diff --git a/docs/about/contact.md b/docs/about/contact.md index 6aceb3d41..762fb1052 100644 --- a/docs/about/contact.md +++ b/docs/about/contact.md @@ -1,6 +1,6 @@ # Contact - + ACCESS-Hive is an initiative of the Australian Earth-System Simulator (ACCESS-NRI). diff --git a/docs/about/contribute/contribute_on_github.md b/docs/about/contribute/contribute_on_github.md index dae394cca..349fdc4ba 100644 --- a/docs/about/contribute/contribute_on_github.md +++ b/docs/about/contribute/contribute_on_github.md @@ -23,17 +23,16 @@ This documentation is written in Markdown format and is based on the ACCESS-Hive GitHub organisation members would have write access to the ACCESS-Hive repository, and they can contribute by creating their own branches instead of maintaining their individual forks. +## Raise a GitHub Issue -Hence, we encourage you to become a member of the ACCESS-Hive GitHub organisation by replying to this issue and ask to be invited to join the organisation. +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. -## Raise a GitHub Issue +## Fork the ACCESS-Hive GitHub repository -Once you are a member of the ACCESS-Hive GitHub organisation, for all additions or modifications to the ACCESS-Hive site, it is recommended to start by opening an issue in the ACCESS-Hive GitHub repository. Feel free to assign that issue to yourself if you intend to work on that issue. +After raising a Github issue about your contribution, you need to fork ACCESS-Hive's Github repository. -## Clone the ACCESS-Hive GitHub repository For cloning this repository onto your local computer, we encourage you to first add your local SSH keys to your GitHub profile. diff --git a/docs/about/contribute/index.md b/docs/about/contribute/index.md index a40f984e5..3a7e8c1d2 100644 --- a/docs/about/contribute/index.md +++ b/docs/about/contribute/index.md @@ -1,6 +1,6 @@ # Contribute to ACCESS-Hive - + ACCESS-Hive is an open user portal which hosts the documentation relevant to the Australian Community Climate and Earth System Simulator (ACCESS) community. diff --git a/docs/about/index.md b/docs/about/index.md index a375a4829..be6ebc748 100644 --- a/docs/about/index.md +++ b/docs/about/index.md @@ -27,7 +27,7 @@
- Code of conduct + Code of conduct
Code of conduct
 diff --git a/docs/assets/jupyterlab_plus_button.png b/docs/assets/jupyterlab_plus_button.png new file mode 100644 index 000000000..6afe68142 Binary files /dev/null and b/docs/assets/jupyterlab_plus_button.png differ diff --git a/docs/assets/launch_are_jupyterlab.gif b/docs/assets/launch_are_jupyterlab.gif new file mode 100644 index 000000000..15bc1847c Binary files /dev/null and b/docs/assets/launch_are_jupyterlab.gif differ diff --git a/docs/assets/launch_are_vdi_desktop.gif b/docs/assets/launch_are_vdi_desktop.gif new file mode 100644 index 000000000..fe6ca44ea Binary files /dev/null and b/docs/assets/launch_are_vdi_desktop.gif differ diff --git a/docs/assets/session_delete_button.png b/docs/assets/session_delete_button.png new file mode 100644 index 000000000..59968d8a8 Binary files /dev/null and b/docs/assets/session_delete_button.png differ diff --git a/docs/getting_started/are.md b/docs/getting_started/are.md index ba2649267..ada5a4491 100644 --- a/docs/getting_started/are.md +++ b/docs/getting_started/are.md @@ -7,36 +7,206 @@ ARE can give you access to NCI’s Gadi supercomputer and data collection There are multiple applications included in ARE, but the two most used for ACCESS-related activities are Virtual Desktop (VDI) and JupyterLab. +## Start an ARE session -
+
- -## Launch the ARE session
- +
+ To start an ARE VDI session go to the ARE VDI Desktop page.
- +
+ To start an ARE JupyterLab session go to the ARE JupyterLab page.
+### Session options +Launching an ARE session is similar to submitting an interactive PBS job that enables you to connect to a Gadi computing node. +
+Therefore, there are multiple PBS directives and other options you can select: + + +### Launch the session +
    +
  1. + Click on the Launch button to launch the session. + You will be prompted to your Interactive Sessions page and you will see your last requested session at the top. +
    2. +
  2. + +
    + +
    + Wait until your session starts and then click on the Launch VDI Desktop button to open a new tab with the VDI interface. +
    + Inside the VDI interface, you can open the terminal by clicking on the black terminal icon at the top of the window. +
    + +
    + Wait until your session starts and then click on the Open JupyterLab button to open a new tab with the JupyterLab interface. +
    + Inside the JupyterLab interface, you can open a new notebook by clicking on the Python3 Notebook button in the Launcher panel (to open a new Laucher panel, click on the plus button Plus button next to your current tab). +
    +
    + +
    3. +
    + +
    + Launch ARE VDI Desktop +
    + +
    + Launch ARE JupyterLab +
    +
    +
+ +## Delete an ARE session +You can delete a session before its automatic expiration (based on the specified Walltime) by clicking on the session's Delete button Session Delete button in the Interactive Sessions page.
References
@@ -44,4 +214,10 @@ There are multiple applications included in ARE, but the two most used for ACCES
  • https://opus.nci.org.au/display/Help/ARE+User+Guide
    • +
  • + https://are.nci.org.au/pun/sys/dashboard/batch_connect/sys/desktop_vnc/ncigadi/session_contexts/new +
    • +
  • + https://are.nci.org.au/pun/sys/dashboard/batch_connect/sys/jupyter/ncigadi/session_contexts/new +
    • \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index fa9ef7e92..eaee2e427 100644 --- a/docs/index.md +++ b/docs/index.md @@ -74,4 +74,4 @@ hide: We at ACCESS-NRI acknowledge the Traditional Owners of the land on which our research infrastructure and community operate across Australia and pay our respects to Elders past and present. We recognise the thousands of years of accumulated knowledge and deep connection they have with all the Earth systems we simulate. - \ No newline at end of file + \ No newline at end of file diff --git a/docs/models/run-a-model/run-access-cm.md b/docs/models/run-a-model/run-access-cm.md index 95c08bc29..34875f572 100644 --- a/docs/models/run-a-model/run-access-cm.md +++ b/docs/models/run-a-model/run-access-cm.md @@ -118,21 +118,20 @@ Before running {{ model }}, you need to fulfil general prerequisites outlined in Project → a project you belong, with allocated SU
    The project, with allocated Service Units (SU), under which you want to run your simulation. Usually (but not always) this corresponds to your $PROJECT. -
    - For more information, check how to join relevant NCI projects. -
    +
    + For more information, check how to join relevant NCI projects.
  • Storage → gdata/access+gdata/hh5+gdata/hr22+gdata/ki32 (minimum)
    - This is the list (joined by + signs) of project data storage needed for the {{ model }} simulation. In ARE, storage locations need to be explicitly defined to access these data from within a VDI instance. + This is the list (joined by + signs) of project data storage needed for the {{ model }} simulation. In ARE, storage locations need to be explicitly defined to access data from within a VDI instance.
    Since every {{ model }} simulation can be unique and input data can come from various sources, if your specific simulation requires data coming from projects other than access, hh5, hr22 or ki32, you need to add those projects to the storage path.
    For example, if your {{ model }} simulation requires data coming from /g/data/tm70 and /scratch/w40, your full storage path will be: gdata/access+gdata/hh5+gdata/hr22+gdata/ki32+/gdata/tm70+scratch/w40
    • - Launch the session and, after the session starts, click on Launch VDI Session. + Launch the session and, after the session starts, click on Launch VDI Desktop. Launch ARE VDI session

    Open the terminal