From 3593fe9a25149600a0472a758d5b7e2bab51eab1 Mon Sep 17 00:00:00 2001
From: jlchang <jlchang@broadinstitute.org>
Date: Wed, 2 Oct 2024 07:54:57 -0400
Subject: [PATCH 01/33] Update README.md to warn of transition state

---
 README.md | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 331faa7d..3179f672 100644
--- a/README.md
+++ b/README.md
@@ -7,11 +7,12 @@ This lesson teaches the basics of interacting with high-performance computing
 
 ## Using this material
 
-NOTE: This is *not* Carpentries boilerplate! Please read carefully.
+NOTE: This lesson is being transitioned to Carpentries Workbench but is still *not* Carpentries boilerplate! 
+Instructions below still need to be edited to reflect the transition. Proceed with caution.
 
-1. Follow the instructions found in The Carpentries' [example lesson][ex-lesson]
+1. ~~Follow the instructions found in The Carpentries' [example lesson][ex-lesson]
   to create a repository for your lesson. Install Ruby, Make, and Jekyll
-  following the instructions [here][setup].
+  following the instructions [here][setup].~~
 
 2. For easier portability, we use snippets of text and code to capture inputs
   and outputs that are host- or site-specific and cannot be scripted. These
@@ -37,17 +38,17 @@ NOTE: This is *not* Carpentries boilerplate! Please read carefully.
   or omit episodes, by editing the configuration block under `episode_names`
   in this file.
 
-4. Set the environment variable `HPC_JEKYLL_CONFIG` to the relative path of the
-  configuration file in your snippets folder:
+4. ~~Set the environment variable `HPC_JEKYLL_CONFIG` to the relative path of the
+  configuration file in your snippets folder:~~
   
   ```bash
   export HPC_JEKYLL_CONFIG=_includes/snippets_library/.../_config_options.yml
   ```
 
-5. Preview the lesson locally, by running `make serve`. You can then view the
+5. ~~Preview the lesson locally, by running `make serve`. You can then view the
   website in your browser, following the links in the output (usually,
   <https://localhost:4000>). Pages will be automatically regenerated every
-  time you write to them.
+  time you write to them.~~
 
 6. If there are discrepancies in the output, edit the snippet file containing
   it, or create a new one and customize.

From 7e1aea24b3a60c06a2564ad7f29f007a1558a9da Mon Sep 17 00:00:00 2001
From: Jean Chang <jlchang@broadinstitute.org>
Date: Thu, 3 Oct 2024 06:59:55 -0400
Subject: [PATCH 02/33] test simpleminded xfer of epcc file

---
 11-epcc-hpc-intro.Rmd       | 190 ++++++++++++++++++++++++++++++++++++
 config.yaml                 |   1 +
 episodes/lesson_config.yaml |  50 ++++++++++
 3 files changed, 241 insertions(+)
 create mode 100644 11-epcc-hpc-intro.Rmd
 create mode 100644 episodes/lesson_config.yaml

diff --git a/11-epcc-hpc-intro.Rmd b/11-epcc-hpc-intro.Rmd
new file mode 100644
index 00000000..b088a07f
--- /dev/null
+++ b/11-epcc-hpc-intro.Rmd
@@ -0,0 +1,190 @@
+---
+title: "Why use an HPC System?"
+teaching: 15
+exercises: 5
+---
+
+```{r load_config, include=FALSE}
+library(yaml)
+config <- yaml.load_file("lesson_config.yaml")
+```
+
+::: questions
+ - "Why would I be interested in High Performance Computing (HPC)?"
+ - "What can I expect to learn from this course?"
+:::
+
+::: objectives
+ - "Be able to describe what an HPC system is"
+ - "Identify how an HPC system could benefit you."
+:::
+
+## HPC research examples
+
+Frequently, research problems that use computing can outgrow the capabilities
+of the desktop or laptop computer where they started:
+
+* A statistics student wants to cross-validate a model. This involves running
+  the model 1000 times &mdash; but each run takes an hour. Running the model on
+  a laptop will take over a month! In this research problem, final results are
+  calculated after all 1000 models have run, but typically only one model is
+  run at a time (in **serial**) on the laptop. Since each of the 1000 runs is
+  independent of all others, and given enough computers, it's theoretically
+  possible to run them all at once (in **parallel**).
+* A genomics researcher has been using small datasets of sequence data, but
+  soon will be receiving a new type of sequencing data that is 10 times as
+  large. It's already challenging to open the datasets on a computer &mdash;
+  analyzing these larger datasets will probably crash it. In this research
+  problem, the calculations required might be impossible to parallelize, but a
+  computer with **more memory** would be required to analyze the much larger
+  future data set.
+* An engineer is using a fluid dynamics package that has an option to run in
+  parallel. So far, this option was not utilized on a desktop. In going from 2D
+  to 3D simulations, the simulation time has more than tripled. It might be
+  useful to take advantage of that option or feature. In this research problem,
+  the calculations in each region of the simulation are largely independent of
+  calculations in other regions of the simulation. It's possible to run each
+  region's calculations simultaneously (in **parallel**), communicate selected
+  results to adjacent regions as needed, and repeat the calculations to
+  converge on a final set of results. In moving from a 2D to a 3D model, **both
+  the amount of data and the amount of calculations increases greatly**, and
+  it's theoretically possible to distribute the calculations across multiple
+  computers communicating over a shared network.
+
+In all these cases, access to more (and larger) computers is needed. Those
+computers should be usable at the same time, **solving many researchers'
+problems in parallel**.
+
+::: discussion
+
+## Break the Ice
+Talk to your neighbour, office mate or [rubber duck](https://rubberduckdebugging.com/) about your research.
+
+ * How does computing help you do your research?
+ * How could more computing help you do more or better research?
+:::
+
+## A Standard Laptop for Standard Tasks
+
+Today, people coding or analysing data typically work with laptops.
+
+![A standard laptop](fig/200px-laptop-openclipartorg-aoguerrero.svg){alt="A standard laptop"}
+
+
+Let's dissect what resources programs running on a laptop require:
+
+* the keyboard and/or touchpad is used to tell the computer what to do
+  (**Input**)
+* the internal computing resources **Central Processing Unit** and **Memory**
+  perform calculation
+* the display depicts progress and results (**Output**)
+
+Schematically, this can be reduced to the following:
+
+![Schematic of how a computer works](fig/Simple_Von_Neumann_Architecture.svg){
+   alt="Schematic of how a computer works"}
+
+## When Tasks Take Too Long
+
+When the task to solve becomes heavy on computations, the operations are
+typically out-sourced from the local laptop or desktop to elsewhere. Take for
+example the task to find the directions for your next vacation. The
+capabilities of your laptop are typically not enough to calculate that route
+spontaneously: [finding the shortest path](https://en.wikipedia.org/wiki/Dijkstra's_algorithm) through a network runs on
+the order of (*v* log *v*) time, where *v* (vertices) represents the number of
+intersections in your map. Instead of doing this yourself, you use a website,
+which in turn runs on a server, that is almost definitely not in the same room
+as you are.
+
+```{asis}
+<figure style="max-width: 30%; text-align: center">
+  <img src="fig/servers-openclipartorg-ericlemerdy.svg" alt="A rack half full with servers" class="figure">
+  <div class="figcaption">A rack half full with servers</div>
+</figure>
+```
+
+Note here, that a server is mostly a noisy computer mounted into a rack cabinet
+which in turn resides in a data center. The internet made it possible that
+these data centers do not require to be nearby your laptop. What people call
+**the cloud** is mostly a web-service where you can rent such servers by
+providing your credit card details and requesting remote resources that satisfy
+your requirements. This is often handled through an online, browser-based
+interface listing the various machines available and their capacities in terms
+of processing power, memory, and storage.
+
+The server itself has no direct display or input methods attached to it. But
+most importantly, it has much more storage, memory and compute capacity than
+your laptop will ever have. In any case, you need a local device (laptop,
+workstation, mobile phone or tablet) to interact with this remote machine,
+which people typically call 'a server'.
+
+## When One Server Is Not Enough
+
+If the computational task or analysis to complete is daunting for a single
+server, larger agglomerations of servers are used. These go by the name of
+"clusters" or "super computers".
+
+```{asis}
+<figure style="max-width: 30%; text-align: center; display: block">
+  <img src="fig/serverrack-openclipartorg-psteinb-basedon-ericlemerdy.svg" alt="A rack with servers" class="figure">
+  <div class="figcaption">A rack with servers</div>
+</figure>
+```
+
+The methodology of providing the input data, configuring the program options,
+and retrieving the results is quite different to using a plain laptop.
+Moreover, using a graphical interface is often discarded in favor of using the
+command line. This imposes a double paradigm shift for prospective users asked
+to
+
+1. work with the command line interface (CLI), rather than a graphical user
+   interface (GUI)
+1. work with a distributed set of computers (called nodes) rather than the
+   machine attached to their keyboard & mouse
+
+::: challenge
+
+## I've Never Used a Server, Have I?
+Take a minute and think about which of your daily interactions with a
+computer may require a remote server or even cluster to provide you with
+results.
+
+::: solution
+
+## Some Ideas
+
+* Checking email: your computer (possibly in your pocket) contacts a remote
+  machine, authenticates, and downloads a list of new messages; it also
+  uploads changes to message status, such as whether you read, marked as
+  junk, or deleted the message. Since yours is not the only account, the
+  mail server is probably one of many in a data center.
+* Searching for a phrase online involves comparing your search term against
+  a massive database of all known sites, looking for matches. This "query"
+  operation can be straightforward, but building that database is a
+  [monumental task](https://en.wikipedia.org/wiki/MapReduce)! Servers are
+  involved at every step.
+* Searching for directions on a mapping website involves connecting your
+  (A) starting and (B) end points by [traversing a graph](
+  https://en.wikipedia.org/wiki/Dijkstra%27s_algorithm) in search of
+  the "shortest" path by distance, time, expense, or another metric.
+  Converting a map into the right form is relatively simple, but
+  calculating all the possible routes between A and B is expensive.
+
+Checking email could be serial: your machine connects to one server and
+exchanges data. Searching by querying the database for your search term (or
+endpoints) could also be serial, in that one machine receives your query
+and returns the result. However, assembling and storing the full database
+is far beyond the capability of any one machine. Therefore, these functions
+are served in parallel by a large, ["hyperscale"](https://en.wikipedia.org/wiki/Hyperscale_computing) 
+collection of servers working together.
+:::
+:::
+
+::: keypoints
+ - "High Performance Computing (HPC) typically involves connecting to very large
+  computing systems elsewhere in the world."
+ - "These other systems can be used to do work that would either be impossible
+  or much slower on smaller systems."
+ - "The standard method of interacting with such systems is via a command line
+  interface called Bash."
+:::
diff --git a/config.yaml b/config.yaml
index 8c7be715..39f42e36 100644
--- a/config.yaml
+++ b/config.yaml
@@ -67,6 +67,7 @@ contact: 'team@carpentries.org'
 episodes: 
 - 10-hpc-intro.md
 - 11-connecting.md
+- 11-epcc-hpc-intro.Rmd
 - 12-cluster.md
 - 13-scheduler.md
 - 14-environment-variables.md
diff --git a/episodes/lesson_config.yaml b/episodes/lesson_config.yaml
new file mode 100644
index 00000000..5425d7b1
--- /dev/null
+++ b/episodes/lesson_config.yaml
@@ -0,0 +1,50 @@
+---
+local:
+  prompt: "[user@laptop ~]$"
+  bash_shebang: "#!/bin/bash"
+
+snippets: EPCC_ARCHER2_slurm
+baseurl: "https://epcced.github.io/2023-06-28-uoe-hpcintro"
+
+remote:
+  name: "ARCHER2"
+  host_id: "EPCC_ARCHER2"
+  login: "login.archer2.ac.uk"
+  host: "ln03"
+  node: "nid001053"
+  location: "EPCC, The University of Edinburgh"
+  homedir: "/home/ta114/ta114/"
+  user: "userid"
+  prompt: "userid@ln03:~>"
+  prompt_work: "userid@uan01:/work/ta114/ta114/userid>"
+  module_python3: "cray-python"
+  bash_shebang: "#!/bin/bash"
+
+sched:
+  name: "Slurm"
+  partition: "standard"
+  reservation: "shortqos"
+  qos: "short"
+  budget: "short"
+  submit:
+    name: "sbatch"
+    options: "--partition=standard --qos=short"
+  queue:
+    debug: ""
+    testing: ""
+  status: "squeue"
+  flag:
+    user: "-u userid"
+    interactive: ""
+    histdetail: "-l -j"
+    name: "--job-name"
+    time: "--time"
+    queue: "--partition"
+    nodes: "--nodes"
+    tasks: ""
+  del: "scancel"
+  interactive: "srun"
+  info: "sinfo"
+  comment: "#SBATCH"
+  hist: "sacct"
+  project: ta114

From b2a3ad89a08e861e62be801158b6702118e6a591 Mon Sep 17 00:00:00 2001
From: Jean Chang <jlchang@broadinstitute.org>
Date: Thu, 3 Oct 2024 07:07:09 -0400
Subject: [PATCH 03/33] get file in right place

---
 11-epcc-hpc-intro.Rmd => episodes/11-epcc-hpc-intro.Rmd | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename 11-epcc-hpc-intro.Rmd => episodes/11-epcc-hpc-intro.Rmd (100%)

diff --git a/11-epcc-hpc-intro.Rmd b/episodes/11-epcc-hpc-intro.Rmd
similarity index 100%
rename from 11-epcc-hpc-intro.Rmd
rename to episodes/11-epcc-hpc-intro.Rmd

From 7f6bf13e4aaadd7a9b7e186db1dc2102eee29ae0 Mon Sep 17 00:00:00 2001
From: Jean Chang <jlchang@broadinstitute.org>
Date: Thu, 3 Oct 2024 07:18:18 -0400
Subject: [PATCH 04/33] trivial change to try out repo's PR process

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 3179f672..e2421275 100644
--- a/README.md
+++ b/README.md
@@ -68,6 +68,7 @@ Instructions below still need to be edited to reflect the transition. Proceed wi
   future will probably not be accepted.
 
 ## Deploying a Customized Lesson
+**While this lesson is in transition, we do not recommend customizing**
 
 The steps above will help you port the default HPC Intro lesson to your
 specific cluster, but the changes will only be visible on your local machine.

From 8a8833407823a325b203c6bf0036942a4a89e763 Mon Sep 17 00:00:00 2001
From: Jean Chang <jlchang@broadinstitute.org>
Date: Thu, 3 Oct 2024 07:33:21 -0400
Subject: [PATCH 05/33] pick a different epcc episode

---
 config.yaml                    |   2 +-
 episodes/11-epcc-hpc-intro.Rmd | 190 ------------------
 episodes/12-epcc-cluster.Rmd   | 351 +++++++++++++++++++++++++++++++++
 3 files changed, 352 insertions(+), 191 deletions(-)
 delete mode 100644 episodes/11-epcc-hpc-intro.Rmd
 create mode 100644 episodes/12-epcc-cluster.Rmd

diff --git a/config.yaml b/config.yaml
index 39f42e36..96dfebfb 100644
--- a/config.yaml
+++ b/config.yaml
@@ -67,8 +67,8 @@ contact: 'team@carpentries.org'
 episodes: 
 - 10-hpc-intro.md
 - 11-connecting.md
-- 11-epcc-hpc-intro.Rmd
 - 12-cluster.md
+- 12-epcc-cluster.Rmd
 - 13-scheduler.md
 - 14-environment-variables.md
 - 15-modules.md
diff --git a/episodes/11-epcc-hpc-intro.Rmd b/episodes/11-epcc-hpc-intro.Rmd
deleted file mode 100644
index b088a07f..00000000
--- a/episodes/11-epcc-hpc-intro.Rmd
+++ /dev/null
@@ -1,190 +0,0 @@
----
-title: "Why use an HPC System?"
-teaching: 15
-exercises: 5
----
-
-```{r load_config, include=FALSE}
-library(yaml)
-config <- yaml.load_file("lesson_config.yaml")
-```
-
-::: questions
- - "Why would I be interested in High Performance Computing (HPC)?"
- - "What can I expect to learn from this course?"
-:::
-
-::: objectives
- - "Be able to describe what an HPC system is"
- - "Identify how an HPC system could benefit you."
-:::
-
-## HPC research examples
-
-Frequently, research problems that use computing can outgrow the capabilities
-of the desktop or laptop computer where they started:
-
-* A statistics student wants to cross-validate a model. This involves running
-  the model 1000 times &mdash; but each run takes an hour. Running the model on
-  a laptop will take over a month! In this research problem, final results are
-  calculated after all 1000 models have run, but typically only one model is
-  run at a time (in **serial**) on the laptop. Since each of the 1000 runs is
-  independent of all others, and given enough computers, it's theoretically
-  possible to run them all at once (in **parallel**).
-* A genomics researcher has been using small datasets of sequence data, but
-  soon will be receiving a new type of sequencing data that is 10 times as
-  large. It's already challenging to open the datasets on a computer &mdash;
-  analyzing these larger datasets will probably crash it. In this research
-  problem, the calculations required might be impossible to parallelize, but a
-  computer with **more memory** would be required to analyze the much larger
-  future data set.
-* An engineer is using a fluid dynamics package that has an option to run in
-  parallel. So far, this option was not utilized on a desktop. In going from 2D
-  to 3D simulations, the simulation time has more than tripled. It might be
-  useful to take advantage of that option or feature. In this research problem,
-  the calculations in each region of the simulation are largely independent of
-  calculations in other regions of the simulation. It's possible to run each
-  region's calculations simultaneously (in **parallel**), communicate selected
-  results to adjacent regions as needed, and repeat the calculations to
-  converge on a final set of results. In moving from a 2D to a 3D model, **both
-  the amount of data and the amount of calculations increases greatly**, and
-  it's theoretically possible to distribute the calculations across multiple
-  computers communicating over a shared network.
-
-In all these cases, access to more (and larger) computers is needed. Those
-computers should be usable at the same time, **solving many researchers'
-problems in parallel**.
-
-::: discussion
-
-## Break the Ice
-Talk to your neighbour, office mate or [rubber duck](https://rubberduckdebugging.com/) about your research.
-
- * How does computing help you do your research?
- * How could more computing help you do more or better research?
-:::
-
-## A Standard Laptop for Standard Tasks
-
-Today, people coding or analysing data typically work with laptops.
-
-![A standard laptop](fig/200px-laptop-openclipartorg-aoguerrero.svg){alt="A standard laptop"}
-
-
-Let's dissect what resources programs running on a laptop require:
-
-* the keyboard and/or touchpad is used to tell the computer what to do
-  (**Input**)
-* the internal computing resources **Central Processing Unit** and **Memory**
-  perform calculation
-* the display depicts progress and results (**Output**)
-
-Schematically, this can be reduced to the following:
-
-![Schematic of how a computer works](fig/Simple_Von_Neumann_Architecture.svg){
-   alt="Schematic of how a computer works"}
-
-## When Tasks Take Too Long
-
-When the task to solve becomes heavy on computations, the operations are
-typically out-sourced from the local laptop or desktop to elsewhere. Take for
-example the task to find the directions for your next vacation. The
-capabilities of your laptop are typically not enough to calculate that route
-spontaneously: [finding the shortest path](https://en.wikipedia.org/wiki/Dijkstra's_algorithm) through a network runs on
-the order of (*v* log *v*) time, where *v* (vertices) represents the number of
-intersections in your map. Instead of doing this yourself, you use a website,
-which in turn runs on a server, that is almost definitely not in the same room
-as you are.
-
-```{asis}
-<figure style="max-width: 30%; text-align: center">
-  <img src="fig/servers-openclipartorg-ericlemerdy.svg" alt="A rack half full with servers" class="figure">
-  <div class="figcaption">A rack half full with servers</div>
-</figure>
-```
-
-Note here, that a server is mostly a noisy computer mounted into a rack cabinet
-which in turn resides in a data center. The internet made it possible that
-these data centers do not require to be nearby your laptop. What people call
-**the cloud** is mostly a web-service where you can rent such servers by
-providing your credit card details and requesting remote resources that satisfy
-your requirements. This is often handled through an online, browser-based
-interface listing the various machines available and their capacities in terms
-of processing power, memory, and storage.
-
-The server itself has no direct display or input methods attached to it. But
-most importantly, it has much more storage, memory and compute capacity than
-your laptop will ever have. In any case, you need a local device (laptop,
-workstation, mobile phone or tablet) to interact with this remote machine,
-which people typically call 'a server'.
-
-## When One Server Is Not Enough
-
-If the computational task or analysis to complete is daunting for a single
-server, larger agglomerations of servers are used. These go by the name of
-"clusters" or "super computers".
-
-```{asis}
-<figure style="max-width: 30%; text-align: center; display: block">
-  <img src="fig/serverrack-openclipartorg-psteinb-basedon-ericlemerdy.svg" alt="A rack with servers" class="figure">
-  <div class="figcaption">A rack with servers</div>
-</figure>
-```
-
-The methodology of providing the input data, configuring the program options,
-and retrieving the results is quite different to using a plain laptop.
-Moreover, using a graphical interface is often discarded in favor of using the
-command line. This imposes a double paradigm shift for prospective users asked
-to
-
-1. work with the command line interface (CLI), rather than a graphical user
-   interface (GUI)
-1. work with a distributed set of computers (called nodes) rather than the
-   machine attached to their keyboard & mouse
-
-::: challenge
-
-## I've Never Used a Server, Have I?
-Take a minute and think about which of your daily interactions with a
-computer may require a remote server or even cluster to provide you with
-results.
-
-::: solution
-
-## Some Ideas
-
-* Checking email: your computer (possibly in your pocket) contacts a remote
-  machine, authenticates, and downloads a list of new messages; it also
-  uploads changes to message status, such as whether you read, marked as
-  junk, or deleted the message. Since yours is not the only account, the
-  mail server is probably one of many in a data center.
-* Searching for a phrase online involves comparing your search term against
-  a massive database of all known sites, looking for matches. This "query"
-  operation can be straightforward, but building that database is a
-  [monumental task](https://en.wikipedia.org/wiki/MapReduce)! Servers are
-  involved at every step.
-* Searching for directions on a mapping website involves connecting your
-  (A) starting and (B) end points by [traversing a graph](
-  https://en.wikipedia.org/wiki/Dijkstra%27s_algorithm) in search of
-  the "shortest" path by distance, time, expense, or another metric.
-  Converting a map into the right form is relatively simple, but
-  calculating all the possible routes between A and B is expensive.
-
-Checking email could be serial: your machine connects to one server and
-exchanges data. Searching by querying the database for your search term (or
-endpoints) could also be serial, in that one machine receives your query
-and returns the result. However, assembling and storing the full database
-is far beyond the capability of any one machine. Therefore, these functions
-are served in parallel by a large, ["hyperscale"](https://en.wikipedia.org/wiki/Hyperscale_computing) 
-collection of servers working together.
-:::
-:::
-
-::: keypoints
- - "High Performance Computing (HPC) typically involves connecting to very large
-  computing systems elsewhere in the world."
- - "These other systems can be used to do work that would either be impossible
-  or much slower on smaller systems."
- - "The standard method of interacting with such systems is via a command line
-  interface called Bash."
-:::
diff --git a/episodes/12-epcc-cluster.Rmd b/episodes/12-epcc-cluster.Rmd
new file mode 100644
index 00000000..8edc631b
--- /dev/null
+++ b/episodes/12-epcc-cluster.Rmd
@@ -0,0 +1,351 @@
+---
+title: "Working on a remote HPC system"
+teaching: 25
+exercises: 10
+---
+
+```{r load_config, include=FALSE}
+library(yaml)
+config <- yaml.load_file("lesson_config.yaml")
+snippets <- paste('files/snippets/', config$snippets, sep='')
+```
+
+::: questions
+ - "What is an HPC system?"
+ - "How does an HPC system work?"
+ - "How do I log on to a remote HPC system?"
+:::
+
+::: objectives
+ - "Connect to a remote HPC system."
+ - "Understand the general HPC system architecture."
+:::
+
+## What Is an HPC System?
+
+The words "cloud", "cluster", and the phrase "high-performance computing" or
+"HPC" are used a lot in different contexts and with various related meanings.
+So what do they mean? And more importantly, how do we use them in our work?
+
+The *cloud* is a generic term commonly used to refer to computing resources
+that are a) *provisioned* to users on demand or as needed and b) represent real
+or *virtual* resources that may be located anywhere on Earth. For example, a
+large company with computing resources in Brazil, Zimbabwe and Japan may manage
+those resources as its own *internal* cloud and that same company may also
+utilize commercial cloud resources provided by Amazon or Google. Cloud
+resources may refer to machines performing relatively simple tasks such as
+serving websites, providing shared storage, providing web services (such as
+e-mail or social media platforms), as well as more traditional compute
+intensive tasks such as running a simulation.
+
+The term *HPC system*, on the other hand, describes a stand-alone resource for
+computationally intensive workloads. They are typically comprised of a
+multitude of integrated processing and storage elements, designed to handle
+high volumes of data and/or large numbers of floating-point operations
+([FLOPS](https://en.wikipedia.org/wiki/FLOPS)) with the highest possible
+performance. For example, all of the machines on the
+[Top-500](https://www.top500.org) list are HPC systems. To support these
+constraints, an HPC resource must exist in a specific, fixed location:
+networking cables can only stretch so far, and electrical and optical signals
+can travel only so fast.
+
+The word "cluster" is often used for small to moderate scale HPC resources less
+impressive than the [Top-500](https://www.top500.org). Clusters are often
+maintained in computing centers that support several such systems, all sharing
+common networking and storage to support common compute intensive tasks.
+
+## Logging In
+
+The first step in using a cluster is to establish a connection from our laptop
+to the cluster. When we are sitting at a computer (or standing, or holding it
+in our hands or on our wrists), we have come to expect a visual display with
+icons, widgets, and perhaps some windows or applications: a graphical user
+interface, or GUI. Since computer clusters are remote resources that we connect
+to over often slow or laggy interfaces (WiFi and VPNs especially), it is more
+practical to use a command-line interface, or CLI, in which commands and
+results are transmitted via text, only. Anything other than text (images, for
+example) must be written to disk and opened with a separate program.
+
+If you have ever opened the Windows Command Prompt or macOS Terminal, you have
+seen a CLI. If you have already taken The Carpentries' courses on the UNIX
+Shell or Version Control, you have used the CLI on your local machine somewhat
+extensively. The only leap to be made here is to open a CLI on a *remote*
+machine, while taking some precautions so that other folks on the network can't
+see (or change) the commands you're running or the results the remote machine
+sends back. We will use the Secure SHell protocol (or SSH) to open an encrypted
+network connection between two machines, allowing you to send & receive text
+and data without having to worry about prying eyes.
+
+![Connect to cluster](fig/connect-to-remote.svg){alt-text="Connect to cluster"}
+
+Make sure you have a SSH client installed on your laptop. Refer to the
+[setup](../index.md) section for more details. SSH clients are
+usually command-line tools, where you provide the remote machine address as the
+only required argument. If your username on the remote system differs from what
+you use locally, you must provide that as well. If your SSH client has a
+graphical front-end, such as PuTTY or MobaXterm, you will set these arguments
+before clicking "connect." From the terminal, you'll write something like `ssh
+userName@hostname`, where the "@" symbol is used to separate the two parts of a
+single argument.
+
+Go ahead and open your terminal or graphical SSH client, then log in to the
+cluster using your username and the remote computer you can reach from the
+outside world, `r config$remote$location`.
+
+```bash
+`r config$local$prompt` ssh `r config$remote$user`@`r config$remote$login`
+```
+
+Remember to replace ``r config$remote$user`` with your username or the one
+supplied by the instructors. You may be asked for your password. Watch out: the
+characters you type after the password prompt are not displayed on the screen.
+Normal output will resume once you press `Enter`.
+
+## Where Are We?
+
+Very often, many users are tempted to think of a high-performance computing
+installation as one giant, magical machine. Sometimes, people will assume that
+the computer they've logged onto is the entire computing cluster. So what's
+really happening? What computer have we logged on to? The name of the current
+computer we are logged onto can be checked with the `hostname` command. (You
+may also notice that the current hostname is also part of our prompt!)
+
+```bash
+`r config$remote$prompt` hostname
+```
+
+```bash
+`r config$remote$host`
+```
+
+::: challenge
+
+## What's in Your Home Directory?
+
+The system administrators may have configured your home directory with some
+helpful files, folders, and links (shortcuts) to space reserved for you on
+other filesystems. Take a look around and see what you can find.
+*Hint:* The shell commands `pwd` and `ls` may come in handy.
+Home directory contents vary from user to user. Please discuss any
+differences you spot with your neighbors.
+
+::: solution
+
+## It's a Beautiful Day in the Neighborhood
+
+The deepest layer should differ: ``r config$remote$user`` is uniquely yours.
+Are there differences in the path at higher levels?
+
+If both of you have empty directories, they will look identical. If you
+or your neighbor has used the system before, there may be differences. What
+are you working on?
+
+
+Use `pwd` to **p**rint the **w**orking **d**irectory path:
+
+```bash
+`r config$remote$prompt` pwd
+```
+
+You can run `ls` to **l**i**s**t the directory contents, though it's
+possible nothing will show up (if no files have been provided). To be sure,
+use the `-a` flag to show hidden files, too.
+
+```bash
+`r config$remote$prompt` ls -a
+```
+
+At a minimum, this will show the current directory as `.`, and the parent
+directory as `..`.
+
+:::
+:::
+
+## Nodes
+
+Individual computers that compose a cluster are typically called *nodes*
+(although you will also hear people call them *servers*, *computers* and
+*machines*). On a cluster, there are different types of nodes for different
+types of tasks. The node where you are right now is called the *head node*,
+*login node*, *landing pad*, or *submit node*. A login node serves as an access
+point to the cluster.
+
+As a gateway, it is well suited for uploading and downloading files, setting up
+software, and running quick tests. Generally speaking, the login node should
+not be used for time-consuming or resource-intensive tasks. You should be alert
+to this, and check with your site's operators or documentation for details of
+what is and isn't allowed. In these lessons, we will avoid running jobs on the
+head node.
+
+::: callout
+## Dedicated Transfer Nodes
+If you want to transfer larger amounts of data to or from the cluster, some
+systems offer dedicated nodes for data transfers only. The motivation for
+this lies in the fact that larger data transfers should not obstruct
+operation of the login node for anybody else. Check with your cluster's
+documentation or its support team if such a transfer node is available. As a
+rule of thumb, consider all transfers of a volume larger than 500 MB to 1 GB
+as large. But these numbers change, e.g., depending on the network connection
+of yourself and of your cluster or other factors.
+:::
+
+The real work on a cluster gets done by the *worker* (or *compute*) *nodes*.
+Worker nodes come in many shapes and sizes, but generally are dedicated to long
+or hard tasks that require a lot of computational resources.
+
+All interaction with the worker nodes is handled by a specialized piece of
+software called a scheduler (the scheduler used in this lesson is called
+**`r config$sched$name`**). We'll learn more about how to use the
+scheduler to submit jobs next, but for now, it can also tell us more
+information about the worker nodes.
+
+For example, we can view all of the worker nodes by running the command
+``r config$sched$info``.
+
+```bash
+`r config$remote$prompt` `r config$sched$info`
+```
+
+```{r, child=paste(snippets, '/cluster/queue-info.snip', sep=''), eval=TRUE}
+```
+
+There are also specialized machines used for managing disk storage, user
+authentication, and other infrastructure-related tasks. Although we do not
+typically logon to or interact with these machines directly, they enable a
+number of key features like ensuring our user account and files are available
+throughout the HPC system.
+
+## What\'s in a Node?
+
+All of the nodes in an HPC system have the same components as your own laptop
+or desktop: *CPUs* (sometimes also called *processors* or *cores*), *memory*
+(or *RAM*), and *disk* space. CPUs are a computer's tool for actually running
+programs and calculations. Information about a current task is stored in the
+computer's memory. Disk refers to all storage that can be accessed like a file
+system. This is generally storage that can hold data permanently, i.e. data is
+still there even if the computer has been restarted. While this storage can be
+local (a hard drive installed inside of it), it is more common for nodes to
+connect to a shared, remote fileserver or cluster of servers.
+
+![Node anatomy](fig/node_anatomy.png){max-width="20%" alt="Node anatomy" caption=""}
+
+::: challenge
+
+## Explore Your Computer
+Try to find out the number of CPUs and amount of memory available on your
+personal computer.
+Note that, if you're logged in to the remote computer cluster, you need to
+log out first. To do so, type `Ctrl+d` or `exit`:
+
+```bash
+`r config$remote$prompt` exit
+`r config$local$prompt`
+```
+
+::: solution
+
+There are several ways to do this. Most operating systems have a graphical
+system monitor, like the Windows Task Manager. More detailed information
+can sometimes be found on the command line. For example, some of the commands used on 
+a Linux system are:
+
+Run system utilities
+```bash
+`r config$local$prompt` nproc --all
+`r config$local$prompt` free -m
+```
+
+Read from `/proc`
+```bash
+`r config$local$prompt` cat /proc/cpuinfo
+`r config$local$prompt` cat /proc/meminfo
+```
+
+Run system monitor
+```bash
+`r config$local$prompt` htop
+```
+
+:::
+:::
+
+
+::: challenge
+## Explore the login node
+
+Now compare the resources of your computer with those of the head node.
+
+::: solution
+
+```bash
+`r config$local$prompt` ssh `r config$remote$user`@`r config$remote$login`
+`r config$remote$prompt` nproc --all
+`r config$remote$prompt` free -m
+```
+
+You can get more information about the processors using `lscpu`,
+and a lot of detail about the memory by reading the file `/proc/meminfo`:
+
+```bash
+`r config$remote$prompt` less /proc/meminfo
+```
+
+You can also explore the available filesystems using `df` to show **d**isk
+**f**ree space. The `-h` flag renders the sizes in a human-friendly format,
+i.e., GB instead of B. The **t**ype flag `-T` shows what kind of filesystem
+each resource is.
+
+```bash
+`r config$remote$prompt` df -Th
+```
+:::
+:::
+
+::: discussion
+The local filesystems (ext, tmp, xfs, zfs) will depend on whether you're
+on the same login node (or compute node, later on). Networked filesystems
+(beegfs, cifs, gpfs, nfs, pvfs) will be similar --- but may include
+`r config$remote$user`, depending on how it is [mounted](
+https://en.wikipedia.org/wiki/Mount_(computing)).
+:::
+
+::: callout
+## Shared Filesystems
+
+This is an important point to remember: files saved on one node
+(computer) are often available everywhere on the cluster!
+
+:::
+
+```{r, child=paste(snippets, '/cluster/specific-node-info.Rmd', sep=''), eval=TRUE}
+```
+
+::: discussion
+## Compare Your Computer, the login node and the compute node
+Compare your laptop's number of processors and memory with the numbers you
+see on the cluster head node and worker node. Discuss the differences with
+your neighbor.
+
+What implications do you think the differences might have on running your
+research work on the different systems and nodes?
+:::
+
+::: callout
+## Differences Between Nodes
+
+Many HPC clusters have a variety of nodes optimized for particular workloads.
+Some nodes may have larger amount of memory, or specialized resources such as
+Graphical Processing Units (GPUs).
+:::
+
+With all of this in mind, we will now cover how to talk to the cluster's
+scheduler, and use it to start running our scripts and programs!
+
+::: keypoints
+ - "An HPC system is a set of networked machines."
+ - "HPC systems typically provide login nodes and a set of worker nodes."
+ - "The resources found on independent (worker) nodes can vary in volume and
+   type (amount of RAM, processor architecture, availability of network mounted
+   filesystems, etc.)."
+ - "Files saved on one node are available on all nodes."
+:::

From 55773d9d9e74d11d36b5a4a4862173545200116c Mon Sep 17 00:00:00 2001
From: Jean Chang <jlchang@broadinstitute.org>
Date: Thu, 3 Oct 2024 07:35:20 -0400
Subject: [PATCH 06/33] indicate EPCC episode

---
 episodes/12-epcc-cluster.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/episodes/12-epcc-cluster.Rmd b/episodes/12-epcc-cluster.Rmd
index 8edc631b..f27d71bd 100644
--- a/episodes/12-epcc-cluster.Rmd
+++ b/episodes/12-epcc-cluster.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "Working on a remote HPC system"
+title: "EPCC version - Working on a remote HPC system"
 teaching: 25
 exercises: 10
 ---

From 27a1bf11a4fdd45728f5c89afa2a48ded798b4eb Mon Sep 17 00:00:00 2001
From: Jean Chang <jlchang@broadinstitute.org>
Date: Thu, 3 Oct 2024 07:39:41 -0400
Subject: [PATCH 07/33] add the EPCC snippets

