The ACCESS-Hive is made available under the Creative Commons Attribution +license. The following is a human-readable summary of +(and not a substitute for) the full legal text of the CC BY 4.0 +license.
+You are free to:
+for any purpose, even commercially.
+The licensor cannot revoke these freedoms as long as you follow the +license terms.
+Under the following terms:
+
ACCESS-Hive is an initiative of the Australian Earth-System Simulator (ACCESS-NRI).
+If you encounter problems/bugs about the content of ACCESS-Hive or you want to contribute, check how to contribute.
+Check the User Support page if you need help, and for information on what is supported and by whom.
+Join the ACCESS-Hive Community Forum and find previous related discussions about the hive or the resources listed here, or start your own and make contacts with your community.
+"Contact" image source: Image by pch.vector on Freepik ↩
+This documentation is written in Markdown format and is based on the Material for MkDocs theme, which is built on top of MkDocs static site generator.
+
+For a quick reference on how to use Markdown syntax you can refer to the Markdown Cheat Sheet.
All contributions need to have an associated Github issue that explains the content and importance of the contribution.
+
+To raise an issue, create a New Issue in the ACCESS-Hive Github repository issue page. Feel free to assign that issue to yourself if you intend to work on it.
After raising a Github issue about your contribution, you need to fork the ACCESS-Hive Github repository.
+For cloning the forked repository onto your local computer, we encourage you to first add your local SSH keys to your GitHub profile.
+To start with, if you have an existing SSH key, then simply add this key to your github account, and you are all set to clone the repository. In case you don't have the SSH keys set up on your local computer, it's easy to create a new SSH key locally, and then feel free to link this key to your github account.
+After cloning the repository locally, create a new branch to make your local changes and then push it to GitHub:
+Work locally on the branch spongebob/fix-hive-title-issue-234, and push the commits using the commands:
While working on a local branch, please make sure to regularly pull changes from the remote main into your local branch, as follows:
This would make sure that the local branch spongebob/fix-hive-title-issue-234 is always in sync with the latest changes in the remote main branch.
MkDocs includes a live preview server, so you can preview your changes as you write your documentation. The server will automatically rebuild the site upon saving.
+To build the site locally, you need to install Material for MkDocs and other plugins. You can find a ful list in the requirements.txt file (in the root of the ACCESS-Hive GitHub repository). Please use pip for the installation as some of the packages are not updated or not available on conda:
To start the server, open terminal and navigate to your ACCESS-Hive local repository and use the command:
+Your documentation will be built on http://127.0.0.1:8000. Open this URL in your browser to see a preview of the documentation. The URL is given in the terminal when running the mkdocs serve command. Make sure you keep the command running so as to see live updates on saving your modifications.
Once the changes on your local branch spongebob/fix-hive-title-issue-234 are ready to be integrated with the development branch, create a pull request and GitHub will automatically build a preview of the documentation using GitHub Actions.
After a PR is created and tested, feel free to ask for reviews by tagging the ACCESS-Hive/reviewers team and reply if any changes are being requested in the PR.
+
ACCESS-Hive is an open user portal which hosts the documentation relevant to the Australian Community Climate and Earth System Simulator (ACCESS) community.
+Contributions are encouraged from any member of the community regarding any aspect of the ACCESS-Hive user portal.
+
+ "How to contribute" sample image source: Image by pch.vector on Freepik ↩
+"Contribute to github?" sample image source:Image by vectorjuice on Freepik ↩
+
+ 
+ 
+ 
+ The Hive forum is a place for the ACCESS Community to come together, share ideas, organise and plan shared activities.
+You can start a new discussion topic on the Hive Forum in just 3 simple steps:
+Register to the ACCESS-Hive Forum
+Create a new topic for your request
+How to write a good help request?
+ Tag the request with the label help
After a discussion topic is posted on the forum, the ACCESS-NRI and community experts will respond with the relevant information by following a 5-step process, as below:
+ ACCESS-NRI monitors the topics tagged with help keyword on a regular basis.
