Callum walley patch 1

.github/workflows/jekyll.yml

@@ -0,0 +1,64 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll site to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["gh-pages-nesi"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@8575951200e472d5f2d95c625da0c7bec8217c42 # v1.161.0
+        with:
+          ruby-version: '3.1' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 0 # Increment this number if you need to re-download cached gems
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v5
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - name: Upload artifact
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v3
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/test_and_build.yml

@@ -4,8 +4,6 @@ name: Check lesson and build for all configs
 on:
   pull_request:
   push:
-    branches:
-      - gh-pages
 
 jobs:
   lint_common_files:
@@ -18,6 +16,21 @@ jobs:
       - name: Check spelling
         run: |
           make spellcheck
+
+  proselint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+      - name: Install proselint
+        run: |
+          python3 -m pip install proselint
+      - name: Check prose
+        run: |
+          proselint **/*.md
       - name: Check top-level Markdown syntax
         uses: DavidAnson/markdownlint-cli2-action@v9
       - name: Check episode Markdown syntax
@@ -60,14 +73,7 @@ jobs:
     strategy:
       matrix:
         HPC_JEKYLL_CONFIG:
-          - Birmingham_Baskerville_slurm
-          - ComputeCanada_Graham_slurm
-          - EPCC_Cirrus_slurm
-          - HPCC_MagicCastle_slurm
-          - Magic_Castle_EESSI_slurm
-          - NIST_CTCMS_slurm
-          - Norway_SIGMA2_SAGA_slurm
-          - UCL_Myriad_sge
+          - NeSI_Mahuika_slurm
     steps:
       - uses: actions/checkout@v2
       - uses: ruby/setup-ruby@v1

Makefile

@@ -6,7 +6,8 @@ export SHELL = /bin/bash
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=bundle config --local set path .vendor/bundle && bundle install && bundle update && bundle exec jekyll
+#JEKYLL=bundle config --local set path .vendor/bundle && bundle install && bundle update && bundle exec jekyll
+JEKYLL=bundle exec jekyll
 HPC_JEKYLL_CONFIG?=
 PARSER=bin/markdown_ast.rb
 DST=_site

README.md

@@ -1,3 +1,22 @@
+
+### For NeSI developers:
+
+
+Our main branches are:
+
+* origin/gh-pages                 <-Do not use, this is for fetching changes from upstream
+* origin/gh-pages-upstream-compat <- This is used for changes we want to share with community
+* origin/gh-pages-nesi            <- Our NeSI specific lessons, not compatible with upstream
+
+To test locally, make your changes and run this. 
+
+```bash
+HPC_JEKYLL_CONFIG=_includes/snippets_library/NeSI_Mahuika_slurm/_config_options.yml make serve
+```
+
+---
+
+### General development notes:
 # Intro to HPC
 
 This lesson teaches the basics of interacting with high-performance computing
@@ -269,3 +288,4 @@ provided to help guide planning and decision-making.
 [mpi4py]: https://mpi4py.readthedocs.io
 [setup]: http://carpentries.github.io/lesson-example/setup.html
 [upstream]: https://github.com/carpentries-incubator/hpc-intro
+

SETUP_FOR_INSTRUCTORS.md

@@ -0,0 +1,29 @@
+# 
+
+Create workshop subdir.
+
+```
+mkdir <workshop name>
+```
+
+Get files.
+
+```
+wget https://raw.githubusercontent.com/nesi/hpc-intro/gh-pages-nesi/_includes/example_scripts/example-job.sh
+wget https://raw.githubusercontent.com/nesi/hpc-intro/gh-pages-nesi/_includes/example_scripts/array_sum2.r -O {{ site.example.script }} 
+wget https://raw.githubusercontent.com/nesi/hpc-intro/gh-pages-nesi/_includes/example_scripts/whothis.sh
+wget 
+wget
+```
+
+```
+mkdir birds
+cd birds
+touch kaka.txt kakapo.jpeg kea.txt kiwi.jpeg pukeko.jpeg
+```
+
+Set permissions.
+
+```
+chmod -R 755*
+```

_config.yml

@@ -1,8 +1,5 @@
-# HPC-Intro Jekyll configuration
----
-
 #------------------------------------------------------------
-# SITE specific configuration
+# NeSI: Mahuika + SLURM
 #------------------------------------------------------------
 
 # Cluster host and scheduler options: the defaults come from
@@ -20,73 +17,76 @@
 # installation. Remember to keep the leading slash on the
 # `snippets` variable below!
 