---
 .../EPCC_ARCHER2_slurm/_config_options.yml    | 65 ++++++++++++++
 .../cluster/queue-info.snip                   |  8 ++
 .../cluster/specific-node-info.Rmd            | 10 +++
 .../EPCC_ARCHER2_slurm/login_output.Rmd       | 26 ++++++
 .../modules/available-modules.Rmd             | 26 ++++++
 .../modules/missing-python.snip               |  1 +
 .../modules/module-load-python.snip           |  2 +
 .../modules/module_list.snip                  | 16 ++++
 .../modules/python-executable-dir.snip        |  1 +
 .../modules/python-ls-dir-command.snip        |  1 +
 .../modules/python-ls-dir-output.snip         |  2 +
 .../modules/python-module-path.snip           |  1 +
 .../modules/software-dependencies.snip        | 80 +++++++++++++++++
 .../modules/wrong-gcc-version.snip            | 73 +++++++++++++++
 .../resources/job-detail.Rmd                  |  2 +
 .../resources/perf-exercise.Rmd               | 67 ++++++++++++++
 .../resources/pi-mpi-details.Rmd              | 16 ++++
 .../resources/runtime-exercise.Rmd            | 47 ++++++++++
 .../resources/serial-submit.Rmd               | 25 ++++++
 .../resources/sharpen-details.snip            | 18 ++++
 .../resources/view-output.snip                | 12 +++
 .../scheduler/basic-job-script.Rmd            |  3 +
 .../scheduler/basic-job-status.Rmd            |  8 ++
 .../EPCC_ARCHER2_slurm/scheduler/del_job.snip |  1 +
 .../scheduler/filesystem_issues.snip          | 20 +++++
 .../scheduler/job-with-name-status.Rmd        |  4 +
 .../scheduler/long_job.snip                   |  9 ++
 .../scheduler/ls-pgm-output.snip              |  2 +
 .../scheduler/option-flags-list.Rmd           |  5 ++
 .../scheduler/parallel-challenge.Rmd          | 25 ++++++
 .../scheduler/parallel-challenge2.Rmd         | 27 ++++++
 .../scheduler/parallel-launch-desc.Rmd        | 13 +++
 .../scheduler/parallel-script.Rmd             | 15 ++++
 .../scheduler/print-sched-variables.Rmd       |  9 ++
 .../scheduler/runtime-exceeded-job.Rmd        |  3 +
 .../scheduler/runtime-exceeded-output.Rmd     |  5 ++
 .../scheduler/squeue_pending.snip             |  2 +
 .../scheduler/squeue_running.snip             |  2 +
 .../scheduler/terminate-job-begin.Rmd         |  6 ++
 .../scheduler/terminate-job-cancel.Rmd        |  3 +
 .../scheduler/terminate-multiple-jobs.Rmd     |  6 ++
 .../scheduler/using-nodes-interactively.Rmd   | 32 +++++++
 episodes/files/snippets/README.md             | 32 +++++++
 episodes/files/snippets/rename-snippets.sh    | 89 +++++++++++++++++++
 44 files changed, 820 insertions(+)
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/login_output.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/available-modules.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/missing-python.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module-load-python.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module_list.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-executable-dir.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-command.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-output.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-module-path.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/software-dependencies.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/wrong-gcc-version.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/job-detail.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/perf-exercise.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/pi-mpi-details.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/runtime-exercise.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/serial-submit.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/sharpen-details.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/view-output.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-status.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/option-flags-list.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-begin.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-cancel.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
 create mode 100644 episodes/files/snippets/README.md
 create mode 100755 episodes/files/snippets/rename-snippets.sh

diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml b/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
new file mode 100644
index 00000000..8d176a4e
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
@@ -0,0 +1,65 @@
+#------------------------------------------------------------
+# ComputeCanada: Graham + Slurm
+#------------------------------------------------------------
+
+# Cluster host and scheduler options: the defaults come from
+# Graham at Compute Canada, running Slurm. Other options can
+# be found in the library of snippets,
+# `_includes/snippets_library`. To use one, replace options
+# below with those in `_config_options.yml` from the
+# library. E.g, to customise for Cirrus at EPCC, running
+# PBS, we could replace the options below with those from
+# 
+# _includes/snippets_library/EPCC_Cirrus_pbs/_config_options.yml
+# 
+# If your cluster is not represented in the library, please
+# copy an existing folder, rename it, and customize for your
+# installation. Remember to keep the leading slash on the
+# `snippets` variable below!
+
+snippets: "/snippets_library/EPCC_ARCHER2_slurm"
+
+local:
+  prompt: "[user@laptop ~]$"
+  bash_shebang: "#!/bin/bash"
+
+remote:
+  name: "ARCHER2"
+  login: "login.archer2.ac.uk"
+  host: "ln03"
+  node: "nid001053"
+  location: "EPCC, The University of Edinburgh"
+  homedir: "/home/ta076/ta076/"
+  user: "userid"
+  prompt: "userid@ln03:~>"
+  prompt-work: "userid@ln03:/work/ta076/ta076/userid>"
+  module_python3: "cray-python"
+  bash_shebang: "#!/bin/bash"
+
+sched:
+  name: "Slurm"
+  reservation: "shortqos"
+  budget: "short"
+  submit:
+    name: "sbatch"
+    options: "--partition=standard --qos=short"
+  queue:
+    debug: ""
+    testing: ""
+  status: "squeue"
+  flag:
+    user: "-u userid"
+    interactive: ""
+    histdetail: "-l -j"
+    name: "--job-name"
+    time: "--time"
+    queue: "--partition"
+    nodes: "--nodes"
+    tasks: ""
+  del: "scancel"
+  interactive: "srun"
+  info: "sinfo"
+  comment: "#SBATCH"
+  hist: "sacct"
+
+
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.snip
new file mode 100644
index 00000000..bdc94879
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.snip
@@ -0,0 +1,8 @@
+```output
+PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST 
+standard     up 1-00:00:00     27 drain* nid[001029,001050,001149,001363,001366,001391,001552,001568,001620,001642,001669,001672-001675,001688,001690-001691,001747,001751,001783,001793,001812,001832-001835] 
+standard     up 1-00:00:00      5  down* nid[001024,001026,001064,001239,001898] 
+standard     up 1-00:00:00      8  drain nid[001002,001028,001030-001031,001360-001362,001745] 
+standard     up 1-00:00:00    945  alloc nid[001000-001001,001003-001023,001025,001027,001032-001037,001040-001049,001051-001063,001065-001108,001110-001145,001147,001150-001238,001240-001264,001266-001271,001274-001334,001337-001359,001364-001365,001367-001390,001392-001551,001553-001567,001569-001619,001621-001637,001639-001641,001643-001668,001670-001671,001676,001679-001687,001692-001734,001736-001744,001746,001748-001750,001752-001782,001784-001792,001794-001811,001813-001824,001826-001831,001836-001890,001892-001897,001899-001918,001920,001923-001934,001936-001945,001947-001965,001967-001981,001984-001991,002006-002023] 
+standard     up 1-00:00:00     37   resv nid[001038-001039,001109,001146,001148,001265,001272-001273,001335-001336,001638,001677-001678,001735,001891,001919,001921-001922,001935,001946,001966,001982-001983,001992-002005] 
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
new file mode 100644
index 00000000..dee005a4
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
@@ -0,0 +1,10 @@
+::: challenge
+## Explore a Worker Node
+
+Finally, let's look at the resources available on the worker nodes where your jobs will actually
+run. Try running this command to see the name, CPUs and memory available on one of the worker nodes:
+
+```bash
+`r config$remote$prompt` sinfo -n nid001053 -o "%n %c %m"
+```
+:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/login_output.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/login_output.Rmd
new file mode 100644
index 00000000..dbba457f
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/login_output.Rmd
@@ -0,0 +1,26 @@
+```output
+This node is running Cray's Linux Environment version 1.3.2
+
+#######################################################################################
+
+        @@@@@@@@@
+     @@@         @@@            _      ____     ____   _   _   _____   ____    ____
+   @@@    @@@@@    @@@         / \    |  _ \   / ___| | | | | | ____| |  _ \  |___ \
+  @@@   @@     @@   @@@       / _ \   | |_) | | |     | |_| | |  _|   | |_) |   __) |
+  @@   @@  @@@  @@   @@      / ___ \  |  _ <  | |___  |  _  | | |___  |  _ <   / __/
+  @@   @@  @@@  @@   @@     /_/   \_\ |_| \_\  \____| |_| |_| |_____| |_| \_\ |_____|
+  @@@   @@     @@   @@@
+   @@@    @@@@@    @@@       https://www.archer2.ac.uk/support-access/
+     @@@         @@@
+        @@@@@@@@@
+
+ -         U K R I         -        E P C C        -         H P E   C r a y         -
+
+Hostname:     uan01
+Distribution: SLES 15.1 1
+CPUS:         256
+Memory:       257.4GB
+Configured:   2021-04-27
+
+######################################################################################
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/available-modules.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/available-modules.Rmd
new file mode 100644
index 00000000..132ecf1f
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/available-modules.Rmd
@@ -0,0 +1,26 @@
+```output
+----------- /work/y07/shared/archer2-modules/modulefiles-cse-pyvenvs -----------
+tensorflow/2.3.1-py38  torch/1.6.0-py38  
+
+----------- /work/y07/shared/archer2-modules/modulefiles-cse-pymods ------------
+python-netCDF4/1.5.5.1  
+
+------------ /work/y07/shared/archer2-modules/modulefiles-cse-utils ------------
+bolt/0.7                  ncview/ncview-2.1.7-gcc-10.1.0  vmd/1.9.3-mpi-gcc10  
+cmake/3.18.4              reframe/3.2                     xios/2.5-gcc10       
+ed/1.16-gcc10             tcl/8.4.20-gcc10                xthi/1.0             
+epcc-job-env              tcl/8.5.0-gcc10                 xthi/1.0-gcc10       
+epcc-reframe/0.1          tcl/8.6.0-gcc10                 
+genmaskcpu/1.0            tcl/8.6.10-gcc10(default)       
+gnuplot/5.4.1-gcc-10.1.0  tk/8.5.6-gcc10                  
+lzip/1.20-gcc10           tk/8.6.10-gcc10(default)        
+nco/4.9.6                 visidata/2.1                    
+nco/4.9.6-gcc-10.1.0      vmd/1.9.3-gcc10(default)        
+
+------------ /work/y07/shared/archer2-modules/modulefiles-cse-libs -------------
+adios/1.13.1     hypre/2.18.0             mumps/5.2.1     superlu-dist/6.1.1  
+boost/1.72.0     libxml2/2.9.7-gcc-9.3.0  parmetis/4.0.3  superlu/5.2.1       
+glm/0.9.9.6      matio/1.5.18             petsc/3.13.3    trilinos/12.18.1    
+gmp/6.1.2-gcc10  metis/5.1.0              scotch/6.0.10   
+...
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/missing-python.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/missing-python.snip
new file mode 100644
index 00000000..381142dc
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/missing-python.snip
@@ -0,0 +1 @@
+/usr/bin/python3
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module-load-python.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module-load-python.snip
new file mode 100644
index 00000000..d0e214d5
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module-load-python.snip
@@ -0,0 +1,2 @@
+{{ site.host_prompt-work }} module load cray-python
+{{ site.host_prompt-work }} which python3
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module_list.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module_list.snip
new file mode 100644
index 00000000..c180fda5
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module_list.snip
@@ -0,0 +1,16 @@
+Currently Loaded Modulefiles:
+ 1) cpe-cray                                                                 
+ 2) cce/10.0.4(default)                                                      
+ 3) craype/2.7.2(default)                                                    
+ 4) craype-x86-rome                                                          
+ 5) libfabric/1.11.0.0.233(default)                                          
+ 6) craype-network-ofi                                                       
+ 7) cray-dsmml/0.1.2(default)                                                
+ 8) perftools-base/20.10.0(default)                                          
+ 9) xpmem/2.2.35-7.0.1.0_1.9__gd50fabf.shasta(default)                       
+10) cray-mpich/8.0.16(default)                                               
+11) cray-libsci/20.10.1.2(default)                                           
+12) bolt/0.7                                                                 
+13) /work/y07/shared/archer2-modules/modulefiles-cse/epcc-setup-env          
+14) /usr/local/share/epcc-module/epcc-module-loader                          
+15) /work/y07/shared/archer2-modules/modulefiles-cse/epcc-setup-env-profile
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-executable-dir.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-executable-dir.snip
new file mode 100644
index 00000000..b9f4b294
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-executable-dir.snip
@@ -0,0 +1 @@
+/opt/cray/pe/python/3.8.5.0/bin/python3
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-command.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-command.snip
new file mode 100644
index 00000000..f87667f8
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-command.snip
@@ -0,0 +1 @@
+{{ site.host_prompt-work }} ls /opt/cray/pe/python/3.8.5.0/bin
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-output.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-output.snip
new file mode 100644
index 00000000..b8411602
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-output.snip
@@ -0,0 +1,2 @@
+2to3	  cygdb   cythonize	easy_install-3.8  f2py3    idle3    nosetests	   pip	 pip3.8  pydoc3.8  py.test  python3    python3.8-config
+2to3-3.8  cython  easy_install	f2py		  f2py3.8  idle3.8  nosetests-3.8  pip3  pydoc3  pytest    python   python3.8  python3-config
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-module-path.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-module-path.snip
new file mode 100644
index 00000000..b8480b0e
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-module-path.snip
@@ -0,0 +1 @@
+/opt/cray/pe/python/3.8.5.0/bin:/lus/cls01095/work/z19/z19/aturner/.local/bin:/lus/cls01095/work/y07/shared/bolt/0.7/bin:/work/y07/shared/utils/bin:/usr/local/maven/bin:/opt/cray/pe/perftools/20.10.0/bin:/opt/cray/pe/papi/6.0.0.4/bin:/opt/cray/libfabric/1.11.0.0.233/bin:/opt/cray/pe/craype/2.7.2/bin:/opt/cray/pe/cce/10.0.4/cce-clang/x86_64/bin:/opt/cray/pe/cce/10.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin:/opt/cray/pe/cce/10.0.4/binutils/cross/x86_64-aarch64/aarch64-linux-gnu/../bin:/opt/cray/pe/cce/10.0.4/utils/x86_64/bin:/usr/local/Modules/bin:/home/z19/z19/aturner/bin:/usr/local/bin:/usr/bin:/bin:/opt/cray/pe/bin:/usr/lib/mit/bin
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/software-dependencies.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/software-dependencies.snip
new file mode 100644
index 00000000..f555f415
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/software-dependencies.snip
@@ -0,0 +1,80 @@
+To demonstrate, let's use `module list`. `module list` shows all loaded software modules.
+
+```
+{{ site.host_prompt }} module list
+```
+{: .language-bash}
+```
+Currently Loaded Modules:
+  1) nixpkgs/.16.09  (H,S)   3) gcccore/.5.4.0    (H)   5) intel/2016.4  (t)   7) StdEnv/2016.4 (S)
+  2) icc/.2016.4.258 (H)     4) ifort/.2016.4.258 (H)   6) openmpi/2.1.1 (m)   8) python/3.5.2  (t)
+
+  Where:
+   S:  Module is Sticky, requires --force to unload or purge
+   m:  MPI implementations / Implémentations MPI
+   t:  Tools for development / Outils de développement
+   H:             Hidden Module
+```
+{: .output}
+
+```
+{{ site.host_prompt }} module load beast
+{{ site.host_prompt }} module list
+```
+{: .language-bash}
+```
+Currently Loaded Modules:
+  1) nixpkgs/.16.09    (H,S)   5) intel/2016.4  (t)   9) java/1.8.0_121   (t)
+  2) icc/.2016.4.258   (H)     6) openmpi/2.1.1 (m)  10) beagle-lib/2.1.2 (bio)
+  3) gcccore/.5.4.0    (H)     7) StdEnv/2016.4 (S)  11) beast/2.4.0      (chem)
+  4) ifort/.2016.4.258 (H)     8) python/3.5.2  (t)
+
+  Where:
+   S:     Module is Sticky, requires --force to unload or purge
+   bio:   Bioinformatic libraries/apps / Logiciels de bioinformatique
+   m:     MPI implementations / Implémentations MPI
+   t:     Tools for development / Outils de développement
+   chem:  Chemistry libraries/apps / Logiciels de chimie
+   H:                Hidden Module
+```
+{: .output}
+
+So in this case, loading the `beast` module (a bioinformatics software package), also loaded
+`java/1.8.0_121` and `beagle-lib/2.1.2` as well. Let's try unloading the `beast` package.
+
+```
+{{ site.host_prompt }} module unload beast
+{{ site.host_prompt }} module list
+```
+{: .language-bash}
+```
+Currently Loaded Modules:
+  1) nixpkgs/.16.09  (H,S)   3) gcccore/.5.4.0    (H)   5) intel/2016.4  (t)   7) StdEnv/2016.4 (S)
+  2) icc/.2016.4.258 (H)     4) ifort/.2016.4.258 (H)   6) openmpi/2.1.1 (m)   8) python/3.5.2  (t)
+
+  Where:
+   S:  Module is Sticky, requires --force to unload or purge
+   m:  MPI implementations / Implémentations MPI
+   t:  Tools for development / Outils de développement
+   H:             Hidden Module
+```
+{: .output}
+
+So using `module unload` "un-loads" a module along with its dependencies.
+If we wanted to unload everything at once, we could run `module purge` (unloads everything).
+
+```
+{{ site.host_prompt }} module purge
+```
+{: .language-bash}
+```
+The following modules were not unloaded:
+  (Use "module --force purge" to unload all):
+
+  1) StdEnv/2016.4    3) icc/.2016.4.258   5) ifort/.2016.4.258   7) imkl/11.3.4.258
+  2) nixpkgs/.16.09   4) gcccore/.5.4.0    6) intel/2016.4        8) openmpi/2.1.1
+```
+{: .output}
+
+Note that `module purge` is informative. It lets us know that all but a default set of packages 
+have been unloaded (and how to actually unload these if we truly so desired).
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/wrong-gcc-version.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/wrong-gcc-version.snip
new file mode 100644
index 00000000..9e0f7666
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/wrong-gcc-version.snip
@@ -0,0 +1,73 @@
+Let's take a closer look at the `gcc` module. GCC is an extremely widely used 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 two different versions: `gcc/4.8.5` and
+`gcc/5.4.0`. How do we load each copy and which copy is the default?
+
+In this case, `gcc/5.4.0` has a `(D)` next to it. This indicates that it is the default - if we type
+`module load gcc`, this is the copy that will be loaded.
+
+```
+{{ site.host_prompt }} module load gcc
+{{ site.host_prompt }} gcc --version
+```
+{: .language-bash}
+```
+Lmod is automatically replacing "intel/2016.4" with "gcc/5.4.0".
+
+
+Due to MODULEPATH changes, the following have been reloaded:
+  1) openmpi/2.1.1
+
+gcc (GCC) 5.4.0
+Copyright (C) 2015 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+```
+{: .output}
+
+Note that three things happened: the default copy of GCC was loaded (version 5.4.0), the Intel
+compilers (which conflict with GCC) were unloaded, and software that is dependent on compiler
+(OpenMPI) was reloaded. The `module` system turned what might be a super-complex operation into a
+single command.
+
+So how do we load the non-default copy of a software package? In this case, the only change we need
+to make is be more specific about the module we are loading. There are two GCC modules: `gcc/5.4.0`
+and `gcc/4.8.5`. To load a non-default module, the only change we need to make to our `module load`
+command is to leave in the version number after the `/`.
+
+```
+{{ site.host_prompt }} module load gcc/4.8.5
+{{ site.host_prompt }} gcc --version
+```
+{: .language-bash}
+```
+Inactive Modules:
+  1) openmpi
+
+The following have been reloaded with a version change:
+  1) gcc/5.4.0 => gcc/4.8.5
+
+gcc (GCC) 4.8.5
+Copyright (C) 2015 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+```
+{: .output}
+
+We now have successfully switched from GCC 5.4.0 to GCC 4.8.5. It is also important to note that
+there was no compatible OpenMPI module available for GCC 4.8.5. Because of this, the `module`
+program has "inactivated" the module. All this means for us is that if we re-load GCC 5.4.0,
+`module` will remember OpenMPI used to be loaded and load that module as well.
+
+```
+{{ site.host_prompt }} module load gcc/5.4.0
+```
+{: .language-bash}
+```
+Activating Modules:
+  1) openmpi/2.1.1
+
+The following have been reloaded with a version change:
+  1) gcc/4.8.5 => gcc/5.4.0
+```
+{: .output}
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/job-detail.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/job-detail.Rmd
new file mode 100644
index 00000000..880b8421
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/job-detail.Rmd
@@ -0,0 +1,2 @@
+JOBID USER         ACCOUNT     NAME           ST REASON START_TIME         T...
+36856 yourUsername yourAccount example-job.sh R  None   2017-07-01T16:47:02 ...
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/perf-exercise.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/perf-exercise.Rmd
new file mode 100644
index 00000000..f79772f7
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/perf-exercise.Rmd
@@ -0,0 +1,67 @@
+::: challenge
+## Computing the speedup and parallel efficiency
+Use your *Overall run times* from above to fill in a table like the one below.
+
+| Cores      | Overall run time (s) | Ideal speedup | Actual speedup | Parallel efficiency |
+|------------|----------------------|---------------|----------------|---------------------|
+| 1 (serial) |                      |               |                |                     |
+| 2          |                      |               |                |                     |
+| 4          |                      |               |                |                     |                   
+| 8          |                      |               |                |                     | 
+| 16         |                      |               |                |                     |
+| 32         |                      |               |                |                     |
+| 64         |                      |               |                |                     |             
+| 128        |                      |               |                |                     |
+| 256        |                      |               |                |                     |
+
+Given your results, try to answer the following questions:
+
+1. What is the core count where you get the **most** efficient use of resources, irrespective
+  of run time?
+2. What is the core count where you get the fastest solution, irrespective of efficiency?
+3. What do you think a good core count choice would be for this application that balances
+   time to solution and efficiency? Why did you choose this option?
+
+::: solution
+
+The table below gives example results for `r config$remote$name` based on the example 
+runtimes given in the solution above.
+
+| Cores      | Overall run time (s) | Ideal speedup | Actual speedup | Parallel efficiency |
+|-----------:|---------------------:|--------------:|---------------:|--------------------:|
+|          1 |                3.931 |         1.000 |          1.000 |               1.000 |
+|          2 |                2.002 |         2.000 |          1.963 |               0.982 |
+|          4 |                1.048 |         4.000 |          3.751 |               0.938 |
+|          8 |                0.572 |         8.000 |          6.872 |               0.859 |
+|         16 |                0.613 |        16.000 |          6.408 |               0.401 |
+|         32 |                0.360 |        32.000 |         10.928 |               0.342 |
+|         64 |                0.249 |        64.000 |         15.767 |               0.246 |
+|        128 |                0.170 |       128.000 |         23.122 |               0.181 |
+|        256 |                0.187 |       256.000 |         21.077 |               0.082 |
+
+### What is the core count where you get the **most** efficient use of resources?
+Just using a single core is the cheapest (and always will be unless your speedup is better
+than perfect – “super-linear” speedup). However, it may not be possible to run on small
+numbers of cores depending on how much memory you need or other technical constraints.
+**Note:** on most high-end systems, nodes are not shared between users. This means you are
+charged for all the CPU-cores on a node regardless of whether you actually use them. Typically
+we would be running on many hundreds of CPU-cores not a few tens, so the real question in
+practice is: what is the optimal number of nodes to use?
+### What is the core count where you get the fastest solution, irrespective of efficiency?
+256 cores gives the fastest time to solution.
+The fastest time to solution does not often make the most efficient use of resources so 
+to use this option, you may end up wasting your resources. Sometimes, when there is 
+time pressure to run the calculations, this may be a valid approach to running 
+applications.
+### What do you think a good core count choice would be for this application to use?
+
+8 cores is probably a good number of cores to use with a parallel efficiency of 86%.
+Usually, the best choice is one that delivers good parallel efficiency with an acceptable
+time to solution. Note that *acceptable time to solution* differs depending on circumstances
+so this is something that the individual researcher will have to assess. Good parallel
+efficiency is often considered to be 70% or greater though many researchers will be happy
+to run in a regime with parallel efficiency greater than 60%. As noted above, running with
+worse parallel efficiency may also be useful if the time to solution is an overriding factor.
+
+:::
+:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/pi-mpi-details.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/pi-mpi-details.Rmd
new file mode 100644
index 00000000..086f90e8
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/pi-mpi-details.Rmd
@@ -0,0 +1,16 @@
+::: prereq
+
+## Required Files
+
+The program used in this example can be retrieved using wget or a browser and copied to the remote.
+
+**Using wget**: 
+```bash
+`r config$remote$prompt` wget `r config$url``r config$baseurl`/files/pi-mpi.py
+```
+
+**Using a web browser**:
+
+[`r config$url``r config$baseurl`/files/pi-mpi.py](`r config$url``r config$baseurl`/files/pi-mpi.py)
+
+:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/runtime-exercise.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/runtime-exercise.Rmd
new file mode 100644
index 00000000..4977a00e
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/runtime-exercise.Rmd
@@ -0,0 +1,47 @@
+::: challenge
+## Benchmarking the parallel performance
+Modify your job script to run on multiple cores and evaluate the performance of `pi-mpi.py`
+on a variety of different core counts and use multiple runs to complete a table like the one
+below.
+If you examine the log file you will see that it contains two timings: the total time taken by the
+entire program and the time taken solely by the calculation. The calculation of Pi from the Monte-Carlo counts
+is not parallelised so this is a serial overhead, performed by a single processor.
+The calculation part is, in theory, perfectly parallel (each processor operates on independent sets of unique random numbers
+) so this should get faster on more cores. The Calculation core seconds is the
+*calculation time* multiplied by the number of cores.
+
+| Cores      | Overall run time (s) | Calculation time (s) | Calculation core seconds |
+|------------|----------------------|----------------------|--------------------------|
+| 1 (serial) |                      |                      |                          |
+| 2          |                      |                      |                          |
+| 4          |                      |                      |                          |                    
+| 8          |                      |                      |                          | 
+| 16         |                      |                      |                          | 
+| 32         |                      |                      |                          | 
+| 64         |                      |                      |                          |              
+| 128        |                      |                      |                          | 
+| 256        |                      |                      |                          |
+
+Look at your results – do they make sense? Given the structure of the code, you would
+expect the performance of the calculation to increase
+linearly with the number of cores: this would give a roughly constant figure for the Calculation core
+seconds. Is this what you observe?
+
+::: solution
+
+The table below shows example timings for runs on `r config$remote$name`
+
+| Cores      | Overall run time (s) | Calculation time (s) |       Calculation core seconds |
+|-----------:|---------------------:|---------------------:|-------------------------------:|
+|          1 |                3.931 |                3.854 |                          3.854 |
+|          2 |                2.002 |                1.930 |                          3.859 |
+|          4 |                1.048 |                0.972 |                          3.888 |
+|          8 |                0.572 |                0.495 |                          3.958 |
+|         16 |                0.613 |                0.536 |                          8.574 |
+|         32 |                0.360 |                0.278 |                          8.880 |
+|         64 |                0.249 |                0.163 |                         10.400 |
+|        128 |                0.170 |                0.083 |                         10.624 |
+|        256 |                0.187 |                0.135 |                         34.560 |
+
+:::
+:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/serial-submit.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/serial-submit.Rmd
new file mode 100644
index 00000000..b7f68819
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/serial-submit.Rmd
@@ -0,0 +1,25 @@
+Creating a file called `submit-pi-mpi.slurm`:
+
+```bash
+#!/bin/bash
+#SBATCH --partition=`r config$sched$partition`
+#SBATCH --qos=`r config$sched$qos`
+#SBATCH --reservation=`r config$sched$reservation`
+
+#SBATCH --job-name=pi-mpi
+#SBATCH --nodes=1
+#SBATCH --tasks-per-node=1
+#SBATCH --time=00:15:00
+srun python pi-mpi.py 10000000
+```
+
+Run application using a single process (i.e. in serial) with a blocking `srun` command:
+```bash
+srun python pi-mpi.py 10000000
+```
+
+Submit with to the batch queue with:
+
+```bash
+`r config$sched$prompt_work` `r config$sched$submit.name` submit-pi-mpi.slurm
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/sharpen-details.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/sharpen-details.snip
new file mode 100644
index 00000000..08172fbe
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/sharpen-details.snip
@@ -0,0 +1,18 @@
+The `sharpen` program has been precompiled on {{ site.remote.name }}, you can add it to your `PATH` variable with the commands:
+
+```
+export PATH=/work/{{ site.sched.project }}/{{ site.sched.project }}/shared/bin:$PATH
+export FUZZY_INPUT=/work/{{ site.sched.project }}/{{ site.sched.project }}/shared/fuzzy.pgm
+``````
+{: .language-bash}
+
+Once you have set the required environment variables, you can access the program as `sharpen-mpi`.
+You will also need to get a copy of the input file for this application.
+To do this, copy it from the 
+central install location to your directory with (note you must have loaded the 
+sharpen module as described above for this to work):
+
+```
+{{ site.host_prompt }} cp $FUZZY_INPUT .
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/view-output.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/view-output.snip
new file mode 100644
index 00000000..5b2a572b
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/view-output.snip
@@ -0,0 +1,12 @@
+> ## Viewing the sharpened output image
+> To see the effect of the sharpening algorithm, you can view the images using the display
+> program from the ImageMagick suite.
+> ```
+> display sharpened.pgm
+> ```
+> Type `q` in the image window to close the program. To view the image you will need an X
+> window client installed and you will have to have logged into {{ site.host_name }} with the `ssh -Y`
+> option to export the display back to your local system. If you are using Windows, the 
+> MobaXterm program provides a login shell with X capability. If you are using macOS, then
+> you will need to install XQuartz. If you are using Linux then X should just work!
+{: .callout}
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
new file mode 100644
index 00000000..2e12f1d8
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
@@ -0,0 +1,3 @@
+```output
+Submitted batch job 36855
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-status.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-status.Rmd
new file mode 100644
index 00000000..e98253bd
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-status.Rmd
@@ -0,0 +1,8 @@
+```output
+JOBID USER         ACCOUNT     NAME           ST REASON START_TIME         T...
+36856 yourUsername yourAccount example-job.sh R  None   2017-07-01T16:47:02 ...
+```
+
+We can see all the details of our job, most importantly that it is in the `R`
+or `RUNNING` state. Sometimes our jobs might need to wait in a queue
+(`PENDING`) or have an error (`E`).
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.snip
new file mode 100644
index 00000000..950788df
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.snip
@@ -0,0 +1 @@
+{{ site.host_prompt }} scancel 38759
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.snip
new file mode 100644
index 00000000..1bc94d83
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.snip
@@ -0,0 +1,20 @@
+> ## Filesystem on ARCHER2
+> At this point it is important to remember that ARCHER2  has two *separate*
+> filesystems: `/home` and `/work`.
+>
+> * `/home` is meant for small files such as source code, and is the
+>    filesystem that you are on when you log in
+> *  `/work` is a much larger and faster filesystem, meant for production
+>    runs and storing large datasets
+>
+> The `/home` filesystem **is not mounted on the compute nodes**
+> meaning that programs run in the batch queues cannot read from or
+> write to files in your home directory. This has not been a problem
+> so far as none of our programs have done file input or
+> output. However, the parallel program we will run here reads and
+> writes large images.
+>
+> * When you log in, you will be in your home directory {{ site.host_homedir }}
+> * Before you run real programs on ARCHER2, you **must change directory** to
+>   {{ site.host_workdir }}
+{: .callout}
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
new file mode 100644
index 00000000..fcd8ee25
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
@@ -0,0 +1,4 @@
+```output
+JOBID USER         ACCOUNT     NAME     ST REASON   START_TIME TIME TIME_LEFT NODES CPUS
+38191 yourUsername yourAccount new_name PD Priority N/A        0:00 1:00:00   1     1
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.snip
new file mode 100644
index 00000000..5a7eafae
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.snip
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+#SBATCH --partition=standard
+#SBATCH --qos=short
+#SBATCH --time=00:00:30
+
+echo 'This script is running on:'
+hostname
+sleep 120
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.snip
new file mode 100644
index 00000000..f67c18fd
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.snip
@@ -0,0 +1,2 @@
+-rw-r--r-- 1 userid ta028 1762743 Jun 26 17:29 fuzzy.pgm
+-rw------- 1 userid ta028 1678630 Jun 26 17:33 sharpened.pgm
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/option-flags-list.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/option-flags-list.Rmd
new file mode 100644
index 00000000..626c6eab
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/option-flags-list.Rmd
@@ -0,0 +1,5 @@
+* `--nodes=<nodes>` - Number of nodes to use
+* `--ntasks-per-node=<tasks-per-node>` - Number of parallel processes per node
+* `--cpus-per-task=<cpus-per-task>` - Number of cores to assign to each parallel process
+* `--time=<days-hours:minutes:seconds>` - Maximum real-world time (walltime)
+your job will be allowed to run. The `<days>` part can be omitted.
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
new file mode 100644
index 00000000..7205ade4
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
@@ -0,0 +1,25 @@
+::: challenge
+## Running parallel jobs
+Modify the pi-mpi-run script that you used above to use all 128 cores on
+one node.  Check the output to confirm that it used the correct number
+of cores in parallel for the calculation.
+
+::: solution
+Here is a modified script
+
+```bash
+#!/bin/bash
+
+#SBATCH --partition=`r config$sched$partition`
+#SBATCH --qos=`r config$sched$qos`
+#SBATCH --reservation=`r config$sched$reservation`
+#SBATCH --time=00:00:30
+
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=128
+
+module load cray-python
+srun python pi-mpi.py 10000000
+```
+:::
+:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
new file mode 100644
index 00000000..328b62d6
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
@@ -0,0 +1,27 @@
+::: challenge
+## Configuring parallel jobs
+You will see in the job output that information is displayed about
+where each MPI process is running, in particular which node it is
+on.
+
+Modify the pi-mpi-run script that you run a total of 2 nodes and 16 processes;
+but to use only 8 tasks on each of two nodes.
+Check the output file to ensure that you understand the job
+distribution.
+
+::: solution
+```bash
+#!/bin/bash
+
+#SBATCH --partition=`r config$sched$partition`
+#SBATCH --qos=`r config$sched$qos`
+#SBATCH --time=00:00:30
+
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-node=8
+
+module load cray-python
+srun python pi-mpi.py 10000000
+```
+:::
+:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
new file mode 100644
index 00000000..d6a797d8
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
@@ -0,0 +1,13 @@
+```bash
+srun python pi-mpi.py 10000000
+```
+
+And this corresponds to the four required items we described above:
+
+  1. Parallel launch program: in this case the parallel launch program is
+     called `srun`; the additional argument controls which cores are used.
+  2. Number of parallel processes per node: in this case this is 16,
+     and is specified by the option `--ntasks-per-node=16` option.
+  2. Total number of parallel processes: in this case this is also 16, because
+     we specified 1 node and 16 parallel processes per node.
+  4. Our program and arguments: in this case this is `python pi-mpi.py 10000000`.
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
new file mode 100644
index 00000000..983799c3
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
@@ -0,0 +1,15 @@
+```bash
+#!/bin/bash
+
+#SBATCH --partition=`r config$sched$partition`
+#SBATCH --qos=`r config$sched$qos`
+#SBATCH --reservation=`r config$sched$reservation`
+#SBATCH --time=00:05:00
+
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=16
+
+module load cray-python
+
+srun python pi-mpi.py 10000000
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
new file mode 100644
index 00000000..b2009095
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
@@ -0,0 +1,9 @@
+::: challenge
+## Job environment variables
+
+When Slurm runs a job, it sets a number of environment variables for the job. One of these will
+let us check our work from the last problem. The `SLURM_CPUS_PER_TASK` variable is set to the
+number of CPUs we requested with `-c`. Using the `SLURM_CPUS_PER_TASK` variable, modify your job
+so that it prints how many CPUs have been allocated.
+
+:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
new file mode 100644
index 00000000..86f57113
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
@@ -0,0 +1,3 @@
+```bash
+`r config$remote$prompt_work` cat slurm-38193.out
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
new file mode 100644
index 00000000..617e03e9
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
@@ -0,0 +1,5 @@
+```output
+This job is running on:
+nid001147
+slurmstepd: error: *** JOB 38193 ON cn01 CANCELLED AT 2017-07-02T16:35:48 DUE TO TIME LIMIT ***
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.snip
new file mode 100644
index 00000000..46997eb0
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.snip
@@ -0,0 +1,2 @@
+        JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+       119867  standard    myjob   userid PD       0:00      1 (Resources) 
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.snip
new file mode 100644
index 00000000..3233cdb7
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.snip
@@ -0,0 +1,2 @@
+        JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+       119867  standard example-   userid  R    0:00:06      1 nid001609 
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-begin.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-begin.Rmd
new file mode 100644
index 00000000..214a8756
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-begin.Rmd
@@ -0,0 +1,6 @@
+```output
+Submitted batch job 38759
+
+JOBID USER         ACCOUNT     NAME           ST REASON   START_TIME TIME TIME_LEFT NODES CPUS
+38759 yourUsername yourAccount example-job.sh PD Priority N/A        0:00 1:00      1     1
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-cancel.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-cancel.Rmd
new file mode 100644
index 00000000..695180ff
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-cancel.Rmd
@@ -0,0 +1,3 @@
+```output
+JOBID  USER  ACCOUNT  NAME  ST  REASON  START_TIME  TIME  TIME_LEFT  NODES  CPUS
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
new file mode 100644
index 00000000..c8d76a27
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
@@ -0,0 +1,6 @@
+::: challenge
+## Cancelling multiple jobs
+We can also cancel all of our jobs at once using the `-u` option. This will delete all jobs for a
+specific user (in this case us). Note that you can only delete your own jobs.
+Try submitting multiple jobs and then cancelling them all with `scancel -u yourUsername`.
+:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
new file mode 100644
index 00000000..9b303a0d
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
@@ -0,0 +1,32 @@
+`srun` runs a single command in the queue system and then exits.
+Let's demonstrate this by running the
+`hostname` command with `srun`. (We can cancel an `srun` job with `Ctrl-c`.)
+
+```bash
+`r config$host_prompt_work` srun `r config$sched$submit$options` --time=00:01:00 hostname
+```
+```output
+nid001976
+```
+
+`srun` accepts all of the same options as `sbatch`. However, instead of specifying these in a
+script, these options are specified on the command-line when starting a job.
+
+Typically, the resulting shell environment will be the same as that for
+`sbatch`.
+
+### Interactive jobs
+
+Sometimes, you will need a lot of resource for interactive use. Perhaps it's our first time running
+an analysis or we are attempting to debug something that went wrong with a previous job.
+Fortunately, SLURM makes it easy to start an interactive job with `srun`:
+
+```bash
+`r config$host_prompt_work` srun `r config$sched$submit$options` --pty /bin/bash
+```
+
+You should be presented with a bash prompt. Note that the prompt may change
+to reflect your new location, in this case the compute node we are logged on.
+You can also verify this with `hostname`.
+
+When you are done with the interactive job, type `exit` to quit your session.
diff --git a/episodes/files/snippets/README.md b/episodes/files/snippets/README.md
new file mode 100644
index 00000000..56b65740
--- /dev/null
+++ b/episodes/files/snippets/README.md
@@ -0,0 +1,32 @@
+# HPC Carpentry Snippets Library
+
+This directory contains snippets of code and output that are specific
+to a particular site. For example, when the lesson shows the status
+of the cluster and its nodes, it is preferable to show *your* cluster
+and *your* nodes. If you replace the contents of the relevant snippet,
+the website gets built with your cluster details, instead of generic
+values (or, more precisely, values taken from ComputeCanada).
+
+The snippets have been named so that the lessons use them in roughly
+alphabetical order, while still reflecting something of the contents
+of each file. So, if you're reading (or teaching) a lesson and notice
+something amiss about half-way through, look to the files about
+half-way through the directory. If it's the first or last snippet,
+you're in particularly good luck.
+
+This alphabetical ordering was not always the case. To reduce the
+headache of keeping forks, branches, and derivative works up-to-date,
+we have included a utility to rename snippets from the older scheme.
+To use it, run the following command, rebuild and test your site, and
+commit the changes.
+
+```bash
+$ ./rename-snippets.sh <your_snippet_directory>
+```
+
+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.
+
+
diff --git a/episodes/files/snippets/rename-snippets.sh b/episodes/files/snippets/rename-snippets.sh
new file mode 100755
index 00000000..85dd5711
--- /dev/null
+++ b/episodes/files/snippets/rename-snippets.sh
@@ -0,0 +1,89 @@
+#!/bin/bash
+
+# This script renames snippets from the argument directory in an effort
+# to make the names more meaningful, thereby simplifying the process of
+# porting to a new site.
+
+if [[ $# != 1 ]] || [[ $1 == "-h" ]] || [[ $1 == "--help" ]]; then
+    echo "Please supply a folder name containing snippets for your site. This"
+    echo "script will rename those snippets based on the script activity. E.g.,"
+    echo "    $0 ComputeCanada_Graham_slurm"
+    exit 1
+fi
+
+if [[ $(which git) == "" ]]; then
+    echo "Error: This script requires git. Please install it and try again."
+    exit 1
+fi
+
+PREFIX=$1
+
+function rename_snip {
+    mv $1 $2
+}
+
+## Episode 12: Working on a remote HPC system
+
+#$ {{ site.sched.info }}
+rename_snip  ${PREFIX}/12/info.snip     ${PREFIX}/12/queue-info.snip
+#$ sinfo -n {{ site.remote.node }} -o "%n %c %m"
+rename_snip  ${PREFIX}/12/explore.snip  ${PREFIX}/12/specific-node-info.snip
+
+## Episode 13: Scheduling jobs
+
+# {{ site.sched.submit.name }} {{ site.sched.submit.options }} example-job.sh
+rename_snip  ${PREFIX}/13/submit_output.snip           ${PREFIX}/13/basic-job-script.snip
+#$ {{ site.sched.status }} {{ site.sched.flag.user }}
+rename_snip  ${PREFIX}/13/statu_output.snip            ${PREFIX}/13/basic-job-status.snip
+#$ {{ site.sched.status }} {{ site.sched.flag.user }}
+rename_snip  ${PREFIX}/13/statu_name_output.snip       ${PREFIX}/13/job-with-name-status.snip
+## The following are several key resource requests:
+rename_snip  ${PREFIX}/13/stat_options.snip            ${PREFIX}/13/option-flags-list.snip
+## Print SLURM_CPUS_PER_TASK, PBS_O_WORKDIR, or similar
+rename_snip  ${PREFIX}/13/env_challenge.snip           ${PREFIX}/13/print-sched-variables.snip
+#$ {{ site.sched.submit.name }} {{ site.sched.submit.options }} example-job.sh
+rename_snip  ${PREFIX}/13/long_job_cat.snip            ${PREFIX}/13/runtime-exceeded-job.snip
+#$ {{ site.sched.status }} {{ site.sched.flag.user }}
+rename_snip  ${PREFIX}/13/long_job_err.snip            ${PREFIX}/13/runtime-exceeded-output.snip
+#$ {{ site.sched.submit.name }} {{ site.sched.submit.options }} example-job.sh
+#$ {{ site.sched.status }} {{ site.sched.flag.user }}
+rename_snip  ${PREFIX}/13/del_job_output1.snip         ${PREFIX}/13/terminate-job-begin.snip
+#$ {{site.sched.del }} 38759
+rename_snip  ${PREFIX}/13/del_job_output2.snip         ${PREFIX}/13/terminate-job-cancel.snip
+#$ {{site.sched.del }} {{ site.sched.flag.user }}
+rename_snip  ${PREFIX}/13/del_multiple_challenge.snip  ${PREFIX}/13/terminate-multiple-jobs.snip
+## use the compute node resources interactively
+rename_snip  ${PREFIX}/13/interactive_example.snip     ${PREFIX}/13/using-nodes-interactively.snip
+
+## Episode 14: Accessing software
+
+#$ module avail
+rename_snip  ${PREFIX}/14/module_avail.snip   ${PREFIX}/14/available-modules.snip
+#$ which python
+rename_snip  ${PREFIX}/14/which_missing.snip  ${PREFIX}/14/missing-python.snip
+#$ module load python[3]
+rename_snip  ${PREFIX}/14/load_python.snip    ${PREFIX}/14/module-load-python.snip
+#$ which python
+rename_snip  ${PREFIX}/14/which_python.snip   ${PREFIX}/14/python-executable-dir.snip
+#$ echo $PATH
+rename_snip  ${PREFIX}/14/path.snip           ${PREFIX}/14/python-module-path.snip
+#$ ls $(dirname $(which python))
+rename_snip  ${PREFIX}/14/ls_dir.snip         ${PREFIX}/14/python-ls-dir-command.snip
+rename_snip  ${PREFIX}/14/ls_dir_output.snip  ${PREFIX}/14/python-ls-dir-output.snip
+## Loading & unloading software and dependencies
+rename_snip  ${PREFIX}/14/depend_demo.snip    ${PREFIX}/14/software-dependencies.snip
+## gcc example
+rename_snip  ${PREFIX}/14/gcc_example.snip    ${PREFIX}/14/wrong-gcc-version.snip
+
+## Episode 15: Transferring files
+
+## Episode 16: Using resources effectively
+
+#$ {{ site.sched.hist }}
+rename_snip  ${PREFIX}/16/stat_output.snip  ${PREFIX}/16/account-history.snip
+#$ top
+rename_snip  ${PREFIX}/16/top_output.snip   ${PREFIX}/16/monitor-processes-top.snip
+#$ free -h
+rename_snip  ${PREFIX}/16/free_output.snip  ${PREFIX}/16/system-memory-free.snip
+
+## Episode 17: Using shared resources responsibly

From a4f2ccad475adf46e5b3ef9b93a3eccf0e1ca24f Mon Sep 17 00:00:00 2001
From: Jean Chang <jlchang@broadinstitute.org>
Date: Thu, 17 Oct 2024 16:45:33 -0400
Subject: [PATCH 08/33] first step converting 13-scheduler.md to Rmd for HPCC