After a request is received, we will let you know within 1 working day if the request is in scope.
A helper will then follow the in scope, help request through to a resolution.
You will receive a progress update at least once a week.
+Request is solved.
+
On this page we answer frequently asked questions (FAQs), and also give additional information for support, in case your question is not yet answered.
+Click on the questions to unfold the answers.
+ACCESS-Hive is the open portal where ACCESS-NRI provides documentation for the ACCESS user community. +The Hive forum is the place where the ACCESS user community and its scientific working groups can exchange ideas and provide support. +
A model component (sometimes referred to simply as component) is a codebase that is typically compiled into a single executable. It usually runs independently and communicates with other components via a coupler.
+We refer to model as a general descriptive name for a particular combination of model components. +For example, ACCESS-CM2 has 3 major model components: atmosphere (including land), ocean, and sea-ice. By contrast, ACCESS-OM2 has 2 major model components: ocean and sea-ice, with the atmospheric forcing provided by a data source.
+A model configuration is a model (as described above) with a specific configuration (e.g. version, set of parameters) for each of its components.
+A run is when a model configuration is executed, usually on an HPC system.
+An experiment typically consists of one or multiple separate sequential runs, with each run picking up where the previous one finished.
+So experiment and run can sometimes be used as synonyms, but at other times an experiment consists of many runs that are linked by passing model state from one run to the next.
+Climate science - like all science - is based on the comparison of different models and hypothesis with observational data. We provide or support the frameworks to perform such comparisons as part of the model evaluation. The different model hypotheses, or more practically speaking model experiments, are created by executing different model configurations with different setups; for example by perturbing initial conditions or by adding new physical prescriptions to the models. +
A "control experiment" (sometimes also called a "control run") is an experiment that is designed to be used as a comparison against which perturbation experiments can be compared.
+Control experiments are typically designed to represent some neutral climate state. For example, pre-industrial control experiments are designed to represent a modern climate state without significant anthropogenic climate forcing (global warming).
+Control experiments are ideally well equilibrated, so that the model doesn't systematically change (often referred to as "drift").
+Control experiments are important because it is an enormous saving in resources if one control experiment can be used by many researchers. It also means researchers can compare their perturbation experiments against not just the control run, but against each other.
+A perturbation experiment is when a model configuration from a control experiment is altered in some way. The altered configuration is then run, restarting from a point in the control experiment.
+The perturbation experiment is run in the same way as the control, each successive run using the state (restarts) from the previous run. The perturbation experiment can then be compared with the control experiment to see the effect of the perturbation.
+Perturbation experiments are a very important way to try and understand complex earth systems, e.g. to isolate potential climate change signals and try and understand their effects.
+Both observational and model DATA is hosted by the National Computational Infrastructure (NCI) under different projects.
+Go to our Observational Data section on the ACCESS-Hive to learn how to find and access observational data.
+Go to our Model Data section on the ACCESS-Hive to learn how to find and access model data.
+In any case, you need to have access to the specific projects and NCI itself in order to read the data. We explain this on our Getting Started Pages.
+Throughout this documentation, we use the term teams to describe ACCESS-NRI's internal employees.
+By contrast, we refer to working groups as the groups of the ACCESS community that work on specific ACCESS components, configurations or research topics. These working groups are formed by the scientific community itself, with ACCESS-NRI liaising between them.
+Consider asking for help on the ACCESS-Hive Forum. For content supported by ACCESS-NRI a team member will provide support. For other content, a fellow member of the community might be able to help.
+For further information on what assistance is available on the forum please visit the forum's Help and Support Page. There is also a Forum Support FAQ covering some of the more common questions you might have about what support is provided, how it is provided and what you can expect.
+ + +The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the contributing guidelines below for how to make contributions to the Hive page content. You can also open an issue highlighting any content you’d like us to provide but aren’t able to contribute yourself.
