Merge pull request #651 from ACCESS-NRI/development

Periodic merge to main

.github/workflows/delete_all_artifacts.sh

@@ -10,8 +10,8 @@ invoke_api() {
 }
 
 list_artifacts() {
-  org=ACCESS-Hive
-  repo=access-hive.github.io
+  org=ACCESS-NRI
+  repo=access-hive.org.au
   invoke_api https://api.github.com/repos/${org}/${repo}/actions/artifacts
 }
 

.github/workflows/deploy_to_github_pages.yml

@@ -12,6 +12,8 @@ on:
       - closed
 env:
   TZ: Australia/Canberra
+permissions:
+  pull-requests: write # to comment on PRs
 
 jobs:
   pr-preview-setup:

docs/css/access-nri.css

@@ -1050,6 +1050,13 @@ img.intro-img {
   margin: 0 0.6em;
 }
 
+.green_prompt_output {
+  color: #00C202
+}
+
+.red_prompt_output {
+  color: #CA1A01;
+}
 
 /* =============================================================== 
   Media queries for website responsiveness

docs/getting_started/first_steps.md

@@ -10,9 +10,11 @@ The steps in this section are aimed at new users who would like to do any of the
 <hr>
 
 ## Create an NCI user account
+
 Most of the data and models you will need are available at the <a href="https://nci.org.au/about-us/who-we-are" target="_blank">National Computing Infrastructure (NCI) </a>.
 <br>
 To access these, you need an <a href="https://opus.nci.org.au/display/Help/How+to+create+an+NCI+user+account" target="_blank">NCI account</a>. If you do not have one, <a href="https://my.nci.org.au/mancini/signup/0" target="_blank">sign up here</a>.
+
 <div class="note">
 You will need an institutional email address with an organisation that allows access to NCI (e.g., an Australian university, ACCESS-NRI, CSIRO, BoM, CLEX, etc.).
 </div>
@@ -28,23 +30,26 @@ Each project has an ID (e.g. `xp65`), which is what the term <i>project</i> actu
 
 If you are interested in datasets and data collections, you can browse the <a href="https://geonetwork.nci.org.au/geonetwork/srv/eng/catalog.search#/search" target="_blank">NCI Data Catalogue</a> and follow the <a href="https://opus.nci.org.au/display/Help/Data+Catalogue+User+Guide" target="_blank">NCI Data Catalogue User Guide</a>.
 
-To perform computations on <i>Gadi</i> instead, you need to join a project with computing resources, also called <i>Service Units (SU)</i>. The project ID will be provided by your supervisor, research project or institution.
+To run models on <i>Gadi</i> instead, you need to join a project with computing resources, also called <i>Service Units (SU)</i>. The project ID will be provided by your supervisor, research project or institution.
 
 To join a project, search for it on <a href="https://my.nci.org.au/mancini/project-search" target="_blank">NCI website</a> and request membership.
+
 <div class="note">
   The first project you join will become your default one. If you would like to change this, check out <a href="#change-default-project-on-gadi">how to change your default project on Gadi</a>.
-</div> 
+</div>
 
-There are several NCI projects that may be relevant to you, depending on the tasks you want to carry out. 
+There are several NCI projects that may be relevant to you, depending on the tasks you want to carry out.
 <br>
 For tasks supported by ACCESS-NRI (e.g., running a supported model configuration, using a supported model evaluation tool, etc.), you will find a list of relevant projects to join in the pages relative to each respective task.
 
 <hr>
 
 ## Login to Gadi
+
 Operations involving model runs and data collections take place on the <a href="https://nci.org.au/our-systems/hpc-systems" target="_blank">Gadi supercomputer</a>.
 
 Before you login to <i>Gadi</i>, you need to possess the following prerequisites:
+
 <ul>
   <li><b>Internet connection</b></li>
   <li>
@@ -62,28 +67,32 @@ Before you login to <i>Gadi</i>, you need to possess the following prerequisites
 </ul>
 
 To login to <i>Gadi</i> using <a href="https://en.wikipedia.org/wiki/Secure_Shell" target="_blank">SSH</a>, on your **local machine's terminal** run the following command, replacing <code>&lt;your-NCI-username&gt;</code> with your NCI <i>username</i> (e.g., <code>ab1234</code>):
+
 <pre><code>ssh &lt;your-NCI-username&gt;@gadi.nci.org.au</code></pre>
+
 You will be prompted to enter your NCI password, and then you will be connected to <i>Gadi</i>:
 <terminal-window lineDelay=0>
-  <terminal-line data="input" lineDelay=300>ssh &lt;your-NCI-username&gt;@gadi.nci.org.au</terminal-line>
-  <terminal-line lineDelay=300>&lt;NCI-username&gt;@gadi.nci.org.au's password: <i class="icon-key" style="display: inline-block; font-size: 0.4em; transform: rotate(-90deg);"></i></terminal-line>
-  <terminal-line lineDelay=3000>###############################################################################</terminal-line>
-  <terminal-line>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Welcome to the NCI National Facility!&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
-  <terminal-line>#&emsp;&emsp;&emsp;&emsp;This service is for authorised clients only. It is a criminal&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;#</terminal-line>
-  <terminal-line>#&emsp;&emsp;&emsp;&emsp;offence to:&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#</terminal-line>
-  <terminal-line>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Obtain access to data without permission;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&emsp;#</terminal-line>
-  <terminal-line>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Damage, delete, alter or insert data without permission;&emsp;&nbsp;#</terminal-line>
-  <terminal-line>#&emsp;&emsp;&emsp;&emsp;Use of this system requires acceptance of the Conditions of Use;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
-  <terminal-line>#&emsp;&emsp;&emsp;&emsp;published at http://nci.org.au/users/nci-terms-and-conditions-access;&emsp;#</terminal-line>
-  <terminal-line>###############################################################################</terminal-line>
-  <terminal-line>|&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;gadi.nci.org.au - 260,760 processor InfiniBand x86_64 cluster&emsp;&emsp;&nbsp;&nbsp;&nbsp;|</terminal-line>
-  <terminal-line>===============================================================================</terminal-line>
-  <terminal-line>===============================================================================</terminal-line>
-  <terminal-line data="input" lineDelay=200></terminal-line>
+<terminal-line data="input" lineDelay=300>ssh &lt;your-NCI-username&gt;@gadi.nci.org.au</terminal-line>
+<terminal-line lineDelay=300>&lt;NCI-username&gt;@gadi.nci.org.au's password: <i class="icon-key" style="display: inline-block; font-size: 0.4em; transform: rotate(-90deg);"></i></terminal-line>
+<terminal-line lineDelay=3000>###############################################################################</terminal-line>
+<terminal-line>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Welcome to the NCI National Facility!&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
+<terminal-line>#&emsp;&emsp;&emsp;&emsp;This service is for authorised clients only. It is a criminal&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;#</terminal-line>
+<terminal-line>#&emsp;&emsp;&emsp;&emsp;offence to:&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#</terminal-line>
+<terminal-line>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Obtain access to data without permission;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&emsp;#</terminal-line>
+<terminal-line>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Damage, delete, alter or insert data without permission;&emsp;&nbsp;#</terminal-line>
+<terminal-line>#&emsp;&emsp;&emsp;&emsp;Use of this system requires acceptance of the Conditions of Use;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
+<terminal-line>#&emsp;&emsp;&emsp;&emsp;published at http://nci.org.au/users/nci-terms-and-conditions-access;&emsp;#</terminal-line>
+<terminal-line>###############################################################################</terminal-line>
+<terminal-line>|&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;gadi.nci.org.au - 260,760 processor InfiniBand x86_64 cluster&emsp;&emsp;&nbsp;&nbsp;&nbsp;|</terminal-line>
+<terminal-line>===============================================================================</terminal-line>
+<terminal-line>===============================================================================</terminal-line>
+<terminal-line data="input" lineDelay=200></terminal-line>
 </terminal-window>
 
 ### Auto login
+
 To simplify the login and avoid being prompted every time to enter your NCI password, follow these steps:
+
 <ol>
   <li>
     <b>Create an SSH key</b>
@@ -217,40 +226,46 @@ Once you complete all the above steps, you should be able to connect to <i>Gadi<
 <pre><code>ssh gadi</code></pre>
 
 ### Change default project on Gadi
+
 It is recommended that you check what your default project on <i>Gadi</i> is set to. The default project should be set to the computational project you will most likely use to run simulations/evaluations and store data.
 <br>
 You can check which is your default project by logging into <i>Gadi</i> and running:
+
 <pre><code>echo $PROJECT</code></pre>
+
 To change your default project on <i>Gadi</i>, you need to manually change the `PROJECT` field in the `~/.config/gadi-login.conf` file.
 <br>
 Alternatively, you can run the following command <b>on <i>Gadi</i>'s terminal</b>:
+
 <pre><code>sed "s/\(PROJECT \).*/\1&lt;new-default-project&gt;/" ~/.config/gadi-login.conf</code></pre>
+
 Once this is done, exit from <i>Gadi</i> and log back in.
 <br>
 For example, if you want to change your default project to `tm70` on <i>Gadi</i>:
 <terminal-window>
-  <terminal-line data="input">echo $PROJECT</terminal-line>
+<terminal-line data="input">echo $PROJECT</terminal-line>
   <terminal-line>&lt;old-default-project&gt;</terminal-line>
   <terminal-line data="input">sed "s/\(PROJECT \).*/\1tm70/" ~/.config/gadi-login.conf</terminal-line>
   <terminal-line data="input">exit</terminal-line>
   <terminal-line>logout</terminal-line>
   <terminal-line>Connection to gadi.nci.org.au closed.</terminal-line>
   <terminal-line data="input" PS1="&lt;span style='color: #9734bb;'&gt;(User PC)$ &lt;/span&gt;">ssh gadi</terminal-line>
-  <terminal-line>###############################################################################</terminal-line>
-  <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Welcome to the NCI National Facility!&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
-  <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;This service is for authorised clients only. It is a criminal&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;#</terminal-line>
-  <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;offence to:&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#</terminal-line>
-  <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Obtain access to data without permission;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&emsp;#</terminal-line>
-  <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Damage, delete, alter or insert data without permission;&emsp;&nbsp;#</terminal-line>
-  <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;Use of this system requires acceptance of the Conditions of Use;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
-  <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;published at http://nci.org.au/users/nci-terms-and-conditions-access;&emsp;#</terminal-line>
-  <terminal-line lineDelay=0>###############################################################################</terminal-line>
-  <terminal-line lineDelay=0>|&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;gadi.nci.org.au - 260,760 processor InfiniBand x86_64 cluster&emsp;&emsp;&nbsp;&nbsp;&nbsp;|</terminal-line>
-  <terminal-line lineDelay=0>===============================================================================</terminal-line>
-  <terminal-line lineDelay=0>===============================================================================</terminal-line>
-  <terminal-line data="input">echo $PROJECT</terminal-line>
-  <terminal-line>tm70</terminal-line>
+<terminal-line>###############################################################################</terminal-line>
+<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Welcome to the NCI National Facility!&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
+<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;This service is for authorised clients only. It is a criminal&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;#</terminal-line>
+<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;offence to:&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#</terminal-line>
+<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Obtain access to data without permission;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&emsp;#</terminal-line>
+<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Damage, delete, alter or insert data without permission;&emsp;&nbsp;#</terminal-line>
+<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;Use of this system requires acceptance of the Conditions of Use;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
+<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;published at http://nci.org.au/users/nci-terms-and-conditions-access;&emsp;#</terminal-line>
+<terminal-line lineDelay=0>###############################################################################</terminal-line>
+<terminal-line lineDelay=0>|&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;gadi.nci.org.au - 260,760 processor InfiniBand x86_64 cluster&emsp;&emsp;&nbsp;&nbsp;&nbsp;|</terminal-line>
+<terminal-line lineDelay=0>===============================================================================</terminal-line>
+<terminal-line lineDelay=0>===============================================================================</terminal-line>
+<terminal-line data="input">echo $PROJECT</terminal-line>
+<terminal-line>tm70</terminal-line>
 </terminal-window>
+
 <hr>
 
 <h6>References</h6>

docs/index.md

@@ -3,6 +3,7 @@ hide:
   - navigation
   - toc
 ---
+
 <h1 class="homepage"></h1>
 <div class="introduction">
     <div>
@@ -74,4 +75,4 @@ 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.
 
-<img src = "assets/acknowledgement_unsplash_david_clode_Bark_Cairns.png"  class="acknowledgement-img" loading="lazy">
+<img src = "assets/acknowledgement_unsplash_david_clode_Bark_Cairns.png"  class="acknowledgement-img" loading="lazy">

docs/js/miscellaneous.js

@@ -62,7 +62,7 @@ function tabFunctionality() {
   document.querySelectorAll('[href^="#"]:not([class^="md"])').forEach(el => {
     let href = el.getAttribute('href');
     let tabEl = document.getElementById(href.slice(1,))
-    if (tabEl.parentElement.classList.contains("tabLabels")) {
+    if (tabEl?.parentElement.classList.contains("tabLabels")) {
       el.addEventListener("click",(e) => openTab(tabEl), false);
     }
   })