---
 .gitignore                                    |   1 +
 config.yaml                                   |   2 +
 episodes/12-epcc-cluster.Rmd                  |   2 +-
 episodes/13-epcc-scheduler.Rmd                | 434 ++++++++++++++++
 episodes/13-hpcc-scheduler.Rmd                | 484 ++++++++++++++++++
 episodes/13-scheduler.md                      |   2 +-
 episodes/epcc_config.yaml                     |  50 ++
 .../_config_options.yml                       |  66 +++
 .../cluster/queue-info.snip                   |   7 +
 .../cluster/specific-node-info.Rmd            |  11 +
 .../cluster/specific-node-info.snip           |  11 +
 .../modules/available-modules.snip            |  21 +
 .../modules/default-modules.snip              |   4 +
 .../modules/missing-python.snip               |  33 ++
 .../modules/module-load-python.snip           |   5 +
 .../modules/python-executable-dir.snip        |   4 +
 .../modules/python-ls-dir-command.snip        |   4 +
 .../modules/python-ls-dir-output.snip         |  16 +
 .../modules/python-module-path.snip           |   4 +
 .../modules/software-dependencies.snip        |  87 ++++
 .../modules/wrong-gcc-version.snip            |   5 +
 .../parallel/eight-tasks-jobscript.snip       |  16 +
 .../parallel/four-tasks-jobscript.snip        |  16 +
 .../parallel/one-task-jobscript.snip          |  14 +
 .../resources/account-history.snip            |  14 +
 .../resources/monitor-processes-top.snip      |  19 +
 .../resources/system-memory-free.snip         |   6 +
 .../scheduler/basic-job-script.Rmd            |   3 +
 .../scheduler/basic-job-script.snip           |   4 +
 .../scheduler/basic-job-status.snip           |   9 +
 .../scheduler/job-with-name-status.snip       |   5 +
 .../scheduler/option-flags-list.snip          |  15 +
 .../scheduler/print-sched-variables.snip      |  30 ++
 .../scheduler/runtime-exceeded-job.snip       |   4 +
 .../scheduler/runtime-exceeded-output.snip    |   6 +
 .../scheduler/terminate-job-begin.snip        |   7 +
 .../scheduler/terminate-job-cancel.snip       |   4 +
 .../scheduler/terminate-multiple-jobs.snip    |  27 +
 .../scheduler/using-nodes-interactively.snip  |  69 +++
 .../filezilla-ssh-tunnel-instructions.snip    |   0
 episodes/lesson_config.yaml                   |  59 +--
 41 files changed, 1549 insertions(+), 31 deletions(-)
 create mode 100644 episodes/13-epcc-scheduler.Rmd
 create mode 100644 episodes/13-hpcc-scheduler.Rmd
 create mode 100644 episodes/epcc_config.yaml
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.Rmd
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/default-modules.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-command.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-output.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-module-path.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/wrong-gcc-version.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks-jobscript.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks-jobscript.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task-jobscript.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/resources/monitor-processes-top.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/resources/system-memory-free.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.Rmd
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/option-flags-list.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/transferring-files/filezilla-ssh-tunnel-instructions.snip

diff --git a/.gitignore b/.gitignore
index 9b846a3c..14ea8afe 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,6 +18,7 @@ site/*
 /*.Rcheck/
 # RStudio files
 .Rproj.user/
+*.Rproj
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
diff --git a/config.yaml b/config.yaml
index 96dfebfb..5519a791 100644
--- a/config.yaml
+++ b/config.yaml
@@ -70,6 +70,8 @@ episodes:
 - 12-cluster.md
 - 12-epcc-cluster.Rmd
 - 13-scheduler.md
+- 13-hpcc-scheduler.Rmd
+- 13-epcc-scheduler.Rmd
 - 14-environment-variables.md
 - 15-modules.md
 - 16-transferring-files.md
diff --git a/episodes/12-epcc-cluster.Rmd b/episodes/12-epcc-cluster.Rmd
index f27d71bd..91a80fb2 100644
--- a/episodes/12-epcc-cluster.Rmd
+++ b/episodes/12-epcc-cluster.Rmd
@@ -6,7 +6,7 @@ exercises: 10
 
 ```{r load_config, include=FALSE}
 library(yaml)
-config <- yaml.load_file("lesson_config.yaml")
+config <- yaml.load_file("epcc_config.yaml")
 snippets <- paste('files/snippets/', config$snippets, sep='')
 ```
 
diff --git a/episodes/13-epcc-scheduler.Rmd b/episodes/13-epcc-scheduler.Rmd
new file mode 100644
index 00000000..08b62b22
--- /dev/null
+++ b/episodes/13-epcc-scheduler.Rmd
@@ -0,0 +1,434 @@
+---
+title: "EPCC version - Working with the scheduler"
+teaching: 50
+exercises: 30
+---
+
+```{r load_config, include=FALSE}
+library(yaml)
+config <- yaml.load_file("epcc_config.yaml")
+snippets <- paste('files/snippets/', config$snippets, sep='')
+```
+
+::: questions
+ - "What is a scheduler and why are they used?"
+ - "How do I launch a program to run on any one node in the cluster?"
+ - "How do I capture the output of a program that is run on a node in the
+   cluster?"
+:::
+
+::: objectives
+ - "Run a simple Hello World style program on the cluster."
+ - "Submit a simple Hello World style script to the cluster."
+ - "Use the batch system command line tools to monitor the execution of your
+   job."
+ - "Inspect the output and error files of your jobs."
+:::
+
+## Job Scheduler
+
+An HPC system might have thousands of nodes and thousands of users. How do we
+decide who gets what and when? How do we ensure that a task is run with the
+resources it needs? This job is handled by a special piece of software called
+the scheduler. On an HPC system, the scheduler manages which jobs run where and
+when.
+
+The following illustration compares these tasks of a job scheduler to a waiter
+in a restaurant. If you can relate to an instance where you had to wait for a
+while in a queue to get in to a popular restaurant, then you may now understand
+why sometimes your job do not start instantly as in your laptop.
+
+![The waiter scheduler](fig/restaurant_queue_manager.svg){caption="" alt="Compare a job scheduler to a waiter in a restaurant"}
+
+The scheduler used in this lesson is `r config$sched$name`. Although
+`r config$sched$name` is not used everywhere, running jobs is quite similar
+regardless of what software is being used. The exact syntax might change, but
+the concepts remain the same.
+
+## Running a Batch Job
+
+The most basic use of the scheduler is to run a command non-interactively. Any
+command (or series of commands) that you want to run on the cluster is called a
+*job*, and the process of using a scheduler to run the job is called *batch job
+submission*.
+
+In this case, the job we want to run is just a shell script. Let's create a
+demo shell script to run as a test. The landing pad will have a number of
+terminal-based text editors installed. Use whichever you prefer. Unsure? `nano`
+is a pretty good, basic choice.
+
+```bash
+`r config$remote$prompt` nano example-job.sh
+`r config$remote$prompt` chmod +x example-job.sh
+`r config$remote$prompt` cat example-job.sh
+```
+
+```output
+`r config$remote$bash_shebang`
+
+echo -n "This script is running on "
+hostname
+```
+
+::: challenge
+## Creating Our Test Job
+
+Run the script. Does it execute on the cluster or just our login node?
+
+```bash
+`r config$remote$prompt` ./example-job.sh
+```
+
+::: solution
+
+```output
+This script is running on `r config$remote$host`
+```
+This job runs on the login node.
+:::
+:::
+
+If you completed the previous challenge successfully, you probably realise that
+there is a distinction between running the job through the scheduler and just
+"running it". To submit this job to the scheduler, we use the
+``r config$sched$submit$name`` command.
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+```
+
+```output
+sbatch: Warning: Your job has no time specification (--time=) and the default time is short. You can cancel your job with 'scancel <JOB_ID>' if you wish to resubmit.
+sbatch: Warning: It appears your working directory may be on the home filesystem. It is /home2/home/ta114/ta114/userid. This is not available from the compute nodes - please check that this is what you intended. You can cancel your job with 'scancel <JOBID>' if you wish to resubmit.
+Submitted batch job 286949
+```
+
+Ah! What went wrong here? Slurm is telling us that the file system we are currently on, `/home`, is not available
+on the compute nodes and that we are getting the default, short runtime. We will deal with the runtime 
+later, but we need to move to a different file system to submit the job and have it visible to the 
+compute nodes. On ARCHER2, this is the `/work` file system. The path is similar to home but with 
+`/work` at the start. Lets move there now, copy our job script across and resubmit:
+
+```bash
+`r config$remote$prompt` cd /work/ta114/ta114/userid
+`r config$remote$prompt_work` cp ~/example-job.sh .
+`r config$remote$prompt_work` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+```
+```{r, child=paste(snippets, '/scheduler/basic-job-script.Rmd', sep=''), eval=TRUE}
+```
+
+That's better! And that's all we need to do to submit a job. Our work is done --- now the
+scheduler takes over and tries to run the job for us. While the job is waiting
+to run, it goes into a list of jobs called the *queue*. To check on our job's
+status, we check the queue using the command
+``r config$sched$status` `r config$sched$flag$user``.
+
+```bash
+`r config$remote$prompt_work` `r config$sched$status` `r config$sched$flag$user`
+```
+
+```{r, child=paste(snippets, '/scheduler/basic-job-status.Rmd', sep=''), eval=TRUE}
+```
+
+The best way to check our job's status is with ``r config$sched$status``. Of
+course, running ``r config$sched$status`` repeatedly to check on things can be
+a little tiresome. To see a real-time view of our jobs, we can use the `watch`
+command. `watch` reruns a given command at 2-second intervals. This is too
+frequent, and will likely upset your system administrator. You can change the
+interval to a more reasonable value, for example 15 seconds, with the `-n 15`
+parameter. Let's try using it to monitor another job.
+
+```bash
+`r config$remote$prompt_work` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt_work` watch -n 15 `r config$sched$status` `r config$sched$flag$user`
+```
+
+You should see an auto-updating display of your job's status. When it finishes,
+it will disappear from the queue. Press `Ctrl-c` when you want to stop the
+`watch` command.
+
+::: discussion
+## Where's the Output?
+On the login node, this script printed output to the terminal --- but
+when we exit `watch`, there's nothing. Where'd it go?
+HPC job output is typically redirected to a file in the directory you
+launched it from. Use `ls` to find and read the file.
+:::
+
+## Customising a Job
+
+The job we just ran used some of the scheduler's default options. In a
+real-world scenario, that's probably not what we want. The default options
+represent a reasonable minimum. Chances are, we will need more cores, more
+memory, more time, among other special considerations. To get access to these
+resources we must customize our job script.
+
+Comments in UNIX shell scripts (denoted by `#`) are typically ignored, but
+there are exceptions. For instance the special `#!` comment at the beginning of
+scripts specifies what program should be used to run it (you'll typically see
+``r config$local$bash_shebang``). Schedulers like `r config$sched$name` also
+have a special comment used to denote special scheduler-specific options.
+Though these comments differ from scheduler to scheduler,
+`r config$sched$name`'s special comment is ``r config$sched$comment``. Anything
+following the ``r config$sched$comment`` comment is interpreted as an
+instruction to the scheduler.
+
+Let's illustrate this by example. By default, a job's name is the name of the
+script, but the ``r config$sched$flag$name`` option can be used to change the
+name of a job. Add an option to the script:
+
+```bash
+`r config$remote$prompt_work` cat example-job.sh
+```
+
+```output
+`r config$remote$bash_shebang`
+`r config$sched$comment` `r config$sched$flag$name` new_name
+
+echo -n "This script is running on "
+hostname
+echo "This script has finished successfully."
+```
+
+Submit the job and monitor its status:
+
+```bash
+`r config$remote$prompt_work` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt_work` `r config$sched$status` `r config$sched$flag$user`
+```
+
+```{r, child=paste(snippets, '/scheduler/job-with-name-status.Rmd', sep=''), eval=TRUE}
+```
+
+Fantastic, we've successfully changed the name of our job!
+
+### Resource Requests
+
+But what about more important changes, such as the number of cores and memory
+for our jobs? One thing that is absolutely critical when working on an HPC
+system is specifying the resources required to run a job. This allows the
+scheduler to find the right time and place to schedule our job. If you do not
+specify requirements (such as the amount of time you need), you will likely be
+stuck with your site's default resources, which is probably not what you want.
+
+The following are several key resource requests:
+
+```{r, child=paste(snippets, '/scheduler/option-flags-list.Rmd', sep=''), eval=TRUE}
+```
+
+Note that just *requesting* these resources does not make your job run faster,
+nor does it necessarily mean that you will consume all of these resources. It
+only means that these are made available to you. Your job may end up using less
+memory, or less time, or fewer tasks or nodes, than you have requested, and it
+will still run.
+
+It's best if your requests accurately reflect your job's requirements. We'll
+talk more about how to make sure that you're using resources effectively in a
+later episode of this lesson.
+
+::: callout
+## Command line options or job script options?
+All of the options we specify can be supplied on the command line (as we
+do here for `--partition=standard`) or in the job script (as we have done
+for the job name above). These are interchangeable. It is often more convenient
+to put the options in the job script as it avoids lots of typing at the command
+line.
+:::
+
+::: challenge
+## Submitting Resource Requests
+Modify our `hostname` script so that it runs for a minute, then submit a job
+for it on the cluster. You should also move all the options we have been specifying
+on the command line (e.g. `--partition`) into the script at this point.
+
+::: solution
+
+```bash
+`r config$remote$prompt_work` cat example-job.sh
+```
+
+```output
+`r config$remote$bash_shebang`
+`r config$sched$comment` `r config$sched$flag$time` 00:01:15
+`r config$sched$comment` --partition=standard
+`r config$sched$comment` --qos=`r config$sched$qos`
+`r config$sched$comment` --reservation=`r config$sched$reservation`
+echo -n "This script is running on "
+sleep 60 # time in seconds
+hostname
+echo "This script has finished successfully."
+```
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` example-job.sh
+```
+
+Why are the `r config$sched$name` runtime and `sleep` time not identical?
+:::
+:::
+
+
+```{r, child=paste(snippets, '/scheduler/print-sched-variables.Rmd', sep=''), eval=TRUE}
+```
+
+Resource requests are typically binding. If you exceed them, your job will be
+killed. Let's use walltime as an example. We will request 30 seconds of
+walltime, and attempt to run a job for two minutes.
+
+```bash
+`r config$remote$prompt_work` cat example-job.sh
+```
+
+```output
+`r config$remote$bash_shebang`
+`r config$sched$comment` `r config$sched$flag$name` long_job
+`r config$sched$comment` `r config$sched$flag$time` 00:00:30
+`r config$sched$comment` --partition=`r config$sched$partition`
+`r config$sched$comment` --qos=`r config$sched$qos`
+`r config$sched$comment` --reservation=`r config$sched$reservation`
+
+echo "This script is running on ... "
+sleep 120 # time in seconds
+hostname
+echo "This script has finished successfully."
+```
+
+Submit the job and wait for it to finish. Once it is has finished, check the
+log file.
+
+```bash
+`r config$remote$prompt_work` `r config$sched$submit$name` example-job.sh
+`r config$remote$prompt_work` watch -n 15 `r config$sched$status` `r config$sched$flag$user`
+```
+
+```{r, child=paste(snippets, '/scheduler/runtime-exceeded-job.Rmd', sep=''), eval=TRUE}
+```
+```{r, child=paste(snippets, '/scheduler/runtime-exceeded-output.Rmd', sep=''), eval=TRUE}
+```
+
+Our job was killed for exceeding the amount of resources it requested. Although
+this appears harsh, this is actually a feature. Strict adherence to resource
+requests allows the scheduler to find the best possible place for your jobs.
+Even more importantly, it ensures that another user cannot use more resources
+than they've been given. If another user messes up and accidentally attempts to
+use all of the cores or memory on a node, `r config$sched$name` will either
+restrain their job to the requested resources or kill the job outright. Other
+jobs on the node will be unaffected. This means that one user cannot mess up
+the experience of others, the only jobs affected by a mistake in scheduling
+will be their own.
+
+::: callout
+## But how much does it cost?
+Although your job will be killed if it exceeds the selected runtime,
+a job that completes within the time limit is only charged for the
+time it actually used. However, you should always try and specify a
+wallclock limit that is close to (but greater than!) the expected
+runtime as this will enable your job to be scheduled more
+quickly.
+If you say your job will run for an hour, the scheduler has
+to wait until a full hour becomes free on the machine. If it only ever
+runs for 5 minutes, you could have set a limit of 10 minutes and it
+might have been run earlier in the gaps between other users' jobs.
+:::
+
+## Cancelling a Job
+
+Sometimes we'll make a mistake and need to cancel a job. This can be done with
+the ``r config$sched$del`` command. Let's submit a job and then cancel it using
+its job number (remember to change the walltime so that it runs long enough for
+you to cancel it before it is killed!).
+
+```bash
+`r config$remote$prompt_work` `r config$sched$submit$name` example-job.sh
+`r config$remote$prompt_work` `r config$sched$status` `r config$sched$flag$user`
+```
+
+```{r, child=paste(snippets, '/scheduler/terminate-job-begin.Rmd', sep=''), eval=TRUE}
+```
+
+Now cancel the job with its job number (printed in your terminal). Absence of any
+job info indicates that the job has been successfully cancelled.
+
+```bash
+`r config$remote$prompt_work` `r config$sched$del` 38759
+# It might take a minute for the job to disappear from the queue...
+`r config$remote$prompt_work` `r config$sched$status` `r config$sched$flag$user`
+```
+
+```{r, child=paste(snippets, '/scheduler/terminate-job-cancel.Rmd', sep=''), eval=TRUE}
+```
+
+```{r, child=paste(snippets, '/scheduler/terminate-multiple-jobs.Rmd', sep=''), eval=TRUE}
+```
+
+## Other Types of Jobs
+
+Up to this point, we've focused on running jobs in batch mode.
+`r config$sched$name` also provides the ability to start an interactive session.
+
+There are very frequently tasks that need to be done interactively. Creating an
+entire job script might be overkill, but the amount of resources required is
+too much for a login node to handle. A good example of this might be building a
+genome index for alignment with a tool like
+[HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml). Fortunately, we can
+run these types of tasks as a one-off with ``r config$sched$interactive``.
+
+```{r, child=paste(snippets, '/scheduler/using-nodes-interactively.Rmd', sep=''), eval=TRUE}
+```
+
+## Running parallel jobs using MPI
+
+As we have already seen, the power of HPC systems comes from *parallelism*, i.e. having lots of
+processors/disks etc. connected together rather than having more powerful components than your
+laptop or workstation. Often, when running research programs on HPC you will need to run a
+program that has been built to use the MPI (Message Passing Interface) parallel library. The MPI
+library allows programs to exploit multiple processing cores in parallel to allow researchers
+to model or simulate faster on larger problem sizes. The details of how MPI work are not important
+for this course or even to use programs that have been built using MPI; however, MPI programs 
+typically have to be launched in job submission scripts in a different way to serial programs and
+users of parallel programs on HPC systems need to know how to do this. Specifically, launching
+parallel MPI programs typically requires four things:
+
+  - A special parallel launch program such as `mpirun`, `mpiexec`, `srun` or `aprun`.
+  - A specification of how many processes to use in parallel. For example, our parallel program
+    may use 256 processes in parallel.
+  - A specification of how many parallel processes to use per compute node. For example, if our
+    compute nodes each have 32 cores we often want to specify 32 parallel processes per node.
+  - The command and arguments for our parallel program.
+
+```{r, child=paste(snippets, '/resources/pi-mpi-details.Rmd', sep=''), eval=TRUE}
+```
+
+To illustrate this process, we will use a simple MPI parallel program that estimates the value of Pi.
+(We will meet this example program in more detail in a later episode.) Here is a job submission
+script that runs the program across two compute nodes on the cluster. Create a file
+(e.g. called: `run-pi-mpi.slurm`) with the contents of this script in it.
+
+```{r, child=paste(snippets, '/scheduler/parallel-script.Rmd', sep=''), eval=TRUE}
+```
+
+The parallel launch line for the sharpen program can be seen towards the bottom of the script:
+
+```{r, child=paste(snippets, '/scheduler/parallel-launch-desc.Rmd', sep=''), eval=TRUE}
+```
+
+As for our other jobs, we launch using the ``r config$sched$submit$name`` command.
+
+```bash
+`r config$remote$prompt_work` `r config$sched$submit$name` run-pi-mpi.slurm
+```
+
+The program generates no output with all details printed to the job log.
+
+```{r, child=paste(snippets, '/scheduler/parallel-challenge.Rmd', sep=''), eval=TRUE}
+```
+
+```{r, child=paste(snippets, '/scheduler/parallel-challenge2.Rmd', sep=''), eval=TRUE}
+```
+
+::: keypoints
+ - "The scheduler handles how compute resources are shared between users."
+ - "Everything you do should be run through the scheduler."
+ - "A job is just a shell script."
+ - "If in doubt, request more resources than you will need."
+:::
diff --git a/episodes/13-hpcc-scheduler.Rmd b/episodes/13-hpcc-scheduler.Rmd
new file mode 100644
index 00000000..ecb37844
--- /dev/null
+++ b/episodes/13-hpcc-scheduler.Rmd
@@ -0,0 +1,484 @@
+---
+title: "HPCC version - Scheduler Fundamentals"
+teaching: 45
+exercises: 30
+---
+
+```{r load_config, include=FALSE}
+library(yaml)
+config <- yaml.load_file("lesson_config.yaml")
+snippets <- paste('files/snippets/', config$snippets, sep='')
+```
+
+::::::::::::::::::::::::::::::::::::::: objectives
+
+- Submit a simple script to the cluster.
+- Monitor the execution of jobs using command line tools.
+- Inspect the output and error files of your jobs.
+- Find the right place to put large datasets on the cluster.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::: questions
+
+- What is a scheduler and why does a cluster need one?
+- How do I launch a program to run on a compute node in the cluster?
+- How do I capture the output of a program that is run on a node in the cluster?
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Job Scheduler
+
+An HPC system might have thousands of nodes and thousands of users. How do we
+decide who gets what and when? How do we ensure that a task is run with the
+resources it needs? This job is handled by a special piece of software called
+the *scheduler*. On an HPC system, the scheduler manages which jobs run where
+and when.
+
+The following illustration compares these tasks of a job scheduler to a waiter
+in a restaurant. If you can relate to an instance where you had to wait for a
+while in a queue to get in to a popular restaurant, then you may now understand
+why sometimes your job do not start instantly as in your laptop.
+
+![](fig/restaurant_queue_manager.svg){alt="Compare a job scheduler to a waiter in a restaurant" max-width="75%"}
+
+The scheduler used in this lesson is `r config$sched$name`. Although
+`r config$sched$name` is not used everywhere, running jobs is quite similar
+regardless of what software is being used. The exact syntax might change, but
+the concepts remain the same.
+
+## Running a Batch Job
+
+The most basic use of the scheduler is to run a command non-interactively. Any
+command (or series of commands) that you want to run on the cluster is called a
+*job*, and the process of using a scheduler to run the job is called *batch job
+submission*.
+
+In this case, the job we want to run is a shell script -- essentially a
+text file containing a list of UNIX commands to be executed in a sequential
+manner. Our shell script will have three parts:
+
+- On the very first line, add ``r config$remote$bash_shebang``. The `#!`
+  (pronounced "hash-bang" or "shebang") tells the computer what program is
+  meant to process the contents of this file. In this case, we are telling it
+  that the commands that follow are written for the command-line shell (what
+  we've been doing everything in so far).
+- Anywhere below the first line, we'll add an `echo` command with a friendly
+  greeting. When run, the shell script will print whatever comes after `echo`
+  in the terminal.
+  - `echo -n` will print everything that follows, *without* ending
+    the line by printing the new-line character.
+- On the last line, we'll invoke the `hostname` command, which will print the
+  name of the machine the script is run on.
+
+```bash
+`r config$remote$prompt`nano example-job.sh
+```
+
+```output
+`r config$remote$bash_shebang`
+
+echo -n "This script is running on "
+hostname
+```
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Creating Our Test Job
+
+Run the script. Does it execute on the cluster or just our login node?
+
+:::::::::::::::  solution
+
+## Solution
+
+```bash
+`r config$remote$prompt`bash example-job.sh
+```
+
+```output
+This script is running on `r config$remote$host`
+```
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+This script ran on the login node, but we want to take advantage of
+the compute nodes: we need the scheduler to queue up `example-job.sh`
+to run on a compute node.
+
+To submit this task to the scheduler, we use the
+``r config$sched$flag$submit$name`` command.
+This creates a *job* which will run the *script* when *dispatched* to
+a compute node which the queuing system has identified as being
+available to perform the work.
+
+```bash
+# `r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+`r config$remote$prompt``r config$sched$submit$name`r config$sched$submit$options` example-job.sh
+```
+
+```{r, child=paste(snippets, '/scheduler/basic-job-script.Rmd', sep=''), eval=TRUE}
+```
+
+And that's all we need to do to submit a job. Our work is done -- now the
+scheduler takes over and tries to run the job for us. While the job is waiting
+to run, it goes into a list of jobs called the *queue*. To check on our job's
+status, we check the queue using the command
+``r config$sched$status` `r config$sched$flag$user``.
+
+```bash
+`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+```
+
+```output
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+    9 cpubase_b example-   user01  R       0:05      1 node1
+```
+
+We can see all the details of our job, most importantly that it is in the `R`
+or `RUNNING` state. Sometimes our jobs might need to wait in a queue
+(`PENDING`) or have an error (`E`).
+
+::::::::::::::::::::::::::::::::::::::  discussion
+
+## Where's the Output?
+
+On the login node, this script printed output to the terminal -- but
+now, when ``r config$sched$status`` shows the job has finished,
+nothing was printed to the terminal.
+
+Cluster job output is typically redirected to a file in the directory you
+launched it from. Use `ls` to find and `cat` to read the file.
+
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Customising a Job
+
+The job we just ran used all of the scheduler's default options. In a
+real-world scenario, that's probably not what we want. The default options
+represent a reasonable minimum. Chances are, we will need more cores, more
+memory, more time, among other special considerations. To get access to these
+resources we must customize our job script.
+
+Comments in UNIX shell scripts (denoted by `#`) are typically ignored, but
+there are exceptions. For instance the special `#!` comment at the beginning of
+scripts specifies what program should be used to run it (you'll typically see
+``r config$local$bash_shebang``). Schedulers like `r config$sched$name` also
+have a special comment used to denote special scheduler-specific options.
+Though these comments differ from scheduler to scheduler,
+`r config$sched$name`'s special comment is ``r config$sched$comment``. Anything
+following the ``r config$sched$comment`` comment is interpreted as an
+instruction to the scheduler.
+
+Let's illustrate this by example. By default, a job's name is the name of the
+script, but the ``r config$sched$flag$name`` option can be used to change the
+name of a job. Add an option to the script:
+
+```bash
+`r config$remote$prompt`cat example-job.sh
+```
+
+```output
+`r config$remote$bash_shebang`
+`r config$sched$comment``r config$sched$flag$name`hello-world
+
+echo -n "This script is running on "
+hostname
+```
+
+Submit the job and monitor its status:
+
+```bash
+`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+```
+
+```output
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+   10 cpubase_b hello-wo   user01  R       0:02      1 node1
+```
+
+Fantastic, we've successfully changed the name of our job!
+
+### Resource Requests
+
+What about more important changes, such as the number of cores and memory for
+our jobs? One thing that is absolutely critical when working on an HPC system
+is specifying the resources required to run a job. This allows the scheduler to
+find the right time and place to schedule our job. If you do not specify
+requirements (such as the amount of time you need), you will likely be stuck
+with your site's default resources, which is probably not what you want.
+
+The following are several key resource requests:
+
+- `--ntasks=<ntasks>` or `-n <ntasks>`: How many CPU cores does your job need,
+  in total?
+
+- `--time <days-hours:minutes:seconds>` or `-t <days-hours:minutes:seconds>`:
+  How much real-world time (walltime) will your job take to run? The `<days>`
+  part can be omitted.
+
+- `--mem=<megabytes>`: How much memory on a node does your job need in
+  megabytes? You can also specify gigabytes using by adding a little "g"
+  afterwards (example: `--mem=5g`)
+
+- `--nodes=<nnodes>` or `-N <nnodes>`: How many separate machines does your job
+  need to run on? Note that if you set `ntasks` to a number greater than what
+  one machine can offer, `r config$sched$name` will set this value
+  automatically.
+
+Note that just *requesting* these resources does not make your job run faster,
+nor does it necessarily mean that you will consume all of these resources. It
+only means that these are made available to you. Your job may end up using less
+memory, or less time, or fewer nodes than you have requested, and it will still
+run.
+
+It's best if your requests accurately reflect your job's requirements. We'll
+talk more about how to make sure that you're using resources effectively in a
+later episode of this lesson.
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Submitting Resource Requests
+
+Modify our `hostname` script so that it runs for a minute, then submit a job
+for it on the cluster.
+
+:::::::::::::::  solution
+
+## Solution
+
+```bash
+`r config$remote$prompt`cat example-job.sh
+```
+
+```output
+`r config$remote$bash_shebang`
+`r config$sched$comment``r config$sched$flag$time`00:01 # timeout in HH:MM
+
+echo -n "This script is running on "
+sleep 20 # time in seconds
+hostname
+```
+
+```bash
+`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+```
+
+Why are the `r config$sched$name` runtime and `sleep` time not identical?
+
+
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+Resource requests are typically binding. If you exceed them, your job will be
+killed. Let's use wall time as an example. We will request 1 minute of
+wall time, and attempt to run a job for two minutes.
+
+```bash
+`r config$remote$prompt`cat example-job.sh
+```
+
+```output
+`r config$remote$bash_shebang`
+`r config$sched$comment``r config$sched$flag$name`long_job
+`r config$sched$comment``r config$sched$flag$time`00:01 # timeout in HH:MM
+
+echo "This script is running on ... "
+sleep 240 # time in seconds
+hostname
+```
+
+Submit the job and wait for it to finish. Once it is has finished, check the
+log file.
+
+```bash
+`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+```
+
+```bash
+`r config$remote$prompt`cat slurm-12.out
+```
+
+```output
+This script is running on ...
+slurmstepd: error: *** JOB 12 ON node1 CANCELLED AT 2021-02-19T13:55:57
+DUE TO TIME LIMIT ***
+```
+
+Our job was killed for exceeding the amount of resources it requested. Although
+this appears harsh, this is actually a feature. Strict adherence to resource
+requests allows the scheduler to find the best possible place for your jobs.
+Even more importantly, it ensures that another user cannot use more resources
+than they've been given. If another user messes up and accidentally attempts to
+use all of the cores or memory on a node, `r config$sched$name` will either
+restrain their job to the requested resources or kill the job outright. Other
+jobs on the node will be unaffected. This means that one user cannot mess up
+the experience of others, the only jobs affected by a mistake in scheduling
+will be their own.
+
+## Cancelling a Job
+
+Sometimes we'll make a mistake and need to cancel a job. This can be done with
+the ``r config$sched$del`` command. Let's submit a job and then cancel it using
+its job number (remember to change the walltime so that it runs long enough for
+you to cancel it before it is killed!).
+
+```bash
+`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+```
+
+```output
+Submitted batch job 13
+
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+   13 cpubase_b long_job   user01  R       0:02      1 node1
+```
+
+Now cancel the job with its job number (printed in your terminal). A clean
+return of your command prompt indicates that the request to cancel the job was
+successful.
+
+```bash
+`r config$remote$prompt`{{site.sched.del }} 38759
+# It might take a minute for the job to disappear from the queue...
+`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+```
+
+```output
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+```
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Cancelling multiple jobs
+
+We can also cancel all of our jobs at once using the `-u` option. This will
+delete all jobs for a specific user (in this case, yourself). Note that you
+can only delete your own jobs.
+
+Try submitting multiple jobs and then cancelling them all.
+
+:::::::::::::::  solution
+
+## Solution
+
+First, submit a trio of jobs:
+
+```bash
+`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+```
+
+Then, cancel them all:
+
+```bash
+`r config$remote$prompt``r config$sched$del` -u `r config$remote$user`
+```
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Other Types of Jobs
+
+Up to this point, we've focused on running jobs in batch mode.
+`r config$sched$name` also provides the ability to start an interactive session.
+
+There are very frequently tasks that need to be done interactively. Creating an
+entire job script might be overkill, but the amount of resources required is
+too much for a login node to handle. A good example of this might be building a
+genome index for alignment with a tool like [HISAT2][hisat]. Fortunately, we
+can run these types of tasks as a one-off with ``r config$sched$interactive``.
+
+``r config$sched$interactive`` runs a single command on the cluster and then
+exits. Let's demonstrate this by running the `hostname` command with
+``r config$sched$interactive``. (We can cancel an ``r config$sched$interactive``
+job with `Ctrl-c`.)
+
+```bash
+`r config$remote$prompt``r config$sched$interactive` hostname
+```
+
+```output
+`r config$remote$node`
+```
+
+``r config$sched$interactive`` accepts all of the same options as
+``r config$sched$flag$submit$name``. However, instead of specifying these in a script,
+these options are specified on the command-line when starting a job. To submit
+a job that uses 2 CPUs for instance, we could use the following command:
+
+```bash
+`r config$remote$prompt``r config$sched$interactive` -n 2 echo "This job will use 2 CPUs."
+```
+
+```output
+This job will use 2 CPUs.
+This job will use 2 CPUs.
+```
+
+Typically, the resulting shell environment will be the same as that for
+``r config$sched$flag$submit$name``.
+
+### Interactive jobs
+
+Sometimes, you will need a lot of resources for interactive use. Perhaps it's
+our first time running an analysis or we are attempting to debug something that
+went wrong with a previous job. Fortunately, `r config$sched$name` makes it
+easy to start an interactive job with ``r config$sched$interactive``:
+
+```bash
+`r config$remote$prompt``r config$sched$interactive` --pty bash
+```
+
+You should be presented with a bash prompt. Note that the prompt will likely
+change to reflect your new location, in this case the compute node we are
+logged on. You can also verify this with `hostname`.
+
+:::::::::::::::::::::::::::::::::::::::::  callout
+
+## Creating remote graphics
+
+To see graphical output inside your jobs, you need to use X11 forwarding. To
+connect with this feature enabled, use the `-Y` option when you login with
+the `ssh` command, e.g., `ssh -Y `r config$remote$user`@`r config$remote$login``.
+
+To demonstrate what happens when you create a graphics window on the remote
+node, use the `xeyes` command. A relatively adorable pair of eyes should pop
+up (press `Ctrl-C` to stop). If you are using a Mac, you must have installed
+XQuartz (and restarted your computer) for this to work.
+
+If your cluster has the
+[slurm-spank-x11](https://github.com/hautreux/slurm-spank-x11) plugin
+installed, you can ensure X11 forwarding within interactive jobs by using the
+`--x11` option for ``r config$sched$interactive`` with the command
+``r config$sched$interactive` --x11 --pty bash`.
+
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+When you are done with the interactive job, type `exit` to quit your session.
+
+
+
+[hisat]: https://daehwankimlab.github.io/hisat2/
+
+
+:::::::::::::::::::::::::::::::::::::::: keypoints
+
+- The scheduler handles how compute resources are shared between users.
+- A job is just a shell script.
+- Request *slightly* more resources than you will need.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
diff --git a/episodes/13-scheduler.md b/episodes/13-scheduler.md
index eebee36e..69889dcb 100644
--- a/episodes/13-scheduler.md
+++ b/episodes/13-scheduler.md
@@ -34,7 +34,7 @@ in a restaurant. If you can relate to an instance where you had to wait for a
 while in a queue to get in to a popular restaurant, then you may now understand
 why sometimes your job do not start instantly as in your laptop.
 
-![](/fig/restaurant\_queue\_manager.svg){alt="Compare a job scheduler to a waiter in a restaurant" max-width="75%"}
+![](/fig/restaurant_queue_manager.svg){alt="Compare a job scheduler to a waiter in a restaurant" max-width="75%"}
 