+Here, we collate lists of useful tools for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our ACCESS-NRI Model Evaluation pages, the information below is not supported by ACCESS-NRI unless stated otherwise.
+Please let us know, if we are missing an important tool. Check How To Contribute to get in touch.
+|
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+Dataset+ |
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+Description+ |
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+ CMOR is used to produce CF-compliant netCDF files. The structure of the files created by CMOR and the metadata they contain fulfill the requirements of many of the climate community’s standard model experiments (which are referred to here as “MIPs” and include, for example, AMIP, PMIP, APE, and IPCC scenario runs).
+
++ Documentation | + Source Code + |
+
| + + | +
+
+ The APP4 is a CMORisation tool designed to convert ACCESS model output to ESGF-compliant formats, primarily for publication to CMIP6. The code was originally built for CMIP5, and was further developed for CMIP6-era activities. It uses CMOR3 and files created with the CMIP6 data request to generate CF-compliant files according to the CMIP6 data standards.
+
++ Documentation | + Source Code + |
+
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+ ACCESS-Archiver
+
+ |
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+
+ The ACCESS Archiver is designed to archive model output from ACCESS simulations. It's focus is to copy ACCESS model output from its initial location to a secondary location (typically from `/scratch` to `/g/data`), while converting UM files to netCDF, compressing MOM/CICE files, and culling restart files to 10-yearly. Saves 50-80% of storage space due to conversion and compression.
+
++ Documentation | + Source Code + |
+
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+
+ Kerchunk
+
+ |
+
+
+ Kerchunk is a library that provides a unified way to represent a variety of chunked, compressed data formats (e.g. NetCDF/HDF5, GRIB2, TIFF, …), allowing efficient access to the data from traditional file systems or cloud object storage. It also provides a flexible way to create virtual datasets from multiple files.
+ Read this blogpost on how to access NetCDF and GRIB file colletions with Kerchunk.
+
++ Documentation | + Source Code + |
+
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+
+ xMIP
+
+ |
+
+
+ This package facilitates the cleaning, organization and interactive analysis of Model Intercomparison Projects (MIPs) within the Pangeo software stack.
+
++ Documentation | + Source Code | + Tutorial + |
+
| + + | +
+
+ esgpull and synda are command line tools to search and download files from the Earth System Grid Federation (ESGF) archive. esgpull is a tool that simplifies usage of the ESGF Search API for data discovery, and manages procedures related to downloading and storing files from ESGF.
+
++ Documentation | + Source Code (esgpull) | + Source Code (synda) + |
+
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+
+ FluxnetLSM
+
+ |
+
+
+ R package for post-processing FLUXNET datasets for use in land surface modelling. Performs quality control and data conversion of FLUXNET data and collated site metadata. Supports FLUXNET2015, La Thuile, OzFlux and ICOS data releases.
+
++ Documentation | + Source Code + |
+
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+
+ MetPy
+
+ |
+
+
+ MetPy is a collection of tools in Python for reading, visualizing, and performing calculations with weather data. Format types are GINI Water Vapor Imagery, NEXRAD Level 3 File, and NEXRAD Level 2 File.
+
++ Documentation | + Source Code + |
+
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+
+ xskillscore
+
+ |
+
+
+ xskillscore is a Python library for computing a wide variety of skill metrics. Its typical application is to verify deterministic and probabilistic forecasts relative to observations.
+
++ Documentation | + Source Code + |
+
Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our ACCESS-NRI Model Evaluation pages, the information below is not supported by ACCESS-NRI unless stated otherwise.
+We are trying to ingest more and more model evaluation and diagnostics recipes in your currated recipe gallery on this website. While this is a continous effort, this site is intented for a list of model evaluation and diagnostics recipes that are not (yet) ingested but may be interesting for the community:
+Please let us know, if we are missing an important tool. Check How To Contribute to get in touch.
+|
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+MED Recipe+ |
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+Components+ |
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+ Pythia Cookbooks
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+
Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our ACCESS-NRI Model Evaluation pages, the information below is not supported by ACCESS-NRI unless stated otherwise.
