Merge branch 'main' into wave_wcag_edits

Author: jen-reeve

.github/workflows/auto_merge.yml

@@ -11,7 +11,7 @@ jobs:
   automerge:
     runs-on: ubuntu-24.04
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
     - run: |

.github/workflows/checks.yml

@@ -42,22 +42,17 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout Repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - name: Get changed files
-        id: get-changed-files
-        uses: tj-actions/changed-files@v40
-        with:
-          files: |
-            docs/**/*.md
       - name: Push Changed files to output
         if: inputs.fileList == ''
         id: diff
         run: |
+          changed_files="$(git diff --name-only origin/${{ github.base_ref }}...HEAD | grep -E '^docs/.*\.md$' | tr '\n' ' ')"
           echo "::info::Workflow triggered by PR"
-          echo "Changed files: '${{steps.get-changed-files.outputs.all_changed_files}}'"
-          echo "filelist=${{steps.get-changed-files.outputs.all_changed_files}}" >> $GITHUB_OUTPUT
+          echo "Changed files: '${changed_files}'"
+          echo "filelist=${changed_files}" >> $GITHUB_OUTPUT
     outputs:
       filelist: ${{steps.diff.outputs.filelist || inputs.fileList}}
   spellcheck:
@@ -71,7 +66,7 @@ jobs:
         run: exit 0
       - if: ${{needs.get.outputs.filelist}}
         name: Check out repo.
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - if: ${{needs.get.outputs.filelist}}
         name: Install dependencies
         run: |
@@ -94,7 +89,7 @@ jobs:
         run: exit 0
       - if: ${{needs.get.outputs.filelist}}
         name: Check out repo.
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - if: ${{needs.get.outputs.filelist}}
         name: Install dependencies
         run: pip3 install $(grep ^proselint requirements.txt)
@@ -114,7 +109,7 @@ jobs:
         run: exit 0
       - if: ${{needs.get.outputs.filelist}}
         name: Check out repo.
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - if: ${{needs.get.outputs.filelist}}
         name: Install dependencies
         run: npm install -g markdownlint-cli
@@ -135,7 +130,7 @@ jobs:
         run: exit 0
       - if: ${{needs.get.outputs.filelist}}
         name: Check out repo.
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - if: ${{needs.get.outputs.filelist}}
         name: Check markdown meta.
         run: |
@@ -153,7 +148,7 @@ jobs:
         run: exit 0
       - if: ${{needs.get.outputs.filelist}}
         name: Check out repo.
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - if: ${{needs.get.outputs.filelist}}
         name: Check markdown meta.
         run: |
@@ -165,7 +160,7 @@ jobs:
     runs-on: ubuntu-24.04
     needs: get
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - run: pip3 install -r requirements.txt

.github/workflows/deploy.yml

@@ -25,7 +25,7 @@ jobs:
           sudo apt-get install -y libxml2-dev libxslt-dev python3-dev
         shell: bash
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
           sparse-checkout: |

.github/workflows/fetch_includes.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
           persist-credentials: true 

docs/Announcements/Accessing_NeSI_Support_during_the_Easter_break.md

@@ -19,7 +19,7 @@ sources of self-service support:
 
 - Changes to system status are reported via our [System Status page](https://status.nesi.org.nz/ "https://status.nesi.org.nz/").
     You can also subscribe for notifications of system updates and
-    unplanned outages sent straight to your inbox. [Sign up here.](../Getting_Started/Getting_Help/System_status.md)
+    unplanned outages sent straight to your inbox. [Sign up here.](../Getting_Started/System_status.md)
 
 - [Consult our User Documentation](https://www.docs.nesi.org.nz) pages
     for instructions and guidelines for using the systems.