 The scheduler used in this lesson is {{ site.sched.name }}. Although
 {{ site.sched.name }} is not used everywhere, running jobs is quite similar
diff --git a/episodes/epcc_config.yaml b/episodes/epcc_config.yaml
new file mode 100644
index 00000000..5425d7b1
--- /dev/null
+++ b/episodes/epcc_config.yaml
@@ -0,0 +1,50 @@
+---
+local:
+  prompt: "[user@laptop ~]$"
+  bash_shebang: "#!/bin/bash"
+
+snippets: EPCC_ARCHER2_slurm
+baseurl: "https://epcced.github.io/2023-06-28-uoe-hpcintro"
+
+remote:
+  name: "ARCHER2"
+  host_id: "EPCC_ARCHER2"
+  login: "login.archer2.ac.uk"
+  host: "ln03"
+  node: "nid001053"
+  location: "EPCC, The University of Edinburgh"
+  homedir: "/home/ta114/ta114/"
+  user: "userid"
+  prompt: "userid@ln03:~>"
+  prompt_work: "userid@uan01:/work/ta114/ta114/userid>"
+  module_python3: "cray-python"
+  bash_shebang: "#!/bin/bash"
+
+sched:
+  name: "Slurm"
+  partition: "standard"
+  reservation: "shortqos"
+  qos: "short"
+  budget: "short"
+  submit:
+    name: "sbatch"
+    options: "--partition=standard --qos=short"
+  queue:
+    debug: ""
+    testing: ""
+  status: "squeue"
+  flag:
+    user: "-u userid"
+    interactive: ""
+    histdetail: "-l -j"
+    name: "--job-name"
+    time: "--time"
+    queue: "--partition"
+    nodes: "--nodes"
+    tasks: ""
+  del: "scancel"
+  interactive: "srun"
+  info: "sinfo"
+  comment: "#SBATCH"
+  hist: "sacct"
+  project: ta114
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml b/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
new file mode 100644
index 00000000..45f7a367
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
@@ -0,0 +1,66 @@
+# ---------------------------------------------------------------
+# 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"
+
+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: "smnode1"
+  location: "cluster.hpc-carpentry.org"
+  homedir: "/home"
+  user: "yourUsername"
+  module_python3: "Python"
+  prompt: "[yourUsername@login1 ~]$"
+  bash_shebang: "#!/bin/bash"
+
+sched:
+  name: "Slurm"
+  submit:
+    name: "sbatch"
+    options: ""
+  queue:
+    debug: "smnode"
+    testing: "cpubase_bycore_b1"
+  status: "squeue"
+  flag:
+    user: "-u yourUsername"
+    interactive: ""
+    histdetail: "-l -j"
+    name: "-J"
+    time: "-t"
+    queue: "-p"
+  del: "scancel"
+  interactive: "srun"
+  info: "sinfo"
+  comment: "#SBATCH"
+  hist: "sacct -u yourUsername"
+  hist_filter: ""
+
+episode_order:
+  - 10-hpc-intro
+  - 11-connecting
+  - 12-cluster
+  - 13-scheduler
+  - 14-environment-variables
+  - 15-modules
+  - 16-transferring-files
+  - 17-parallel
+  - 18-resources
+  - 19-responsibility
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.snip
new file mode 100644
index 00000000..decfc331
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.snip
@@ -0,0 +1,7 @@
+```
+PARTITION          AVAIL  TIMELIMIT  NODES  STATE NODELIST
+cpubase_bycore_b1*    up   infinite      4   idle node[1-2],smnode[1-2]
+node                  up   infinite      2   idle node[1-2]
+smnode                up   infinite      2   idle smnode[1-2]
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.Rmd
new file mode 100644
index 00000000..3a86da2c
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.Rmd
@@ -0,0 +1,11 @@
+::: challenge
+## Explore a Worker Node
+
+Finally, let's look at the resources available on the worker nodes where your jobs will actually
+run. Try running this command to see the name, CPUs and memory available on one of the worker nodes:
+
+```bash
+`r config$remote$prompt` sinfo -o "%n %c %m" | column -t
+```
+:::
+
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.snip
new file mode 100644
index 00000000..b70845bd
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.snip
@@ -0,0 +1,11 @@
+> ## Explore a Worker Node
+>
+> Finally, let's look at the resources available on the worker nodes where your
+> jobs will actually run. Try running this command to see the name, CPUs and
+> memory available on the worker nodes:
+>
+> ```
+> {{ site.remote.prompt }} sinfo -o "%n %c %m" | column -t
+> ```
+> {: .language-bash}
+{: .challenge}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.snip
new file mode 100644
index 00000000..f6f3f50b
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.snip
@@ -0,0 +1,21 @@
+```
+~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
+  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
+  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
+  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
+  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
+  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a
+
+[removed most of the output here for clarity]
+
+  Where:
+   L:        Module is loaded
+   Aliases:  Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
+             will load foo/1.2.3
+   D:        Default Module
+
+Use "module spider" to find all possible modules and extensions.
+Use "module keyword key1 key2 ..." to search for all possible modules matching
+any of the "keys".
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/default-modules.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/default-modules.snip
new file mode 100644
index 00000000..a448dd96
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/default-modules.snip
@@ -0,0 +1,4 @@
+```
+No Modulefiles Currently Loaded.
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.snip
new file mode 100644
index 00000000..89039d32
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.snip
@@ -0,0 +1,33 @@
+If the `python3` command was unavailable, we would see output like
+
+```
+/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/{{site.remote.user}}/.local/bin:/home/{{site.remote.user}}/bin)
+```
+{: .output}
+
+Note that this wall of text is really a list, with values separated
+by the `:` character. The output is telling us that the `which` command
+searched the following directories for `python3`, without success:
+
+```
+/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin
+/opt/software/slurm/bin
+/usr/local/bin
+/usr/bin
+/usr/local/sbin
+/usr/sbin
+/opt/puppetlabs/bin
+/home/{{site.remote.user}}/.local/bin
+/home/{{site.remote.user}}/bin
+```
+{: .output}
+
+However, in our case we do have an existing `python3` available so we see
+
+```
+/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin/python3
+```
+{: .output}
+
+We need a different Python than the system provided one though, so let us load
+a module to access it.
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.snip
new file mode 100644
index 00000000..d9bab7b4
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.snip
@@ -0,0 +1,5 @@
+```
+{{ site.remote.prompt }} module load {{ site.remote.module_python3 }}
+{{ site.remote.prompt }} which python3
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.snip
new file mode 100644
index 00000000..46dec092
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.snip
@@ -0,0 +1,4 @@
+```
+/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-command.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-command.snip
new file mode 100644
index 00000000..80319d0a
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-command.snip
@@ -0,0 +1,4 @@
+```
+{{ site.remote.prompt }} ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-output.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-output.snip
new file mode 100644
index 00000000..01d010ba
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-output.snip
@@ -0,0 +1,16 @@
+```
+2to3              nosetests-3.8  python                 rst2s5.py
+2to3-3.8          pasteurize     python3                rst2xetex.py
+chardetect        pbr            python3.8              rst2xml.py
+cygdb             pip            python3.8-config       rstpep2html.py
+cython            pip3           python3-config         runxlrd.py
+cythonize         pip3.8         rst2html4.py           sphinx-apidoc
+easy_install      pybabel        rst2html5.py           sphinx-autogen
+easy_install-3.8  __pycache__    rst2html.py            sphinx-build
+futurize          pydoc3         rst2latex.py           sphinx-quickstart
+idle3             pydoc3.8       rst2man.py             tabulate
+idle3.8           pygmentize     rst2odt_prepstyles.py  virtualenv
+netaddr           pytest         rst2odt.py             wheel
+nosetests         py.test        rst2pseudoxml.py
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-module-path.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-module-path.snip
new file mode 100644
index 00000000..68e97df1
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-module-path.snip
@@ -0,0 +1,4 @@
+```
+/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/SQLite/3.31.1-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Tcl/8.6.10-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/GCCcore/x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/user01/.local/bin:/home/user01/bin
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip
new file mode 100644
index 00000000..fe107f2e
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip
@@ -0,0 +1,87 @@
+To demonstrate, let's use `module list`. `module list` shows all loaded
+software modules.
+
+```
+{{ site.remote.prompt }} module list
+```
+{: .language-bash}
+
+```
+Currently Loaded Modules:
+  1) GCCcore/x.y.z                 4) GMP/6.2.0-GCCcore-x.y.z
+  2) Tcl/8.6.10-GCCcore-x.y.z      5) libffi/3.3-GCCcore-x.y.z
+  3) SQLite/3.31.1-GCCcore-x.y.z   6) Python/3.x.y-GCCcore-x.y.z
+```
+{: .output}
+
+```
+{{ site.remote.prompt }} module load GROMACS
+{{ site.remote.prompt }} module list
+```
+{: .language-bash}
+
+```
+Currently Loaded Modules:
+  1) GCCcore/x.y.z                    14) libfabric/1.11.0-GCCcore-x.y.z
+  2) Tcl/8.6.10-GCCcore-x.y.z         15) PMIx/3.1.5-GCCcore-x.y.z
+  3) SQLite/3.31.1-GCCcore-x.y.z      16) OpenMPI/4.0.3-GCC-x.y.z
+  4) GMP/6.2.0-GCCcore-x.y.z          17) OpenBLAS/0.3.9-GCC-x.y.z
+  5) libffi/3.3-GCCcore-x.y.z         18) gompi/2020a
+  6) Python/3.x.y-GCCcore-x.y.z       19) FFTW/3.3.8-gompi-2020a
+  7) GCC/x.y.z                        20) ScaLAPACK/2.1.0-gompi-2020a
+  8) numactl/2.0.13-GCCcore-x.y.z     21) foss/2020a
+  9) libxml2/2.9.10-GCCcore-x.y.z     22) pybind11/2.4.3-GCCcore-x.y.z-Pytho...
+ 10) libpciaccess/0.16-GCCcore-x.y.z  23) SciPy-bundle/2020.03-foss-2020a-Py...
+ 11) hwloc/2.2.0-GCCcore-x.y.z        24) networkx/2.4-foss-2020a-Python-3.8...
+ 12) libevent/2.1.11-GCCcore-x.y.z    25) GROMACS/2020.1-foss-2020a-Python-3...
+ 13) UCX/1.8.0-GCCcore-x.y.z
+```
+{: .output}
+
+So in this case, loading the `GROMACS` module (a bioinformatics software
+package), also loaded `GMP/6.2.0-GCCcore-x.y.z` and
+`SciPy-bundle/2020.03-foss-2020a-Python-3.x.y` as well. Let's try unloading the
+`GROMACS` package.
+
+```
+{{ site.remote.prompt }} module unload GROMACS
+{{ site.remote.prompt }} module list
+```
+{: .language-bash}
+
+```
+Currently Loaded Modules:
+  1) GCCcore/x.y.z                    13) UCX/1.8.0-GCCcore-x.y.z
+  2) Tcl/8.6.10-GCCcore-x.y.z         14) libfabric/1.11.0-GCCcore-x.y.z
+  3) SQLite/3.31.1-GCCcore-x.y.z      15) PMIx/3.1.5-GCCcore-x.y.z
+  4) GMP/6.2.0-GCCcore-x.y.z          16) OpenMPI/4.0.3-GCC-x.y.z
+  5) libffi/3.3-GCCcore-x.y.z         17) OpenBLAS/0.3.9-GCC-x.y.z
+  6) Python/3.x.y-GCCcore-x.y.z       18) gompi/2020a
+  7) GCC/x.y.z                        19) FFTW/3.3.8-gompi-2020a
+  8) numactl/2.0.13-GCCcore-x.y.z     20) ScaLAPACK/2.1.0-gompi-2020a
+  9) libxml2/2.9.10-GCCcore-x.y.z     21) foss/2020a
+ 10) libpciaccess/0.16-GCCcore-x.y.z  22) pybind11/2.4.3-GCCcore-x.y.z-Pytho...
+ 11) hwloc/2.2.0-GCCcore-x.y.z        23) SciPy-bundle/2020.03-foss-2020a-Py...
+ 12) libevent/2.1.11-GCCcore-x.y.z    24) networkx/2.4-foss-2020a-Python-3.x.y
+```
+{: .output}
+
+So using `module unload` "un-loads" a module, and depending on how a site is
+ configured it may also unload all of the dependencies (in our case it does
+ not). If we wanted to unload everything at once, we could run `module purge`
+ (unloads everything).
+
+```
+{{ site.remote.prompt }} module purge
+{{ site.remote.prompt }} module list
+```
+{: .language-bash}
+
+```
+No modules loaded
+```
+{: .output}
+
+Note that `module purge` is informative. It will also let us know if a default
+set of "sticky" packages cannot be unloaded (and how to actually unload these
+if we truly so desired).
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/wrong-gcc-version.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/wrong-gcc-version.snip
new file mode 100644
index 00000000..8fbd2825
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/wrong-gcc-version.snip
@@ -0,0 +1,5 @@
+<!--- There is a long additional section on some specific features of Lmod in
+snippets_library/ComputeCanada_Graham_slurm/modules/wrong-gcc-version.snip,
+particular covering the concept of a module hierarchy. While this is not
+relevant to the EESSI configuration right now, it may become so in the future
+if we change the default module naming scheme to hierarchical. -->
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks-jobscript.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks-jobscript.snip
new file mode 100644
index 00000000..2f643071
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks-jobscript.snip
@@ -0,0 +1,16 @@
+```
+{{ site.remote.bash_shebang }}
+{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
+{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
+{{ site.sched.comment }} -N 1
+{{ site.sched.comment }} -n 8
+
+# Load the computing environment we need
+# (mpi4py and numpy are in SciPy-bundle)
+module load {{ site.remote.module_python3 }}
+module load SciPy-bundle
+
+# Execute the task
+mpiexec amdahl
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks-jobscript.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks-jobscript.snip
new file mode 100644
index 00000000..19804d74
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks-jobscript.snip
@@ -0,0 +1,16 @@
+```
+{{ site.remote.bash_shebang }}
+{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
+{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
+{{ site.sched.comment }} -N 1
+{{ site.sched.comment }} -n 4
+
+# Load the computing environment we need
+# (mpi4py and numpy are in SciPy-bundle)
+module load {{ site.remote.module_python3 }}
+module load SciPy-bundle
+
+# Execute the task
+mpiexec amdahl
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task-jobscript.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task-jobscript.snip
new file mode 100644
index 00000000..1941ef04
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task-jobscript.snip
@@ -0,0 +1,14 @@
+```
+{{ 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
+
+# Load the computing environment we need
+module load {{ site.remote.module_python3 }}
+
+# Execute the task
+amdahl
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.snip
new file mode 100644
index 00000000..d5a87620
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.snip
@@ -0,0 +1,14 @@
+```
+       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
+------------ ---------- ---------- ---------- ---------- ---------- --------
+7               file.sh cpubase_b+ def-spons+          1  COMPLETED      0:0
+7.batch           batch            def-spons+          1  COMPLETED      0:0
+7.extern         extern            def-spons+          1  COMPLETED      0:0
+8               file.sh cpubase_b+ def-spons+          1  COMPLETED      0:0
+8.batch           batch            def-spons+          1  COMPLETED      0:0
+8.extern         extern            def-spons+          1  COMPLETED      0:0
+9            example-j+ cpubase_b+ def-spons+          1  COMPLETED      0:0
+9.batch           batch            def-spons+          1  COMPLETED      0:0
+9.extern         extern            def-spons+          1  COMPLETED      0:0
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/monitor-processes-top.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/monitor-processes-top.snip
new file mode 100644
index 00000000..12685735
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/monitor-processes-top.snip
@@ -0,0 +1,19 @@
+```
+top - 21:00:19 up  3:07,  1 user,  load average: 1.06, 1.05, 0.96
+Tasks: 311 total,   1 running, 222 sleeping,   0 stopped,   0 zombie
+%Cpu(s):  7.2 us,  3.2 sy,  0.0 ni, 89.0 id,  0.0 wa,  0.2 hi,  0.2 si,  0.0 st
+KiB Mem : 16303428 total,  8454704 free,  3194668 used,  4654056 buff/cache
+KiB Swap:  8220668 total,  8220668 free,        0 used. 11628168 avail Mem
+
+  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
+ 1693 jeff      20   0 4270580 346944 171372 S  29.8  2.1   9:31.89 gnome-shell
+ 3140 jeff      20   0 3142044 928972 389716 S  27.5  5.7  13:30.29 Web Content
+ 3057 jeff      20   0 3115900 521368 231288 S  18.9  3.2  10:27.71 firefox
+ 6007 jeff      20   0  813992 112336  75592 S   4.3  0.7   0:28.25 tilix
+ 1742 jeff      20   0  975080 164508 130624 S   2.0  1.0   3:29.83 Xwayland
+    1 root      20   0  230484  11924   7544 S   0.3  0.1   0:06.08 systemd
+   68 root      20   0       0      0      0 I   0.3  0.0   0:01.25 kworker/4:1
+ 2913 jeff      20   0  965620  47892  37432 S   0.3  0.3   0:11.76 code
+    2 root      20   0       0      0      0 S   0.0  0.0   0:00.02 kthreadd
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/system-memory-free.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/system-memory-free.snip
new file mode 100644
index 00000000..ec4c0d3f
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/system-memory-free.snip
@@ -0,0 +1,6 @@
+```
+total        used        free      shared  buff/cache   available
+Mem:           3.8G        1.5G        678M        327M        1.6G        1.6G
+Swap:          3.9G        170M        3.7G
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.Rmd
new file mode 100644
index 00000000..5f76fb2c
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.Rmd
@@ -0,0 +1,3 @@
+```output
+Submitted batch job 7
+```
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.snip
new file mode 100644
index 00000000..06b7fc91
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.snip
@@ -0,0 +1,4 @@
+```
+Submitted batch job 7
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.snip
new file mode 100644
index 00000000..6bb1b93e
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.snip
@@ -0,0 +1,9 @@
+```
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+    9 cpubase_b example-   user01  R       0:05      1 node1
+```
+{: .output}
+
+We can see all the details of our job, most importantly that it is in the `R`
+or `RUNNING` state. Sometimes our jobs might need to wait in a queue
+(`PENDING`) or have an error (`E`).
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.snip
new file mode 100644
index 00000000..838c5464
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.snip
@@ -0,0 +1,5 @@
+```
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+   10 cpubase_b hello-wo   user01  R       0:02      1 node1
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/option-flags-list.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/option-flags-list.snip
new file mode 100644
index 00000000..5e80b164
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/option-flags-list.snip
@@ -0,0 +1,15 @@
+* `--ntasks=<ntasks>` or `-n <ntasks>`: How many CPU cores does your job need,
+  in total?
+
+* `--time <days-hours:minutes:seconds>` or `-t <days-hours:minutes:seconds>`:
+  How much real-world time (walltime) will your job take to run? The `<days>`
+  part can be omitted.
+
+* `--mem=<megabytes>`: How much memory on a node does your job need in
+  megabytes? You can also specify gigabytes using by adding a little "g"
+  afterwards (example: `--mem=5g`)
+
+* `--nodes=<nnodes>` or `-N <nnodes>`: How many separate machines does your job
+  need to run on? Note that if you set `ntasks` to a number greater than what
+  one machine can offer, {{ site.sched.name }} will set this value
+  automatically.
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.snip
new file mode 100644
index 00000000..5234a4ed
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.snip
@@ -0,0 +1,30 @@
+> ## Job environment variables
+>
+> When {{ site.sched.name }} runs a job, it sets a number of environment
+> variables for the job. One of these will let us check what directory our job
+> script was submitted from. The `SLURM_SUBMIT_DIR` variable is set to the
+> directory from which our job was submitted. Using the `SLURM_SUBMIT_DIR`
+> variable, modify your job so that it prints out the location from which the
+> job was submitted.
+>
+> > ## Solution
+> >
+> > ```
+> > {{ site.remote.prompt }} nano example-job.sh
+> > {{ site.remote.prompt }} cat example-job.sh
+> > ```
+> > {: .language-bash}
+> >
+> > ```
+> > {{ site.remote.bash_shebang }}
+> > #SBATCH -t 00:00:30
+> >
+> > echo -n "This script is running on "
+> > hostname
+> >
+> > echo "This job was launched in the following directory:"
+> > echo ${SLURM_SUBMIT_DIR}
+> > ```
+> > {: .output}
+> {: .solution}
+{: .challenge}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.snip
new file mode 100644
index 00000000..a9eae8de
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.snip
@@ -0,0 +1,4 @@
+```
+{{ site.remote.prompt }} cat slurm-12.out
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.snip
new file mode 100644
index 00000000..180d3ea4
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.snip
@@ -0,0 +1,6 @@
+```
+This script is running on ...
+slurmstepd: error: *** JOB 12 ON node1 CANCELLED AT 2021-02-19T13:55:57
+DUE TO TIME LIMIT ***
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.snip
new file mode 100644
index 00000000..c7af2eef
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.snip
@@ -0,0 +1,7 @@
+```
+Submitted batch job 13
+
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+   13 cpubase_b long_job   user01  R       0:02      1 node1
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.snip
new file mode 100644
index 00000000..5429787d
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.snip
@@ -0,0 +1,4 @@
+```
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+```
+{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.snip
new file mode 100644
index 00000000..3a229b55
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.snip
@@ -0,0 +1,27 @@
+> ## Cancelling multiple jobs
+>
+> We can also cancel all of our jobs at once using the `-u` option. This will
+> delete all jobs for a specific user (in this case, yourself). Note that you
+> can only delete your own jobs.
+>
+> Try submitting multiple jobs and then cancelling them all.
+>
+> > ## Solution
+> >
+> > First, submit a trio of jobs:
+> >
+> > ```
+> > {{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
+> > {{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
+> > {{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
+> > ```
+> > {: .language-bash}
+> >
+> > Then, cancel them all:
+> >
+> > ```
+> > {{ site.remote.prompt }} {{ site.sched.del }} -u {{ site.remote.user }}
+> > ```
+> > {: .language-bash}
+> {: .solution}
+{: .challenge}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.snip
new file mode 100644
index 00000000..40b11437
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.snip
@@ -0,0 +1,69 @@
+`{{ site.sched.interactive }}` runs a single command on the cluster and then
+exits. Let's demonstrate this by running the `hostname` command with
+`{{ site.sched.interactive }}`. (We can cancel an `{{ site.sched.interactive }}`
+job with `Ctrl-c`.)
+
+```
+{{ site.remote.prompt }} {{ site.sched.interactive }} hostname
+```
+{: .language-bash}
+
+```
+{{ site.remote.node }}
+```
+{: .output}
+
+`{{ site.sched.interactive }}` accepts all of the same options as
+`{{ site.sched.submit.name }}`. However, instead of specifying these in a script,
+these options are specified on the command-line when starting a job. To submit
+a job that uses 2 CPUs for instance, we could use the following command:
+
+```
+{{ site.remote.prompt }} {{ site.sched.interactive }} -n 2 echo "This job will use 2 CPUs."
+```
+{: .language-bash}
+
+```
+This job will use 2 CPUs.
+This job will use 2 CPUs.
+```
+{: .output}
+
+Typically, the resulting shell environment will be the same as that for
+`{{ site.sched.submit.name }}`.
+
+### Interactive jobs
+
+Sometimes, you will need a lot of resources for interactive use. Perhaps it's
+our first time running an analysis or we are attempting to debug something that
+went wrong with a previous job. Fortunately, {{ site.sched.name }} makes it
+easy to start an interactive job with `{{ site.sched.interactive }}`:
+
+```
+{{ site.remote.prompt }} {{ site.sched.interactive }} --pty bash
+```
+{: .language-bash}
+
+You should be presented with a bash prompt. Note that the prompt will likely
+change to reflect your new location, in this case the compute node we are
+logged on. You can also verify this with `hostname`.
+
+> ## Creating remote graphics
+>
+> To see graphical output inside your jobs, you need to use X11 forwarding. To
+> connect with this feature enabled, use the `-Y` option when you login with
+> the `ssh` command, e.g., `ssh -Y {{ site.remote.user }}@{{ site.remote.login }}`.
+>
+> To demonstrate what happens when you create a graphics window on the remote
+> node, use the `xeyes` command. A relatively adorable pair of eyes should pop
+> up (press `Ctrl-C` to stop). If you are using a Mac, you must have installed
+> XQuartz (and restarted your computer) for this to work.
+>
+> If your cluster has the
+> [slurm-spank-x11](https://github.com/hautreux/slurm-spank-x11) plugin
+> installed, you can ensure X11 forwarding within interactive jobs by using the
+> `--x11` option for `{{ site.sched.interactive }}` with the command
+> `{{ site.sched.interactive }} --x11 --pty bash`.
+{: .callout}
+
+When you are done with the interactive job, type `exit` to quit your session.
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/transferring-files/filezilla-ssh-tunnel-instructions.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/transferring-files/filezilla-ssh-tunnel-instructions.snip
new file mode 100644
index 00000000..e69de29b
diff --git a/episodes/lesson_config.yaml b/episodes/lesson_config.yaml
index 5425d7b1..3575aad9 100644
--- a/episodes/lesson_config.yaml
+++ b/episodes/lesson_config.yaml
@@ -1,50 +1,51 @@
 ---
 local:
-  prompt: "[user@laptop ~]$"
-  bash_shebang: "#!/bin/bash"
+  prompt: "[you@laptop:~]$"
+  bash_shebang: "#!/usr/bin/env bash"
 
-snippets: EPCC_ARCHER2_slurm
-baseurl: "https://epcced.github.io/2023-06-28-uoe-hpcintro"
+snippets: HPCC_MagicCastle_slurm
+baseurl: "https://jlchang.github.io/probable-pancake/"
 
 remote:
-  name: "ARCHER2"
-  host_id: "EPCC_ARCHER2"
-  login: "login.archer2.ac.uk"
-  host: "ln03"
-  node: "nid001053"
-  location: "EPCC, The University of Edinburgh"
-  homedir: "/home/ta114/ta114/"
-  user: "userid"
-  prompt: "userid@ln03:~>"
-  prompt_work: "userid@uan01:/work/ta114/ta114/userid>"
-  module_python3: "cray-python"
+  name: "HPC Carpentry's Cloud Cluster"
+  host_id: #"EPCC_ARCHER2"
+  login: "cluster.hpc-carpentry.org"
+  host: "login1"
+  node: "smnode1"
+  location: "cluster.hpc-carpentry.org"
+  homedir: "/home"
+  user: "yourUsername"
+  prompt: 'yourUsername@login1 ~]'
+  prompt_work: #"userid@uan01:/work/ta114/ta114/userid>"
+  module_python3: "Python"
   bash_shebang: "#!/bin/bash"
 
 sched:
   name: "Slurm"
-  partition: "standard"
-  reservation: "shortqos"
-  qos: "short"
-  budget: "short"
   submit:
     name: "sbatch"
-    options: "--partition=standard --qos=short"
+    options: ""
   queue:
-    debug: ""
-    testing: ""
+    debug: "smnode"
+    testing: "cpubase_bycore_b1"
   status: "squeue"
   flag:
-    user: "-u userid"
+    user: "-u yourUsername"
     interactive: ""
     histdetail: "-l -j"
-    name: "--job-name"
-    time: "--time"
-    queue: "--partition"
-    nodes: "--nodes"
+    name: "-J"
+    time: "-t"
+    queue: "-p"
+    nodes: ""
     tasks: ""
   del: "scancel"
   interactive: "srun"
   info: "sinfo"
   comment: "#SBATCH"
-  hist: "sacct"
-  project: ta114
+  hist: "sacct -u yourUsername"
+  hist_filter: ""
+  partition: "standard"
+  reservation: "shortqos"
+  qos: "short"
+  budget: "short"
+  project: 

From 52967a935436bbe9095be5acd8692f07040a8581 Mon Sep 17 00:00:00 2001
From: Jean Chang <jlchang@broadinstitute.org>
Date: Wed, 15 Jan 2025 08:30:55 -0500
Subject: [PATCH 09/33] update workflows

---
 .github/workflows/pr-close-signal.yaml       |  6 ++---
 .github/workflows/pr-comment.yaml            | 24 +++++++++-----------
 .github/workflows/pr-post-remove-branch.yaml |  6 ++---
 .github/workflows/pr-preflight.yaml          |  8 +++----
 .github/workflows/pr-receive.yaml            |  5 ++--
 .github/workflows/sandpaper-main.yaml        | 13 ++++++-----
 .github/workflows/sandpaper-version.txt      |  2 +-
 .github/workflows/update-cache.yaml          |  9 ++++----
 .github/workflows/update-workflows.yaml      | 10 ++++----
 9 files changed, 38 insertions(+), 45 deletions(-)

diff --git a/.github/workflows/pr-close-signal.yaml b/.github/workflows/pr-close-signal.yaml
index d20a2991..3268909b 100644
--- a/.github/workflows/pr-close-signal.yaml
+++ b/.github/workflows/pr-close-signal.yaml
@@ -2,13 +2,12 @@ name: "Bot: Send Close Pull Request Signal"
 
 on:
   pull_request:
-    types:
-      [closed]
+    types: [closed]
 
 jobs:
   send-close-signal:
     name: "Send closing signal"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ github.event.action == 'closed' }}
     steps:
       - name: "Create PRtifact"
@@ -20,4 +19,3 @@ jobs:
         with:
           name: pr
           path: ./pr
-
diff --git a/.github/workflows/pr-comment.yaml b/.github/workflows/pr-comment.yaml
index 8a2bd3ce..014235dd 100644
--- a/.github/workflows/pr-comment.yaml
+++ b/.github/workflows/pr-comment.yaml
@@ -12,7 +12,6 @@ concurrency:
   group: pr-${{ github.event.workflow_run.pull_requests[0].number }}
   cancel-in-progress: true
 
-
 jobs:
   # Pull requests are valid if:
   #  - they match the sha of the workflow run head commit
@@ -20,7 +19,7 @@ jobs:
   #  - no .github files were committed
   test-pr:
     name: "Test if pull request is valid"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: >
       github.event.workflow_run.event == 'pull_request' &&
       github.event.workflow_run.conclusion == 'success'
@@ -30,12 +29,12 @@ jobs:
       number: ${{ steps.get-pr.outputs.NUM }}
       msg: ${{ steps.check-pr.outputs.MSG }}
     steps:
-      - name: 'Download PR artifact'
+      - name: "Download PR artifact"
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
-          name: 'pr'
+          name: "pr"
 
       - name: "Get PR Number"
         if: ${{ steps.dl.outputs.success == 'true' }}
@@ -81,19 +80,19 @@ jobs:
     permissions:
       contents: write
     steps:
-      - name: 'Checkout md outputs'
+      - name: "Checkout md outputs"
         uses: actions/checkout@v4
         with:
           ref: md-outputs
           path: built
           fetch-depth: 1
 
-      - name: 'Download built markdown'
+      - name: "Download built markdown"
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
-          name: 'built'
+          name: "built"
 
       - if: ${{ steps.dl.outputs.success == 'true' }}
         run: unzip built.zip
@@ -127,12 +126,12 @@ jobs:
     permissions:
       pull-requests: write
     steps:
-      - name: 'Download comment artifact'
+      - name: "Download comment artifact"
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
-          name: 'diff'
+          name: "diff"
 
       - if: ${{ steps.dl.outputs.success == 'true' }}
         run: unzip ${{ github.workspace }}/diff.zip
@@ -158,14 +157,14 @@ jobs:
     permissions:
       pull-requests: write
     steps:
-      - name: 'Check for spoofing'
+      - name: "Check for spoofing"
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
-          name: 'built'
+          name: "built"
 
-      - name: 'Alert if spoofed'
+      - name: "Alert if spoofed"
         id: spoof
         if: ${{ steps.dl.outputs.success == 'true' }}
         run: |
@@ -182,4 +181,3 @@ jobs:
         with:
           pr: ${{ env.NR }}
           body: ${{ env.body }}
-
diff --git a/.github/workflows/pr-post-remove-branch.yaml b/.github/workflows/pr-post-remove-branch.yaml
index 62c2e98d..1f8dd158 100644
--- a/.github/workflows/pr-post-remove-branch.yaml
+++ b/.github/workflows/pr-post-remove-branch.yaml
@@ -9,14 +9,14 @@ on:
 jobs:
   delete:
     name: "Delete branch from Pull Request"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: >
       github.event.workflow_run.event == 'pull_request' &&
       github.event.workflow_run.conclusion == 'success'
     permissions:
       contents: write
     steps:
-      - name: 'Download artifact'
+      - name: "Download artifact"
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
@@ -26,7 +26,7 @@ jobs:
         run: |
           unzip pr.zip
           echo "NUM=$(<./NUM)" >> $GITHUB_OUTPUT
-      - name: 'Remove branch'
+      - name: "Remove branch"
         uses: carpentries/actions/remove-branch@main
         with:
           pr: ${{ steps.get-pr.outputs.NUM }}
diff --git a/.github/workflows/pr-preflight.yaml b/.github/workflows/pr-preflight.yaml
index d0d7420d..fcd098ab 100644
--- a/.github/workflows/pr-preflight.yaml
+++ b/.github/workflows/pr-preflight.yaml
@@ -2,16 +2,14 @@ name: "Pull Request Preflight Check"
 
 on:
   pull_request_target:
-    branches:
-      ["main"]
-    types:
-      ["opened", "synchronize", "reopened"]
+    branches: ["main"]
+    types: ["opened", "synchronize", "reopened"]
 
 jobs:
   test-pr:
     name: "Test if pull request is valid"
     if: ${{ github.event.action != 'closed' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       is_valid: ${{ steps.check-pr.outputs.VALID }}
     permissions:
diff --git a/.github/workflows/pr-receive.yaml b/.github/workflows/pr-receive.yaml
index 0204cc17..3886a3ba 100644
--- a/.github/workflows/pr-receive.yaml
+++ b/.github/workflows/pr-receive.yaml
@@ -2,8 +2,7 @@ name: "Receive Pull Request"
 
 on:
   pull_request:
-    types:
-      [opened, synchronize, reopened]
+    types: [opened, synchronize, reopened]
 
 concurrency:
   group: ${{ github.ref }}
@@ -13,7 +12,7 @@ jobs:
   test-pr:
     name: "Record PR number"
     if: ${{ github.event.action != 'closed' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       is_valid: ${{ steps.check-pr.outputs.VALID }}
     steps:
diff --git a/.github/workflows/sandpaper-main.yaml b/.github/workflows/sandpaper-main.yaml
index a4f8dc40..5a34c11a 100644
--- a/.github/workflows/sandpaper-main.yaml
+++ b/.github/workflows/sandpaper-main.yaml
@@ -6,22 +6,24 @@ on:
       - main
       - master
   schedule:
-    - cron: '0 0 * * 2'
+    - cron: "0 0 * * 2"
   workflow_dispatch:
     inputs:
       name:
-        description: 'Who triggered this build?'
+        description: "Who triggered this build?"
         required: true
-        default: 'Maintainer (via GitHub)'
+        default: "Maintainer (via GitHub)"
       reset:
-        description: 'Reset cached markdown files'
+        description: "Reset cached markdown files"
         required: false
         default: false
         type: boolean
 jobs:
   full-build:
     name: "Build Full Site"
-    runs-on: ubuntu-latest
+    # 2024-10-01: ubuntu-latest is now 24.04 and R is not installed by default in the runner image
+    # pin to 22.04 for now
+    runs-on: ubuntu-22.04
     permissions:
       checks: write
       contents: write
@@ -30,7 +32,6 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RENV_PATHS_ROOT: ~/.local/share/renv/
     steps:
-
       - name: "Checkout Lesson"
         uses: actions/checkout@v4
 
diff --git a/.github/workflows/sandpaper-version.txt b/.github/workflows/sandpaper-version.txt
index 427cda05..ce62dc55 100644
--- a/.github/workflows/sandpaper-version.txt
+++ b/.github/workflows/sandpaper-version.txt
@@ -1 +1 @@
-0.16.7
+0.16.9
diff --git a/.github/workflows/update-cache.yaml b/.github/workflows/update-cache.yaml
index 08ea9c97..c3033a4a 100644
--- a/.github/workflows/update-cache.yaml
+++ b/.github/workflows/update-cache.yaml
@@ -4,17 +4,17 @@ on:
   workflow_dispatch:
     inputs:
       name:
-        description: 'Who triggered this build (enter github username to tag yourself)?'
+        description: "Who triggered this build (enter github username to tag yourself)?"
         required: true
-        default: 'monthly run'
+        default: "monthly run"
   schedule:
     # Run every tuesday
-    - cron: '0 0 * * 2'
+    - cron: "0 0 * * 2"
 
 jobs:
   preflight:
     name: "Preflight Check"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       ok: ${{ steps.check.outputs.ok }}
     steps:
@@ -74,7 +74,6 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RENV_PATHS_ROOT: ~/.local/share/renv/
     steps:
-
       - name: "Checkout Lesson"
         uses: actions/checkout@v4
 
diff --git a/.github/workflows/update-workflows.yaml b/.github/workflows/update-workflows.yaml
index a2d6fee1..2b556567 100644
--- a/.github/workflows/update-workflows.yaml
+++ b/.github/workflows/update-workflows.yaml
@@ -4,21 +4,21 @@ on:
   workflow_dispatch:
     inputs:
       name:
-        description: 'Who triggered this build (enter github username to tag yourself)?'
+        description: "Who triggered this build (enter github username to tag yourself)?"
         required: true
-        default: 'weekly run'
+        default: "weekly run"
       clean:
         description: 'Workflow files/file extensions to clean (no wildcards, enter "" for none)'
         required: false
-        default: '.yaml'
+        default: ".yaml"
   schedule:
     # Run every Tuesday
-    - cron: '0 0 * * 2'
+    - cron: "0 0 * * 2"
 
 jobs:
   check_token:
     name: "Check SANDPAPER_WORKFLOW token"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     outputs:
       workflow: ${{ steps.validate.outputs.wf }}
       repo: ${{ steps.validate.outputs.repo }}

From 700d7ecde23ff3cfe65ef2d4386406c50db2e279 Mon Sep 17 00:00:00 2001
From: jlchang <jlchang@users.noreply.github.com>
Date: Thu, 23 Jan 2025 14:07:03 +0000
Subject: [PATCH 10/33] [actions] update sandpaper workflow to version 0.16.11

---
 .github/workflows/pr-close-signal.yaml       |  3 ++-
 .github/workflows/pr-comment.yaml            | 27 ++++++++++----------
 .github/workflows/pr-post-remove-branch.yaml |  4 +--
 .github/workflows/pr-preflight.yaml          |  6 +++--
 .github/workflows/pr-receive.yaml            |  5 ++--
 .github/workflows/sandpaper-main.yaml        | 10 +++++---
 .github/workflows/sandpaper-version.txt      |  2 +-
 .github/workflows/update-cache.yaml          | 13 +++++-----
 .github/workflows/update-workflows.yaml      | 10 ++++----
 9 files changed, 44 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/pr-close-signal.yaml b/.github/workflows/pr-close-signal.yaml
index 3268909b..b1303c26 100644
--- a/.github/workflows/pr-close-signal.yaml
+++ b/.github/workflows/pr-close-signal.yaml
@@ -2,7 +2,8 @@ name: "Bot: Send Close Pull Request Signal"
 
 on:
   pull_request:
-    types: [closed]
+    types:
+      [closed]
 
 jobs:
   send-close-signal:
diff --git a/.github/workflows/pr-comment.yaml b/.github/workflows/pr-comment.yaml
index 014235dd..f80d9d0c 100644
--- a/.github/workflows/pr-comment.yaml
+++ b/.github/workflows/pr-comment.yaml
@@ -12,6 +12,7 @@ concurrency:
   group: pr-${{ github.event.workflow_run.pull_requests[0].number }}
   cancel-in-progress: true
 
+
 jobs:
   # Pull requests are valid if:
   #  - they match the sha of the workflow run head commit
@@ -29,12 +30,12 @@ jobs:
       number: ${{ steps.get-pr.outputs.NUM }}
       msg: ${{ steps.check-pr.outputs.MSG }}
     steps:
-      - name: "Download PR artifact"
+      - name: 'Download PR artifact'
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
-          name: "pr"
+          name: 'pr'
 
       - name: "Get PR Number"
         if: ${{ steps.dl.outputs.success == 'true' }}
@@ -73,26 +74,26 @@ jobs:
   create-branch:
     name: "Create Git Branch"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       NR: ${{ needs.test-pr.outputs.number }}
     permissions:
       contents: write
     steps:
-      - name: "Checkout md outputs"
+      - name: 'Checkout md outputs'
         uses: actions/checkout@v4
         with:
           ref: md-outputs
           path: built
           fetch-depth: 1
 
-      - name: "Download built markdown"
+      - name: 'Download built markdown'
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
-          name: "built"
+          name: 'built'
 
       - if: ${{ steps.dl.outputs.success == 'true' }}
         run: unzip built.zip
@@ -119,19 +120,19 @@ jobs:
   comment-pr:
     name: "Comment on Pull Request"
     needs: [test-pr, create-branch]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       NR: ${{ needs.test-pr.outputs.number }}
     permissions:
       pull-requests: write
     steps:
-      - name: "Download comment artifact"
+      - name: 'Download comment artifact'
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
-          name: "diff"
+          name: 'diff'
 
       - if: ${{ steps.dl.outputs.success == 'true' }}
         run: unzip ${{ github.workspace }}/diff.zip
@@ -149,7 +150,7 @@ jobs:
   comment-changed-workflow:
     name: "Comment if workflow files have changed"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ always() && needs.test-pr.outputs.is_valid == 'false' }}
     env:
       NR: ${{ github.event.workflow_run.pull_requests[0].number }}
@@ -157,14 +158,14 @@ jobs:
     permissions:
       pull-requests: write
     steps:
-      - name: "Check for spoofing"
+      - name: 'Check for spoofing'
         id: dl
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
-          name: "built"
+          name: 'built'
 
-      - name: "Alert if spoofed"
+      - name: 'Alert if spoofed'
         id: spoof
         if: ${{ steps.dl.outputs.success == 'true' }}
         run: |
diff --git a/.github/workflows/pr-post-remove-branch.yaml b/.github/workflows/pr-post-remove-branch.yaml
index 1f8dd158..9419e2be 100644
--- a/.github/workflows/pr-post-remove-branch.yaml
+++ b/.github/workflows/pr-post-remove-branch.yaml
@@ -16,7 +16,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - name: "Download artifact"
+      - name: 'Download artifact'
         uses: carpentries/actions/download-workflow-artifact@main
         with:
           run: ${{ github.event.workflow_run.id }}
@@ -26,7 +26,7 @@ jobs:
         run: |
           unzip pr.zip
           echo "NUM=$(<./NUM)" >> $GITHUB_OUTPUT
-      - name: "Remove branch"
+      - name: 'Remove branch'
         uses: carpentries/actions/remove-branch@main
         with:
           pr: ${{ steps.get-pr.outputs.NUM }}
diff --git a/.github/workflows/pr-preflight.yaml b/.github/workflows/pr-preflight.yaml
index fcd098ab..34ad7aed 100644
--- a/.github/workflows/pr-preflight.yaml
+++ b/.github/workflows/pr-preflight.yaml
@@ -2,8 +2,10 @@ name: "Pull Request Preflight Check"
 
 on:
   pull_request_target:
-    branches: ["main"]
-    types: ["opened", "synchronize", "reopened"]
+    branches:
+      ["main"]
+    types:
+      ["opened", "synchronize", "reopened"]
 
 jobs:
   test-pr:
diff --git a/.github/workflows/pr-receive.yaml b/.github/workflows/pr-receive.yaml
index 3886a3ba..7fbff6cd 100644
--- a/.github/workflows/pr-receive.yaml
+++ b/.github/workflows/pr-receive.yaml
@@ -2,7 +2,8 @@ name: "Receive Pull Request"
 
 on:
   pull_request:
-    types: [opened, synchronize, reopened]
+    types:
+      [opened, synchronize, reopened]
 
 concurrency:
   group: ${{ github.ref }}
@@ -47,7 +48,7 @@ jobs:
   build-md-source:
     name: "Build markdown source files if valid"
     needs: test-pr
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: ${{ needs.test-pr.outputs.is_valid == 'true' }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/sandpaper-main.yaml b/.github/workflows/sandpaper-main.yaml
index 5a34c11a..b3d1de8c 100644
--- a/.github/workflows/sandpaper-main.yaml
+++ b/.github/workflows/sandpaper-main.yaml
@@ -6,21 +6,22 @@ on:
       - main
       - master
   schedule:
-    - cron: "0 0 * * 2"
+    - cron: '0 0 * * 2'
   workflow_dispatch:
     inputs:
       name:
-        description: "Who triggered this build?"
+        description: 'Who triggered this build?'
         required: true
-        default: "Maintainer (via GitHub)"
+        default: 'Maintainer (via GitHub)'
       reset:
-        description: "Reset cached markdown files"
+        description: 'Reset cached markdown files'
         required: false
         default: false
         type: boolean
 jobs:
   full-build:
     name: "Build Full Site"
+
     # 2024-10-01: ubuntu-latest is now 24.04 and R is not installed by default in the runner image
     # pin to 22.04 for now
     runs-on: ubuntu-22.04
@@ -32,6 +33,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RENV_PATHS_ROOT: ~/.local/share/renv/
     steps:
+
       - name: "Checkout Lesson"
         uses: actions/checkout@v4
 
diff --git a/.github/workflows/sandpaper-version.txt b/.github/workflows/sandpaper-version.txt
index ce62dc55..f2f6c138 100644
--- a/.github/workflows/sandpaper-version.txt
+++ b/.github/workflows/sandpaper-version.txt
@@ -1 +1 @@
-0.16.9
+0.16.11
diff --git a/.github/workflows/update-cache.yaml b/.github/workflows/update-cache.yaml
index c3033a4a..a011c0c0 100644
--- a/.github/workflows/update-cache.yaml
+++ b/.github/workflows/update-cache.yaml
@@ -4,12 +4,12 @@ on:
   workflow_dispatch:
     inputs:
       name:
-        description: "Who triggered this build (enter github username to tag yourself)?"
+        description: 'Who triggered this build (enter github username to tag yourself)?'
         required: true
-        default: "monthly run"
+        default: 'monthly run'
   schedule:
     # Run every tuesday
-    - cron: "0 0 * * 2"
+    - cron: '0 0 * * 2'
 
 jobs:
   preflight:
@@ -36,7 +36,7 @@ jobs:
 
   check_renv:
     name: "Check if We Need {renv}"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: preflight
     if: ${{ needs.preflight.outputs.ok == 'true'}}
     outputs:
@@ -52,7 +52,7 @@ jobs:
 
   check_token:
     name: "Check SANDPAPER_WORKFLOW token"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: check_renv
     if: ${{ needs.check_renv.outputs.needed == 'true' }}
     outputs:
@@ -69,11 +69,12 @@ jobs:
     name: "Update Package Cache"
     needs: check_token
     if: ${{ needs.check_token.outputs.repo== 'true' }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RENV_PATHS_ROOT: ~/.local/share/renv/
     steps:
+
       - name: "Checkout Lesson"
         uses: actions/checkout@v4
 
diff --git a/.github/workflows/update-workflows.yaml b/.github/workflows/update-workflows.yaml
index 2b556567..6414cf28 100644
--- a/.github/workflows/update-workflows.yaml
+++ b/.github/workflows/update-workflows.yaml
@@ -4,16 +4,16 @@ on:
   workflow_dispatch:
     inputs:
       name:
-        description: "Who triggered this build (enter github username to tag yourself)?"
+        description: 'Who triggered this build (enter github username to tag yourself)?'
         required: true
-        default: "weekly run"
+        default: 'weekly run'
       clean:
         description: 'Workflow files/file extensions to clean (no wildcards, enter "" for none)'
         required: false
-        default: ".yaml"
+        default: '.yaml'
   schedule:
     # Run every Tuesday
-    - cron: "0 0 * * 2"
+    - cron: '0 0 * * 2'
 
 jobs:
   check_token:
@@ -31,7 +31,7 @@ jobs:
 
   update_workflow:
     name: "Update Workflow"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: check_token
     if: ${{ needs.check_token.outputs.workflow == 'true' }}
     steps:

From 2a3a4b20e4baace7e068a4bb3382998730978392 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 5 Mar 2025 12:41:46 +0100
Subject: [PATCH 11/33] Use a configuration script to control things

---
 episodes/13-hpcc-scheduler.Rmd                | 13 +++--
 episodes/13-hpcc-scheduler/hpcc/section1.rmd  |  1 +
 .../13-hpcc-scheduler/hpcc_test/section1.rmd  |  1 +
 episodes/lesson_config.yaml                   |  3 +-
 episodes/lesson_config_hpcc.yaml              |  2 +
 episodes/load_config.R                        | 48 +++++++++++++++++++
 6 files changed, 63 insertions(+), 5 deletions(-)
 create mode 100644 episodes/13-hpcc-scheduler/hpcc/section1.rmd
 create mode 100644 episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
 create mode 100644 episodes/lesson_config_hpcc.yaml
 create mode 100644 episodes/load_config.R

diff --git a/episodes/13-hpcc-scheduler.Rmd b/episodes/13-hpcc-scheduler.Rmd
index ecb37844..9596e970 100644
--- a/episodes/13-hpcc-scheduler.Rmd
+++ b/episodes/13-hpcc-scheduler.Rmd
@@ -4,10 +4,9 @@ teaching: 45
 exercises: 30
 ---
 
-```{r load_config, include=FALSE}
-library(yaml)
-config <- yaml.load_file("lesson_config.yaml")
-snippets <- paste('files/snippets/', config$snippets, sep='')
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives
@@ -27,6 +26,12 @@ snippets <- paste('files/snippets/', config$snippets, sep='')
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
+### Section 1
+```{r child=choose_doc("section1.rmd")}
+```
+
+Tester
+
 ## Job Scheduler
 