+Please let us know, if we are missing an important catalogue. Check How To Contribute to get in touch.
+|
+
+
+Dataset+ |
+
+
+
+Description+ |
+
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+ NCI datasets
+
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+ NCI has an extensive catalogue of datasets of interest to the weather and climate community. These datasets are directly available on the NCI supercomputer and the Australian Research Environment.
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+ This is an intake catalogue maintained by the ARC Centre of Excellence for Climate Extremes CLEX.
+ Only datasets from the NCI Catalog are referenced.
+ The catalogue is available in intake's default catalogue list in the CLEX Conda environment.
+ Two notebooks are provided in the docs folder showing how to access the ERA5 and CMIP6 datasets.
+
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+ The ACDG portal is a metadata portal listing climate research resources available in Australia from multiple data repositories.
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+ The Australian Ocean Data Network (AODN) is an interoperable online network of marine and climate data resources.
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+ The Intake-Ilamb catalog provides an yaml-style intake catalogue of the reference data used for ESM model benchmarking in the International Land Model Benchmarking (ILAMB) effort.
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+ FLUXNET
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+ FLUXNET scientists use the eddy covariance technique to measure the cycling of carbon, water, and energy between the biosphere and atmosphere.
+
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+ This dataset is available as intake-esm catalogue.
+
+ |
+
Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our ACCESS-NRI Model Evaluation pages, the information below is not supported by ACCESS-NRI unless stated otherwise.
+Please let us know if we are missing an important catalogue. Check How To Contribute to get in touch.
+|
+
+
+Dataset+ |
+
+
+
+Description+ |
+
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+
+ The Copernicus Climate Change Service (C3S) combines observations of the climate system with the latest science to develop authoritative, quality-assured information about the past, current and future states of the climate in Europe and worldwide. C3S data is provided via its Climate Data Store (CDS).
+ You can search its available datasets via this interface.
+ You can use the CDS API as well as command line tools to download data. To download ERA5 from CDS, you can use for example this era5cli command line tool.
+
+ |
+
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+
+ The CEDA (Centre for Environmental Data Analysis) Archive hosts atmospheric and earth observation data.
+ It provids an interactive Catalogue Search and Tools for downloading data.
+ It holds environmental data related to atmospheric and earth observation fields, such as Climate, Compisition, Observations, Numerical Weather Predictions, Airborne or Satellite data and imagery.
+
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+ The range of data held by the Environmental Data Service (EDS) is vast, covering all aspects of environmental science: atmosphere, climate and earth observation, geoscience, marine, polar and cryosphere, terrestrial and freshwater
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+ CEDA Archive
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+ The CEDA Archive forms part of NERC's Environmental Data Service (EDS) and is responsible for looking after data from atmospheric and earth observation research. They host over 18 Petabytes of data from climate models, satellites, aircraft, met observations, and other sources.
+
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+ OZFlux
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+ OzFlux is an ecosystem research network set up to provide Australian, New Zealand and global ecosystem modelling communities with consistent observations of energy, carbon and water exchange between the atmosphere and key Australian and New Zealand ecosystems.
+
+ |
+
Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our ACCESS-NRI Model Evaluation pages, the information below is not supported by ACCESS-NRI unless stated otherwise.
+The ACCESS Community and the ACCESS-NRI have established Community Working Groups to assess and prioritise the needs of the modelling community as well as encourage collaboration within. These working groups are open to the community and welcome new members.
+The working group activities are coordinated through the ACCESS Hive Community Forum. +To join a working group follow the instructions on the ACCESS-NRI website.
+
+ 
+ 
+ 
+ 
+ 
+ Coupled climate models like ACCESS-CM involve, among other things, calculation of complex mathematical equations that explain the physics of the atmosphere and oceans. Performed at hundreds of millions of points around the Earth, these calculations require vast computing power to complete them in a reasonable amount of time, thus relying on the power of high-performance computing (HPC) like Gadi. The Gadi supercomputer can handle more than 10 million billion (10 quadrillion) calculations per second and is connected to 100,000 Terabytes of high-performance research data storage.
