Update Gemfile and fix some typos

.codespell-ignore

@@ -0,0 +1,6 @@
+Fram
+dropse
+figurestyle
+hist
+namd
+rouge

.github/workflows/test_and_build.yml

@@ -8,28 +8,35 @@ on:
       - gh-pages
 
 jobs:
-  spellcheck:
+  lint_common_files:
     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 codespell
         run: |
-          python3 -m pip install codespell
+          sudo apt-get install codespell
       - name: Check spelling
         run: |
           make spellcheck
+      - name: Check top-level Markdown syntax
+        uses: DavidAnson/markdownlint-cli2-action@v9
+      - name: Check episode Markdown syntax
+        uses: DavidAnson/markdownlint-cli2-action@v9
+        with:
+          globs: _episodes/*.md
+      - name: Check extra Markdown syntax
+        uses: DavidAnson/markdownlint-cli2-action@v9
+        with:
+          globs: _extras/*.md
 
   check_lesson_and_build_default:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0.4'
+          bundler-cache: true
       - name: Install basic requirements
         run: |
           # Need this library for nokogiri
@@ -38,9 +45,6 @@ jobs:
           bundle config set path '.vendor/bundle'
           bundle config build.nokogiri --use-system-libraries
           bundle install
-      - name: "Lint episode markdown"
-        run: |
-          find _episodes -name \*.md -exec bundle exec mdl -r MD001,MD003,MD005,MD006,MD007,MD008,MD009,MD010,MD011,MD012,MD015,MD016,MD017,MD018,MD019,MD020,MD021,MD022,MD023,MD025,MD035,MD036,MD037,MD038,MD039,MD046 {} \;
       - name: "Check lesson for warnings"
         run: |
           make lesson-check-all
@@ -56,17 +60,20 @@ jobs:
     strategy:
       matrix:
         HPC_JEKYLL_CONFIG:
+          - Birmingham_Baskerville_slurm
           - ComputeCanada_Graham_slurm
           - EPCC_Cirrus_pbs
+          - HPCC_MagicCastle_slurm
+          - Magic_Castle_EESSI_slurm
           - NIST_CTCMS_slurm
           - Norway_SIGMA2_SAGA_slurm
           - UCL_Myriad_sge
-          - Magic_Castle_EESSI_slurm
     steps:
       - uses: actions/checkout@v2
       - uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0.4'
+          bundler-cache: true
       - name: Install basic requirements
         run: |
           # Need this library for nokogiri
@@ -78,6 +85,7 @@ jobs:
       - name: Check build ${{matrix.HPC_JEKYLL_CONFIG}}
         run: |
           make --always-make site HPC_JEKYLL_CONFIG=_includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}}/_config_options.yml
-      - name: "Lint snippet markdown"
-        run: |
-          find _includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}} -name \*.snip -exec bundle exec mdl -r MD001,MD003,MD005,MD006,MD007,MD008,MD009,MD010,MD011,MD012,MD015,MD016,MD017,MD018,MD019,MD020,MD021,MD022,MD023,MD025,MD035,MD036,MD037,MD038,MD039,MD046 {} \;
+      - name: Lint snippet markdown
+        uses: DavidAnson/markdownlint-cli2-action@v9
+        with:
+          globs: _includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}}/**/*.snip

.markdownlint-cli2.yaml

@@ -0,0 +1,73 @@
+# markdownlint-cli2:
+# - Example: <https://github.com/DavidAnson/markdownlint-cli2/blob/main/test/markdownlint-cli2-yaml-example/.markdownlint-cli2.yaml>
+# - Rules:   <https://github.com/DavidAnson/markdownlint/blob/main/README.md#rules--aliases>
+---
+config:
+  MD001: false  # heading-increment
+  MD002: false  # mdl rule undefined
+  MD003: true   # heading-style
+  MD004: true   # ul-style
+  MD005: true   # list-indent
+  MD006: false  # mdl rule undefined
+  MD007: true   # ul-indent
+  MD008: false  # mdl rule undefined
+  MD009: true   # no-trailing-spaces
+  MD010: true   # no-hard-tabs
+  MD011: true   # no-reversed-links
+  MD012: true   # no-multiple-blanks
+  MD013: false  # line-length
+  MD014: false  # commands-show-output
+  MD015: false  # mdl rule undefined
+  MD016: false  # mdl rule undefined
+  MD017: false  # mdl rule undefined
+  MD018: true   # no-missing-space-atx
+  MD019: true   # no-multiple-space-atx
+  MD020: true   # no-missing-space-closed-atx
+  MD021: true   # no-multiple-space-closed-atx
+  MD022: true   # blanks-around-headings
+  MD023: true   # heading-start-left
+  MD024: false  # no-duplicate-heading
+  MD025: true   # single-h1
+  MD026: false  # no-trailing-punctuation
+  MD027: false  # no-multiple-space-blockquote
+  MD028: false  # no-blanks-blockquote
+  MD029: true   # ol-prefix
+  MD030: true   # list-marker-space
+  MD031: false  # blanks-around-fences
+  MD032: true   # blanks-around-lists
+  MD033: false  # no-inline-html
+  MD034: true   # no-bare-urls
+  MD035: true   # hr-style
+  MD036: true   # no-emphasis-as-heading
+  MD037: true   # no-space-in-emphasis
+  MD038: true   # no-space-in-code
+  MD039: true   # no-space-in-links
+  MD040: false  # fenced-code-language
+  MD041: false  # first-line-h1
+  MD042: true   # no-empty-links
+  MD043: false  # required-headings
+  MD044: true   # proper-names
+  MD045: true   # no-alt-text
+  MD046: true   # code-block-style
+  MD047: true   # single-trailing-newline
+  MD048: true   # code-fence-style
+  MD049: false  # emphasis-style
+  MD050: false  # strong-style
+  MD051: true   # link-fragments
+  MD052: true   # reference-links-images
+  MD053: false  # link-image-reference-definitions
+  MD054: false  # link-image-style
+  MD055: true   # table-pipe-style
+  MD056: true   # table-column-count
+
+ignores:
+  - .vendor
+  - .bundle
+  - _extras/figures.md  # really HTML
+  - _includes/links.md  # just a list of links
+  - "**/*.html"
+  - "**/*.sh"
+  - "**/*.yaml"
+  - "**/*.yml"
+
+# noProgress: true