 An HPC system might have thousands of nodes and thousands of users. How do we
diff --git a/episodes/13-hpcc-scheduler/hpcc/section1.rmd b/episodes/13-hpcc-scheduler/hpcc/section1.rmd
new file mode 100644
index 00000000..eaf423ac
--- /dev/null
+++ b/episodes/13-hpcc-scheduler/hpcc/section1.rmd
@@ -0,0 +1 @@
+I was hoping this would appear.
\ No newline at end of file
diff --git a/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd b/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
new file mode 100644
index 00000000..9712c571
--- /dev/null
+++ b/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
@@ -0,0 +1 @@
+I was hoping this would appear first.
\ No newline at end of file
diff --git a/episodes/lesson_config.yaml b/episodes/lesson_config.yaml
index 3575aad9..c257ba17 100644
--- a/episodes/lesson_config.yaml
+++ b/episodes/lesson_config.yaml
@@ -48,4 +48,5 @@ sched:
   reservation: "shortqos"
   qos: "short"
   budget: "short"
-  project: 
+  project: ""
+main_config: "lesson_config_hpcc.yaml"
diff --git a/episodes/lesson_config_hpcc.yaml b/episodes/lesson_config_hpcc.yaml
new file mode 100644
index 00000000..f2044649
--- /dev/null
+++ b/episodes/lesson_config_hpcc.yaml
@@ -0,0 +1,2 @@
+main_snippets: "hpcc_test"
+fallback_snippets: "hpcc"
diff --git a/episodes/load_config.R b/episodes/load_config.R
new file mode 100644
index 00000000..872489eb
--- /dev/null
+++ b/episodes/load_config.R
@@ -0,0 +1,48 @@
+
+# Function to merge two lists (with overrides)
+merge_lists <- function(base, override) {
+  modifyList(base, override)
+}
+
+# Load required package
+library(yaml)
+# Load primary configuration
+config <- yaml.load_file("lesson_config.yaml")
+# If 'config' key exists, load the second configuration and merge
+if (!is.null(config$main_config) && file.exists(config$main_config)) {
+  override_config <- yaml.load_file(config$main_config)
+  config <- merge_lists(config, override_config)
+}
+
+snippets <- paste('files/snippets/', config$snippets, sep='')
+
+# Extract main and fallback paths from config
+main_snippets <- config$main_snippets
+fallback_snippets <- config$fallback_snippets
+
+# Function to choose the correct document path (or return NULL if neither exists)
+choose_doc <- function(child_file) {
+  # Get the current document name (without extension)
+  current_doc <- tools::file_path_sans_ext(knitr::current_input(dir = TRUE))
+  
+  # Build paths for the child document inside subdirectories
+  doc_paths <- list(
+    main = file.path(current_doc, main_snippets, child_file),
+    fallback = file.path(current_doc, fallback_snippets, child_file)
+  )
+  print(doc_paths)
+  print(getwd())
+  # Return the valid path, or NULL if neither exists
+  if (file.exists(doc_paths$main)) {
+    print("Returning")
+    print(doc_paths$main)
+    return(doc_paths$main)
+  } else if (file.exists(doc_paths$fallback)) {
+    print("Returning")
+    print(doc_paths$fallback)
+    return(doc_paths$fallback)
+  } else {
+    print("Returning NULL")
+    return(NULL)  # Return NULL if neither path exists
+  }
+}
\ No newline at end of file

From 025c734f4e1040d9189fd13d2b3a2116de593755 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 5 Mar 2025 12:43:49 +0100
Subject: [PATCH 12/33] Update sandpaper-main.yaml

---
 .github/workflows/sandpaper-main.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/sandpaper-main.yaml b/.github/workflows/sandpaper-main.yaml
index b3d1de8c..ff447dd7 100644
--- a/.github/workflows/sandpaper-main.yaml
+++ b/.github/workflows/sandpaper-main.yaml
@@ -5,8 +5,6 @@ on:
     branches:
       - main
       - master
-  schedule:
-    - cron: '0 0 * * 2'
   workflow_dispatch:
     inputs:
       name:

From 4bd329a7b70dcc4f61dd942dccaa6aeb69d6a801 Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Wed, 5 Mar 2025 07:50:35 -0500
Subject: [PATCH 13/33] Comments! ... and POSIX compliance

---
 episodes/13-hpcc-scheduler.Rmd                    | 8 ++++++--
 episodes/13-hpcc-scheduler/hpcc/section1.rmd      | 7 ++++++-
 episodes/13-hpcc-scheduler/hpcc_test/section1.rmd | 2 +-
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/episodes/13-hpcc-scheduler.Rmd b/episodes/13-hpcc-scheduler.Rmd
index 9596e970..0d9914e7 100644
--- a/episodes/13-hpcc-scheduler.Rmd
+++ b/episodes/13-hpcc-scheduler.Rmd
@@ -27,10 +27,14 @@ source("load_config.R")
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 ### Section 1
-```{r child=choose_doc("section1.rmd")}
+
+We are testing the snippet library mechanism, stay tuned!
+
+```{r comment="Does this work??",
+    child=choose_doc("section1.rmd")}
 ```
 
-Tester
+How does spacing look?
 
 ## Job Scheduler
 
diff --git a/episodes/13-hpcc-scheduler/hpcc/section1.rmd b/episodes/13-hpcc-scheduler/hpcc/section1.rmd
index eaf423ac..7c419e3a 100644
--- a/episodes/13-hpcc-scheduler/hpcc/section1.rmd
+++ b/episodes/13-hpcc-scheduler/hpcc/section1.rmd
@@ -1 +1,6 @@
-I was hoping this would appear.
\ No newline at end of file
+---
+layout: page
+author: Alan O'Cais
+comment: Snippet test
+---
+I was hoping this would appear.
diff --git a/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd b/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
index 9712c571..673021ac 100644
--- a/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
+++ b/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
@@ -1 +1 @@
-I was hoping this would appear first.
\ No newline at end of file
+I was hoping this would appear first.

From a704f159ae76356614fde8c5ebe6b645e0073a16 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 5 Mar 2025 14:32:53 +0100
Subject: [PATCH 14/33] Try to fix lesson building

---
 episodes/13-hpcc-scheduler.Rmd                |    3 +-
 renv/activate.R                               | 1307 +++++++++++++++++
 renv/profile                                  |    1 +
 renv/profiles/lesson-requirements/renv.lock   |  342 +++++
 .../lesson-requirements/renv/.gitignore       |    7 +
 .../lesson-requirements/renv/settings.json    |   19 +
 6 files changed, 1677 insertions(+), 2 deletions(-)
 create mode 100644 renv/activate.R
 create mode 100644 renv/profile
 create mode 100644 renv/profiles/lesson-requirements/renv.lock
 create mode 100644 renv/profiles/lesson-requirements/renv/.gitignore
 create mode 100644 renv/profiles/lesson-requirements/renv/settings.json

diff --git a/episodes/13-hpcc-scheduler.Rmd b/episodes/13-hpcc-scheduler.Rmd
index 0d9914e7..5735775a 100644
--- a/episodes/13-hpcc-scheduler.Rmd
+++ b/episodes/13-hpcc-scheduler.Rmd
@@ -30,8 +30,7 @@ source("load_config.R")
 
 We are testing the snippet library mechanism, stay tuned!
 
-```{r comment="Does this work??",
-    child=choose_doc("section1.rmd")}
+```{r child=choose_doc("section1.rmd")}
 ```
 
 How does spacing look?
diff --git a/renv/activate.R b/renv/activate.R
new file mode 100644
index 00000000..2ebe4034
--- /dev/null
+++ b/renv/activate.R
@@ -0,0 +1,1307 @@
+
+local({
+
+  # the requested version of renv
+  version <- "1.0.8"
+  attr(version, "sha") <- NULL
+
+  # the project directory
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    project <- getwd()
+
+  # use start-up diagnostics if enabled
+  diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+  if (diagnostics) {
+    start <- Sys.time()
+    profile <- tempfile("renv-startup-", fileext = ".Rprof")
+    utils::Rprof(profile)
+    on.exit({
+      utils::Rprof(NULL)
+      elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+      writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+      writeLines(sprintf("- Profile: %s", profile))
+      print(utils::summaryRprof(profile))
+    }, add = TRUE)
+  }
+
+  # figure out whether the autoloader is enabled
+  enabled <- local({
+
+    # first, check config option
+    override <- getOption("renv.config.autoloader.enabled")
+    if (!is.null(override))
+      return(override)
+
+    # if we're being run in a context where R_LIBS is already set,
+    # don't load -- presumably we're being run as a sub-process and
+    # the parent process has already set up library paths for us
+    rcmd <- Sys.getenv("R_CMD", unset = NA)
+    rlibs <- Sys.getenv("R_LIBS", unset = NA)
+    if (!is.na(rlibs) && !is.na(rcmd))
+      return(FALSE)
+
+    # next, check environment variables
+    # TODO: prefer using the configuration one in the future
+    envvars <- c(
+      "RENV_CONFIG_AUTOLOADER_ENABLED",
+      "RENV_AUTOLOADER_ENABLED",
+      "RENV_ACTIVATE_PROJECT"
+    )
+
+    for (envvar in envvars) {
+      envval <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(envval))
+        return(tolower(envval) %in% c("true", "t", "1"))
+    }
+
+    # enable by default
+    TRUE
+
+  })
+
+  # bail if we're not enabled
+  if (!enabled) {
+
+    # if we're not enabled, we might still need to manually load
+    # the user profile here
+    profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+    if (file.exists(profile)) {
+      cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+      if (tolower(cfg) %in% c("true", "t", "1"))
+        sys.source(profile, envir = globalenv())
+    }
+
+    return(FALSE)
+
+  }
+
+  # avoid recursion
+  if (identical(getOption("renv.autoloader.running"), TRUE)) {
+    warning("ignoring recursive attempt to run renv autoloader")
+    return(invisible(TRUE))
+  }
+
+  # signal that we're loading renv during R startup
+  options(renv.autoloader.running = TRUE)
+  on.exit(options(renv.autoloader.running = NULL), add = TRUE)
+
+  # signal that we've consented to use renv
+  options(renv.consent = TRUE)
+
+  # load the 'utils' package eagerly -- this ensures that renv shims, which
+  # mask 'utils' packages, will come first on the search path
+  library(utils, lib.loc = .Library)
+
+  # unload renv if it's already been loaded
+  if ("renv" %in% loadedNamespaces())
+    unloadNamespace("renv")
+
+  # load bootstrap tools   
+  ansify <- function(text) {
+    if (renv_ansify_enabled())
+      renv_ansify_enhanced(text)
+    else
+      renv_ansify_default(text)
+  }
+  
+  renv_ansify_enabled <- function() {
+  
+    override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
+    if (!is.na(override))
+      return(as.logical(override))
+  
+    pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
+    if (identical(pane, "build"))
+      return(FALSE)
+  
+    testthat <- Sys.getenv("TESTTHAT", unset = "false")
+    if (tolower(testthat) %in% "true")
+      return(FALSE)
+  
+    iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
+    if (tolower(iderun) %in% "false")
+      return(FALSE)
+  
+    TRUE
+  
+  }
+  
+  renv_ansify_default <- function(text) {
+    text
+  }
+  
+  renv_ansify_enhanced <- function(text) {
+  
+    # R help links
+    pattern <- "`\\?(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # runnable code
+    pattern <- "`(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # return ansified text
+    text
+  
+  }
+  
+  renv_ansify_init <- function() {
+  
+    envir <- renv_envir_self()
+    if (renv_ansify_enabled())
+      assign("ansify", renv_ansify_enhanced, envir = envir)
+    else
+      assign("ansify", renv_ansify_default, envir = envir)
+  
+  }
+  
+  `%||%` <- function(x, y) {
+    if (is.null(x)) y else x
+  }
+  
+  catf <- function(fmt, ..., appendLF = TRUE) {
+  
+    quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
+    if (quiet)
+      return(invisible())
+  
+    msg <- sprintf(fmt, ...)
+    cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
+  
+    invisible(msg)
+  
+  }
+  
+  header <- function(label,
+                     ...,
+                     prefix = "#",
+                     suffix = "-",
+                     n = min(getOption("width"), 78))
+  {
+    label <- sprintf(label, ...)
+    n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
+    if (n <= 0)
+      return(paste(prefix, label))
+  
+    tail <- paste(rep.int(suffix, n), collapse = "")
+    paste0(prefix, " ", label, " ", tail)
+  
+  }
+  
+  heredoc <- function(text, leave = 0) {
+  
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+  
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+  
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    text <- paste(substring(lines, common), collapse = "\n")
+  
+    # substitute in ANSI links for executable renv code
+    ansify(text)
+  
+  }
+  
+  startswith <- function(string, prefix) {
+    substring(string, 1, nchar(prefix)) == prefix
+  }
+  
+  bootstrap <- function(version, library) {
+  
+    friendly <- renv_bootstrap_version_friendly(version)
+    section <- header(sprintf("Bootstrapping renv %s", friendly))
+    catf(section)
+  
+    # attempt to download renv
+    catf("- Downloading renv ... ", appendLF = FALSE)
+    withCallingHandlers(
+      tarball <- renv_bootstrap_download(version),
+      error = function(err) {
+        catf("FAILED")
+        stop("failed to download:\n", conditionMessage(err))
+      }
+    )
+    catf("OK")
+    on.exit(unlink(tarball), add = TRUE)
+  
+    # now attempt to install
+    catf("- Installing renv  ... ", appendLF = FALSE)
+    withCallingHandlers(
+      status <- renv_bootstrap_install(version, tarball, library),
+      error = function(err) {
+        catf("FAILED")
+        stop("failed to install:\n", conditionMessage(err))
+      }
+    )
+    catf("OK")
+  
+    # add empty line to break up bootstrapping from normal output
+    catf("")
+  
+    return(invisible())
+  }
+  
+  renv_bootstrap_tests_running <- function() {
+    getOption("renv.tests.running", default = FALSE)
+  }
+  
+  renv_bootstrap_repos <- function() {
+  
+    # get CRAN repository
+    cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
+  
+    # check for repos override
+    repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+    if (!is.na(repos)) {
+  
+      # check for RSPM; if set, use a fallback repository for renv
+      rspm <- Sys.getenv("RSPM", unset = NA)
+      if (identical(rspm, repos))
+        repos <- c(RSPM = rspm, CRAN = cran)
+  
+      return(repos)
+  
+    }
+  
+    # check for lockfile repositories
+    repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
+    if (!inherits(repos, "error") && length(repos))
+      return(repos)
+  
+    # retrieve current repos
+    repos <- getOption("repos")
+  
+    # ensure @CRAN@ entries are resolved
+    repos[repos == "@CRAN@"] <- cran
+  
+    # add in renv.bootstrap.repos if set
+    default <- c(FALLBACK = "https://cloud.r-project.org")
+    extra <- getOption("renv.bootstrap.repos", default = default)
+    repos <- c(repos, extra)
+  
+    # remove duplicates that might've snuck in
+    dupes <- duplicated(repos) | duplicated(names(repos))
+    repos[!dupes]
+  
+  }
+  
+  renv_bootstrap_repos_lockfile <- function() {
+  
+    lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
+    if (!file.exists(lockpath))
+      return(NULL)
+  
+    lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
+    if (inherits(lockfile, "error")) {
+      warning(lockfile)
+      return(NULL)
+    }
+  
+    repos <- lockfile$R$Repositories
+    if (length(repos) == 0)
+      return(NULL)
+  
+    keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
+    vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
+    names(vals) <- keys
+  
+    return(vals)
+  
+  }
+  
+  renv_bootstrap_download <- function(version) {
+  
+    sha <- attr(version, "sha", exact = TRUE)
+  
+    methods <- if (!is.null(sha)) {
+  
+      # attempting to bootstrap a development version of renv
+      c(
+        function() renv_bootstrap_download_tarball(sha),
+        function() renv_bootstrap_download_github(sha)
+      )
+  
+    } else {
+  
+      # attempting to bootstrap a release version of renv
+      c(
+        function() renv_bootstrap_download_tarball(version),
+        function() renv_bootstrap_download_cran_latest(version),
+        function() renv_bootstrap_download_cran_archive(version)
+      )
+  
+    }
+  
+    for (method in methods) {
+      path <- tryCatch(method(), error = identity)
+      if (is.character(path) && file.exists(path))
+        return(path)
+    }
+  
+    stop("All download methods failed")
+  
+  }
+  
+  renv_bootstrap_download_impl <- function(url, destfile) {
+  
+    mode <- "wb"
+  
+    # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+    fixup <-
+      Sys.info()[["sysname"]] == "Windows" &&
+      substring(url, 1L, 5L) == "file:"
+  
+    if (fixup)
+      mode <- "w+b"
+  
+    args <- list(
+      url      = url,
+      destfile = destfile,
+      mode     = mode,
+      quiet    = TRUE
+    )
+  
+    if ("headers" %in% names(formals(utils::download.file)))
+    {
+      headers <- renv_bootstrap_download_custom_headers(url)
+      if (length(headers) && is.character(headers))
+        args$headers <- headers
+    }
+  
+    do.call(utils::download.file, args)
+  
+  }
+  
+  renv_bootstrap_download_custom_headers <- function(url) {
+  
+    headers <- getOption("renv.download.headers")
+    if (is.null(headers))
+      return(character())
+  
+    if (!is.function(headers))
+      stopf("'renv.download.headers' is not a function")
+  
+    headers <- headers(url)
+    if (length(headers) == 0L)
+      return(character())
+  
+    if (is.list(headers))
+      headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
+  
+    ok <-
+      is.character(headers) &&
+      is.character(names(headers)) &&
+      all(nzchar(names(headers)))
+  
+    if (!ok)
+      stop("invocation of 'renv.download.headers' did not return a named character vector")
+  
+    headers
+  
+  }
+  
+  renv_bootstrap_download_cran_latest <- function(version) {
+  
+    spec <- renv_bootstrap_download_cran_latest_find(version)
+    type  <- spec$type
+    repos <- spec$repos
+  
+    baseurl <- utils::contrib.url(repos = repos, type = type)
+    ext <- if (identical(type, "source"))
+      ".tar.gz"
+    else if (Sys.info()[["sysname"]] == "Windows")
+      ".zip"
+    else
+      ".tgz"
+    name <- sprintf("renv_%s%s", version, ext)
+    url <- paste(baseurl, name, sep = "/")
+  
+    destfile <- file.path(tempdir(), name)
+    status <- tryCatch(
+      renv_bootstrap_download_impl(url, destfile),
+      condition = identity
+    )
+  
+    if (inherits(status, "condition"))
+      return(FALSE)
+  
+    # report success and return
+    destfile
+  
+  }
+  
+  renv_bootstrap_download_cran_latest_find <- function(version) {
+  
+    # check whether binaries are supported on this system
+    binary <-
+      getOption("renv.bootstrap.binary", default = TRUE) &&
+      !identical(.Platform$pkgType, "source") &&
+      !identical(getOption("pkgType"), "source") &&
+      Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
+  
+    types <- c(if (binary) "binary", "source")
+  
+    # iterate over types + repositories
+    for (type in types) {
+      for (repos in renv_bootstrap_repos()) {
+  
+        # build arguments for utils::available.packages() call
+        args <- list(type = type, repos = repos)
+  
+        # add custom headers if available -- note that
+        # utils::available.packages() will pass this to download.file()
+        if ("headers" %in% names(formals(utils::download.file)))
+        {
+          headers <- renv_bootstrap_download_custom_headers(url)
+          if (length(headers) && is.character(headers))
+            args$headers <- headers
+        }
+  
+        # retrieve package database
+        db <- tryCatch(
+          as.data.frame(
+            do.call(utils::available.packages, args),
+            stringsAsFactors = FALSE
+          ),
+          error = identity
+        )
+  
+        if (inherits(db, "error"))
+          next
+  
+        # check for compatible entry
+        entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+        if (nrow(entry) == 0)
+          next
+  
+        # found it; return spec to caller
+        spec <- list(entry = entry, type = type, repos = repos)
+        return(spec)
+  
+      }
+    }
+  
+    # if we got here, we failed to find renv
+    fmt <- "renv %s is not available from your declared package repositories"
+    stop(sprintf(fmt, version))
+  
+  }
+  
+  renv_bootstrap_download_cran_archive <- function(version) {
+  
+    name <- sprintf("renv_%s.tar.gz", version)
+    repos <- renv_bootstrap_repos()
+    urls <- file.path(repos, "src/contrib/Archive/renv", name)
+    destfile <- file.path(tempdir(), name)
+  
+    for (url in urls) {
+  
+      status <- tryCatch(
+        renv_bootstrap_download_impl(url, destfile),
+        condition = identity
+      )
+  
+      if (identical(status, 0L))
+        return(destfile)
+  
+    }
+  
+    return(FALSE)
+  
+  }
+  
+  renv_bootstrap_download_tarball <- function(version) {
+  
+    # if the user has provided the path to a tarball via
+    # an environment variable, then use it
+    tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
+    if (is.na(tarball))
+      return()
+  
+    # allow directories
+    if (dir.exists(tarball)) {
+      name <- sprintf("renv_%s.tar.gz", version)
+      tarball <- file.path(tarball, name)
+    }
+  
+    # bail if it doesn't exist
+    if (!file.exists(tarball)) {
+  
+      # let the user know we weren't able to honour their request
+      fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
+      msg <- sprintf(fmt, tarball)
+      warning(msg)
+  
+      # bail
+      return()
+  
+    }
+  
+    catf("- Using local tarball '%s'.", tarball)
+    tarball
+  
+  }
+  
+  renv_bootstrap_github_token <- function() {
+    for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) {
+      envval <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(envval))
+        return(envval)
+    }
+  }
+  
+  renv_bootstrap_download_github <- function(version) {
+  
+    enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
+    if (!identical(enabled, "TRUE"))
+      return(FALSE)
+  
+    # prepare download options
+    token <- renv_bootstrap_github_token()
+    if (nzchar(Sys.which("curl")) && nzchar(token)) {
+      fmt <- "--location --fail --header \"Authorization: token %s\""
+      extra <- sprintf(fmt, token)
+      saved <- options("download.file.method", "download.file.extra")
+      options(download.file.method = "curl", download.file.extra = extra)
+      on.exit(do.call(base::options, saved), add = TRUE)
+    } else if (nzchar(Sys.which("wget")) && nzchar(token)) {
+      fmt <- "--header=\"Authorization: token %s\""
+      extra <- sprintf(fmt, token)
+      saved <- options("download.file.method", "download.file.extra")
+      options(download.file.method = "wget", download.file.extra = extra)
+      on.exit(do.call(base::options, saved), add = TRUE)
+    }
+  
+    url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
+    name <- sprintf("renv_%s.tar.gz", version)
+    destfile <- file.path(tempdir(), name)
+  
+    status <- tryCatch(
+      renv_bootstrap_download_impl(url, destfile),
+      condition = identity
+    )
+  
+    if (!identical(status, 0L))
+      return(FALSE)
+  
+    renv_bootstrap_download_augment(destfile)
+  
+    return(destfile)
+  
+  }
+  
+  # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
+  # can use renv::install() to fully capture metadata.
+  renv_bootstrap_download_augment <- function(destfile) {
+    sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
+    if (is.null(sha)) {
+      return()
+    }
+  
+    # Untar
+    tempdir <- tempfile("renv-github-")
+    on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
+    untar(destfile, exdir = tempdir)
+    pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
+  
+    # Modify description
+    desc_path <- file.path(pkgdir, "DESCRIPTION")
+    desc_lines <- readLines(desc_path)
+    remotes_fields <- c(
+      "RemoteType: github",
+      "RemoteHost: api.github.com",
+      "RemoteRepo: renv",
+      "RemoteUsername: rstudio",
+      "RemotePkgRef: rstudio/renv",
+      paste("RemoteRef: ", sha),
+      paste("RemoteSha: ", sha)
+    )
+    writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
+  
+    # Re-tar
+    local({
+      old <- setwd(tempdir)
+      on.exit(setwd(old), add = TRUE)
+  
+      tar(destfile, compression = "gzip")
+    })
+    invisible()
+  }
+  
+  # Extract the commit hash from a git archive. Git archives include the SHA1
+  # hash as the comment field of the tarball pax extended header
+  # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
+  # For GitHub archives this should be the first header after the default one
+  # (512 byte) header.
+  renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
+  
+    # open the bundle for reading
+    # We use gzcon for everything because (from ?gzcon)
+    # > Reading from a connection which does not supply a 'gzip' magic
+    # > header is equivalent to reading from the original connection
+    conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
+    on.exit(close(conn))
+  
+    # The default pax header is 512 bytes long and the first pax extended header
+    # with the comment should be 51 bytes long
+    # `52 comment=` (11 chars) + 40 byte SHA1 hash
+    len <- 0x200 + 0x33
+    res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
+  
+    if (grepl("^52 comment=", res)) {
+      sub("52 comment=", "", res)
+    } else {
+      NULL
+    }
+  }
+  
+  renv_bootstrap_install <- function(version, tarball, library) {
+  
+    # attempt to install it into project library
+    dir.create(library, showWarnings = FALSE, recursive = TRUE)
+    output <- renv_bootstrap_install_impl(library, tarball)
+  
+    # check for successful install
+    status <- attr(output, "status")
+    if (is.null(status) || identical(status, 0L))
+      return(status)
+  
+    # an error occurred; report it
+    header <- "installation of renv failed"
+    lines <- paste(rep.int("=", nchar(header)), collapse = "")
+    text <- paste(c(header, lines, output), collapse = "\n")
+    stop(text)
+  
+  }
+  
+  renv_bootstrap_install_impl <- function(library, tarball) {
+  
+    # invoke using system2 so we can capture and report output
+    bin <- R.home("bin")
+    exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
+    R <- file.path(bin, exe)
+  
+    args <- c(
+      "--vanilla", "CMD", "INSTALL", "--no-multiarch",
+      "-l", shQuote(path.expand(library)),
+      shQuote(path.expand(tarball))
+    )
+  
+    system2(R, args, stdout = TRUE, stderr = TRUE)
+  
+  }
+  
+  renv_bootstrap_platform_prefix <- function() {
+  
+    # construct version prefix
+    version <- paste(R.version$major, R.version$minor, sep = ".")
+    prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
+  
+    # include SVN revision for development versions of R
+    # (to avoid sharing platform-specific artefacts with released versions of R)
+    devel <-
+      identical(R.version[["status"]],   "Under development (unstable)") ||
+      identical(R.version[["nickname"]], "Unsuffered Consequences")
+  
+    if (devel)
+      prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
+  
+    # build list of path components
+    components <- c(prefix, R.version$platform)
+  
+    # include prefix if provided by user
+    prefix <- renv_bootstrap_platform_prefix_impl()
+    if (!is.na(prefix) && nzchar(prefix))
+      components <- c(prefix, components)
+  
+    # build prefix
+    paste(components, collapse = "/")
+  
+  }
+  
+  renv_bootstrap_platform_prefix_impl <- function() {
+  
+    # if an explicit prefix has been supplied, use it
+    prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
+    if (!is.na(prefix))
+      return(prefix)
+  
+    # if the user has requested an automatic prefix, generate it
+    auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+  
+    if (auto %in% c("TRUE", "True", "true", "1"))
+      return(renv_bootstrap_platform_prefix_auto())
+  
+    # empty string on failure
+    ""
+  
+  }
+  
+  renv_bootstrap_platform_prefix_auto <- function() {
+  
+    prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
+    if (inherits(prefix, "error") || prefix %in% "unknown") {
+  
+      msg <- paste(
+        "failed to infer current operating system",
+        "please file a bug report at https://github.com/rstudio/renv/issues",
+        sep = "; "
+      )
+  
+      warning(msg)
+  
+    }
+  
+    prefix
+  
+  }
+  
+  renv_bootstrap_platform_os <- function() {
+  
+    sysinfo <- Sys.info()
+    sysname <- sysinfo[["sysname"]]
+  
+    # handle Windows + macOS up front
+    if (sysname == "Windows")
+      return("windows")
+    else if (sysname == "Darwin")
+      return("macos")
+  
+    # check for os-release files
+    for (file in c("/etc/os-release", "/usr/lib/os-release"))
+      if (file.exists(file))
+        return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
+  
+    # check for redhat-release files
+    if (file.exists("/etc/redhat-release"))
+      return(renv_bootstrap_platform_os_via_redhat_release())
+  
+    "unknown"
+  
+  }
+  
+  renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
+  
+    # read /etc/os-release
+    release <- utils::read.table(
+      file             = file,
+      sep              = "=",
+      quote            = c("\"", "'"),
+      col.names        = c("Key", "Value"),
+      comment.char     = "#",
+      stringsAsFactors = FALSE
+    )
+  
+    vars <- as.list(release$Value)
+    names(vars) <- release$Key
+  
+    # get os name
+    os <- tolower(sysinfo[["sysname"]])
+  
+    # read id
+    id <- "unknown"
+    for (field in c("ID", "ID_LIKE")) {
+      if (field %in% names(vars) && nzchar(vars[[field]])) {
+        id <- vars[[field]]
+        break
+      }
+    }
+  
+    # read version
+    version <- "unknown"
+    for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
+      if (field %in% names(vars) && nzchar(vars[[field]])) {
+        version <- vars[[field]]
+        break
+      }
+    }
+  
+    # join together
+    paste(c(os, id, version), collapse = "-")
+  
+  }
+  
+  renv_bootstrap_platform_os_via_redhat_release <- function() {
+  
+    # read /etc/redhat-release
+    contents <- readLines("/etc/redhat-release", warn = FALSE)
+  
+    # infer id
+    id <- if (grepl("centos", contents, ignore.case = TRUE))
+      "centos"
+    else if (grepl("redhat", contents, ignore.case = TRUE))
+      "redhat"
+    else
+      "unknown"
+  
+    # try to find a version component (very hacky)
+    version <- "unknown"
+  
+    parts <- strsplit(contents, "[[:space:]]")[[1L]]
+    for (part in parts) {
+  
+      nv <- tryCatch(numeric_version(part), error = identity)
+      if (inherits(nv, "error"))
+        next
+  
+      version <- nv[1, 1]
+      break
+  
+    }
+  
+    paste(c("linux", id, version), collapse = "-")
+  
+  }
+  
+  renv_bootstrap_library_root_name <- function(project) {
+  
+    # use project name as-is if requested
+    asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
+    if (asis)
+      return(basename(project))
+  
+    # otherwise, disambiguate based on project's path
+    id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
+    paste(basename(project), id, sep = "-")
+  
+  }
+  
+  renv_bootstrap_library_root <- function(project) {
+  
+    prefix <- renv_bootstrap_profile_prefix()
+  
+    path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+    if (!is.na(path))
+      return(paste(c(path, prefix), collapse = "/"))
+  
+    path <- renv_bootstrap_library_root_impl(project)
+    if (!is.null(path)) {
+      name <- renv_bootstrap_library_root_name(project)
+      return(paste(c(path, prefix, name), collapse = "/"))
+    }
+  
+    renv_bootstrap_paths_renv("library", project = project)
+  
+  }
+  
+  renv_bootstrap_library_root_impl <- function(project) {
+  
+    root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+    if (!is.na(root))
+      return(root)
+  
+    type <- renv_bootstrap_project_type(project)
+    if (identical(type, "package")) {
+      userdir <- renv_bootstrap_user_dir()
+      return(file.path(userdir, "library"))
+    }
+  
+  }
+  
+  renv_bootstrap_validate_version <- function(version, description = NULL) {
+  
+    # resolve description file
+    #
+    # avoid passing lib.loc to `packageDescription()` below, since R will
+    # use the loaded version of the package by default anyhow. note that
+    # this function should only be called after 'renv' is loaded
+    # https://github.com/rstudio/renv/issues/1625
+    description <- description %||% packageDescription("renv")
+  
+    # check whether requested version 'version' matches loaded version of renv
+    sha <- attr(version, "sha", exact = TRUE)
+    valid <- if (!is.null(sha))
+      renv_bootstrap_validate_version_dev(sha, description)
+    else
+      renv_bootstrap_validate_version_release(version, description)
+  
+    if (valid)
+      return(TRUE)
+  
+    # the loaded version of renv doesn't match the requested version;
+    # give the user instructions on how to proceed
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
+      paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
+    else
+      paste("renv", description[["Version"]], sep = "@")
+  
+    # display both loaded version + sha if available
+    friendly <- renv_bootstrap_version_friendly(
+      version = description[["Version"]],
+      sha     = if (dev) description[["RemoteSha"]]
+    )
+  
+    fmt <- heredoc("
+      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+    ")
+    catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
+  
+    FALSE
+  
+  }
+  
+  renv_bootstrap_validate_version_dev <- function(version, description) {
+    expected <- description[["RemoteSha"]]
+    is.character(expected) && startswith(expected, version)
+  }
+  
+  renv_bootstrap_validate_version_release <- function(version, description) {
+    expected <- description[["Version"]]
+    is.character(expected) && identical(expected, version)
+  }
+  
+  renv_bootstrap_hash_text <- function(text) {
+  
+    hashfile <- tempfile("renv-hash-")
+    on.exit(unlink(hashfile), add = TRUE)
+  
+    writeLines(text, con = hashfile)
+    tools::md5sum(hashfile)
+  
+  }
+  
+  renv_bootstrap_load <- function(project, libpath, version) {
+  
+    # try to load renv from the project library
+    if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
+      return(FALSE)
+  
+    # warn if the version of renv loaded does not match
+    renv_bootstrap_validate_version(version)
+  
+    # execute renv load hooks, if any
+    hooks <- getHook("renv::autoload")
+    for (hook in hooks)
+      if (is.function(hook))
+        tryCatch(hook(), error = warnify)
+  
+    # load the project
+    renv::load(project)
+  
+    TRUE
+  
+  }
+  
+  renv_bootstrap_profile_load <- function(project) {
+  
+    # if RENV_PROFILE is already set, just use that
+    profile <- Sys.getenv("RENV_PROFILE", unset = NA)
+    if (!is.na(profile) && nzchar(profile))
+      return(profile)
+  
+    # check for a profile file (nothing to do if it doesn't exist)
+    path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project)
+    if (!file.exists(path))
+      return(NULL)
+  
+    # read the profile, and set it if it exists
+    contents <- readLines(path, warn = FALSE)
+    if (length(contents) == 0L)
+      return(NULL)
+  
+    # set RENV_PROFILE
+    profile <- contents[[1L]]
+    if (!profile %in% c("", "default"))
+      Sys.setenv(RENV_PROFILE = profile)
+  
+    profile
+  
+  }
+  
+  renv_bootstrap_profile_prefix <- function() {
+    profile <- renv_bootstrap_profile_get()
+    if (!is.null(profile))
+      return(file.path("profiles", profile, "renv"))
+  }
+  
+  renv_bootstrap_profile_get <- function() {
+    profile <- Sys.getenv("RENV_PROFILE", unset = "")
+    renv_bootstrap_profile_normalize(profile)
+  }
+  
+  renv_bootstrap_profile_set <- function(profile) {
+    profile <- renv_bootstrap_profile_normalize(profile)
+    if (is.null(profile))
+      Sys.unsetenv("RENV_PROFILE")
+    else
+      Sys.setenv(RENV_PROFILE = profile)
+  }
+  
+  renv_bootstrap_profile_normalize <- function(profile) {
+  
+    if (is.null(profile) || profile %in% c("", "default"))
+      return(NULL)
+  
+    profile
+  
+  }
+  
+  renv_bootstrap_path_absolute <- function(path) {
+  
+    substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
+      substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
+      substr(path, 2L, 3L) %in% c(":/", ":\\")
+    )
+  
+  }
+  
+  renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
+    renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
+    root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
+    prefix <- if (profile) renv_bootstrap_profile_prefix()
+    components <- c(root, renv, prefix, ...)
+    paste(components, collapse = "/")
+  }
+  
+  renv_bootstrap_project_type <- function(path) {
+  
+    descpath <- file.path(path, "DESCRIPTION")
+    if (!file.exists(descpath))
+      return("unknown")
+  
+    desc <- tryCatch(
+      read.dcf(descpath, all = TRUE),
+      error = identity
+    )
+  
+    if (inherits(desc, "error"))
+      return("unknown")
+  
+    type <- desc$Type
+    if (!is.null(type))
+      return(tolower(type))
+  
+    package <- desc$Package
+    if (!is.null(package))
+      return("package")
+  
+    "unknown"
+  
+  }
+  
+  renv_bootstrap_user_dir <- function() {
+    dir <- renv_bootstrap_user_dir_impl()
+    path.expand(chartr("\\", "/", dir))
+  }
+  
+  renv_bootstrap_user_dir_impl <- function() {
+  
+    # use local override if set
+    override <- getOption("renv.userdir.override")
+    if (!is.null(override))
+      return(override)
+  
+    # use R_user_dir if available
+    tools <- asNamespace("tools")
+    if (is.function(tools$R_user_dir))
+      return(tools$R_user_dir("renv", "cache"))
+  
+    # try using our own backfill for older versions of R
+    envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
+    for (envvar in envvars) {
+      root <- Sys.getenv(envvar, unset = NA)
+      if (!is.na(root))
+        return(file.path(root, "R/renv"))
+    }
+  
+    # use platform-specific default fallbacks
+    if (Sys.info()[["sysname"]] == "Windows")
+      file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
+    else if (Sys.info()[["sysname"]] == "Darwin")
+      "~/Library/Caches/org.R-project.R/R/renv"
+    else
+      "~/.cache/R/renv"
+  
+  }
+  
+  renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
+    sha <- sha %||% attr(version, "sha", exact = TRUE)
+    parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+    paste(parts, collapse = "")
+  }
+  
+  renv_bootstrap_exec <- function(project, libpath, version) {
+    if (!renv_bootstrap_load(project, libpath, version))
+      renv_bootstrap_run(version, libpath)
+  }
+  
+  renv_bootstrap_run <- function(version, libpath) {
+  
+    # perform bootstrap
+    bootstrap(version, libpath)
+  
+    # exit early if we're just testing bootstrap
+    if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+      return(TRUE)
+  
+    # try again to load
+    if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
+      return(renv::load(project = getwd()))
+    }
+  
+    # failed to download or load renv; warn the user
+    msg <- c(
+      "Failed to find an renv installation: the project will not be loaded.",
+      "Use `renv::activate()` to re-initialize the project."
+    )
+  
+    warning(paste(msg, collapse = "\n"), call. = FALSE)
+  
+  }
+  
+  renv_json_read <- function(file = NULL, text = NULL) {
+  
+    jlerr <- NULL
+  
+    # if jsonlite is loaded, use that instead
+    if ("jsonlite" %in% loadedNamespaces()) {
+  
+      json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
+      if (!inherits(json, "error"))
+        return(json)
+  
+      jlerr <- json
+  
+    }
+  
+    # otherwise, fall back to the default JSON reader
+    json <- tryCatch(renv_json_read_default(file, text), error = identity)
+    if (!inherits(json, "error"))
+      return(json)
+  
+    # report an error
+    if (!is.null(jlerr))
+      stop(jlerr)
+    else
+      stop(json)
+  
+  }
+  
+  renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+    jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
+  }
+  
+  renv_json_read_default <- function(file = NULL, text = NULL) {
+  
+    # find strings in the JSON
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+    pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
+    locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
+  
+    # if any are found, replace them with placeholders
+    replaced <- text
+    strings <- character()
+    replacements <- character()
+  
+    if (!identical(c(locs), -1L)) {
+  
+      # get the string values
+      starts <- locs
+      ends <- locs + attr(locs, "match.length") - 1L
+      strings <- substring(text, starts, ends)
+  
+      # only keep those requiring escaping
+      strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE)
+  
+      # compute replacements
+      replacements <- sprintf('"\032%i\032"', seq_along(strings))
+  
+      # replace the strings
+      mapply(function(string, replacement) {
+        replaced <<- sub(string, replacement, replaced, fixed = TRUE)
+      }, strings, replacements)
+  
+    }
+  
+    # transform the JSON into something the R parser understands
+    transformed <- replaced
+    transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
+    transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
+    transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
+    transformed <- gsub(":", "=", transformed, fixed = TRUE)
+    text <- paste(transformed, collapse = "\n")
+  
+    # parse it
+    json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]]
+  
+    # construct map between source strings, replaced strings
+    map <- as.character(parse(text = strings))
+    names(map) <- as.character(parse(text = replacements))
+  
+    # convert to list
+    map <- as.list(map)
+  
+    # remap strings in object
+    remapped <- renv_json_read_remap(json, map)
+  
+    # evaluate
+    eval(remapped, envir = baseenv())
+  
+  }
+  
+  renv_json_read_remap <- function(json, map) {
+  
+    # fix names
+    if (!is.null(names(json))) {
+      lhs <- match(names(json), names(map), nomatch = 0L)
+      rhs <- match(names(map), names(json), nomatch = 0L)
+      names(json)[rhs] <- map[lhs]
+    }
+  
+    # fix values
+    if (is.character(json))
+      return(map[[json]] %||% json)
+  
+    # handle true, false, null
+    if (is.name(json)) {
+      text <- as.character(json)
+      if (text == "true")
+        return(TRUE)
+      else if (text == "false")
+        return(FALSE)
+      else if (text == "null")
+        return(NULL)
+    }
+  
+    # recurse
+    if (is.recursive(json)) {
+      for (i in seq_along(json)) {
+        json[i] <- list(renv_json_read_remap(json[[i]], map))
+      }
+    }
+  
+    json
+  
+  }
+
+  # load the renv profile, if any
+  renv_bootstrap_profile_load(project)
+
+  # construct path to library root
+  root <- renv_bootstrap_library_root(project)
+
+  # construct library prefix for platform
+  prefix <- renv_bootstrap_platform_prefix()
+
+  # construct full libpath
+  libpath <- file.path(root, prefix)
+
+  # run bootstrap code
+  renv_bootstrap_exec(project, libpath, version)
+
+  invisible()
+
+})
diff --git a/renv/profile b/renv/profile
new file mode 100644
index 00000000..6d4023b5
--- /dev/null
+++ b/renv/profile
@@ -0,0 +1 @@
+lesson-requirements
diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
new file mode 100644
index 00000000..b1b476a1
--- /dev/null
+++ b/renv/profiles/lesson-requirements/renv.lock
@@ -0,0 +1,342 @@
+{
+  "R": {
+    "Version": "4.4.0",
+    "Repositories": [
+      {
+        "Name": "carpentries",
+        "URL": "https://carpentries.r-universe.dev"
+      },
+      {
+        "Name": "carpentries_archive",
+        "URL": "https://carpentries.github.io/drat"
+      },
+      {
+        "Name": "CRAN",
+        "URL": "https://cran.rstudio.com"
+      }
+    ]
+  },
+  "Packages": {
+    "R6": {
+      "Package": "R6",
+      "Version": "2.5.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+    },
+    "base64enc": {
+      "Package": "base64enc",
+      "Version": "0.1-3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "543776ae6848fde2f48ff3816d0628bc"
+    },
+    "bslib": {
+      "Package": "bslib",
+      "Version": "0.8.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "cachem",
+        "fastmap",
+        "grDevices",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "lifecycle",
+        "memoise",
+        "mime",
+        "rlang",
+        "sass"
+      ],
+      "Hash": "b299c6741ca9746fb227debcb0f9fb6c"
+    },
+    "cachem": {
+      "Package": "cachem",
+      "Version": "1.1.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "fastmap",
+        "rlang"
+      ],
+      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
+    },
+    "cli": {
+      "Package": "cli",
+      "Version": "3.6.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "b21916dd77a27642b447374a5d30ecf3"
+    },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.37",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "33698c4b3127fc9f506654607fb73676"
+    },
+    "evaluate": {
+      "Package": "evaluate",
+      "Version": "1.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "6b567375113ceb7d9f800de4dd42218e"
+    },
+    "fastmap": {
+      "Package": "fastmap",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
+    },
+    "fontawesome": {
+      "Package": "fontawesome",
+      "Version": "0.5.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "rlang"
+      ],
+      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
+    },
+    "fs": {
+      "Package": "fs",
+      "Version": "1.6.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
+    },
+    "glue": {
+      "Package": "glue",
+      "Version": "1.7.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "e0b3a53876554bd45879e596cdb10a52"
+    },
+    "highr": {
+      "Package": "highr",
+      "Version": "0.11",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "xfun"
+      ],
+      "Hash": "d65ba49117ca223614f71b60d85b8ab7"
+    },
+    "htmltools": {
+      "Package": "htmltools",
+      "Version": "0.5.8.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "digest",
+        "fastmap",
+        "grDevices",
+        "rlang",
+        "utils"
+      ],
+      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
+    },
+    "jquerylib": {
+      "Package": "jquerylib",
+      "Version": "0.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "htmltools"
+      ],
+      "Hash": "5aab57a3bd297eee1c1d862735972182"
+    },
+    "jsonlite": {
+      "Package": "jsonlite",
+      "Version": "1.8.9",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "methods"
+      ],
+      "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b"
+    },
+    "knitr": {
+      "Package": "knitr",
+      "Version": "1.48",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "evaluate",
+        "highr",
+        "methods",
+        "tools",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "acf380f300c721da9fde7df115a5f86f"
+    },
+    "lifecycle": {
+      "Package": "lifecycle",
+      "Version": "1.0.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "rlang"
+      ],
+      "Hash": "b8552d117e1b808b09a832f589b79035"
+    },
+    "memoise": {
+      "Package": "memoise",
+      "Version": "2.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "cachem",
+        "rlang"
+      ],
+      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
+    },
+    "mime": {
+      "Package": "mime",
+      "Version": "0.12",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "tools"
+      ],
+      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
+    },
+    "rappdirs": {
+      "Package": "rappdirs",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
+    },
+    "renv": {
+      "Package": "renv",
+      "Version": "1.0.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "e082251834fa427514e68bec8afc8fda"
+    },
+    "rlang": {
+      "Package": "rlang",
+      "Version": "1.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
+    },
+    "rmarkdown": {
+      "Package": "rmarkdown",
+      "Version": "2.28",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bslib",
+        "evaluate",
+        "fontawesome",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "knitr",
+        "methods",
+        "tinytex",
+        "tools",
+        "utils",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "062470668513dcda416927085ee9bdc7"
+    },
+    "sass": {
+      "Package": "sass",
+      "Version": "0.4.9",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R6",
+        "fs",
+        "htmltools",
+        "rappdirs",
+        "rlang"
+      ],
+      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
+    },
+    "tinytex": {
+      "Package": "tinytex",
+      "Version": "0.53",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "xfun"
+      ],
+      "Hash": "9db859e8aabbb474293dde3097839420"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.47",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "stats",
+        "tools"
+      ],
+      "Hash": "36ab21660e2d095fef0d83f689e0477c"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.10",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
+    }
+  }
+}
diff --git a/renv/profiles/lesson-requirements/renv/.gitignore b/renv/profiles/lesson-requirements/renv/.gitignore
new file mode 100644
index 00000000..0ec0cbba
--- /dev/null
+++ b/renv/profiles/lesson-requirements/renv/.gitignore
@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/
diff --git a/renv/profiles/lesson-requirements/renv/settings.json b/renv/profiles/lesson-requirements/renv/settings.json
new file mode 100644
index 00000000..ffdbb320
--- /dev/null
+++ b/renv/profiles/lesson-requirements/renv/settings.json
@@ -0,0 +1,19 @@
+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.type": "implicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}