+An overview of Gadi resources such as compute, storage and PBS jobs are described below.
+Useful NCI commands to check your available compute resources are:
+| Command | +Purpose | +
|---|---|
logout or Ctrl+D |
+To exit a session | +
hostname |
+Displays login node details | +
module list |
+Modules currently loaded | +
module avail |
+Available modules | +
nci_account -P [proj] |
+Compute allocation for [proj] | +
nqstat -P [proj] |
+Jobs running/queued in [proj] | +
lquota |
+Storage allocation and usage for all your projects | +
Compute allocations are granted to projects instead of directly to users and, hence, you need to be a member of a project in order to use its compute allocation. To run jobs on Gadi, you need to have sufficient allocated compute hours available, where the job cost depends on the resources reserved for the job and the amount of walltime it uses.
+Each user has a project-independent $HOME directory, which has a storage limit of 10 GiB. All data on /home is backed up.
Through project membership, the user gets access to the storage space within the
+project folders /scratch and /g/data filesystems for that particular project.
To run compute tasks such as an ACCESS-CM suite on Gadi, users need to submit them as jobs to queues. Within a job submission, you can specify the queue, duration and computational resources needed for your job. When a job submission is accepted, it is assigned a jobID (shown in the return message) that can then be used to monitor the job’s status.
+On job completion, contents of the job’s standard output/error stream gets copied to a file in the working directory with the respective format: <jobname>.o<jobid> and <jobname>.e<jobid>. Users should check these two log files before proceeding with post-processing of any output from their corresponding job.
We encourage members of the community to list any workshops, tutorials, conferences that might be of interest to the community.
+The easiest way for you to add your event is to make an issue with the template provided. This provides a form which guides you through the process of providing the required information.
+This process requires some knowledge of git, GitHub and Markdown. If you do not feel comfortable doing this then it is sufficient to just add an issue as above. The issue will be assigned to someone else to finish.
+If you do feel confident adding your event to the list, then create a Markdown text file, identified with the .md extension, to the correct subdirectory in the events folder of the ACCESS-Hive repository. The subdirectories are named by year, put your new file in the year in which the event will take place. Avoid spaces in your filename: use an underscore _ where you would normally have a space. e.g. regional_dowscaling_cordex.md
The file must contain a header with the metadata as in the example below:
+
+ 
+ 
+ 
+ ---
+title: Regional climate downscaling for Australia within the CORDEX framework
+start_date: 27/11/2022
+end_date: 27/11/2022
+location: Adelaide, SA
+link: https://www.amos2022.org.au/
+description: This workshop is relevant for those performing regional climate simulations or downscaling with empirical/statistical downscaling approaches including machine learning, as well as those using regional climate projection data in their work. The focus will be on CORDEX related data and modelling. The workshop will have some presentations with extended discussion.
+---
+Make sure to follow all the steps described in the contribution guidelines to submit this addition for approval for publication.
+ +This workshop is relevant for those performing regional climate simulations or downscaling with empirical/statistical downscaling approaches including machine learning, as well as those using regional climate projection data in their work. The focus will be on CORDEX related data and modelling. The workshop will have some presentations with extended discussion. Some topics to be covered include: +- Accessing the existing CORDEX-CMIP5 data. How to access and use the data +- Explain the CORDEX-CMIP6 protocol +- What does it say? How can you contribute? +- Who is planning to contribute (or is already working on contributions) to the Australasia domain?
+ +The UM Partnership Team and GC Programme Team are running a GC5 assessment workshop, to assess the latest configuration of the Global Coupled model.