docs/Announcements/December_holiday_support_restrictions.md

@@ -30,7 +30,7 @@ END: 9:00am 5 January 2026
   </tr>
   <tr>
     <td>Email: <a href="../General/Announcements/support@nesi.org.nz">support@nesi.org.nz</a></td>
-    <td>- <a href="../Getting_Started/Getting_Help/System_status.md">Sign up for system status updates</a> for advance warning of any system updates or unplanned outages.<br>- <a href="https://www.docs.nesi.org.nz">Consult our User Documentation</a> pages for instructions and guidelines for using the systems.<br>- <a href="https://www.youtube.com/playlist?list=PLvbRzoDQPkuGMWazx5LPA6y8Ji6tyl0Sp">Visit our YouTube channel</a>  for introductory training webinars.</td>
+    <td>- <a href="../Getting_Started/System_status.md">Sign up for system status updates</a> for advance warning of any system updates or unplanned outages.<br>- <a href="https://www.docs.nesi.org.nz">Consult our User Documentation</a> pages for instructions and guidelines for using the systems.<br>- <a href="https://www.youtube.com/playlist?list=PLvbRzoDQPkuGMWazx5LPA6y8Ji6tyl0Sp">Visit our YouTube channel</a>  for introductory training webinars.</td>
   </tr>
   </tbody>
   </table>

docs/Announcements/Known_Issues_HPC3.md

@@ -11,30 +11,31 @@ Below is a list issues that we're actively working on. We hope to have these res
 
 For differences between the new platforms and Mahuika, see the more permanent [differences from Mahuika](../Getting_Started/FAQs/Mahuika_HPC3_Differences.md).
 
-## Access
 
-### OnDemand Apps
-* The resources dedicated to interactive work via a web browser are smaller, and so computations requiring large amounts of memory or many CPU cores are not yet supported. 
+## OnDemand Apps
+* Firefox Browser will fail to render the _HPC Shell Access_ app correctly.  Please switch to a Chrome or Safari browser until the vendor provides a fix.
 
-* Slurm `sbatch` jobs can be submitted directly from your apps, such as the terminal in Jupyterlab, RSudio or code-server.  However, interactive jobs (`srun` or `salloc`) can only run from the `Clusters > NeSI HPC SHell Access` dropdown menu which opens a standard terminal window in the browser. [Watch a demo here](https://youtu.be/bkq6tpRrAwc?si=kS2KBifnCf4d6tWz).
+* The resources dedicated to interactive work via a web browser are smaller, and so computations requiring large amounts of memory or many CPU cores are not yet supported. 
 
 * Missing user Namespaces in Kubernetes pods will interfere with most Apptainer operations.  One can run `apptainer pull` command, `apptainer exec,run,shell` commands can not be executed.
 
+## UCX ERROR
+Multi-node MPI jobs may fail on the four nodes mg[13-16] with errors like `UCX ERROR: no active messages transport`. If you encounter this, add the sbatch option `-x mg[13-16]` to avoid those nodes. Single-task jobs are not affected.
 
-## Software
-As was already the case on the Milan nodes in Mahuika (where they had a Rocky 8 OS), some of our environment modules cause system software to stop working, e.g: load `module load Perl` and `svn` stops working. This is usually the case if they load `LegacySystem/7` as a dependency. The solutions are to ask us to re-build the problem environment module, or just don't have it loaded while doing other things.
-
-**Delft3D_FM** wasn't working in Mahuika's Milan partition so probably needs rebuilding.
+## Core dump files
+Contrary to what is stated in [our documentation on core files](../Getting_Started/FAQs/What_is_a_core_file.md), these are not currently available, even if `ulimit -c unlimited` is set.
 
-**MPI** software using 2020 or earlier toolchains eg intel-2020a, may not work correctly across nodes. Trying with more recent toolchains is recommended eg intel-2022a. 
+## Software
+* FileSender - If you modify the `default_transfer_days_valid` parameter in your `~/.filesender/filesender.py.ini` to > 20 it will cause the transfer to fail with a 500 error code.  Please do not modify this parameter.
 