From 3c6959c39413b749c0eab1e77575f89702f7c196 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 5 Mar 2025 14:49:57 +0100
Subject: [PATCH 15/33] Update lesson config

---
 config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/config.yaml b/config.yaml
index 5519a791..fa48e8ec 100644
--- a/config.yaml
+++ b/config.yaml
@@ -33,7 +33,7 @@ life_cycle: 'alpha'
 license: 'CC-BY 4.0'
 
 # Link to the source repository for this lesson
-source: 'https://github.com/tobyhodges/probable-pancake'
+source: 'https://github.com/ocaisa/probable-pancake'
 
 # Default branch of your lesson
 branch: 'main'
@@ -95,6 +95,6 @@ profiles:
 
 
 carpentry_description: Lesson Description
-url: 'https://tkphd.github.io/hpc-intro-online'
+url: 'https://ocaisa.github.io/probable_pancake'
 analytics: carpentries
 lang: en

From 9cd9187b2c2ffc51aaa6eb5a33168bd9663990f2 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 5 Mar 2025 15:11:03 +0100
Subject: [PATCH 16/33] Tweak a few things

---
 episodes/13-hpcc-scheduler.Rmd | 8 ++++----
 episodes/lesson_config.yaml    | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/episodes/13-hpcc-scheduler.Rmd b/episodes/13-hpcc-scheduler.Rmd
index 5735775a..9b1134dd 100644
--- a/episodes/13-hpcc-scheduler.Rmd
+++ b/episodes/13-hpcc-scheduler.Rmd
@@ -186,12 +186,12 @@ script, but the ``r config$sched$flag$name`` option can be used to change the
 name of a job. Add an option to the script:
 
 ```bash
-`r config$remote$prompt`cat example-job.sh
+`r config$remote$prompt` cat example-job.sh
 ```
 
 ```output
 `r config$remote$bash_shebang`
-`r config$sched$comment``r config$sched$flag$name`hello-world
+`r config$sched$comment` `r config$sched$flag$name` hello-world
 
 echo -n "This script is running on "
 hostname
@@ -200,8 +200,8 @@ hostname
 Submit the job and monitor its status:
 
 ```bash
-`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
-`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$status` `r config$sched$flag$user`
 ```
 
 ```output
diff --git a/episodes/lesson_config.yaml b/episodes/lesson_config.yaml
index c257ba17..52f0a9d7 100644
--- a/episodes/lesson_config.yaml
+++ b/episodes/lesson_config.yaml
@@ -4,7 +4,7 @@ local:
   bash_shebang: "#!/usr/bin/env bash"
 
 snippets: HPCC_MagicCastle_slurm
-baseurl: "https://jlchang.github.io/probable-pancake/"
+baseurl: "https://ocaisa.github.io/probable-pancake/"
 
 remote:
   name: "HPC Carpentry's Cloud Cluster"
@@ -15,7 +15,7 @@ remote:
   location: "cluster.hpc-carpentry.org"
   homedir: "/home"
   user: "yourUsername"
-  prompt: 'yourUsername@login1 ~]'
+  prompt: '[yourUsername@login1 ~]'
   prompt_work: #"userid@uan01:/work/ta114/ta114/userid>"
   module_python3: "Python"
   bash_shebang: "#!/bin/bash"

From 1940ebbd267a4c29a1f33339baa07ff217f34aae Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 5 Mar 2025 15:26:22 +0100
Subject: [PATCH 17/33] Explore the configuration a bit

---
 episodes/13-hpcc-scheduler.Rmd               | 16 ++++++++++++++--
 episodes/13-hpcc-scheduler/hpcc/section2.rmd |  8 ++++++++
 2 files changed, 22 insertions(+), 2 deletions(-)
 create mode 100644 episodes/13-hpcc-scheduler/hpcc/section2.rmd

diff --git a/episodes/13-hpcc-scheduler.Rmd b/episodes/13-hpcc-scheduler.Rmd
index 9b1134dd..b27453b7 100644
--- a/episodes/13-hpcc-scheduler.Rmd
+++ b/episodes/13-hpcc-scheduler.Rmd
@@ -28,12 +28,24 @@ source("load_config.R")
 
 ### Section 1
 
-We are testing the snippet library mechanism, stay tuned!
+We are testing the snippet library mechanism, stay tuned! This appears in the as part of the main configuration.
 
 ```{r child=choose_doc("section1.rmd")}
 ```
 
-How does spacing look?
+### Section 2
+
+This one is only part of the backup.
+
+```{r child=choose_doc("section2.rmd")}
+```
+
+### Section 3
+
+```{r child=choose_doc("section3.rmd")}
+```
+
+And the above shouldn't appear at all.
 
 ## Job Scheduler
 
diff --git a/episodes/13-hpcc-scheduler/hpcc/section2.rmd b/episodes/13-hpcc-scheduler/hpcc/section2.rmd
new file mode 100644
index 00000000..48ec3cdb
--- /dev/null
+++ b/episodes/13-hpcc-scheduler/hpcc/section2.rmd
@@ -0,0 +1,8 @@
+---
+layout: page
+author: Alan O'Cais
+comment: Snippet test
+---
+::: discussion
+This is a second snippet that only appears in the backup.
+:::

From 313a9c9d43c4c7730ef2ad4a844d5969f03b2a57 Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 12:36:45 -0400
Subject: [PATCH 18/33] Workbenchify 10 & 11, including Portal conditional

---
 MAINTENANCE.md                                |   4 +-
 config.yaml                                   |   2 +-
 episodes/10-hpc-intro.md                      |   2 +-
 .../{11-connecting.md => 11-connecting.Rmd}   |  92 +-
 episodes/13-hpcc-scheduler.Rmd                |   4 +-
 episodes/files/jargon.html                    | 178 ++++
 index.md                                      |  14 +-
 renv.lock                                     | 988 ++++++++++++++++++
 renv/.gitignore                               |   7 +
 renv/activate.R                               | 202 ++--
 renv/profile                                  |   1 -
 renv/profiles/lesson-requirements/renv.lock   | 902 +++++++++++++---
 renv/settings.json                            |  19 +
 13 files changed, 2129 insertions(+), 286 deletions(-)
 rename episodes/{11-connecting.md => 11-connecting.Rmd} (89%)
 create mode 100644 episodes/files/jargon.html
 create mode 100644 renv.lock
 create mode 100644 renv/.gitignore
 delete mode 100644 renv/profile
 create mode 100644 renv/settings.json

diff --git a/MAINTENANCE.md b/MAINTENANCE.md
index b70c98c4..57278b8d 100644
--- a/MAINTENANCE.md
+++ b/MAINTENANCE.md
@@ -1,4 +1,6 @@
-# Site Structure and Maintenance
+---
+title: "Site Structure and Maintenance"
+---
 
 This site depends strongly on GitHub infrastructure, and a number of
 operational decisions have been made during the development process
diff --git a/config.yaml b/config.yaml
index fa48e8ec..4b045ef6 100644
--- a/config.yaml
+++ b/config.yaml
@@ -66,7 +66,7 @@ contact: 'team@carpentries.org'
 # Order of episodes in your lesson
 episodes: 
 - 10-hpc-intro.md
-- 11-connecting.md
+- 11-connecting.Rmd
 - 12-cluster.md
 - 12-epcc-cluster.Rmd
 - 13-scheduler.md
diff --git a/episodes/10-hpc-intro.md b/episodes/10-hpc-intro.md
index 5b48859c..4292cedc 100644
--- a/episodes/10-hpc-intro.md
+++ b/episodes/10-hpc-intro.md
@@ -54,7 +54,7 @@ problems in parallel**.
 
 ## Jargon Busting Presentation
 
-Open the [HPC Jargon Buster]({{ site.url }}files/jargon#p1)
+Open the [HPC Jargon Buster](../files/jargon#p1)
 in a new tab. To present the content, press `C` to open a **c**lone in a
 separate window, then press `P` to toggle **p**resentation mode.
 
diff --git a/episodes/11-connecting.md b/episodes/11-connecting.Rmd
similarity index 89%
rename from episodes/11-connecting.md
rename to episodes/11-connecting.Rmd
index 1d756e82..83f22c08 100644
--- a/episodes/11-connecting.md
+++ b/episodes/11-connecting.Rmd
@@ -17,6 +17,11 @@ exercises: 10
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ## Secure Connections
 
 The first step in using a cluster is to establish a connection from our laptop
@@ -56,7 +61,7 @@ When logging in to a laptop, tablet, or other personal device, a username,
 password, or pattern are normally required to prevent unauthorized access. In
 these situations, the likelihood of somebody else intercepting your password is
 low, since logging your keystrokes requires a malicious exploit or physical
-access. For systems like {{ site.remote.host }} running an SSH server, anybody
+access. For systems like ``r config$remote$host`` running an SSH server, anybody
 on the network can log in, or try to. Since usernames are often public or easy
 to guess, your password is often the weakest link in the security chain. Many
 clusters therefore forbid password-based login, requiring instead that you
@@ -121,7 +126,7 @@ Once you have opened a terminal, check for existing SSH keys and filenames
 since existing SSH keys are overwritten.
 
 ```bash
-{{ site.local.prompt }} ls ~/.ssh/
+`r config$local$prompt` ls ~/.ssh/
 ```
 
 If `~/.ssh/id_ed25519` already exists, you will need to specify
@@ -140,7 +145,7 @@ produce a stronger key than the `ssh-keygen` default by invoking these flags:
   extension added.
 
 ```bash
-{{ site.local.prompt }} ssh-keygen -a 100 -f ~/.ssh/id_ed25519 -t ed25519
+`r config$local$prompt` ssh-keygen -a 100 -f ~/.ssh/id_ed25519 -t ed25519
 ```
 
 When prompted, enter a strong password with the
@@ -165,7 +170,7 @@ If key generation failed because ed25519 is not available, try using the older
 check for an existing key:
 
 ```bash
-{{ site.local.prompt }} ls ~/.ssh/
+`r config$local$prompt` ls ~/.ssh/
 ```
 
 If `~/.ssh/id_rsa` already exists, you will need to specify choose a different
@@ -177,7 +182,7 @@ name for the new key-pair. Generate it as above, with the following extra flags:
   rather than PEM.
 
 ```bash
-{{ site.local.prompt }} ssh-keygen -a 100 -b 4096 -f ~/.ssh/id_rsa -o -t rsa
+`r config$local$prompt` ssh-keygen -a 100 -b 4096 -f ~/.ssh/id_rsa -o -t rsa
 ```
 
 When prompted, enter a strong password with the
@@ -233,7 +238,7 @@ type it in again.
 Open your terminal application and check if an agent is running:
 
 ```bash
-{{ site.local.prompt }} ssh-add -l
+`r config$local$prompt` ssh-add -l
 ```
 
 - If you get an error like this one,
@@ -245,7 +250,7 @@ Open your terminal application and check if an agent is running:
   ... then you need to launch the agent as follows:
   
   ```bash
-  {{ site.local.prompt }} eval $(ssh-agent)
+  `r config$local$prompt` eval $(ssh-agent)
   ```
   
   :::::::::::::::::::::::::::::::::::::::::  callout
@@ -258,7 +263,7 @@ Open your terminal application and check if an agent is running:
   shell commands that can be used to reach it -- but *does not execute them!*
   
   ```bash
-  {{ site.local.prompt }} ssh-agent
+  `r config$local$prompt` ssh-agent
   ```
   
   ```output
@@ -283,7 +288,7 @@ Open your terminal application and check if an agent is running:
 Add your key to the agent, with session expiration after 8 hours:
 
 ```bash
-{{ site.local.prompt }} ssh-add -t 8h ~/.ssh/id_ed25519
+`r config$local$prompt` ssh-add -t 8h ~/.ssh/id_ed25519
 ```
 
 ```output
@@ -302,27 +307,40 @@ See the [PuTTY documentation][putty-agent].
 
 ### Transfer Your Public Key
 
-{% if site.remote.portal %}
-Visit [{{ site.remote.portal }}]({{ site.remote.portal }}) to upload your SSH
-public key. (Remember, it's the one ending in `.pub`!)
-
-{% else %}
-Use the **s**ecure **c**o**p**y tool to send your public key to the cluster.
-
-```bash
-{{ site.local.prompt }} scp ~/.ssh/id_ed25519.pub {{ site.remote.user }}@{{ site.remote.login }}:~/
+```{r, eval=is.null(config$remote$portal), echo=FALSE, results="asis"}
+cat(
+    paste(
+        "```bash\n",
+        config$local$prompt,
+        " scp ~/.ssh/id_ed25519.pub ",
+        config$remote$user,
+        "@",
+        config$remote$login,
+        ":~/\n```",
+        sep="")
+)
 ```
 
-{% endif %}
+```{r, eval=!is.null(config$remote$portal), echo=FALSE, results="asis"}
+cat(
+    paste(
+        "Visit [",
+        config$remote$portal,
+        "](",
+        config$remote$portal,
+        ") to upload your SSH public key. (Remember, it's the one ending in `.pub`!)",
+        sep="")
+)
+```
 
 ## Log In to the Cluster
 
 Go ahead and open your terminal or graphical SSH client, then log in to the
-cluster. Replace `{{ site.remote.user }}` with your username or the one
+cluster. Replace ``r config$remote$user`` with your username or the one
 supplied by the instructors.
 
 ```bash
-{{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }}
+`r config$local$prompt` ssh `r config$remote$user`@`r config$remote$login`
 ```
 
 You may be asked for your password. Watch out: the characters you type after
@@ -340,9 +358,9 @@ connected to the local system and the remote system will typically be different
 for every user. We still need to indicate which system we are entering commands
 on though so we will adopt the following convention:
 
-- `{{ site.local.prompt }}` when the command is to be entered on a terminal
+- ``r config$local$prompt`` when the command is to be entered on a terminal
   connected to your local computer
-- `{{ site.remote.prompt }}` when the command is to be entered on a
+- ``r config$remote$prompt`` when the command is to be entered on a
   terminal connected to the remote system
 - `$` when it really doesn't matter which system the terminal is connected to.
 
@@ -356,28 +374,28 @@ computer we are logged onto can be checked with the `hostname` command. (You
 may also notice that the current hostname is also part of our prompt!)
 
 ```bash
-{{ site.remote.prompt }} hostname
+`r config$remote$prompt` hostname
 ```
 
 ```output
-{{ site.remote.host }}
+`r config$remote$host`
 ```
 
 So, we're definitely on the remote machine. Next, let's find out where we are
 by running `pwd` to **p**rint the **w**orking **d**irectory.
 
 ```bash
-{{ site.remote.prompt }} pwd
+`r config$remote$prompt` pwd
 ```
 
 ```output
-{{ site.remote.homedir }}/{{ site.remote.user }}
+`r config$remote$homedir`/`r config$remote$user`
 ```
 
 Great, we know where we are! Let's see what's in our current directory:
 
 ```bash
-{{ site.remote.prompt }} ls
+`r config$remote$prompt` ls
 ```
 
 ```output
@@ -390,7 +408,7 @@ other filesystems. If they did not, your home directory may appear empty. To
 double-check, include hidden files in your directory listing:
 
 ```bash
-{{ site.remote.prompt }} ls -a
+`r config$remote$prompt` ls -a
 ```
 
 ```output
@@ -399,13 +417,11 @@ double-check, include hidden files in your directory listing:
 ```
 
 In the first column, `.` is a reference to the current directory and `..` a
-reference to its parent (`{{ site.remote.homedir }}`). You may or may not see
+reference to its parent (``r config$remote$homedir``). You may or may not see
 the other files, or files like them: `.bashrc` is a shell configuration file,
 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
 
 :::::::::::::::::::::::::::::::::::::::::  callout
@@ -428,14 +444,14 @@ If the `.ssh` folder was not listed above, then it does not yet
 exist: create it.
 
 ```bash
-{{ site.remote.prompt }} mkdir ~/.ssh
+`r config$remote$prompt` mkdir ~/.ssh
 ```
 
 Now, use `cat` to print your public key, but redirect the output, appending it
 to the `authorized_keys` file:
 
 ```bash
-{{ site.remote.prompt }} cat ~/id_ed25519.pub >> ~/.ssh/authorized_keys
+`r config$remote$prompt` cat ~/id_ed25519.pub >> ~/.ssh/authorized_keys
 ```
 
 That's all! Disconnect, then try to log back into the remote: if your key and
@@ -443,17 +459,13 @@ agent have been configured correctly, you should not be prompted for the
 password for your SSH key.
 
 ```bash
-{{ site.remote.prompt }} logout
+`r config$remote$prompt` logout
 ```
 
 ```bash
-{{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }}
+`r config$local$prompt` ssh `r config$remote$user`@`r config$remote$login`
 ```
 
-{% endunless %}
-
-
-
 [gh-ssh]: https://docs.github.com/en/authentication/connecting-to-github-with-ssh
 [keepass]: https://keepass.info
 [bitwarden]: https://bitwarden.com
diff --git a/episodes/13-hpcc-scheduler.Rmd b/episodes/13-hpcc-scheduler.Rmd
index 5735775a..d5ca99e2 100644
--- a/episodes/13-hpcc-scheduler.Rmd
+++ b/episodes/13-hpcc-scheduler.Rmd
@@ -80,7 +80,7 @@ manner. Our shell script will have three parts:
   name of the machine the script is run on.
 
 ```bash
-`r config$remote$prompt`nano example-job.sh
+`r config$remote$prompt` nano example-job.sh
 ```
 
 ```output
@@ -101,7 +101,7 @@ Run the script. Does it execute on the cluster or just our login node?
 ## Solution
 
 ```bash
-`r config$remote$prompt`bash example-job.sh
+`r config$remote$prompt` bash example-job.sh
 ```
 
 ```output
diff --git a/episodes/files/jargon.html b/episodes/files/jargon.html
new file mode 100644
index 00000000..11d35eeb
--- /dev/null
+++ b/episodes/files/jargon.html
@@ -0,0 +1,178 @@
+<!DOCTYPE html>
+<!--
+ This is a <a href="https://github.com/gnab/remark">remark</a>
+ presentation: plain Markdown with an HTML wrapper. Each "slide"
+ begins with "---"; presenter notes for each slide begin with "???"
+ and are not rendered. To see the finished presentation, please visit
+ https://carpentries-incubator.github.io/hpc-intro/files/jargon.html
+-->
+<html>
+  <head>
+    <title>HPC Jargon Buster</title>
+    <link href="favicon.png" rel="icon" type="image/png"/>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
+    <style type="text/css">
+      @import url(https://fonts.googleapis.com/css?family=Yanone+Kaffeesatz);
+      @import url(https://fonts.googleapis.com/css?family=Droid+Serif:400,700,400italic);
+      @import url(https://fonts.googleapis.com/css?family=Ubuntu+Mono:400,700,400italic);
+
+      body { font-family: 'Droid Serif'; }
+      h1, h2, h3 {
+        font-family: 'Yanone Kaffeesatz';
+        font-weight: normal;
+      }
+      .remark-code, .remark-inline-code { font-family: 'Ubuntu Mono'; }
+    </style>
+  </head>
+  <body>
+    <textarea id="source">
+class: center, middle
+
+# High Performance Computing Jargon Buster
+
+[The HPC Carpentry Community](https://www.hpc-carpentry.org)
+
+???
+
+> Press `C` to open a "clone", then `P` to toggle Presentation Mode.
+
+HPC Carpentry is a community effort to develop educational materials
+in the pedagogical style of The Carpentries.
+
+The point of this presentation is to briefly introduce some scale-up
+options, so that learners get a sense of the variety of ways this can
+be done, and the source of some of the overloading of terminology
+that will be used later in the lesson.
+
+This non-interactive activity should be kept brief.
+
+---
+
+# Your Personal Computer
+
+.center[
+![Standalone computers (banana for scale)](../fig/jargon_standalone.svg)
+]
+
+- Familiar starting point, accessed locally
+- Good for local computational tasks
+- Highly flexible, easy to reconfigure for new tasks
+
+???
+
+A laptop and a desktop computer: you sit at the keyboard & mouse and
+log in to the computer directly, often as the sole user.
+
+Good at performing local and personal tasks: familiar but limited resources.
+
+---
+
+# Shared Computing Resources
+
+.center[
+![An HPC resource (img: [Julian Herzog](https://commons.wikimedia.org/wiki/File:High_Performance_Computing_Center_Stuttgart_HLRS_2015_07_Cray_XC40_Hazel_Hen_IO.jpg))](../fig/HPCCStuttgart_Hazel_Hen_XC40.png)
+]
+<!-- Image: https://commons.wikimedia.org/wiki/File:High_Performance_Computing_Center_Stuttgart_HLRS_2015_07_Cray_XC40_Hazel_Hen_IO.jpg, Julian Herzog. -->
+
+- Large-scale computation is different
+- It has a rich history, and confusing terminology
+- Many terms overloaded
+
+???
+
+Computation at larger scales typically involves changes in how
+things are done, and connection to remote computer systems and
+transfer of data between systems.
+
+There are many ways to do it, and the terminology can be confusing.
+
+This presentation will step through some scale-up scenarios to help
+frame the problem.
+
+---
+
+# A large computer
+
+.center[
+![A large computer (banana for scale)](../fig/jargon_large_computer.svg)
+]
+
+- More powerful "compute server"
+- Accessed remotely, likely shared by a small group
+- Less flexible &mdash; need to accommodate other users
+
+???
+
+First obvious way to scale, has more CPUs and memory, and more or
+faster storage. Typically shared, run commercial or open-source
+operating systems, may be called a "compute server". Typical tasks
+are operations of large user-facing programs, like scientific models
+or visualizations.
+
+---
+
+# Cloud Systems
+
+.center[
+![Cloud computers (bananas for scale)](../fig/jargon_multi_cluster.svg)
+]
+
+- Generally quite heterogeneous
+- Many types of servers
+
+???
+
+Cloud systems physically resemble clusters or supercomputers, but
+with greater heterogeneity among components, and less coupling, often
+without an interconnect at all. Cloud servers are generally accessed
+by connecting to their services over the network. Multiple virtual
+machines may reside on individual physical machines. Typical tasks
+are driven by user connections from the outside to the various "front
+end" services (e.g. web sites) which pass traffic on to the "back
+end" servers (e.g. databases) to present results to users.
+
+---
+
+# A cluster or supercomputer
+
+.center[
+![A cluster (banana for scale)](../fig/jargon_cluster.svg)
+]
+
+- Special "login node" or "head node" accessed remotely by users
+- Compute service accessed via resource manager
+- Some flexibility on local accounts
+- Specially-built software for best performance
+
+???
+
+A collection of standalone computers that are networked together. They will
+frequently have software installed that allow the coordinated running of other
+software across all of these computers. This allows these networked computers
+to work together to accomplish computing tasks faster. 
+
+---
+
+# HPC workflow
+
+.center[
+![Schematic HPC workflow](../fig/jargon_workflow.png)
+]
+
+- You talk to the cluster head node
+- The cluster head node distributes compute tasks
+- You view results
+
+???
+
+In the usual HPC workflow, users do not communicate directly with
+compute nodes, but work through a scheduling system to distribute
+tasks.
+    </textarea>
+    <script src="https://remarkjs.com/downloads/remark-latest.min.js" type="text/javascript">
+    </script>
+    <script type="text/javascript">
+      var slideshow = remark.create();
+    </script>
+  </body>
+</html>
diff --git a/index.md b/index.md
index 02b64977..39ed73cc 100644
--- a/index.md
+++ b/index.md
@@ -2,8 +2,6 @@
 site: sandpaper::sandpaper_site
 ---
 
-{% include gh\_variables.html %}
-
 This workshop is an introduction to using high-performance computing systems
 effectively. We can't cover every case or give an exhaustive course on parallel
 programming in just two days' teaching time. Instead, this workshop is intended
@@ -19,7 +17,6 @@ participants to go through
 [shell-novice](https://swcarpentry.github.io/shell-novice/), if new to the
 command line (also known as terminal or shell).
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 By the end of this workshop, students will know how to:
@@ -35,10 +32,8 @@ By the end of this workshop, students will know how to:
 