CONTRIBUTING.md

@@ -130,4 +130,3 @@ which everyone is welcome to join. You can also [reach us by email][email].
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: https://software-carpentry.org/lessons/
 [swc-site]: https://software-carpentry.org/
-

Gemfile

@@ -1,4 +1,18 @@
-source "https://rubygems.org"
-gem "github-pages", group: :jekyll_plugins
+# frozen_string_literal: true
+
+source 'https://rubygems.org'
+
+git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
+
+# Synchronize with https://pages.github.com/versions
+ruby '3.0.4'
+
+gem 'github-pages', group: :jekyll_plugins
+
+if Gem::Version.new(RUBY_VERSION) >= Gem::Version.new('3.0.0')
+  gem 'webrick', '>= 1.6.1'
+end
+
 gem "kramdown-parser-gfm"
+
 gem "mdl"

LICENSE.md

@@ -1,9 +1,7 @@
 ---
-title: "Licenses"
+title: "License: CC BY 4.0"
 ---
 
-# CC BY 4.0
-
 ## Instructional Material
 
 All High Performance Computing Carpentry instructional material is

Makefile

@@ -154,7 +154,7 @@ lesson-fixme :
 
 ## spellcheck
 spellcheck:
-	codespell --skip="assets,*.svg,.vendor" --quiet-level=2  -L "dropse,figurestyle,hist,namd,rouge"
+	codespell --skip=".bundle,.vendor,assets,*.svg" --quiet-level=2 --ignore-words=".codespell-ignore"
 
 ##
 ## IV. Auxililary (plumbing) commands

_config.yml

@@ -94,7 +94,7 @@ episode_order:
 # "swc": Software Carpentry
 # "dc":  Data Carpentry
 # "lc":  Library Carpentry
-# "cp":  Carpentries (e.g., instructor traning)
+# "cp":  Carpentries (e.g., instructor training)
 carpentry: "incubator"
 
 # Overall title for pages.

_episodes/11-connecting.md

@@ -409,6 +409,7 @@ which you can edit with your preferences; and `.ssh` is a directory storing SSH
 keys and a record of authorized connections.
 
 {% unless site.remote.portal %}
+
 ### Install Your SSH Key
 
 > ## There May Be a Better Way

_episodes/13-scheduler.md

@@ -181,7 +181,6 @@ Submit the job and monitor its status:
 
 Fantastic, we've successfully changed the name of our job!
 
-
 ### Resource Requests
 
 What about more important changes, such as the number of cores and memory for

_extras/discuss.md

@@ -82,20 +82,19 @@ individual to individual!
 >
 > - Vary the number of threads used per process
 > - Reduce the number of cores used per node
-> - Allow the calculation to use Symmetric Mutithreading (SMT) if enabled
+> - Allow the calculation to use Symmetric Multithreading (SMT) if enabled
 >
 > Please ask for more information on these options from a helper!
 {: .challenge}
 
 > ## Running Many Serial BLAST+ Analyses in Parallel
 >
-> [BLAST+](
-https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+> [BLAST+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
 > finds regions of similarity between biological sequences. The program
 > compares nucleotide or protein sequences to sequence databases and calculates
 > the statistical significance.
 >
-> In this exercise, you should use what you have learnt so far to set up a way
+> In this exercise, you should use what you have learned so far to set up a way
 > to run multiple serial BLAST+ analyses in parallel. There are many different
 > ways to do this that can be used on their own or in combination. Some ideas
 > include:
@@ -107,14 +106,12 @@ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do
 >
 > We have prepared an example dataset that has 100 sequences to analyse
 > (actually this is 10 sequences repeated 10 times). This set is based on the
-> [BLAST GNU Parallel example](
-https://github.com/LangilleLab/microbiome_helper/wiki/Quick-Introduction-to-GNU-Parallel)
+> [BLAST GNU Parallel example](https://github.com/LangilleLab/microbiome_helper/wiki/Quick-Introduction-to-GNU-Parallel)
 >
 > This exercise involves:
 >
 > - Downloading and expanding the dataset to the HPC system from:
->   [{{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz](
->   {{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz)
+>   [{{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz]({{ site.url }}{{site.baseurl}}/files/parallel_example.tar.gz)
 > - Writing a job submission script to run a single analysis using the `blast`
 >   module and the following command:
 >

_extras/guide.md

@@ -66,8 +66,7 @@ is a great way to contribute.
 :    *to be defined*
 
 [Supercomputer](https://en.wikipedia.org/wiki/Supercomputer)
-:    ["... a major scientific instrument ..."](
-https://www.hpcnotes.com/2015/10/essential-analogies-for-hpc-advocate.html)
+:    ["... a major scientific instrument ..."](https://www.hpcnotes.com/2015/10/essential-analogies-for-hpc-advocate.html)
 
 [Workstation](https://en.wikipedia.org/wiki/Workstation)
 :    *to be defined*

_extras/learner-prerequisites.md

@@ -14,8 +14,7 @@ bring all prerequisites to the course.
 ## Pre-Workshop Survey
 
 For a motivation of this survey type, see Greg Wilson's template in [Teaching
-Tech Together](
-https://teachtogether.tech/en/index.html#s:checklists-preassess).
+Tech Together](https://teachtogether.tech/en/index.html#s:checklists-preassess).
 
 ### Shell
 

_includes/snippets_library/Birmingham_Baskerville_slurm/modules/wrong-gcc-version.snip

@@ -3,32 +3,29 @@ C/C++/Fortran compiler. Tons of software is dependent on the GCC version, and
 might not compile or run if the wrong version is loaded. In this case, there
 are few different versions:
 
-`GCC/7.3.0-2.30    GCC/8.2.0-2.31.1    GCC/8.3.0    GCC/9.3.0`
+`GCC/7.3.0    GCC/8.2.0    GCC/8.3.0    GCC/9.3.0`
 
 How do we load each copy and which copy is the default?
 
-On SAGA and Fram we do not have default modules and we must use the full name
-to load it.
-
 ```
-{{ site.host_prompt }} module load gcc
+{{ site.host_prompt }} module load GCC
 ```
 {: .language-bash}
 
 ```
 Lmod has detected the following error:  The following module(s) are unknown:
-"gcc"
+"GCC"
 
 Please check the spelling or version number. Also try "module spider ..."
 It is also possible your cache file is out-of-date; it may help to try:
-  $ module --ignore-cache load "gcc"
+  $ module --ignore-cache load "GCC"
 ```
 {: .output}
 
 To load a software module we must specify the full module name:
 
 ```
-{{ site.host_prompt }} module load GCC/8.2.0-2.31.1
+{{ site.host_prompt }} module load GCC/8.2.0
 {{ site.host_prompt }} gcc --version
 ```
 {: .language-bash}

_includes/snippets_library/Birmingham_Baskerville_slurm/parallel/eight-tasks-jobscript.snip

@@ -0,0 +1,15 @@
+```
+{{ site.remote.bash_shebang }}
+{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-pi
+{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
+{{ site.sched.comment }} -N 1
+{{ site.sched.comment }} -n 8
+{{ site.sched.comment }} --mem=3G
+
+# Load the computing environment we need
+module load python3
+
+# Execute the task
+mpiexec amdahl
+```
+{: .language-bash}

_includes/snippets_library/Birmingham_Baskerville_slurm/parallel/one-task-jobscript.snip

@@ -0,0 +1,15 @@
+```
+{{ site.remote.bash_shebang }}
+{{ site.sched.comment }} {{ site.sched.flag.name }} solo-job
+{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
+{{ site.sched.comment }} -N 1
+{{ site.sched.comment }} -n 1
+{{ site.sched.comment }} --mem=3G
+
+# Load the computing environment we need
+module load python
+
+# Execute the task
+mpiexec amdahl
+```
+{: .language-bash}

_includes/snippets_library/EPCC_Cirrus_pbs/modules/wrong-gcc-version.snip

@@ -89,4 +89,3 @@ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 {: .output}
 
 This achieves the same result as unload followed by load but in a single step.
-

_includes/snippets_library/EPCC_Cirrus_pbs/scheduler/terminate-multiple-jobs.snip

@@ -1,2 +0,0 @@
-
-

_includes/snippets_library/README.md

@@ -28,5 +28,3 @@ If the naming seems counter-intuitive, please feel free to make
 changes locally, and file an issue of submit a pull request to fix it
 upstream. None of this is set in stone, and improvements are always
 welcome.
-
-