-Please let us know if you find any additional problems.
+* Legacy Code - Some of our environment modules cause system software to stop working, e.g: do `module load Perl/5.38.2-GCC-12.3.0` and find that `svn` stops working. This is usually the case if they load `LegacySystem/7` as a dependency. The solutions are to ask us to re-build the problem environment module, or just don't have it loaded while doing other things.
+ 
+* MPI software using 2020 or earlier toolchains eg intel/2020a, may not work correctly across nodes. Trying with more recent toolchains is recommended. 
 
 ## Slurm
 
-### GPUs
+### Requesting GPUs
 If you request a GPU without specifying which *type* of GPU, you will get a random one. So please always specify a GPU type. 
 
 ### BadConstraints
-This uninformative message can appear as a reason for a job pending in the `squeue` output when the job is submitted to both `milan` and `genoa` partitions (which is the default behaviour). It does not appear to reflect a real problem though, just a side-effect of the mechanism we are using to target jobs to the right-sized node(s). 
-
+This uninformative message can appear in the `squeue` output as the reason for a job pending. It does not always reflect a real problem though, just a side-effect of the mechanism we are using to target jobs to the right-sized node(s) together with a small bug in Slurm. If it causes your job to be put on hold (ie: its priority gets appears as zero in output from `squeue --me  -S -p  --Format=jobid:10,partition:13,reason:22,numnodes:.6,prioritylong:.6`) then please try `scontrol release <jobid>` or {% include "partials/support_request.html" %} if the issue persists.

docs/Getting_Started/.pages.yml

@@ -4,7 +4,7 @@ nav:
  - Projects 
  - Allocations
  - Accessing_the_HPCs
- - Getting_Help
+ - Getting_Help.md
  - Cheat_Sheets
  - "*"
  - my.nesi.org.nz: my-nesi-org-nz

…ting_Started/Getting_Help/Consultancy.md docs/Getting_Started/Consultancy.mddocs/Getting_Started/Getting_Help/Consultancy.md renamed to docs/Getting_Started/Consultancy.md docs/Getting_Started/Getting_Help/Consultancy.md renamed to docs/Getting_Started/Consultancy.md

@@ -9,17 +9,16 @@ Our Consultancy service provides scientific and HPC-focused
 computational and data science support to research projects across a
 range of domains.
 
-![Consultancy](../../assets/images/consultancy.png){ width=75% }
+![Consultancy](../assets/images/consultancy.png){ width=75% }
 
 !!! success "Case studies"
     [See our case studies page for examples of projects our Consultancy service has supported](https://www.reannz.co.nz/case-studies).
 
-
 ## Need support with your research project?
 
 If you would like to learn more about our Consultancy service and how
 you can work with our Research Software Engineers on
-a project, please {% include "partials/support_request.html" %} to set up an
+a project, please {% include "partials/support_request.html" %} to set up an
 initial meeting. We can discuss your needs and complete a Consultancy
 application form together.
 

docs/Getting_Started/Creating_an_Account.md

@@ -2,21 +2,20 @@
 created_at: '2018-04-18T23:56:10Z'
 tags:
 - onboarding
-- howto
-- access
 - mynesi
+description: How to create a REANNZ HPC account.
 ---
 
 
 !!! prerequisite
-     Either an active login at a Tuakiri member institution, or 
+     Either an active login at a Tuakiri member institution, or
      [a Tuakiri Virtual Home account in respect of your current place of work or study](../Policy/Account_Requests_for_non_Tuakiri_Members.md).
 
 1. Access [my.nesi.org.nz](https://my.nesi.org.nz) via your browser and
     log in with either your institutional credentials, or your Tuakiri
     Virtual Home account, whichever applies.
 
-2. If this is your first time logging in to my.nesi and you do not have
+2. If this is your first time logging in to `my.nesi` and you do not have
     an entry in our database (you have not previously had a NeSI
     account) you will be asked to fill out some fields, such as your
     role at your institution and contact telephone number, and submit