 ## Getting Started
 
-To get started, follow the directions in the "[Setup](
-{{ page.root }}/setup.html)" tab to download data to your computer and follow
-any installation instructions.
-
+To get started, please follow the "[Setup Instructions](../learners/setup.md)
+to ensure you have a terminal and SSH application.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -52,9 +47,4 @@ welcome.
 If you are teaching this lesson in a workshop, please see the
 [Instructor notes](instructors/instructor-notes.md).
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
-
-
-
-
diff --git a/renv.lock b/renv.lock
new file mode 100644
index 00000000..d90ed3be
--- /dev/null
+++ b/renv.lock
@@ -0,0 +1,988 @@
+{
+  "R": {
+    "Version": "4.4.2",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://mirrors.nics.utk.edu/cran"
+      }
+    ]
+  },
+  "Packages": {
+    "R6": {
+      "Package": "R6",
+      "Version": "2.6.1",
+      "Source": "Repository",
+      "Title": "Encapsulated Classes with Reference Semantics",
+      "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://r6.r-lib.org, https://github.com/r-lib/R6",
+      "BugReports": "https://github.com/r-lib/R6/issues",
+      "Depends": [
+        "R (>= 3.6)"
+      ],
+      "Suggests": [
+        "lobstr",
+        "testthat (>= 3.0.0)"
+      ],
+      "Config/Needs/website": "tidyverse/tidytemplate, ggplot2, microbenchmark, scales",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "no",
+      "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Winston Chang <winston@posit.co>",
+      "Repository": "CRAN"
+    },
+    "base64enc": {
+      "Package": "base64enc",
+      "Version": "0.1-3",
+      "Source": "Repository",
+      "Title": "Tools for base64 encoding",
+      "Author": "Simon Urbanek <Simon.Urbanek@r-project.org>",
+      "Maintainer": "Simon Urbanek <Simon.Urbanek@r-project.org>",
+      "Depends": [
+        "R (>= 2.9.0)"
+      ],
+      "Enhances": [
+        "png"
+      ],
+      "Description": "This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.",
+      "License": "GPL-2 | GPL-3",
+      "URL": "http://www.rforge.net/base64enc",
+      "NeedsCompilation": "yes",
+      "Repository": "CRAN"
+    },
+    "bslib": {
+      "Package": "bslib",
+      "Version": "0.9.0",
+      "Source": "Repository",
+      "Title": "Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'",
+      "Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Javi\", \"Aguilar\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap colorpicker library\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch library\"), person(, \"PayPal\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap accessibility plugin\") )",
+      "Description": "Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rstudio.github.io/bslib/, https://github.com/rstudio/bslib",
+      "BugReports": "https://github.com/rstudio/bslib/issues",
+      "Depends": [
+        "R (>= 2.10)"
+      ],
+      "Imports": [
+        "base64enc",
+        "cachem",
+        "fastmap (>= 1.1.1)",
+        "grDevices",
+        "htmltools (>= 0.5.8)",
+        "jquerylib (>= 0.1.3)",
+        "jsonlite",
+        "lifecycle",
+        "memoise (>= 2.0.1)",
+        "mime",
+        "rlang",
+        "sass (>= 0.4.9)"
+      ],
+      "Suggests": [
+        "bsicons",
+        "curl",
+        "fontawesome",
+        "future",
+        "ggplot2",
+        "knitr",
+        "magrittr",
+        "rappdirs",
+        "rmarkdown (>= 2.7)",
+        "shiny (> 1.8.1)",
+        "testthat",
+        "thematic",
+        "tools",
+        "utils",
+        "withr",
+        "yaml"
+      ],
+      "Config/Needs/deploy": "BH, chiflights22, colourpicker, commonmark, cpp11, cpsievert/chiflights22, cpsievert/histoslider, dplyr, DT, ggplot2, ggridges, gt, hexbin, histoslider, htmlwidgets, lattice, leaflet, lubridate, markdown, modelr, plotly, reactable, reshape2, rprojroot, rsconnect, rstudio/shiny, scales, styler, tibble",
+      "Config/Needs/routine": "chromote, desc, renv",
+      "Config/Needs/website": "brio, crosstalk, dplyr, DT, ggplot2, glue, htmlwidgets, leaflet, lorem, palmerpenguins, plotly, purrr, rprojroot, rstudio/htmltools, scales, stringr, tidyr, webshot2",
+      "Config/testthat/edition": "3",
+      "Config/testthat/parallel": "true",
+      "Config/testthat/start-first": "zzzz-bs-sass, fonts, zzz-precompile, theme-*, rmd-*",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "Collate": "'accordion.R' 'breakpoints.R' 'bs-current-theme.R' 'bs-dependencies.R' 'bs-global.R' 'bs-remove.R' 'bs-theme-layers.R' 'bs-theme-preset-bootswatch.R' 'bs-theme-preset-brand.R' 'bs-theme-preset-builtin.R' 'bs-theme-preset.R' 'utils.R' 'bs-theme-preview.R' 'bs-theme-update.R' 'bs-theme.R' 'bslib-package.R' 'buttons.R' 'card.R' 'deprecated.R' 'files.R' 'fill.R' 'imports.R' 'input-dark-mode.R' 'input-switch.R' 'layout.R' 'nav-items.R' 'nav-update.R' 'navbar_options.R' 'navs-legacy.R' 'navs.R' 'onLoad.R' 'page.R' 'popover.R' 'precompiled.R' 'print.R' 'shiny-devmode.R' 'sidebar.R' 'staticimports.R' 'tooltip.R' 'utils-deps.R' 'utils-shiny.R' 'utils-tags.R' 'value-box.R' 'version-default.R' 'versions.R'",
+      "NeedsCompilation": "no",
+      "Author": "Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Joe Cheng [aut], Garrick Aden-Buie [aut] (<https://orcid.org/0000-0002-7111-0077>), Posit Software, PBC [cph, fnd], Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Javi Aguilar [ctb, cph] (Bootstrap colorpicker library), Thomas Park [ctb, cph] (Bootswatch library), PayPal [ctb, cph] (Bootstrap accessibility plugin)",
+      "Maintainer": "Carson Sievert <carson@posit.co>",
+      "Repository": "CRAN"
+    },
+    "cachem": {
+      "Package": "cachem",
+      "Version": "1.1.0",
+      "Source": "Repository",
+      "Title": "Cache R Objects with Automatic Pruning",
+      "Description": "Key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.",
+      "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", c(\"aut\", \"cre\")), person(family = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")))",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "ByteCompile": "true",
+      "URL": "https://cachem.r-lib.org/, https://github.com/r-lib/cachem",
+      "Imports": [
+        "rlang",
+        "fastmap (>= 1.2.0)"
+      ],
+      "Suggests": [
+        "testthat"
+      ],
+      "RoxygenNote": "7.2.3",
+      "Config/Needs/routine": "lobstr",
+      "Config/Needs/website": "pkgdown",
+      "NeedsCompilation": "yes",
+      "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Winston Chang <winston@posit.co>",
+      "Repository": "CRAN"
+    },
+    "cli": {
+      "Package": "cli",
+      "Version": "3.6.4",
+      "Source": "Repository",
+      "Title": "Helpers for Developing Command Line Interfaces",
+      "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"gabor@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Kirill\", \"Müller\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", , \"salim-b@pm.me\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli",
+      "BugReports": "https://github.com/r-lib/cli/issues",
+      "Depends": [
+        "R (>= 3.4)"
+      ],
+      "Imports": [
+        "utils"
+      ],
+      "Suggests": [
+        "callr",
+        "covr",
+        "crayon",
+        "digest",
+        "glue (>= 1.6.0)",
+        "grDevices",
+        "htmltools",
+        "htmlwidgets",
+        "knitr",
+        "methods",
+        "processx",
+        "ps (>= 1.3.4.9000)",
+        "rlang (>= 1.0.2.9003)",
+        "rmarkdown",
+        "rprojroot",
+        "rstudioapi",
+        "testthat (>= 3.2.0)",
+        "tibble",
+        "whoami",
+        "withr"
+      ],
+      "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "yes",
+      "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Gábor Csárdi <gabor@posit.co>",
+      "Repository": "CRAN"
+    },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.37",
+      "Source": "Repository",
+      "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))",
+      "Date": "2024-08-19",
+      "Title": "Create Compact Hash Digests of R Objects",
+      "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.",
+      "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html",
+      "BugReports": "https://github.com/eddelbuettel/digest/issues",
+      "Depends": [
+        "R (>= 3.3.0)"
+      ],
+      "Imports": [
+        "utils"
+      ],
+      "License": "GPL (>= 2)",
+      "Suggests": [
+        "tinytest",
+        "simplermarkdown"
+      ],
+      "VignetteBuilder": "simplermarkdown",
+      "Encoding": "UTF-8",
+      "NeedsCompilation": "yes",
+      "Author": "Dirk Eddelbuettel [aut, cre] (<https://orcid.org/0000-0001-6419-907X>), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (<https://orcid.org/0000-0002-7579-5165>), Simon Urbanek [ctb] (<https://orcid.org/0000-0003-2297-1732>), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (<https://orcid.org/0000-0001-5180-0567>), Qiang Kou [ctb] (<https://orcid.org/0000-0001-6786-5453>), Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>), Michel Lang [ctb] (<https://orcid.org/0000-0001-9754-0393>), Viliam Simko [ctb], Kurt Hornik [ctb] (<https://orcid.org/0000-0003-4198-9911>), Radford Neal [ctb] (<https://orcid.org/0000-0002-2473-3407>), Kendon Bell [ctb] (<https://orcid.org/0000-0002-9093-8312>), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (<https://orcid.org/0000-0003-1878-3253>), Floris Vanderhaeghe [ctb] (<https://orcid.org/0000-0002-6378-6229>), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (<https://orcid.org/0000-0001-7813-818X>), Mark van der Loo [ctb] (<https://orcid.org/0000-0002-9807-4686>), Chris Muir [ctb] (<https://orcid.org/0000-0003-2555-3878>), Moritz Beller [ctb] (<https://orcid.org/0000-0003-4852-0526>), Sebastian Campbell [ctb], Winston Chang [ctb] (<https://orcid.org/0000-0002-1576-2126>), Dean Attali [ctb] (<https://orcid.org/0000-0002-5645-3493>), Michael Chirico [ctb] (<https://orcid.org/0000-0003-0787-087X>), Kevin Ushey [ctb]",
+      "Maintainer": "Dirk Eddelbuettel <edd@debian.org>",
+      "Repository": "CRAN"
+    },
+    "evaluate": {
+      "Package": "evaluate",
+      "Version": "1.0.3",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Parsing and Evaluation Tools that Provide More Details than the Default",
+      "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"aut\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Michael\", \"Lawrence\", role = \"ctb\"), person(\"Thomas\", \"Kluyver\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Adam\", \"Ryczkowski\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Michel\", \"Lang\", role = \"ctb\"), person(\"Karolis\", \"Koncevičius\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://evaluate.r-lib.org/, https://github.com/r-lib/evaluate",
+      "BugReports": "https://github.com/r-lib/evaluate/issues",
+      "Depends": [
+        "R (>= 3.6.0)"
+      ],
+      "Suggests": [
+        "callr",
+        "covr",
+        "ggplot2 (>= 3.3.6)",
+        "lattice",
+        "methods",
+        "pkgload",
+        "rlang",
+        "knitr",
+        "testthat (>= 3.0.0)",
+        "withr"
+      ],
+      "Config/Needs/website": "tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "no",
+      "Author": "Hadley Wickham [aut, cre], Yihui Xie [aut] (<https://orcid.org/0000-0003-0645-5666>), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb], Karolis Koncevičius [ctb], Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Hadley Wickham <hadley@posit.co>",
+      "Repository": "CRAN"
+    },
+    "fastmap": {
+      "Package": "fastmap",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Title": "Fast Data Structures",
+      "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )",
+      "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. Environments are commonly used as key-value stores in R, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.2.3",
+      "Suggests": [
+        "testthat (>= 2.1.1)"
+      ],
+      "URL": "https://r-lib.github.io/fastmap/, https://github.com/r-lib/fastmap",
+      "BugReports": "https://github.com/r-lib/fastmap/issues",
+      "NeedsCompilation": "yes",
+      "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd], Tessil [cph] (hopscotch_map library)",
+      "Maintainer": "Winston Chang <winston@posit.co>",
+      "Repository": "CRAN"
+    },
+    "fontawesome": {
+      "Package": "fontawesome",
+      "Version": "0.5.3",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Easily Work with 'Font Awesome' Icons",
+      "Description": "Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents and 'Shiny' apps. These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. There is also a utility function for exporting 'Font Awesome' icons as 'PNG' images for those situations where raster graphics are needed.",
+      "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"rich@posit.co\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"ctb\"), person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome font\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "License": "MIT + file LICENSE",
+      "URL": "https://github.com/rstudio/fontawesome, https://rstudio.github.io/fontawesome/",
+      "BugReports": "https://github.com/rstudio/fontawesome/issues",
+      "Encoding": "UTF-8",
+      "ByteCompile": "true",
+      "RoxygenNote": "7.3.2",
+      "Depends": [
+        "R (>= 3.3.0)"
+      ],
+      "Imports": [
+        "rlang (>= 1.0.6)",
+        "htmltools (>= 0.5.1.1)"
+      ],
+      "Suggests": [
+        "covr",
+        "dplyr (>= 1.0.8)",
+        "gt (>= 0.9.0)",
+        "knitr (>= 1.31)",
+        "testthat (>= 3.0.0)",
+        "rsvg"
+      ],
+      "Config/testthat/edition": "3",
+      "NeedsCompilation": "no",
+      "Author": "Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Winston Chang [ctb], Dave Gandy [ctb, cph] (Font-Awesome font), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Richard Iannone <rich@posit.co>",
+      "Repository": "CRAN"
+    },
+    "fs": {
+      "Package": "fs",
+      "Version": "1.6.5",
+      "Source": "Repository",
+      "Title": "Cross-Platform File System Operations Based on 'libuv'",
+      "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "A cross-platform interface to file system operations, built on top of the 'libuv' C library.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://fs.r-lib.org, https://github.com/r-lib/fs",
+      "BugReports": "https://github.com/r-lib/fs/issues",
+      "Depends": [
+        "R (>= 3.6)"
+      ],
+      "Imports": [
+        "methods"
+      ],
+      "Suggests": [
+        "covr",
+        "crayon",
+        "knitr",
+        "pillar (>= 1.0.0)",
+        "rmarkdown",
+        "spelling",
+        "testthat (>= 3.0.0)",
+        "tibble (>= 1.1.0)",
+        "vctrs (>= 0.3.0)",
+        "withr"
+      ],
+      "VignetteBuilder": "knitr",
+      "ByteCompile": "true",
+      "Config/Needs/website": "tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Copyright": "file COPYRIGHTS",
+      "Encoding": "UTF-8",
+      "Language": "en-US",
+      "RoxygenNote": "7.2.3",
+      "SystemRequirements": "GNU make",
+      "NeedsCompilation": "yes",
+      "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut, cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>",
+      "Repository": "CRAN"
+    },
+    "glue": {
+      "Package": "glue",
+      "Version": "1.8.0",
+      "Source": "Repository",
+      "Title": "Interpreted String Literals",
+      "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://glue.tidyverse.org/, https://github.com/tidyverse/glue",
+      "BugReports": "https://github.com/tidyverse/glue/issues",
+      "Depends": [
+        "R (>= 3.6)"
+      ],
+      "Imports": [
+        "methods"
+      ],
+      "Suggests": [
+        "crayon",
+        "DBI (>= 1.2.0)",
+        "dplyr",
+        "knitr",
+        "magrittr",
+        "rlang",
+        "rmarkdown",
+        "RSQLite",
+        "testthat (>= 3.2.0)",
+        "vctrs (>= 0.3.0)",
+        "waldo (>= 0.5.3)",
+        "withr"
+      ],
+      "VignetteBuilder": "knitr",
+      "ByteCompile": "true",
+      "Config/Needs/website": "bench, forcats, ggbeeswarm, ggplot2, R.utils, rprintf, tidyr, tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "yes",
+      "Author": "Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Jennifer Bryan <jenny@posit.co>",
+      "Repository": "CRAN"
+    },
+    "highr": {
+      "Package": "highr",
+      "Version": "0.11",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Syntax Highlighting for R Source Code",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )",
+      "Description": "Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package (<https://gitlab.com/saalen/highlight>).",
+      "Depends": [
+        "R (>= 3.3.0)"
+      ],
+      "Imports": [
+        "xfun (>= 0.18)"
+      ],
+      "Suggests": [
+        "knitr",
+        "markdown",
+        "testit"
+      ],
+      "License": "GPL",
+      "URL": "https://github.com/yihui/highr",
+      "BugReports": "https://github.com/yihui/highr/issues",
+      "VignetteBuilder": "knitr",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.1",
+      "NeedsCompilation": "no",
+      "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
+    },
+    "htmltools": {
+      "Package": "htmltools",
+      "Version": "0.5.8.1",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Tools for HTML",
+      "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Yihui\", \"Xie\", , \"yihui@posit.co\", role = \"aut\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Tools for HTML generation and output.",
+      "License": "GPL (>= 2)",
+      "URL": "https://github.com/rstudio/htmltools, https://rstudio.github.io/htmltools/",
+      "BugReports": "https://github.com/rstudio/htmltools/issues",
+      "Depends": [
+        "R (>= 2.14.1)"
+      ],
+      "Imports": [
+        "base64enc",
+        "digest",
+        "fastmap (>= 1.1.0)",
+        "grDevices",
+        "rlang (>= 1.0.0)",
+        "utils"
+      ],
+      "Suggests": [
+        "Cairo",
+        "markdown",
+        "ragg",
+        "shiny",
+        "testthat",
+        "withr"
+      ],
+      "Enhances": [
+        "knitr"
+      ],
+      "Config/Needs/check": "knitr",
+      "Config/Needs/website": "rstudio/quillt, bench",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.1",
+      "Collate": "'colors.R' 'fill.R' 'html_dependency.R' 'html_escape.R' 'html_print.R' 'htmltools-package.R' 'images.R' 'known_tags.R' 'selector.R' 'staticimports.R' 'tag_query.R' 'utils.R' 'tags.R' 'template.R'",
+      "NeedsCompilation": "yes",
+      "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>), Winston Chang [aut] (<https://orcid.org/0000-0002-1576-2126>), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Carson Sievert <carson@posit.co>",
+      "Repository": "CRAN"
+    },
+    "jquerylib": {
+      "Package": "jquerylib",
+      "Version": "0.1.4",
+      "Source": "Repository",
+      "Title": "Obtain 'jQuery' as an HTML Dependency Object",
+      "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )",
+      "Description": "Obtain any major version of 'jQuery' (<https://code.jquery.com/>) and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "Config/testthat/edition": "3",
+      "RoxygenNote": "7.0.2",
+      "Imports": [
+        "htmltools"
+      ],
+      "Suggests": [
+        "testthat"
+      ],
+      "NeedsCompilation": "no",
+      "Author": "Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)",
+      "Maintainer": "Carson Sievert <carson@rstudio.com>",
+      "Repository": "CRAN"
+    },
+    "jsonlite": {
+      "Package": "jsonlite",
+      "Version": "1.9.1",
+      "Source": "Repository",
+      "Title": "A Simple and Robust JSON Parser and Generator for R",
+      "License": "MIT + file LICENSE",
+      "Depends": [
+        "methods"
+      ],
+      "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))",
+      "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805",
+      "BugReports": "https://github.com/jeroen/jsonlite/issues",
+      "Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>",
+      "VignetteBuilder": "knitr, R.rsp",
+      "Description": "A reasonably fast JSON parser and generator, optimized for statistical  data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API.  The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains  functions to stream, validate, and prettify JSON data. The unit tests included  with the package verify that all edge cases are encoded and decoded consistently  for use with dynamic data in systems and applications.",
+      "Suggests": [
+        "httr",
+        "vctrs",
+        "testthat",
+        "knitr",
+        "rmarkdown",
+        "R.rsp",
+        "sf"
+      ],
+      "RoxygenNote": "7.2.3",
+      "Encoding": "UTF-8",
+      "NeedsCompilation": "yes",
+      "Author": "Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)",
+      "Repository": "CRAN"
+    },
+    "knitr": {
+      "Package": "knitr",
+      "Version": "1.49",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "A General-Purpose Package for Dynamic Report Generation in R",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de\"), person(\"Aron\", \"Atkins\", role = \"ctb\"), person(\"Aaron\", \"Wolen\", role = \"ctb\"), person(\"Ashley\", \"Manton\", role = \"ctb\"), person(\"Atsushi\", \"Yasumoto\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8335-495X\")), person(\"Ben\", \"Baumer\", role = \"ctb\"), person(\"Brian\", \"Diggs\", role = \"ctb\"), person(\"Brian\", \"Zhang\", role = \"ctb\"), person(\"Bulat\", \"Yapparov\", role = \"ctb\"), person(\"Cassio\", \"Pereira\", role = \"ctb\"), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person(\"David\", \"Hall\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", role = \"ctb\"), person(\"David\", \"Robinson\", role = \"ctb\"), person(\"Doug\", \"Hemken\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", role = \"ctb\"), person(\"Elio\", \"Campitelli\", role = \"ctb\"), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Emily\", \"Riederer\", role = \"ctb\"), person(\"Fabian\", \"Hirschmann\", role = \"ctb\"), person(\"Fitch\", \"Simeon\", role = \"ctb\"), person(\"Forest\", \"Fang\", role = \"ctb\"), person(c(\"Frank\", \"E\", \"Harrell\", \"Jr\"), role = \"ctb\", comment = \"the Sweavel package at inst/misc/Sweavel.sty\"), person(\"Garrick\", \"Aden-Buie\", role = \"ctb\"), person(\"Gregoire\", \"Detrez\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Hao\", \"Zhu\", role = \"ctb\"), person(\"Heewon\", \"Jeon\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Hodges\", \"Daniel\", role = \"ctb\"), person(\"Jacob\", \"Bien\", role = \"ctb\"), person(\"Jake\", \"Burkhead\", role = \"ctb\"), person(\"James\", \"Manton\", role = \"ctb\"), person(\"Jared\", \"Lander\", role = \"ctb\"), person(\"Jason\", \"Punyon\", role = \"ctb\"), person(\"Javier\", \"Luraschi\", role = \"ctb\"), person(\"Jeff\", \"Arnold\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", role = \"ctb\"), person(\"Jeremy\", \"Ashkenas\", role = c(\"ctb\", \"cph\"), comment = \"the CSS file at inst/misc/docco-classic.css\"), person(\"Jeremy\", \"Stephens\", role = \"ctb\"), person(\"Jim\", \"Hester\", role = \"ctb\"), person(\"Joe\", \"Cheng\", role = \"ctb\"), person(\"Johannes\", \"Ranke\", role = \"ctb\"), person(\"John\", \"Honaker\", role = \"ctb\"), person(\"John\", \"Muschelli\", role = \"ctb\"), person(\"Jonathan\", \"Keane\", role = \"ctb\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Johan\", \"Toloe\", role = \"ctb\"), person(\"Jonathan\", \"Sidi\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Julien\", \"Barnier\", role = \"ctb\"), person(\"Kaiyin\", \"Zhong\", role = \"ctb\"), person(\"Kamil\", \"Slowikowski\", role = \"ctb\"), person(\"Karl\", \"Forner\", role = \"ctb\"), person(c(\"Kevin\", \"K.\"), \"Smith\", role = \"ctb\"), person(\"Kirill\", \"Mueller\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Lorenz\", \"Walthert\", role = \"ctb\"), person(\"Lucas\", \"Gallindo\", role = \"ctb\"), person(\"Marius\", \"Hofert\", role = \"ctb\"), person(\"Martin\", \"Modrák\", role = \"ctb\"), person(\"Michael\", \"Chirico\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"Michel\", \"Kuhlmann\", role = \"ctb\"), person(\"Miller\", \"Patrick\", role = \"ctb\"), person(\"Nacho\", \"Caballero\", role = \"ctb\"), person(\"Nick\", \"Salkowski\", role = \"ctb\"), person(\"Niels Richard\", \"Hansen\", role = \"ctb\"), person(\"Noam\", \"Ross\", role = \"ctb\"), person(\"Obada\", \"Mahdi\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = \"ctb\", comment=c(ORCID = \"0000-0002-9101-3362\")), person(\"Pedro\", \"Faria\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\"), person(\"Ramnath\", \"Vaidyanathan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Robert\", \"Krzyzanowski\", role = \"ctb\"), person(\"Rodrigo\", \"Copetti\", role = \"ctb\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Ruaridh\", \"Williamson\", role = \"ctb\"), person(\"Sagiru\", \"Mati\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1413-3974\")), person(\"Scott\", \"Kostyshak\", role = \"ctb\"), person(\"Sebastian\", \"Meyer\", role = \"ctb\"), person(\"Sietse\", \"Brouwer\", role = \"ctb\"), person(c(\"Simon\", \"de\"), \"Bernard\", role = \"ctb\"), person(\"Sylvain\", \"Rousseau\", role = \"ctb\"), person(\"Taiyun\", \"Wei\", role = \"ctb\"), person(\"Thibaut\", \"Assus\", role = \"ctb\"), person(\"Thibaut\", \"Lamadon\", role = \"ctb\"), person(\"Thomas\", \"Leeper\", role = \"ctb\"), person(\"Tim\", \"Mastny\", role = \"ctb\"), person(\"Tom\", \"Torsney-Weir\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = \"ctb\"), person(\"Viktoras\", \"Veitas\", role = \"ctb\"), person(\"Weicheng\", \"Zhu\", role = \"ctb\"), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Zachary\", \"Foster\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.",
+      "Depends": [
+        "R (>= 3.6.0)"
+      ],
+      "Imports": [
+        "evaluate (>= 0.15)",
+        "highr (>= 0.11)",
+        "methods",
+        "tools",
+        "xfun (>= 0.48)",
+        "yaml (>= 2.1.19)"
+      ],
+      "Suggests": [
+        "bslib",
+        "codetools",
+        "DBI (>= 0.4-1)",
+        "digest",
+        "formatR",
+        "gifski",
+        "gridSVG",
+        "htmlwidgets (>= 0.7)",
+        "jpeg",
+        "JuliaCall (>= 0.11.1)",
+        "magick",
+        "litedown",
+        "markdown (>= 1.3)",
+        "png",
+        "ragg",
+        "reticulate (>= 1.4)",
+        "rgl (>= 0.95.1201)",
+        "rlang",
+        "rmarkdown",
+        "sass",
+        "showtext",
+        "styler (>= 1.2.0)",
+        "targets (>= 0.6.0)",
+        "testit",
+        "tibble",
+        "tikzDevice (>= 0.10)",
+        "tinytex (>= 0.46)",
+        "webshot",
+        "rstudioapi",
+        "svglite"
+      ],
+      "License": "GPL",
+      "URL": "https://yihui.org/knitr/",
+      "BugReports": "https://github.com/yihui/knitr/issues",
+      "Encoding": "UTF-8",
+      "VignetteBuilder": "litedown, knitr",
+      "SystemRequirements": "Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org). The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).",
+      "Collate": "'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R' 'plot.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'",
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "no",
+      "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (<https://orcid.org/0000-0002-9101-3362>), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (<https://orcid.org/0000-0003-1413-3974>), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
+    },
+    "lifecycle": {
+      "Package": "lifecycle",
+      "Version": "1.0.4",
+      "Source": "Repository",
+      "Title": "Manage the Life Cycle of your Package Functions",
+      "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Manage the life cycle of your exported functions with shared conventions, documentation badges, and user-friendly deprecation warnings.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://lifecycle.r-lib.org/, https://github.com/r-lib/lifecycle",
+      "BugReports": "https://github.com/r-lib/lifecycle/issues",
+      "Depends": [
+        "R (>= 3.6)"
+      ],
+      "Imports": [
+        "cli (>= 3.4.0)",
+        "glue",
+        "rlang (>= 1.1.0)"
+      ],
+      "Suggests": [
+        "covr",
+        "crayon",
+        "knitr",
+        "lintr",
+        "rmarkdown",
+        "testthat (>= 3.0.1)",
+        "tibble",
+        "tidyverse",
+        "tools",
+        "vctrs",
+        "withr"
+      ],
+      "VignetteBuilder": "knitr",
+      "Config/Needs/website": "tidyverse/tidytemplate, usethis",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.2.1",
+      "NeedsCompilation": "no",
+      "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Lionel Henry <lionel@posit.co>",
+      "Repository": "CRAN"
+    },
+    "memoise": {
+      "Package": "memoise",
+      "Version": "2.0.1",
+      "Source": "Repository",
+      "Title": "'Memoisation' of Functions",
+      "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = \"aut\", email = \"hadley@rstudio.com\"), person(given = \"Jim\", family = \"Hester\", role = \"aut\"), person(given = \"Winston\", family = \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@rstudio.com\"), person(given = \"Kirill\", family = \"Müller\", role = \"aut\", email = \"krlmlr+r@mailbox.org\"), person(given = \"Daniel\", family = \"Cook\", role = \"aut\", email = \"danielecook@gmail.com\"), person(given = \"Mark\", family = \"Edmondson\", role = \"ctb\", email = \"r@sunholo.com\"))",
+      "Description": "Cache the results of a function so that when you call it again with the same arguments it returns the previously computed value.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://memoise.r-lib.org, https://github.com/r-lib/memoise",
+      "BugReports": "https://github.com/r-lib/memoise/issues",
+      "Imports": [
+        "rlang (>= 0.4.10)",
+        "cachem"
+      ],
+      "Suggests": [
+        "digest",
+        "aws.s3",
+        "covr",
+        "googleAuthR",
+        "googleCloudStorageR",
+        "httr",
+        "testthat"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.1.2",
+      "NeedsCompilation": "no",
+      "Author": "Hadley Wickham [aut], Jim Hester [aut], Winston Chang [aut, cre], Kirill Müller [aut], Daniel Cook [aut], Mark Edmondson [ctb]",
+      "Maintainer": "Winston Chang <winston@rstudio.com>",
+      "Repository": "CRAN"
+    },
+    "mime": {
+      "Package": "mime",
+      "Version": "0.12",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Map Filenames to MIME Types",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"Beilei\", \"Bian\", role = \"ctb\") )",
+      "Description": "Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.",
+      "Imports": [
+        "tools"
+      ],
+      "License": "GPL",
+      "URL": "https://github.com/yihui/mime",
+      "BugReports": "https://github.com/yihui/mime/issues",
+      "RoxygenNote": "7.1.1",
+      "Encoding": "UTF-8",
+      "NeedsCompilation": "yes",
+      "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jeffrey Horner [ctb], Beilei Bian [ctb]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
+    },
+    "rappdirs": {
+      "Package": "rappdirs",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Application Directories: Determine Where to Save Data, Caches, and Logs",
+      "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = c(\"trl\", \"cre\", \"cph\"), email = \"hadley@rstudio.com\"), person(given = \"RStudio\", role = \"cph\"), person(given = \"Sridhar\", family = \"Ratnakumar\", role = \"aut\"), person(given = \"Trent\", family = \"Mick\", role = \"aut\"), person(given = \"ActiveState\", role = \"cph\", comment = \"R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs\"), person(given = \"Eddy\", family = \"Petrisor\", role = \"ctb\"), person(given = \"Trevor\", family = \"Davis\", role = c(\"trl\", \"aut\")), person(given = \"Gabor\", family = \"Csardi\", role = \"ctb\"), person(given = \"Gregory\", family = \"Jefferis\", role = \"ctb\"))",
+      "Description": "An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's 'Appdirs' (<https://github.com/ActiveState/appdirs>) to R.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rappdirs.r-lib.org, https://github.com/r-lib/rappdirs",
+      "BugReports": "https://github.com/r-lib/rappdirs/issues",
+      "Depends": [
+        "R (>= 3.2)"
+      ],
+      "Suggests": [
+        "roxygen2",
+        "testthat (>= 3.0.0)",
+        "covr",
+        "withr"
+      ],
+      "Copyright": "Original python appdirs module copyright (c) 2010 ActiveState Software Inc. R port copyright Hadley Wickham, RStudio. See file LICENSE for details.",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.1.1",
+      "Config/testthat/edition": "3",
+      "NeedsCompilation": "yes",
+      "Author": "Hadley Wickham [trl, cre, cph], RStudio [cph], Sridhar Ratnakumar [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs), Eddy Petrisor [ctb], Trevor Davis [trl, aut], Gabor Csardi [ctb], Gregory Jefferis [ctb]",
+      "Maintainer": "Hadley Wickham <hadley@rstudio.com>",
+      "Repository": "CRAN"
+    },
+    "renv": {
+      "Package": "renv",
+      "Version": "1.1.2",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Project Environments",
+      "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@rstudio.com\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv",
+      "BugReports": "https://github.com/rstudio/renv/issues",
+      "Imports": [
+        "utils"
+      ],
+      "Suggests": [
+        "BiocManager",
+        "cli",
+        "compiler",
+        "covr",
+        "cpp11",
+        "devtools",
+        "gitcreds",
+        "jsonlite",
+        "jsonvalidate",
+        "knitr",
+        "miniUI",
+        "modules",
+        "packrat",
+        "pak",
+        "R6",
+        "remotes",
+        "reticulate",
+        "rmarkdown",
+        "rstudioapi",
+        "shiny",
+        "testthat",
+        "uuid",
+        "waldo",
+        "yaml",
+        "webfakes"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "VignetteBuilder": "knitr",
+      "Config/Needs/website": "tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Config/testthat/parallel": "true",
+      "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes",
+      "NeedsCompilation": "no",
+      "Author": "Kevin Ushey [aut, cre] (<https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
+      "Repository": "CRAN"
+    },
+    "rlang": {
+      "Package": "rlang",
+      "Version": "1.1.5",
+      "Source": "Repository",
+      "Title": "Functions for Base Types and Core R and 'Tidyverse' Features",
+      "Description": "A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.",
+      "Authors@R": "c( person(\"Lionel\", \"Henry\", ,\"lionel@posit.co\", c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", ,\"hadley@posit.co\", \"aut\"), person(given = \"mikefc\", email = \"mikefc@coolbutuseless.com\",  role = \"cph\",  comment = \"Hash implementation based on Mike's xxhashlite\"), person(given = \"Yann\", family = \"Collet\", role = \"cph\",  comment = \"Author of the embedded xxHash library\"), person(given = \"Posit, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "License": "MIT + file LICENSE",
+      "ByteCompile": "true",
+      "Biarch": "true",
+      "Depends": [
+        "R (>= 3.5.0)"
+      ],
+      "Imports": [
+        "utils"
+      ],
+      "Suggests": [
+        "cli (>= 3.1.0)",
+        "covr",
+        "crayon",
+        "fs",
+        "glue",
+        "knitr",
+        "magrittr",
+        "methods",
+        "pillar",
+        "rmarkdown",
+        "stats",
+        "testthat (>= 3.0.0)",
+        "tibble",
+        "usethis",
+        "vctrs (>= 0.2.3)",
+        "withr"
+      ],
+      "Enhances": [
+        "winch"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "URL": "https://rlang.r-lib.org, https://github.com/r-lib/rlang",
+      "BugReports": "https://github.com/r-lib/rlang/issues",
+      "Config/testthat/edition": "3",
+      "Config/Needs/website": "dplyr, tidyverse/tidytemplate",
+      "NeedsCompilation": "yes",
+      "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], mikefc [cph] (Hash implementation based on Mike's xxhashlite), Yann Collet [cph] (Author of the embedded xxHash library), Posit, PBC [cph, fnd]",
+      "Maintainer": "Lionel Henry <lionel@posit.co>",
+      "Repository": "CRAN"
+    },
+    "rmarkdown": {
+      "Package": "rmarkdown",
+      "Version": "2.29",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Dynamic Documents for R",
+      "Authors@R": "c( person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\"), person(\"Yihui\", \"Xie\", , \"xie@yihui.name\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Jonathan\", \"McPherson\", , \"jonathan@posit.co\", role = \"aut\"), person(\"Javier\", \"Luraschi\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevin@posit.co\", role = \"aut\"), person(\"Aron\", \"Atkins\", , \"aron@posit.co\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\"), person(\"Richard\", \"Iannone\", , \"rich@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Andrew\", \"Dunning\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0464-5036\")), person(\"Atsushi\", \"Yasumoto\", role = c(\"ctb\", \"cph\"), comment = c(ORCID = \"0000-0002-8335-495X\", cph = \"Number sections Lua filter\")), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Carson\", \"Sievert\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4958-2844\")),  person(\"Devon\", \"Ryan\", , \"dpryan79@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8549-0971\")), person(\"Frederik\", \"Aust\", , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Jeff\", \"Allen\", , \"jeff@posit.co\", role = \"ctb\"),  person(\"JooYoung\", \"Seo\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4064-6012\")), person(\"Malcolm\", \"Barrett\", role = \"ctb\"), person(\"Rob\", \"Hyndman\", , \"Rob.Hyndman@monash.edu\", role = \"ctb\"), person(\"Romain\", \"Lesur\", role = \"ctb\"), person(\"Roy\", \"Storey\", role = \"ctb\"), person(\"Ruben\", \"Arslan\", , \"ruben.arslan@uni-goettingen.de\", role = \"ctb\"), person(\"Sergio\", \"Oller\", role = \"ctb\"), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"jQuery UI contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Alexander\", \"Farkas\", role = c(\"ctb\", \"cph\"), comment = \"html5shiv library\"), person(\"Scott\", \"Jehl\", role = c(\"ctb\", \"cph\"), comment = \"Respond.js library\"), person(\"Ivan\", \"Sagalaev\", role = c(\"ctb\", \"cph\"), comment = \"highlight.js library\"), person(\"Greg\", \"Franko\", role = c(\"ctb\", \"cph\"), comment = \"tocify library\"), person(\"John\", \"MacFarlane\", role = c(\"ctb\", \"cph\"), comment = \"Pandoc templates\"), person(, \"Google, Inc.\", role = c(\"ctb\", \"cph\"), comment = \"ioslides library\"), person(\"Dave\", \"Raggett\", role = \"ctb\", comment = \"slidy library\"), person(, \"W3C\", role = \"cph\", comment = \"slidy library\"), person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome\"), person(\"Ben\", \"Sperry\", role = \"ctb\", comment = \"Ionicons\"), person(, \"Drifty\", role = \"cph\", comment = \"Ionicons\"), person(\"Aidan\", \"Lister\", role = c(\"ctb\", \"cph\"), comment = \"jQuery StickyTabs\"), person(\"Benct Philip\", \"Jonsson\", role = c(\"ctb\", \"cph\"), comment = \"pagebreak Lua filter\"), person(\"Albert\", \"Krewinkel\", role = c(\"ctb\", \"cph\"), comment = \"pagebreak Lua filter\") )",
+      "Description": "Convert R Markdown documents into a variety of formats.",
+      "License": "GPL-3",
+      "URL": "https://github.com/rstudio/rmarkdown, https://pkgs.rstudio.com/rmarkdown/",
+      "BugReports": "https://github.com/rstudio/rmarkdown/issues",
+      "Depends": [
+        "R (>= 3.0)"
+      ],
+      "Imports": [
+        "bslib (>= 0.2.5.1)",
+        "evaluate (>= 0.13)",
+        "fontawesome (>= 0.5.0)",
+        "htmltools (>= 0.5.1)",
+        "jquerylib",
+        "jsonlite",
+        "knitr (>= 1.43)",
+        "methods",
+        "tinytex (>= 0.31)",
+        "tools",
+        "utils",
+        "xfun (>= 0.36)",
+        "yaml (>= 2.1.19)"
+      ],
+      "Suggests": [
+        "digest",
+        "dygraphs",
+        "fs",
+        "rsconnect",
+        "downlit (>= 0.4.0)",
+        "katex (>= 1.4.0)",
+        "sass (>= 0.4.0)",
+        "shiny (>= 1.6.0)",
+        "testthat (>= 3.0.3)",
+        "tibble",
+        "vctrs",
+        "cleanrmd",
+        "withr (>= 2.4.2)",
+        "xml2"
+      ],
+      "VignetteBuilder": "knitr",
+      "Config/Needs/website": "rstudio/quillt, pkgdown",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "SystemRequirements": "pandoc (>= 1.14) - http://pandoc.org",
+      "NeedsCompilation": "no",
+      "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Christophe Dervieux [aut] (<https://orcid.org/0000-0003-4474-2498>), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>), Atsushi Yasumoto [ctb, cph] (<https://orcid.org/0000-0002-8335-495X>, Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (<https://orcid.org/0000-0002-4958-2844>), Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>), Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Jeff Allen [ctb], JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], Posit Software, PBC [cph, fnd], jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
+    },
+    "sass": {
+      "Package": "sass",
+      "Version": "0.4.9",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Syntactically Awesome Style Sheets ('Sass')",
+      "Description": "An 'SCSS' compiler, powered by the 'LibSass' library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the 'Sass CSS' extension language, which is stable, powerful, and CSS compatible.",
+      "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@rstudio.com\", \"aut\"), person(\"Timothy\", \"Mastny\", , \"tim.mastny@gmail.com\", \"aut\"), person(\"Richard\", \"Iannone\", , \"rich@rstudio.com\", \"aut\", comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Barret\", \"Schloerke\", , \"barret@rstudio.com\", \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Carson\", \"Sievert\", , \"carson@rstudio.com\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Christophe\", \"Dervieux\", , \"cderv@rstudio.com\", c(\"ctb\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(family = \"RStudio\", role = c(\"cph\", \"fnd\")), person(family = \"Sass Open Source Foundation\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Greter\", \"Marcel\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Mifsud\", \"Michael\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Hampton\", \"Catlin\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Natalie\", \"Weizenbaum\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Chris\", \"Eppstein\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Adams\", \"Joseph\", role = c(\"ctb\", \"cph\"), comment = \"json.cpp\"), person(\"Trifunovic\", \"Nemanja\", role = c(\"ctb\", \"cph\"), comment = \"utf8.h\") )",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rstudio.github.io/sass/, https://github.com/rstudio/sass",
+      "BugReports": "https://github.com/rstudio/sass/issues",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.1",
+      "SystemRequirements": "GNU make",
+      "Imports": [
+        "fs (>= 1.2.4)",
+        "rlang (>= 0.4.10)",
+        "htmltools (>= 0.5.1)",
+        "R6",
+        "rappdirs"
+      ],
+      "Suggests": [
+        "testthat",
+        "knitr",
+        "rmarkdown",
+        "withr",
+        "shiny",
+        "curl"
+      ],
+      "VignetteBuilder": "knitr",
+      "Config/testthat/edition": "3",
+      "NeedsCompilation": "yes",
+      "Author": "Joe Cheng [aut], Timothy Mastny [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>), Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), RStudio [cph, fnd], Sass Open Source Foundation [ctb, cph] (LibSass library), Greter Marcel [ctb, cph] (LibSass library), Mifsud Michael [ctb, cph] (LibSass library), Hampton Catlin [ctb, cph] (LibSass library), Natalie Weizenbaum [ctb, cph] (LibSass library), Chris Eppstein [ctb, cph] (LibSass library), Adams Joseph [ctb, cph] (json.cpp), Trifunovic Nemanja [ctb, cph] (utf8.h)",
+      "Maintainer": "Carson Sievert <carson@rstudio.com>",
+      "Repository": "CRAN"
+    },
+    "tinytex": {
+      "Package": "tinytex",
+      "Version": "0.56",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Devon\", \"Ryan\", role = \"ctb\", email = \"dpryan79@gmail.com\", comment = c(ORCID = \"0000-0002-8549-0971\")), person(\"Ethan\", \"Heinzen\", role = \"ctb\"), person(\"Fernando\", \"Cagua\", role = \"ctb\"), person() )",
+      "Description": "Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.",
+      "Imports": [
+        "xfun (>= 0.48)"
+      ],
+      "Suggests": [
+        "testit",
+        "rstudioapi"
+      ],
+      "License": "MIT + file LICENSE",
+      "URL": "https://github.com/rstudio/tinytex",
+      "BugReports": "https://github.com/rstudio/tinytex/issues",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "no",
+      "Author": "Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>), Ethan Heinzen [ctb], Fernando Cagua [ctb]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.51",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )",
+      "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.",
+      "Depends": [
+        "R (>= 3.2.0)"
+      ],
+      "Imports": [
+        "grDevices",
+        "stats",
+        "tools"
+      ],
+      "Suggests": [
+        "testit",
+        "parallel",
+        "codetools",
+        "methods",
+        "rstudioapi",
+        "tinytex (>= 0.30)",
+        "mime",
+        "litedown (>= 0.4)",
+        "commonmark",
+        "knitr (>= 1.47)",
+        "remotes",
+        "pak",
+        "rhub",
+        "renv",
+        "curl",
+        "xml2",
+        "jsonlite",
+        "magick",
+        "yaml",
+        "qs",
+        "rmarkdown"
+      ],
+      "License": "MIT + file LICENSE",
+      "URL": "https://github.com/yihui/xfun",
+      "BugReports": "https://github.com/yihui/xfun/issues",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "VignetteBuilder": "litedown",
+      "NeedsCompilation": "yes",
+      "Author": "Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>, https://yihui.org), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>), Christophe Dervieux [ctb]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.10",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Methods to Convert R Data to YAML and Back",
+      "Date": "2024-07-22",
+      "Suggests": [
+        "RUnit"
+      ],
+      "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]",
+      "Maintainer": "Shawn Garbett <shawn.garbett@vumc.org>",
+      "License": "BSD_3_clause + file LICENSE",
+      "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter (<https://pyyaml.org/wiki/LibYAML>) for R.",
+      "URL": "https://github.com/vubiostat/r-yaml/",
+      "BugReports": "https://github.com/vubiostat/r-yaml/issues",
+      "NeedsCompilation": "yes",
+      "Repository": "CRAN"
+    }
+  }
+}
diff --git a/renv/.gitignore b/renv/.gitignore
new file mode 100644
index 00000000..0ec0cbba
--- /dev/null
+++ b/renv/.gitignore
@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/
diff --git a/renv/activate.R b/renv/activate.R
index 2ebe4034..0862e8b1 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -42,7 +42,7 @@ local({
       return(FALSE)
 
     # next, check environment variables
-    # TODO: prefer using the configuration one in the future
+    # prefer using the configuration one in the future
     envvars <- c(
       "RENV_CONFIG_AUTOLOADER_ENABLED",
       "RENV_AUTOLOADER_ENABLED",
@@ -135,12 +135,12 @@ local({
   
     # R help links
     pattern <- "`\\?(renv::(?:[^`])+)`"
-    replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
+    replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`"
     text <- gsub(pattern, replacement, text, perl = TRUE)
   
     # runnable code
     pattern <- "`(renv::(?:[^`])+)`"
-    replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
+    replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`"
     text <- gsub(pattern, replacement, text, perl = TRUE)
   
     # return ansified text
@@ -209,10 +209,6 @@ local({
   
   }
   
-  startswith <- function(string, prefix) {
-    substring(string, 1, nchar(prefix)) == prefix
-  }
-  
   bootstrap <- function(version, library) {
   
     friendly <- renv_bootstrap_version_friendly(version)
@@ -368,8 +364,7 @@ local({
       quiet    = TRUE
     )
   
-    if ("headers" %in% names(formals(utils::download.file)))
-    {
+    if ("headers" %in% names(formals(utils::download.file))) {
       headers <- renv_bootstrap_download_custom_headers(url)
       if (length(headers) && is.character(headers))
         args$headers <- headers
@@ -457,9 +452,8 @@ local({
   
         # add custom headers if available -- note that
         # utils::available.packages() will pass this to download.file()
-        if ("headers" %in% names(formals(utils::download.file)))
-        {
-          headers <- renv_bootstrap_download_custom_headers(url)
+        if ("headers" %in% names(formals(utils::download.file))) {
+          headers <- renv_bootstrap_download_custom_headers(repos)
           if (length(headers) && is.character(headers))
             args$headers <- headers
         }
@@ -565,6 +559,9 @@ local({
   
     # prepare download options
     token <- renv_bootstrap_github_token()
+    if (is.null(token))
+      token <- ""
+  
     if (nzchar(Sys.which("curl")) && nzchar(token)) {
       fmt <- "--location --fail --header \"Authorization: token %s\""
       extra <- sprintf(fmt, token)
@@ -953,8 +950,14 @@ local({
   }
   
   renv_bootstrap_validate_version_dev <- function(version, description) {
+    
     expected <- description[["RemoteSha"]]
-    is.character(expected) && startswith(expected, version)
+    if (!is.character(expected))
+      return(FALSE)
+    
+    pattern <- sprintf("^\\Q%s\\E", version)
+    grepl(pattern, expected, perl = TRUE)
+    
   }
   
   renv_bootstrap_validate_version_release <- function(version, description) {
@@ -1134,10 +1137,10 @@ local({
   
   renv_bootstrap_exec <- function(project, libpath, version) {
     if (!renv_bootstrap_load(project, libpath, version))
-      renv_bootstrap_run(version, libpath)
+      renv_bootstrap_run(project, libpath, version)
   }
   
-  renv_bootstrap_run <- function(version, libpath) {
+  renv_bootstrap_run <- function(project, libpath, version) {
   
     # perform bootstrap
     bootstrap(version, libpath)
@@ -1148,7 +1151,7 @@ local({
   
     # try again to load
     if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
-      return(renv::load(project = getwd()))
+      return(renv::load(project = project))
     }
   
     # failed to download or load renv; warn the user
@@ -1194,98 +1197,101 @@ local({
     jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
   }
   
-  renv_json_read_default <- function(file = NULL, text = NULL) {
-  
-    # find strings in the JSON
-    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
-    pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
-    locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
-  
-    # if any are found, replace them with placeholders
-    replaced <- text
-    strings <- character()
-    replacements <- character()
-  
-    if (!identical(c(locs), -1L)) {
-  
-      # get the string values
-      starts <- locs
-      ends <- locs + attr(locs, "match.length") - 1L
-      strings <- substring(text, starts, ends)
-  
-      # only keep those requiring escaping
-      strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE)
-  
-      # compute replacements
-      replacements <- sprintf('"\032%i\032"', seq_along(strings))
-  
-      # replace the strings
-      mapply(function(string, replacement) {
-        replaced <<- sub(string, replacement, replaced, fixed = TRUE)
-      }, strings, replacements)
+  renv_json_read_patterns <- function() {
+    
+    list(
+      
+      # objects
+      list("{", "\t\n\tobject(\t\n\t"),
+      list("}", "\t\n\t)\t\n\t"),
+      
+      # arrays
+      list("[", "\t\n\tarray(\t\n\t"),
+      list("]", "\n\t\n)\n\t\n"),
+      
+      # maps
+      list(":", "\t\n\t=\t\n\t")
+      
+    )
+    
+  }
   
+  renv_json_read_envir <- function() {
+  
+    envir <- new.env(parent = emptyenv())
+    
+    envir[["+"]] <- `+`
+    envir[["-"]] <- `-`
+    
+    envir[["object"]] <- function(...) {
+      result <- list(...)
+      names(result) <- as.character(names(result))
+      result
     }
-  
-    # transform the JSON into something the R parser understands
-    transformed <- replaced
-    transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
-    transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
-    transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
-    transformed <- gsub(":", "=", transformed, fixed = TRUE)
-    text <- paste(transformed, collapse = "\n")
-  
-    # parse it
-    json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]]
-  
-    # construct map between source strings, replaced strings
-    map <- as.character(parse(text = strings))
-    names(map) <- as.character(parse(text = replacements))
-  
-    # convert to list
-    map <- as.list(map)
-  
-    # remap strings in object
-    remapped <- renv_json_read_remap(json, map)
-  
-    # evaluate
-    eval(remapped, envir = baseenv())
-  
+    
+    envir[["array"]] <- list
+    
+    envir[["true"]]  <- TRUE
+    envir[["false"]] <- FALSE
+    envir[["null"]]  <- NULL
+    
+    envir
+    
   }
   
-  renv_json_read_remap <- function(json, map) {
-  
-    # fix names
-    if (!is.null(names(json))) {
-      lhs <- match(names(json), names(map), nomatch = 0L)
-      rhs <- match(names(map), names(json), nomatch = 0L)
-      names(json)[rhs] <- map[lhs]
+  renv_json_read_remap <- function(object, patterns) {
+    
+    # repair names if necessary
+    if (!is.null(names(object))) {
+      
+      nms <- names(object)
+      for (pattern in patterns)
+        nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE)
+      names(object) <- nms
+      
     }
-  
-    # fix values
-    if (is.character(json))
-      return(map[[json]] %||% json)
-  
-    # handle true, false, null
-    if (is.name(json)) {
-      text <- as.character(json)
-      if (text == "true")
-        return(TRUE)
-      else if (text == "false")
-        return(FALSE)
-      else if (text == "null")
-        return(NULL)
+    
+    # repair strings if necessary
+    if (is.character(object)) {
+      for (pattern in patterns)
+        object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE)
     }
+    
+    # recurse for other objects
+    if (is.recursive(object))
+      for (i in seq_along(object))
+        object[i] <- list(renv_json_read_remap(object[[i]], patterns))
+    
+    # return remapped object
+    object
+    
+  }
   
-    # recurse
-    if (is.recursive(json)) {
-      for (i in seq_along(json)) {
-        json[i] <- list(renv_json_read_remap(json[[i]], map))
-      }
-    }
+  renv_json_read_default <- function(file = NULL, text = NULL) {
   
-    json
+    # read json text
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+    
+    # convert into something the R parser will understand
+    patterns <- renv_json_read_patterns()
+    transformed <- text
+    for (pattern in patterns)
+      transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE)
+    
+    # parse it
+    rfile <- tempfile("renv-json-", fileext = ".R")
+    on.exit(unlink(rfile), add = TRUE)
+    writeLines(transformed, con = rfile)
+    json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]]
   
+    # evaluate in safe environment
+    result <- eval(json, envir = renv_json_read_envir())
+  
+    # fix up strings if necessary
+    renv_json_read_remap(result, patterns)
+    
   }
+  
 