+The workshop will be a hybrid event with an option to attend online or in-person at Met Office Collaboration Building, Exeter. We will discuss the assessment of the latest GC5 configuration in a range of model simulations in a seamless context and sessions will broadly consist of: +- Summary of GC5 physics changes +- General model assessment +- Summary from Priority Evaluation Groups (PEGs) +- Summary from Collaboration Groups (CoGs) +- Upcoming changes in GC science and tools +- Discussions
+Please fill in the registration form to confirm attendance by 21st October
+For any further questions please contact Luke Roberts, Prince Xavier or Charline Marzin at the Met Office.
+ +Scientific ocean drilling provides the robust baseline data on global climate evolution over extended geologic time periods that are critical for improving climate model performance. By targeting how the climate system operates across a wide array of past climate states, scientific ocean drilling has, and continues to, obtain the data necessary to calibrate and improve numerical models used to project future climate impacts and inform mitigation strategies.
+Join us in this session where we aim to connect climate and ocean modellers to our rich (50+ years of drilling) database and unanswered questions in scientific ocean drilling. By addressing key questions about Earth’s past, present, and future through interdisciplinary research, we are aiming to spark new collaborations and proposals that will lead to a more profound understanding of Earth as one integrated, interconnected system.
+ +The Surface Water and Ocean Topography (SWOT) satellite, which will launch in November 2022, is a ground-breaking wide-swath altimetry mission that will observe fine details of the ocean dynamics at a resolution 10 times finer than current satellites. SWOT is jointly developed by NASA and CNES with contributions from researchers around the world, including Australia. The Australian government, the Integrated Marine Observing System, and the Australian marine science community are investing in SWOT through calibration/validation and synergistic in situ measurements of fine-scale ocean dynamics in the Australian region. This workshop will present a primer on the principles of the satellite and instrument, how it works, and what are its possibilities and limitations compared to existing altimetry products. This will be complemented with a brief summary of ocean research related to and enabled by SWOT, including internal waves and tides, sub-mesoscale dynamics, the geoid, and mean dynamic topography. The goal of the workshop is to provide oceanographers, hydrologists and other users of altimetry data with the information they need to prepare for the arrival of SWOT data in late 2023.
+ +We are maintaining a list of upcoming events for the community on the ACCESS-NRI website.
+
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+
+ 
+ This page is intended to provide access to training material directly related to ACCESS models and model components. This material can cover topics such as but not limited to:
+The JULES tutorials explain how to use FCM, Rose and Cylc both for using the model and for development work. They can be useful to ACCESS users as practical demonstrations of the Rose and Cylc infrastructure.
+ +To learn the basics of Git and GitHub. It also includes ACCESS-NRI's recommendations to setup GitHub.
+ + +
The National Computational Infrastructure (NCI) provides training resources and in-person training courses throughout the year to help develop the skills of the NCI user community.
+A full calendar of upcoming training opportunities can be found on their Opus page.
+Users can find important information and resources about using NCI systems and services in the NCI User Guides.
+ +This space is intended to promote training material relevant to ACCESS and its community. The training material can be directly relevant to ACCESS and its model components, such as:
+It is also intended for training material around more peripheral topics that are essential for the community, such as:
+ACCESS-NRI encourages the members of the community to contact us to share their suggestions.
+Finally, you will also find ACCESS-NRI's policies in this space.
+ +
+
+ To find out more information about the workshop, check the ACCESS Community Workshop 2023 page on the ACCESS-NRI website.
+ +For the training on Intake, ILAMB and ESMValTool, you will need to clone this Github repo to Gadi as follows:
+Log in to Gadi +
+ 
+ ssh <your_nci_username>@gadi.nci.org.au
+ssh connection setup for Gadi, you can use ARE's Gadi Terminal.
+Clone this Github repo to your user directory within /scratch/nf33 on Gadi. Depending on whether or not you've used the nf33 project before, your user directory may or may not already exist.
+
mkdir -p /scratch/nf33/$USER
+cd /scratch/nf33/$USER
+git clone https://github.com/ACCESS-NRI/workshop-training-2023.git
+ACCESS Community Workshop 2023
+ +