-# ---------------------------------------------------------------
-# HPC Carpentries in the Cloud: Slurm + Software Stack from EESSI
-# ---------------------------------------------------------------
-#
-# The HPC Carpentry Cluster in the Cloud is provided as a public
-# service by volunteers. It is provisioned with Magic Castle
-# <https://github.com/ComputeCanada/magic_castle> using the EESSI
-# <https://eessi.github.io/docs/> software stack. If you need an
-# account, please visit <cluster.hpc-carpentry.org>.
-#
-# Compute responsibly.
-
-snippets: "/snippets_library/HPCC_MagicCastle_slurm"
+snippets: "/snippets_library/NeSI_Mahuika_slurm"
 
 local:
   prompt: "[you@laptop:~]$"
   bash_shebang: "#!/usr/bin/env bash"
 
 remote:
-  name: "HPC Carpentry's Cloud Cluster"
-  login: "cluster.hpc-carpentry.org"
-  portal: "https://mokey.cluster.hpc-carpentry.org"
-  host: "login1"
-  node: "node1"
-  location: "cluster.hpc-carpentry.org"
+  name: "mahuika"
+  login: "nesi.org.nz"
+  portal: ""
+  host: "mahuika02"
+  node: "mahuika02"
+  location: "Greta Point Datacenter"
   homedir: "/home"
   user: "yourUsername"
+  prompt: "[yourUsername@mahuika ~]$"
+  bash_shebang: "#!/bin/bash -e"
   module_python3: "Python"
-  prompt: "[yourUsername@login1 ~]$"
-  bash_shebang: "#!/bin/bash"
+
 
 sched:
   name: "Slurm"
   submit:
     name: "sbatch"
     options: ""
   queue:
-    debug: "smnode"
-    testing: "cpubase_bycore_b1"
+    debug: "debug"
+    testing: ""
   status: "squeue"
   flag:
     user: "-u yourUsername"
+    me: "--me"
     interactive: ""
     histdetail: "-l -j"
-    name: "-J"
-    time: "-t"
-    queue: "-p"
-    nodes: "-N"
-    tasks: "-n"
+    name: "--job-name"
+    time: "--time"
+    queue: "--partition"
   del: "scancel"
   interactive: "srun"
   info: "sinfo"
   comment: "#SBATCH"
-  hist: "sacct -u yourUsername"
-  hist_filter: ""
+  hist: "sacct"
+  efficiency: "nn_seff"
+  projectcode: "nesi99991"
+
+# For 'R'
+example:
+  lang: "R"
+  shell: "Rscript "
+  script: "array_sum.r"
+  module: "R/4.3.1-gimkl-2022a"
+
+# For 'python'
+# example:
+#   lang: "Python"
+#   shell: "python"
+#   script: "array_sum.py"
+#   module: "Python/3.11.3-gimkl-2022a"
 
 episode_order:
-  - 10-hpc-intro
-  - 11-connecting
-  - 12-cluster
-  - 13-scheduler
-  - 14-environment-variables
-  - 15-modules
-  - 16-transferring-files
-  - 17-parallel
-  - 18-resources
-  - 19-responsibility
+  - 01-cluster
+  - 02-filesystem
+  - 04-modules
+  - 03-break1
+  - 05-scheduler
+  - 064-parallel
+  - 08-break2
+  - 07-resources
+  - 09-scaling
+
 
 #------------------------------------------------------------
 # Values for this lesson
@@ -103,10 +103,10 @@ carpentry: "incubator"
 title: "Introduction to High-Performance Computing"
 
 # Email address, no mailto:
-email: "team@carpentries.org"
+email: "support@nesi.org.nz"
 
 # Life cycle stage of the lesson ("pre-alpha", "alpha", "beta", "stable")?
-life_cycle: "alpha"
+life_cycle: "stable"
 
 #------------------------------------------------------------
 # Generic settings (should not need to change).
@@ -115,8 +115,20 @@ life_cycle: "alpha"
 # What kind of thing is this ("workshop" or "lesson")?
 kind: "lesson"
 
+# Workshop working directory.
+working_dir:
+  - /nesi/nobackup/nesi99991
+  - introhpc2403
+
 # Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
-start_time: 0
+# 600 is 10am
+start_time: 540
+# Start time for people wanting to skip bash content
+hpc_start_time: 780
+# Lesson to start at.
+hpc_start_lesson: 01-cluster
+# Script to run if skipping bash lessons. Should create neccicery files to get started.
+hpc_start_script: late_start.sh
 
 # Magic to make URLs resolve both locally and on GitHub. Please don't change.
 repository: <USERNAME>/<PROJECT>
@@ -141,6 +153,10 @@ training_site: "https://carpentries.github.io/instructor-training"
 workshop_repo: "https://github.com/carpentries/workshop-template"
 workshop_site: "https://carpentries.github.io/workshop-template"
 cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
+support_docs: "https://support.nesi.org.nz/hc/en-gb"
+exercise: "https://docs.google.com/spreadsheets/d/1D5PnhE6iJOB3ZKkDCiBHnk5CNZlhmj_gS-IXKGkkVoI/edit?usp=sharing"
+
+
 
 # Specify that things in the Episodes and Extras collections should be output.
 collections: