi/index.md b/docs/model_evaluation/model_evaluation_on_gadi/index.md
index 17f0a33a6..bce9227f8 100644
--- a/docs/model_evaluation/model_evaluation_on_gadi/index.md
+++ b/docs/model_evaluation/model_evaluation_on_gadi/index.md
@@ -1,7 +1,6 @@
-# Model Evaluation on Gadi/NCI
-
-At the moment, we are providing support for an the following model evaluation frameworks on Gadi/NCI:
+# Model Evaluation on Gadi
+ACCESS-NRI currently provides support for the following model evaluation frameworks on
Gadi:
-The best way to get our help is by raising an issue on the
community forum with tags `help` and another tag for the specific framework.
-
-In the future, we are also aiming to support a broader range of frameworks and recipes which are currently not supported (see [our community resource lists](../../community_resources/community_med/index.md) for this collection).
\ No newline at end of file
+
+
+In future, ACCESS-NRI aims to support a broader range of frameworks and recipes that are currently not supported, but are listed in
Community Resources.
\ No newline at end of file
diff --git a/docs/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool.md b/docs/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool.md
index 79c5a2918..76e15a240 100644
--- a/docs/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool.md
+++ b/docs/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool.md
@@ -1,13 +1,16 @@
-# Tutorial for using `esmvaltool` on Gadi@NCI
+# Tutorial for using ESMValTool on Gadi
-`esmvaltool` is the Earth System Model Evaluation Tool.
+## What is ESMValTool?
+The Earth System Model Evaluation Tool (
ESMValTool) is a climate model diagnostics and evaluation software package to better understand the causes and effects of model biases and inter-model spread.
-???+ warning "Support Level: Supported on Gadi, but not owned by ACCESS-NRI"
-
- ESMValTool is a community-developed climate model diagnostics and evaluation software package.
+???+ warning "Support Level: Supported on
Gadi, but not owned by ACCESS-NRI"
- ACCESS-NRI does not own the code of ESMValTool, but actively supports the use of ESMValTool on Gadi.
- ACCESS-NRI provides access to the latest version of ESMValTool via the `xp65` access-med conda environment deployed on NCI-Gadi.
+
ESMValTool is a community-developed climate model diagnostics and evaluation software package. While ACCESS-NRI does not own the code, it actively supports the use of
ESMValTool software on
Gadi. ACCESS-NRI provides access to the latest version of
ESMValTool via the `xp65` `access-med`
conda environment for Model Evaluation on Gadi.
+
+
+The
ESMValTool mainly focuses on evaluating results from the Coupled Model Intercomparison Project (CMIP) ensemble.
+
+For more information, refer to the official
ESMValTool documentation.
-## About ESMValTool
-
-The Earth System Model Evaluation Tool (ESMValTool) is a community-development that aims at improving diagnosing and understanding of the causes and effects of model biases and inter-model spread. The ESMValTool mainly focus on evaluating results from the Coupled Model Intercomparison Project (CMIP) ensemble. The goal is to build a common framework for the evaluation of Earth System Models (ESMs) against observations available through the Earth System Grid Federation (ESGF) in standard formats (obs4MIPs) or made available at ESGF nodes.
-
-More information on ESMValTool scope is available in the extensive
ESMValTool documentation.
-
-ACCESS-NRI provides access to the latest version of ESMValTool via the `xp65` access-med conda environment deployed on NCI-Gadi.
-Our plan is to routinely run benchmarks and comparisons of the ACCESS models CMIP submissions. We will also provide support for running recipes on NCI-Gadi.
+## Using ESMValTool on Gadi
-## Running `esmvaltool` on Gadi
+
ESMValTool is provided through the `xp65` `access-med`
conda environment for Model Evaluation on Gadi.
+
+ACCESS-NRI plans to routinely run benchmarks and comparisons of CMIP submissions for ACCESS models, as well as providing support to run
ESMValTool recipes on
Gadi.
-#### Pre-requisites
+### Pre-requisites
-NCI Projects requires to run the set of ESMValTool recipes:
+To run
ESMValTool recipes, you need to be a member of the following NCI projects:
-- xp65, ct11, fs38, oi10, rr3, al33, rt52, zz93, qv56
-
-
-#### Load the `access-med` conda environment
+- `xp65`, `ct11`, `fs38`, `oi10`, `rr3`, `al33`, `rt52`, `zz93` and `qv56`.
+### Running ESMValTool recipes
+
+To load the the `access-med` conda environment, execute the following commands:
```
module use /g/data/xp65/public/modules
module load conda/access-med
```
-#### What recipes are available?
+To list which
ESMValTool recipes are available on
Gadi, run:
```
esmvaltool recipes list
```
-#### Details of a recipe
+To find out details of a specific `recipe_name.yml`, execute:
```
esmvaltool recipes show recipe_name.yml
```
-#### Running an recipe yourself
+To execute `recipe_name.yml` and automatically download the required climate data to the default directory, run:
```
esmvaltool run examples/recipe_python.yml --search_esgf=when_missing
```
-
-## Support
-
-ACCESS and NCI-Gadi users can get help from ACCESS-NRI for running their recipe on Gadi via Github Issue on the
ESMValTool-Workflow github repository or by opening a thread on the
ACCESS-Hive Forum.
-
-General support for ESMValTool (non-specific to NCI-Gadi) can be found in
ESMValTool Discussions page where users can open an issue and a member of the User Engagement Team of ESMValTool will reply as soon as possible. This is open for all general and technical questions on the ESMValTool: installation, application, development, or any other question or comment you may have.
-
-### Recipes and diagnostics
-
-Contacts for specific diagnostic sets are the respective authors, as listed in the corresponding
recipe and diagnostic documentation and in the source code.
-
-The current status of ESMValTool recipes for the `xp65` conda environment is available
here
-
-## License
-
-The ESMValTool is released under the Apache License, version 2.0. Citation of the ESMValTool paper (“Software Documentation Paper”) is kindly requested upon use, alongside with the software DOI for ESMValTool (doi:10.5281/zenodo.3401363) and ESMValCore (doi:10.5281/zenodo.3387139) and version number:
-
-> Righi, M., Andela, B., Eyring, V., Lauer, A., Predoi, V., Schlund, M., Vegas-Regidor, J., Bock, L., Brötz, B., de Mora, L., Diblen, F., Dreyer, L., Drost, N., Earnshaw, P., Hassler, B., Koldunov, N., Little, B., Loosveldt Tomas, S., and Zimmermann, K.: Earth System Model Evaluation Tool (ESMValTool) v2.0 – technical overview, Geosci. Model Dev., 13, 1179–1199, https://doi.org/10.5194/gmd-13-1179-2020, 2020.
-
-Besides the above citation, users are kindly asked to register any journal articles (or other scientific documents) that use the software at the ESMValTool webpage (http://www.esmvaltool.org/). Citing the Software Documentation Paper and registering your paper(s) will serve to document the scientific impact of the Software, which is of vital importance for securing future funding. You should consider this an obligation if you have taken advantage of the ESMValTool, which represents the end product of considerable effort by the development team.
+The `--search_esgf=when_missing` option tells
ESMValTool to search for and download the necessary climate data files from Earth System Grid Federation (ESGF), if they cannot be found locally.
## ESMValTool recipe examples
-To find the available recipes, please go see the
ACCESS ESMValTool Worflow recipe status
+A list of
ESMValTool recipes available on
Gadi can be found on the
ACCESS-NRI MED ESMValTool Workflow GitHub repository. Some example recipes are provided below:
-Below we showcase example recipes from `esmvaltool` that we are providing to run on Gadi:
@@ -110,6 +88,27 @@ Below we showcase example recipes from `esmvaltool` that we are providing to run
+
ACCESS-Hive is an initiative of the 
+
+ 
+ 
+ 
+ 
+ 
+ 
-
-We highly appreciate any contributions received from our community and do our best to engage the wider community through shared 
+ 
+ 
+ 
+ 
+ 
next to your current tab).
+ 
+ 
+ 
in the 
+ 
\ No newline at end of file
+
diff --git a/docs/model_evaluation/model_evaluation_getting_started/index.md b/docs/model_evaluation/model_evaluation_getting_started/index.md
index 9be25276e..ff07c0ded 100644
--- a/docs/model_evaluation/model_evaluation_getting_started/index.md
+++ b/docs/model_evaluation/model_evaluation_getting_started/index.md
@@ -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.
diff --git a/docs/models/index.md b/docs/models/index.md
index abf10f781..58ddcd285 100644
--- a/docs/models/index.md
+++ b/docs/models/index.md
@@ -9,7 +9,7 @@ ACCESS models are computer codes comprising complex mathematical representations
## Supported ACCESS Model Configurations
-
diff --git a/docs/models/model_components/ocean.md b/docs/models/model_components/ocean.md
index 26702917f..4a1e3c35c 100644
--- a/docs/models/model_components/ocean.md
+++ b/docs/models/model_components/ocean.md
@@ -11,8 +11,8 @@ MOM is an open source development by a consortium of scientists across several g
There are 2 MOM versions currently used in ACCESS models: 
+ 
-
+ 
+ 
.
+To ensure that your suite is run under the correct NCI project for which you are a member, edit the Compute project field in suite conf → Machine and Runtime Options, and click the Save button 
.
+
+ 
+ 
+
+ 
+ 
- 
+ 
+ 
+ 
+ 
+ 
+ 