   # load the renv profile, if any
   renv_bootstrap_profile_load(project)
diff --git a/renv/profile b/renv/profile
deleted file mode 100644
index 6d4023b5..00000000
--- a/renv/profile
+++ /dev/null
@@ -1 +0,0 @@
-lesson-requirements
diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
index b1b476a1..57824b77 100644
--- a/renv/profiles/lesson-requirements/renv.lock
+++ b/renv/profiles/lesson-requirements/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.4.0",
+    "Version": "4.4.2",
     "Repositories": [
       {
         "Name": "carpentries",
@@ -21,322 +21,964 @@
       "Package": "R6",
       "Version": "2.5.1",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
+      "Title": "Encapsulated Classes with Reference Semantics",
+      "Authors@R": "person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@stdout.org\")",
+      "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.",
+      "Depends": [
+        "R (>= 3.0)"
       ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+      "Suggests": [
+        "testthat",
+        "pryr"
+      ],
+      "License": "MIT + file LICENSE",
+      "URL": "https://r6.r-lib.org, https://github.com/r-lib/R6/",
+      "BugReports": "https://github.com/r-lib/R6/issues",
+      "RoxygenNote": "7.1.1",
+      "NeedsCompilation": "no",
+      "Author": "Winston Chang [aut, cre]",
+      "Maintainer": "Winston Chang <winston@stdout.org>",
+      "Repository": "CRAN"
     },
     "base64enc": {
       "Package": "base64enc",
       "Version": "0.1-3",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
+      "Title": "Tools for base64 encoding",
+      "Author": "Simon Urbanek <Simon.Urbanek@r-project.org>",
+      "Maintainer": "Simon Urbanek <Simon.Urbanek@r-project.org>",
+      "Depends": [
+        "R (>= 2.9.0)"
+      ],
+      "Enhances": [
+        "png"
       ],
-      "Hash": "543776ae6848fde2f48ff3816d0628bc"
+      "Description": "This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.",
+      "License": "GPL-2 | GPL-3",
+      "URL": "http://www.rforge.net/base64enc",
+      "NeedsCompilation": "yes",
+      "Repository": "CRAN"
     },
     "bslib": {
       "Package": "bslib",
       "Version": "0.8.0",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
+      "Title": "Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'",
+      "Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Javi\", \"Aguilar\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap colorpicker library\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch library\"), person(, \"PayPal\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap accessibility plugin\") )",
+      "Description": "Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rstudio.github.io/bslib/, https://github.com/rstudio/bslib",
+      "BugReports": "https://github.com/rstudio/bslib/issues",
+      "Depends": [
+        "R (>= 2.10)"
+      ],
+      "Imports": [
         "base64enc",
         "cachem",
-        "fastmap",
+        "fastmap (>= 1.1.1)",
         "grDevices",
-        "htmltools",
-        "jquerylib",
+        "htmltools (>= 0.5.8)",
+        "jquerylib (>= 0.1.3)",
         "jsonlite",
         "lifecycle",
-        "memoise",
+        "memoise (>= 2.0.1)",
         "mime",
         "rlang",
-        "sass"
+        "sass (>= 0.4.9)"
+      ],
+      "Suggests": [
+        "bsicons",
+        "curl",
+        "fontawesome",
+        "future",
+        "ggplot2",
+        "knitr",
+        "magrittr",
+        "rappdirs",
+        "rmarkdown (>= 2.7)",
+        "shiny (> 1.8.1)",
+        "testthat",
+        "thematic",
+        "withr"
       ],
-      "Hash": "b299c6741ca9746fb227debcb0f9fb6c"
+      "Config/Needs/deploy": "BH, chiflights22, colourpicker, commonmark, cpp11, cpsievert/chiflights22, cpsievert/histoslider, dplyr, DT, ggplot2, ggridges, gt, hexbin, histoslider, htmlwidgets, lattice, leaflet, lubridate, modelr, plotly, reactable, reshape2, rprojroot, rsconnect, rstudio/shiny, scales, styler, tibble",
+      "Config/Needs/routine": "chromote, desc, renv",
+      "Config/Needs/website": "brio, crosstalk, dplyr, DT, ggplot2, glue, htmlwidgets, leaflet, lorem, palmerpenguins, plotly, purrr, rprojroot, rstudio/htmltools, scales, stringr, tidyr, webshot2",
+      "Config/testthat/edition": "3",
+      "Config/testthat/parallel": "true",
+      "Config/testthat/start-first": "zzzz-bs-sass, fonts, zzz-precompile, theme-*, rmd-*",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "Collate": "'accordion.R' 'breakpoints.R' 'bs-current-theme.R' 'bs-dependencies.R' 'bs-global.R' 'bs-remove.R' 'bs-theme-layers.R' 'bs-theme-preset-bootswatch.R' 'bs-theme-preset-builtin.R' 'bs-theme-preset.R' 'utils.R' 'bs-theme-preview.R' 'bs-theme-update.R' 'bs-theme.R' 'bslib-package.R' 'buttons.R' 'card.R' 'deprecated.R' 'files.R' 'fill.R' 'imports.R' 'input-dark-mode.R' 'input-switch.R' 'layout.R' 'nav-items.R' 'nav-update.R' 'navs-legacy.R' 'navs.R' 'onLoad.R' 'page.R' 'popover.R' 'precompiled.R' 'print.R' 'shiny-devmode.R' 'sidebar.R' 'staticimports.R' 'tooltip.R' 'utils-deps.R' 'utils-shiny.R' 'utils-tags.R' 'value-box.R' 'version-default.R' 'versions.R'",
+      "NeedsCompilation": "no",
+      "Author": "Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Joe Cheng [aut], Garrick Aden-Buie [aut] (<https://orcid.org/0000-0002-7111-0077>), Posit Software, PBC [cph, fnd], Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Javi Aguilar [ctb, cph] (Bootstrap colorpicker library), Thomas Park [ctb, cph] (Bootswatch library), PayPal [ctb, cph] (Bootstrap accessibility plugin)",
+      "Maintainer": "Carson Sievert <carson@posit.co>",
+      "Repository": "CRAN"
     },
     "cachem": {
       "Package": "cachem",
       "Version": "1.1.0",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "fastmap",
-        "rlang"
+      "Title": "Cache R Objects with Automatic Pruning",
+      "Description": "Key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.",
+      "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", c(\"aut\", \"cre\")), person(family = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")))",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "ByteCompile": "true",
+      "URL": "https://cachem.r-lib.org/, https://github.com/r-lib/cachem",
+      "Imports": [
+        "rlang",
+        "fastmap (>= 1.2.0)"
+      ],
+      "Suggests": [
+        "testthat"
       ],
-      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
+      "RoxygenNote": "7.2.3",
+      "Config/Needs/routine": "lobstr",
+      "Config/Needs/website": "pkgdown",
+      "NeedsCompilation": "yes",
+      "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Winston Chang <winston@posit.co>",
+      "Repository": "CRAN"
     },
     "cli": {
       "Package": "cli",
       "Version": "3.6.3",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
+      "Title": "Helpers for Developing Command Line Interfaces",
+      "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Kirill\", \"Müller\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", , \"salim-b@pm.me\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli",
+      "BugReports": "https://github.com/r-lib/cli/issues",
+      "Depends": [
+        "R (>= 3.4)"
+      ],
+      "Imports": [
         "utils"
       ],
-      "Hash": "b21916dd77a27642b447374a5d30ecf3"
+      "Suggests": [
+        "callr",
+        "covr",
+        "crayon",
+        "digest",
+        "glue (>= 1.6.0)",
+        "grDevices",
+        "htmltools",
+        "htmlwidgets",
+        "knitr",
+        "methods",
+        "mockery",
+        "processx",
+        "ps (>= 1.3.4.9000)",
+        "rlang (>= 1.0.2.9003)",
+        "rmarkdown",
+        "rprojroot",
+        "rstudioapi",
+        "testthat",
+        "tibble",
+        "whoami",
+        "withr"
+      ],
+      "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.2.3",
+      "NeedsCompilation": "yes",
+      "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>",
+      "Repository": "CRAN"
     },
     "digest": {
       "Package": "digest",
       "Version": "0.6.37",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
+      "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))",
+      "Date": "2024-08-19",
+      "Title": "Create Compact Hash Digests of R Objects",
+      "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.",
+      "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html",
+      "BugReports": "https://github.com/eddelbuettel/digest/issues",
+      "Depends": [
+        "R (>= 3.3.0)"
+      ],
+      "Imports": [
         "utils"
       ],
-      "Hash": "33698c4b3127fc9f506654607fb73676"
+      "License": "GPL (>= 2)",
+      "Suggests": [
+        "tinytest",
+        "simplermarkdown"
+      ],
+      "VignetteBuilder": "simplermarkdown",
+      "Encoding": "UTF-8",
+      "NeedsCompilation": "yes",
+      "Author": "Dirk Eddelbuettel [aut, cre] (<https://orcid.org/0000-0001-6419-907X>), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (<https://orcid.org/0000-0002-7579-5165>), Simon Urbanek [ctb] (<https://orcid.org/0000-0003-2297-1732>), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (<https://orcid.org/0000-0001-5180-0567>), Qiang Kou [ctb] (<https://orcid.org/0000-0001-6786-5453>), Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>), Michel Lang [ctb] (<https://orcid.org/0000-0001-9754-0393>), Viliam Simko [ctb], Kurt Hornik [ctb] (<https://orcid.org/0000-0003-4198-9911>), Radford Neal [ctb] (<https://orcid.org/0000-0002-2473-3407>), Kendon Bell [ctb] (<https://orcid.org/0000-0002-9093-8312>), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (<https://orcid.org/0000-0003-1878-3253>), Floris Vanderhaeghe [ctb] (<https://orcid.org/0000-0002-6378-6229>), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (<https://orcid.org/0000-0001-7813-818X>), Mark van der Loo [ctb] (<https://orcid.org/0000-0002-9807-4686>), Chris Muir [ctb] (<https://orcid.org/0000-0003-2555-3878>), Moritz Beller [ctb] (<https://orcid.org/0000-0003-4852-0526>), Sebastian Campbell [ctb], Winston Chang [ctb] (<https://orcid.org/0000-0002-1576-2126>), Dean Attali [ctb] (<https://orcid.org/0000-0002-5645-3493>), Michael Chirico [ctb] (<https://orcid.org/0000-0003-0787-087X>), Kevin Ushey [ctb]",
+      "Maintainer": "Dirk Eddelbuettel <edd@debian.org>",
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       "Package": "evaluate",
       "Version": "1.0.0",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
+      "Type": "Package",
+      "Title": "Parsing and Evaluation Tools that Provide More Details than the Default",
+      "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"aut\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Michael\", \"Lawrence\", role = \"ctb\"), person(\"Thomas\", \"Kluyver\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Adam\", \"Ryczkowski\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Michel\", \"Lang\", role = \"ctb\"), person(\"Karolis\", \"Koncevičius\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://evaluate.r-lib.org/, https://github.com/r-lib/evaluate",
+      "BugReports": "https://github.com/r-lib/evaluate/issues",
+      "Depends": [
+        "R (>= 3.6.0)"
+      ],
+      "Suggests": [
+        "covr",
+        "ggplot2 (>= 3.3.6)",
+        "lattice",
+        "methods",
+        "rlang",
+        "testthat (>= 3.0.0)",
+        "withr"
       ],
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+      "Config/Needs/website": "tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "no",
+      "Author": "Hadley Wickham [aut, cre], Yihui Xie [aut] (<https://orcid.org/0000-0003-0645-5666>), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb], Karolis Koncevičius [ctb], Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Hadley Wickham <hadley@posit.co>",
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       "Version": "1.2.0",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
+      "Title": "Fast Data Structures",
+      "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )",
+      "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. Environments are commonly used as key-value stores in R, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.2.3",
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+      "BugReports": "https://github.com/r-lib/fastmap/issues",
+      "NeedsCompilation": "yes",
+      "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd], Tessil [cph] (hopscotch_map library)",
+      "Maintainer": "Winston Chang <winston@posit.co>",
+      "Repository": "CRAN"
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       "Package": "fontawesome",
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       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "htmltools",
-        "rlang"
+      "Type": "Package",
+      "Title": "Easily Work with 'Font Awesome' Icons",
+      "Description": "Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents and 'Shiny' apps. These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. There is also a utility function for exporting 'Font Awesome' icons as 'PNG' images for those situations where raster graphics are needed.",
+      "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"rich@posit.co\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"ctb\"), person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome font\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "License": "MIT + file LICENSE",
+      "URL": "https://github.com/rstudio/fontawesome, https://rstudio.github.io/fontawesome/",
+      "BugReports": "https://github.com/rstudio/fontawesome/issues",
+      "Encoding": "UTF-8",
+      "ByteCompile": "true",
+      "RoxygenNote": "7.2.3",
+      "Depends": [
+        "R (>= 3.3.0)"
+      ],
+      "Imports": [
+        "rlang (>= 1.0.6)",
+        "htmltools (>= 0.5.1.1)"
       ],
-      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
+      "Suggests": [
+        "covr",
+        "dplyr (>= 1.0.8)",
+        "knitr (>= 1.31)",
+        "testthat (>= 3.0.0)",
+        "rsvg"
+      ],
+      "Config/testthat/edition": "3",
+      "NeedsCompilation": "no",
+      "Author": "Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Winston Chang [ctb], Dave Gandy [ctb, cph] (Font-Awesome font), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Richard Iannone <rich@posit.co>",
+      "Repository": "CRAN"
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     "fs": {
       "Package": "fs",
       "Version": "1.6.4",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
+      "Title": "Cross-Platform File System Operations Based on 'libuv'",
+      "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "A cross-platform interface to file system operations, built on top of the 'libuv' C library.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://fs.r-lib.org, https://github.com/r-lib/fs",
+      "BugReports": "https://github.com/r-lib/fs/issues",
+      "Depends": [
+        "R (>= 3.6)"
+      ],
+      "Imports": [
         "methods"
       ],
-      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
+      "Suggests": [
+        "covr",
+        "crayon",
+        "knitr",
+        "pillar (>= 1.0.0)",
+        "rmarkdown",
+        "spelling",
+        "testthat (>= 3.0.0)",
+        "tibble (>= 1.1.0)",
+        "vctrs (>= 0.3.0)",
+        "withr"
+      ],
+      "VignetteBuilder": "knitr",
+      "ByteCompile": "true",
+      "Config/Needs/website": "tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Copyright": "file COPYRIGHTS",
+      "Encoding": "UTF-8",
+      "Language": "en-US",
+      "RoxygenNote": "7.2.3",
+      "SystemRequirements": "GNU make",
+      "NeedsCompilation": "yes",
+      "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut, cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>",
+      "Repository": "CRAN"
     },
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       "Package": "glue",
       "Version": "1.7.0",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
+      "Title": "Interpreted String Literals",
+      "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://glue.tidyverse.org/, https://github.com/tidyverse/glue",
+      "BugReports": "https://github.com/tidyverse/glue/issues",
+      "Depends": [
+        "R (>= 3.6)"
+      ],
+      "Imports": [
         "methods"
       ],
-      "Hash": "e0b3a53876554bd45879e596cdb10a52"
+      "Suggests": [
+        "crayon",
+        "DBI (>= 1.2.0)",
+        "dplyr",
+        "knitr",
+        "magrittr",
+        "rlang",
+        "rmarkdown",
+        "RSQLite",
+        "testthat (>= 3.2.0)",
+        "vctrs (>= 0.3.0)",
+        "waldo (>= 0.3.0)",
+        "withr"
+      ],
+      "VignetteBuilder": "knitr",
+      "ByteCompile": "true",
+      "Config/Needs/website": "bench, forcats, ggbeeswarm, ggplot2, R.utils, rprintf, tidyr, tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.2.3.9000",
+      "NeedsCompilation": "yes",
+      "Author": "Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Jennifer Bryan <jenny@posit.co>",
+      "Repository": "CRAN"
     },
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       "Package": "highr",
       "Version": "0.11",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "xfun"
+      "Type": "Package",
+      "Title": "Syntax Highlighting for R Source Code",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )",
+      "Description": "Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package (<https://gitlab.com/saalen/highlight>).",
+      "Depends": [
+        "R (>= 3.3.0)"
+      ],
+      "Imports": [
+        "xfun (>= 0.18)"
       ],
-      "Hash": "d65ba49117ca223614f71b60d85b8ab7"
+      "Suggests": [
+        "knitr",
+        "markdown",
+        "testit"
+      ],
+      "License": "GPL",
+      "URL": "https://github.com/yihui/highr",
+      "BugReports": "https://github.com/yihui/highr/issues",
+      "VignetteBuilder": "knitr",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.1",
+      "NeedsCompilation": "no",
+      "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
     },
     "htmltools": {
       "Package": "htmltools",
       "Version": "0.5.8.1",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
+      "Type": "Package",
+      "Title": "Tools for HTML",
+      "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Yihui\", \"Xie\", , \"yihui@posit.co\", role = \"aut\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Tools for HTML generation and output.",
+      "License": "GPL (>= 2)",
+      "URL": "https://github.com/rstudio/htmltools, https://rstudio.github.io/htmltools/",
+      "BugReports": "https://github.com/rstudio/htmltools/issues",
+      "Depends": [
+        "R (>= 2.14.1)"
+      ],
+      "Imports": [
         "base64enc",
         "digest",
-        "fastmap",
+        "fastmap (>= 1.1.0)",
         "grDevices",
-        "rlang",
+        "rlang (>= 1.0.0)",
         "utils"
       ],
-      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
+      "Suggests": [
+        "Cairo",
+        "markdown",
+        "ragg",
+        "shiny",
+        "testthat",
+        "withr"
+      ],
+      "Enhances": [
+        "knitr"
+      ],
+      "Config/Needs/check": "knitr",
+      "Config/Needs/website": "rstudio/quillt, bench",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.1",
+      "Collate": "'colors.R' 'fill.R' 'html_dependency.R' 'html_escape.R' 'html_print.R' 'htmltools-package.R' 'images.R' 'known_tags.R' 'selector.R' 'staticimports.R' 'tag_query.R' 'utils.R' 'tags.R' 'template.R'",
+      "NeedsCompilation": "yes",
+      "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>), Winston Chang [aut] (<https://orcid.org/0000-0002-1576-2126>), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Carson Sievert <carson@posit.co>",
+      "Repository": "CRAN"
     },
     "jquerylib": {
       "Package": "jquerylib",
       "Version": "0.1.4",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
+      "Title": "Obtain 'jQuery' as an HTML Dependency Object",
+      "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )",
+      "Description": "Obtain any major version of 'jQuery' (<https://code.jquery.com/>) and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.",
+      "License": "MIT + file LICENSE",
+      "Encoding": "UTF-8",
+      "Config/testthat/edition": "3",
+      "RoxygenNote": "7.0.2",
+      "Imports": [
         "htmltools"
       ],
-      "Hash": "5aab57a3bd297eee1c1d862735972182"
+      "Suggests": [
+        "testthat"
+      ],
+      "NeedsCompilation": "no",
+      "Author": "Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)",
+      "Maintainer": "Carson Sievert <carson@rstudio.com>",
+      "Repository": "CRAN"
     },
     "jsonlite": {
       "Package": "jsonlite",
       "Version": "1.8.9",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
+      "Title": "A Simple and Robust JSON Parser and Generator for R",
+      "License": "MIT + file LICENSE",
+      "Depends": [
         "methods"
       ],
-      "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b"
+      "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))",
+      "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805",
+      "BugReports": "https://github.com/jeroen/jsonlite/issues",
+      "Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>",
+      "VignetteBuilder": "knitr, R.rsp",
+      "Description": "A reasonably fast JSON parser and generator, optimized for statistical  data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API.  The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains  functions to stream, validate, and prettify JSON data. The unit tests included  with the package verify that all edge cases are encoded and decoded consistently  for use with dynamic data in systems and applications.",
+      "Suggests": [
+        "httr",
+        "vctrs",
+        "testthat",
+        "knitr",
+        "rmarkdown",
+        "R.rsp",
+        "sf"
+      ],
+      "RoxygenNote": "7.2.3",
+      "Encoding": "UTF-8",
+      "NeedsCompilation": "yes",
+      "Author": "Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)",
+      "Repository": "CRAN"
     },
     "knitr": {
       "Package": "knitr",
       "Version": "1.48",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "evaluate",
-        "highr",
+      "Type": "Package",
+      "Title": "A General-Purpose Package for Dynamic Report Generation in R",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de\"), person(\"Aron\", \"Atkins\", role = \"ctb\"), person(\"Aaron\", \"Wolen\", role = \"ctb\"), person(\"Ashley\", \"Manton\", role = \"ctb\"), person(\"Atsushi\", \"Yasumoto\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8335-495X\")), person(\"Ben\", \"Baumer\", role = \"ctb\"), person(\"Brian\", \"Diggs\", role = \"ctb\"), person(\"Brian\", \"Zhang\", role = \"ctb\"), person(\"Bulat\", \"Yapparov\", role = \"ctb\"), person(\"Cassio\", \"Pereira\", role = \"ctb\"), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person(\"David\", \"Hall\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", role = \"ctb\"), person(\"David\", \"Robinson\", role = \"ctb\"), person(\"Doug\", \"Hemken\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", role = \"ctb\"), person(\"Elio\", \"Campitelli\", role = \"ctb\"), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Emily\", \"Riederer\", role = \"ctb\"), person(\"Fabian\", \"Hirschmann\", role = \"ctb\"), person(\"Fitch\", \"Simeon\", role = \"ctb\"), person(\"Forest\", \"Fang\", role = \"ctb\"), person(c(\"Frank\", \"E\", \"Harrell\", \"Jr\"), role = \"ctb\", comment = \"the Sweavel package at inst/misc/Sweavel.sty\"), person(\"Garrick\", \"Aden-Buie\", role = \"ctb\"), person(\"Gregoire\", \"Detrez\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Hao\", \"Zhu\", role = \"ctb\"), person(\"Heewon\", \"Jeon\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Hodges\", \"Daniel\", role = \"ctb\"), person(\"Jacob\", \"Bien\", role = \"ctb\"), person(\"Jake\", \"Burkhead\", role = \"ctb\"), person(\"James\", \"Manton\", role = \"ctb\"), person(\"Jared\", \"Lander\", role = \"ctb\"), person(\"Jason\", \"Punyon\", role = \"ctb\"), person(\"Javier\", \"Luraschi\", role = \"ctb\"), person(\"Jeff\", \"Arnold\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", role = \"ctb\"), person(\"Jeremy\", \"Ashkenas\", role = c(\"ctb\", \"cph\"), comment = \"the CSS file at inst/misc/docco-classic.css\"), person(\"Jeremy\", \"Stephens\", role = \"ctb\"), person(\"Jim\", \"Hester\", role = \"ctb\"), person(\"Joe\", \"Cheng\", role = \"ctb\"), person(\"Johannes\", \"Ranke\", role = \"ctb\"), person(\"John\", \"Honaker\", role = \"ctb\"), person(\"John\", \"Muschelli\", role = \"ctb\"), person(\"Jonathan\", \"Keane\", role = \"ctb\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Johan\", \"Toloe\", role = \"ctb\"), person(\"Jonathan\", \"Sidi\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Julien\", \"Barnier\", role = \"ctb\"), person(\"Kaiyin\", \"Zhong\", role = \"ctb\"), person(\"Kamil\", \"Slowikowski\", role = \"ctb\"), person(\"Karl\", \"Forner\", role = \"ctb\"), person(c(\"Kevin\", \"K.\"), \"Smith\", role = \"ctb\"), person(\"Kirill\", \"Mueller\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Lorenz\", \"Walthert\", role = \"ctb\"), person(\"Lucas\", \"Gallindo\", role = \"ctb\"), person(\"Marius\", \"Hofert\", role = \"ctb\"), person(\"Martin\", \"Modrák\", role = \"ctb\"), person(\"Michael\", \"Chirico\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"Michel\", \"Kuhlmann\", role = \"ctb\"), person(\"Miller\", \"Patrick\", role = \"ctb\"), person(\"Nacho\", \"Caballero\", role = \"ctb\"), person(\"Nick\", \"Salkowski\", role = \"ctb\"), person(\"Niels Richard\", \"Hansen\", role = \"ctb\"), person(\"Noam\", \"Ross\", role = \"ctb\"), person(\"Obada\", \"Mahdi\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = \"ctb\", comment=c(ORCID = \"0000-0002-9101-3362\")), person(\"Pedro\", \"Faria\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\"), person(\"Ramnath\", \"Vaidyanathan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Robert\", \"Krzyzanowski\", role = \"ctb\"), person(\"Rodrigo\", \"Copetti\", role = \"ctb\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Ruaridh\", \"Williamson\", role = \"ctb\"), person(\"Sagiru\", \"Mati\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1413-3974\")), person(\"Scott\", \"Kostyshak\", role = \"ctb\"), person(\"Sebastian\", \"Meyer\", role = \"ctb\"), person(\"Sietse\", \"Brouwer\", role = \"ctb\"), person(c(\"Simon\", \"de\"), \"Bernard\", role = \"ctb\"), person(\"Sylvain\", \"Rousseau\", role = \"ctb\"), person(\"Taiyun\", \"Wei\", role = \"ctb\"), person(\"Thibaut\", \"Assus\", role = \"ctb\"), person(\"Thibaut\", \"Lamadon\", role = \"ctb\"), person(\"Thomas\", \"Leeper\", role = \"ctb\"), person(\"Tim\", \"Mastny\", role = \"ctb\"), person(\"Tom\", \"Torsney-Weir\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = \"ctb\"), person(\"Viktoras\", \"Veitas\", role = \"ctb\"), person(\"Weicheng\", \"Zhu\", role = \"ctb\"), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Zachary\", \"Foster\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.",
+      "Depends": [
+        "R (>= 3.3.0)"
+      ],
+      "Imports": [
+        "evaluate (>= 0.15)",
+        "highr (>= 0.11)",
         "methods",
         "tools",
-        "xfun",
-        "yaml"
+        "xfun (>= 0.44)",
+        "yaml (>= 2.1.19)"
+      ],
+      "Suggests": [
+        "bslib",
+        "codetools",
+        "DBI (>= 0.4-1)",
+        "digest",
+        "formatR",
+        "gifski",
+        "gridSVG",
+        "htmlwidgets (>= 0.7)",
+        "jpeg",
+        "JuliaCall (>= 0.11.1)",
+        "magick",
+        "markdown (>= 1.3)",
+        "png",
+        "ragg",
+        "reticulate (>= 1.4)",
+        "rgl (>= 0.95.1201)",
+        "rlang",
+        "rmarkdown",
+        "sass",
+        "showtext",
+        "styler (>= 1.2.0)",
+        "targets (>= 0.6.0)",
+        "testit",
+        "tibble",
+        "tikzDevice (>= 0.10)",
+        "tinytex (>= 0.46)",
+        "webshot",
+        "rstudioapi",
+        "svglite"
       ],
-      "Hash": "acf380f300c721da9fde7df115a5f86f"
+      "License": "GPL",
+      "URL": "https://yihui.org/knitr/",
+      "BugReports": "https://github.com/yihui/knitr/issues",
+      "Encoding": "UTF-8",
+      "VignetteBuilder": "knitr",
+      "SystemRequirements": "Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org). The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).",
+      "Collate": "'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R' 'plot.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'",
+      "RoxygenNote": "7.3.2",
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+      "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (<https://orcid.org/0000-0002-9101-3362>), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (<https://orcid.org/0000-0003-1413-3974>), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
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       "Version": "1.0.4",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
+      "Title": "Manage the Life Cycle of your Package Functions",
+      "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "Manage the life cycle of your exported functions with shared conventions, documentation badges, and user-friendly deprecation warnings.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://lifecycle.r-lib.org/, https://github.com/r-lib/lifecycle",
+      "BugReports": "https://github.com/r-lib/lifecycle/issues",
+      "Depends": [
+        "R (>= 3.6)"
+      ],
+      "Imports": [
+        "cli (>= 3.4.0)",
         "glue",
-        "rlang"
+        "rlang (>= 1.1.0)"
+      ],
+      "Suggests": [
+        "covr",
+        "crayon",
+        "knitr",
+        "lintr",
+        "rmarkdown",
+        "testthat (>= 3.0.1)",
+        "tibble",
+        "tidyverse",
+        "tools",
+        "vctrs",
+        "withr"
       ],
-      "Hash": "b8552d117e1b808b09a832f589b79035"
+      "VignetteBuilder": "knitr",
+      "Config/Needs/website": "tidyverse/tidytemplate, usethis",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.2.1",
+      "NeedsCompilation": "no",
+      "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Lionel Henry <lionel@posit.co>",
+      "Repository": "CRAN"
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       "Version": "2.0.1",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "cachem",
-        "rlang"
+      "Title": "'Memoisation' of Functions",
+      "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = \"aut\", email = \"hadley@rstudio.com\"), person(given = \"Jim\", family = \"Hester\", role = \"aut\"), person(given = \"Winston\", family = \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@rstudio.com\"), person(given = \"Kirill\", family = \"Müller\", role = \"aut\", email = \"krlmlr+r@mailbox.org\"), person(given = \"Daniel\", family = \"Cook\", role = \"aut\", email = \"danielecook@gmail.com\"), person(given = \"Mark\", family = \"Edmondson\", role = \"ctb\", email = \"r@sunholo.com\"))",
+      "Description": "Cache the results of a function so that when you call it again with the same arguments it returns the previously computed value.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://memoise.r-lib.org, https://github.com/r-lib/memoise",
+      "BugReports": "https://github.com/r-lib/memoise/issues",
+      "Imports": [
+        "rlang (>= 0.4.10)",
+        "cachem"
       ],
-      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
+      "Suggests": [
+        "digest",
+        "aws.s3",
+        "covr",
+        "googleAuthR",
+        "googleCloudStorageR",
+        "httr",
+        "testthat"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.1.2",
+      "NeedsCompilation": "no",
+      "Author": "Hadley Wickham [aut], Jim Hester [aut], Winston Chang [aut, cre], Kirill Müller [aut], Daniel Cook [aut], Mark Edmondson [ctb]",
+      "Maintainer": "Winston Chang <winston@rstudio.com>",
+      "Repository": "CRAN"
     },
     "mime": {
       "Package": "mime",
       "Version": "0.12",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
+      "Type": "Package",
+      "Title": "Map Filenames to MIME Types",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"Beilei\", \"Bian\", role = \"ctb\") )",
+      "Description": "Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.",
+      "Imports": [
         "tools"
       ],
-      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
+      "License": "GPL",
+      "URL": "https://github.com/yihui/mime",
+      "BugReports": "https://github.com/yihui/mime/issues",
+      "RoxygenNote": "7.1.1",
+      "Encoding": "UTF-8",
+      "NeedsCompilation": "yes",
+      "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jeffrey Horner [ctb], Beilei Bian [ctb]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
     },
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       "Package": "rappdirs",
       "Version": "0.3.3",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
+      "Type": "Package",
+      "Title": "Application Directories: Determine Where to Save Data, Caches, and Logs",
+      "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = c(\"trl\", \"cre\", \"cph\"), email = \"hadley@rstudio.com\"), person(given = \"RStudio\", role = \"cph\"), person(given = \"Sridhar\", family = \"Ratnakumar\", role = \"aut\"), person(given = \"Trent\", family = \"Mick\", role = \"aut\"), person(given = \"ActiveState\", role = \"cph\", comment = \"R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs\"), person(given = \"Eddy\", family = \"Petrisor\", role = \"ctb\"), person(given = \"Trevor\", family = \"Davis\", role = c(\"trl\", \"aut\")), person(given = \"Gabor\", family = \"Csardi\", role = \"ctb\"), person(given = \"Gregory\", family = \"Jefferis\", role = \"ctb\"))",
+      "Description": "An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's 'Appdirs' (<https://github.com/ActiveState/appdirs>) to R.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rappdirs.r-lib.org, https://github.com/r-lib/rappdirs",
+      "BugReports": "https://github.com/r-lib/rappdirs/issues",
+      "Depends": [
+        "R (>= 3.2)"
+      ],
+      "Suggests": [
+        "roxygen2",
+        "testthat (>= 3.0.0)",
+        "covr",
+        "withr"
       ],
-      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
+      "Copyright": "Original python appdirs module copyright (c) 2010 ActiveState Software Inc. R port copyright Hadley Wickham, RStudio. See file LICENSE for details.",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.1.1",
+      "Config/testthat/edition": "3",
+      "NeedsCompilation": "yes",
+      "Author": "Hadley Wickham [trl, cre, cph], RStudio [cph], Sridhar Ratnakumar [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs), Eddy Petrisor [ctb], Trevor Davis [trl, aut], Gabor Csardi [ctb], Gregory Jefferis [ctb]",
+      "Maintainer": "Hadley Wickham <hadley@rstudio.com>",
+      "Repository": "CRAN"
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     "renv": {
       "Package": "renv",
       "Version": "1.0.8",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
+      "Type": "Package",
+      "Title": "Project Environments",
+      "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@rstudio.com\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv",
+      "BugReports": "https://github.com/rstudio/renv/issues",
+      "Imports": [
         "utils"
       ],
-      "Hash": "e082251834fa427514e68bec8afc8fda"
+      "Suggests": [
+        "BiocManager",
+        "cli",
+        "covr",
+        "cpp11",
+        "devtools",
+        "gitcreds",
+        "jsonlite",
+        "jsonvalidate",
+        "knitr",
+        "miniUI",
+        "packrat",
+        "pak",
+        "R6",
+        "remotes",
+        "reticulate",
+        "rmarkdown",
+        "rstudioapi",
+        "shiny",
+        "testthat",
+        "uuid",
+        "waldo",
+        "yaml",
+        "webfakes"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "VignetteBuilder": "knitr",
+      "Config/Needs/website": "tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Config/testthat/parallel": "true",
+      "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes",
+      "NeedsCompilation": "no",
+      "Author": "Kevin Ushey [aut, cre] (<https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
+      "Repository": "CRAN"
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       "Package": "rlang",
       "Version": "1.1.4",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
+      "Title": "Functions for Base Types and Core R and 'Tidyverse' Features",
+      "Description": "A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.",
+      "Authors@R": "c( person(\"Lionel\", \"Henry\", ,\"lionel@posit.co\", c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", ,\"hadley@posit.co\", \"aut\"), person(given = \"mikefc\", email = \"mikefc@coolbutuseless.com\",  role = \"cph\",  comment = \"Hash implementation based on Mike's xxhashlite\"), person(given = \"Yann\", family = \"Collet\", role = \"cph\",  comment = \"Author of the embedded xxHash library\"), person(given = \"Posit, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "License": "MIT + file LICENSE",
+      "ByteCompile": "true",
+      "Biarch": "true",
+      "Depends": [
+        "R (>= 3.5.0)"
+      ],
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         "utils"
       ],
-      "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
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+        "cli (>= 3.1.0)",
+        "covr",
+        "crayon",
+        "fs",
+        "glue",
+        "knitr",
+        "magrittr",
+        "methods",
+        "pillar",
+        "rmarkdown",
+        "stats",
+        "testthat (>= 3.0.0)",
+        "tibble",
+        "usethis",
+        "vctrs (>= 0.2.3)",
+        "withr"
+      ],
+      "Enhances": [
+        "winch"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.1",
+      "URL": "https://rlang.r-lib.org, https://github.com/r-lib/rlang",
+      "BugReports": "https://github.com/r-lib/rlang/issues",
+      "Config/testthat/edition": "3",
+      "Config/Needs/website": "dplyr, tidyverse/tidytemplate",
+      "NeedsCompilation": "yes",
+      "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], mikefc [cph] (Hash implementation based on Mike's xxhashlite), Yann Collet [cph] (Author of the embedded xxHash library), Posit, PBC [cph, fnd]",
+      "Maintainer": "Lionel Henry <lionel@posit.co>",
+      "Repository": "CRAN"
     },
     "rmarkdown": {
       "Package": "rmarkdown",
       "Version": "2.28",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bslib",
-        "evaluate",
-        "fontawesome",
-        "htmltools",
+      "Type": "Package",
+      "Title": "Dynamic Documents for R",
+      "Authors@R": "c( person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\"), person(\"Yihui\", \"Xie\", , \"xie@yihui.name\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Jonathan\", \"McPherson\", , \"jonathan@posit.co\", role = \"aut\"), person(\"Javier\", \"Luraschi\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevin@posit.co\", role = \"aut\"), person(\"Aron\", \"Atkins\", , \"aron@posit.co\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\"), person(\"Richard\", \"Iannone\", , \"rich@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Andrew\", \"Dunning\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0464-5036\")), person(\"Atsushi\", \"Yasumoto\", role = c(\"ctb\", \"cph\"), comment = c(ORCID = \"0000-0002-8335-495X\", cph = \"Number sections Lua filter\")), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Carson\", \"Sievert\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4958-2844\")),  person(\"Devon\", \"Ryan\", , \"dpryan79@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8549-0971\")), person(\"Frederik\", \"Aust\", , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Jeff\", \"Allen\", , \"jeff@posit.co\", role = \"ctb\"),  person(\"JooYoung\", \"Seo\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4064-6012\")), person(\"Malcolm\", \"Barrett\", role = \"ctb\"), person(\"Rob\", \"Hyndman\", , \"Rob.Hyndman@monash.edu\", role = \"ctb\"), person(\"Romain\", \"Lesur\", role = \"ctb\"), person(\"Roy\", \"Storey\", role = \"ctb\"), person(\"Ruben\", \"Arslan\", , \"ruben.arslan@uni-goettingen.de\", role = \"ctb\"), person(\"Sergio\", \"Oller\", role = \"ctb\"), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"jQuery UI contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Alexander\", \"Farkas\", role = c(\"ctb\", \"cph\"), comment = \"html5shiv library\"), person(\"Scott\", \"Jehl\", role = c(\"ctb\", \"cph\"), comment = \"Respond.js library\"), person(\"Ivan\", \"Sagalaev\", role = c(\"ctb\", \"cph\"), comment = \"highlight.js library\"), person(\"Greg\", \"Franko\", role = c(\"ctb\", \"cph\"), comment = \"tocify library\"), person(\"John\", \"MacFarlane\", role = c(\"ctb\", \"cph\"), comment = \"Pandoc templates\"), person(, \"Google, Inc.\", role = c(\"ctb\", \"cph\"), comment = \"ioslides library\"), person(\"Dave\", \"Raggett\", role = \"ctb\", comment = \"slidy library\"), person(, \"W3C\", role = \"cph\", comment = \"slidy library\"), person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome\"), person(\"Ben\", \"Sperry\", role = \"ctb\", comment = \"Ionicons\"), person(, \"Drifty\", role = \"cph\", comment = \"Ionicons\"), person(\"Aidan\", \"Lister\", role = c(\"ctb\", \"cph\"), comment = \"jQuery StickyTabs\"), person(\"Benct Philip\", \"Jonsson\", role = c(\"ctb\", \"cph\"), comment = \"pagebreak Lua filter\"), person(\"Albert\", \"Krewinkel\", role = c(\"ctb\", \"cph\"), comment = \"pagebreak Lua filter\") )",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Description": "Convert R Markdown documents into a variety of formats.",
+      "License": "GPL-3",
+      "URL": "https://github.com/rstudio/rmarkdown, https://pkgs.rstudio.com/rmarkdown/",
+      "BugReports": "https://github.com/rstudio/rmarkdown/issues",
+      "Depends": [
+        "R (>= 3.0)"
+      ],
+      "Imports": [
+        "bslib (>= 0.2.5.1)",
+        "evaluate (>= 0.13)",
+        "fontawesome (>= 0.5.0)",
+        "htmltools (>= 0.5.1)",
         "jquerylib",
         "jsonlite",
-        "knitr",
+        "knitr (>= 1.43)",
         "methods",
-        "tinytex",
+        "tinytex (>= 0.31)",
         "tools",
         "utils",
-        "xfun",
-        "yaml"
+        "xfun (>= 0.36)",
+        "yaml (>= 2.1.19)"
+      ],
+      "Suggests": [
+        "digest",
+        "dygraphs",
+        "fs",
+        "rsconnect",
+        "downlit (>= 0.4.0)",
+        "katex (>= 1.4.0)",
+        "sass (>= 0.4.0)",
+        "shiny (>= 1.6.0)",
+        "testthat (>= 3.0.3)",
+        "tibble",
+        "vctrs",
+        "cleanrmd",
+        "withr (>= 2.4.2)",
+        "xml2"
       ],
-      "Hash": "062470668513dcda416927085ee9bdc7"
+      "VignetteBuilder": "knitr",
+      "Config/Needs/website": "rstudio/quillt, pkgdown",
+      "Config/testthat/edition": "3",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.1",
+      "SystemRequirements": "pandoc (>= 1.14) - http://pandoc.org",
+      "NeedsCompilation": "no",
+      "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Christophe Dervieux [aut] (<https://orcid.org/0000-0003-4474-2498>), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>), Atsushi Yasumoto [ctb, cph] (<https://orcid.org/0000-0002-8335-495X>, Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (<https://orcid.org/0000-0002-4958-2844>), Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>), Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Jeff Allen [ctb], JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], Posit Software, PBC [cph, fnd], jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)",
+      "Repository": "CRAN"
     },
     "sass": {
       "Package": "sass",
       "Version": "0.4.9",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
+      "Type": "Package",
+      "Title": "Syntactically Awesome Style Sheets ('Sass')",
+      "Description": "An 'SCSS' compiler, powered by the 'LibSass' library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the 'Sass CSS' extension language, which is stable, powerful, and CSS compatible.",
+      "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@rstudio.com\", \"aut\"), person(\"Timothy\", \"Mastny\", , \"tim.mastny@gmail.com\", \"aut\"), person(\"Richard\", \"Iannone\", , \"rich@rstudio.com\", \"aut\", comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Barret\", \"Schloerke\", , \"barret@rstudio.com\", \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Carson\", \"Sievert\", , \"carson@rstudio.com\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Christophe\", \"Dervieux\", , \"cderv@rstudio.com\", c(\"ctb\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(family = \"RStudio\", role = c(\"cph\", \"fnd\")), person(family = \"Sass Open Source Foundation\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Greter\", \"Marcel\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Mifsud\", \"Michael\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Hampton\", \"Catlin\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Natalie\", \"Weizenbaum\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Chris\", \"Eppstein\", role = c(\"ctb\", \"cph\"), comment = \"LibSass library\"), person(\"Adams\", \"Joseph\", role = c(\"ctb\", \"cph\"), comment = \"json.cpp\"), person(\"Trifunovic\", \"Nemanja\", role = c(\"ctb\", \"cph\"), comment = \"utf8.h\") )",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rstudio.github.io/sass/, https://github.com/rstudio/sass",
+      "BugReports": "https://github.com/rstudio/sass/issues",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.1",
+      "SystemRequirements": "GNU make",
+      "Imports": [
+        "fs (>= 1.2.4)",
+        "rlang (>= 0.4.10)",
+        "htmltools (>= 0.5.1)",
         "R6",
-        "fs",
-        "htmltools",
-        "rappdirs",
-        "rlang"
+        "rappdirs"
+      ],
+      "Suggests": [
+        "testthat",
+        "knitr",
+        "rmarkdown",
+        "withr",
+        "shiny",
+        "curl"
       ],
-      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
+      "VignetteBuilder": "knitr",
+      "Config/testthat/edition": "3",
+      "NeedsCompilation": "yes",
+      "Author": "Joe Cheng [aut], Timothy Mastny [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>), Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), RStudio [cph, fnd], Sass Open Source Foundation [ctb, cph] (LibSass library), Greter Marcel [ctb, cph] (LibSass library), Mifsud Michael [ctb, cph] (LibSass library), Hampton Catlin [ctb, cph] (LibSass library), Natalie Weizenbaum [ctb, cph] (LibSass library), Chris Eppstein [ctb, cph] (LibSass library), Adams Joseph [ctb, cph] (json.cpp), Trifunovic Nemanja [ctb, cph] (utf8.h)",
+      "Maintainer": "Carson Sievert <carson@rstudio.com>",
+      "Repository": "CRAN"
     },
     "tinytex": {
       "Package": "tinytex",
       "Version": "0.53",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "xfun"
+      "Type": "Package",
+      "Title": "Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Devon\", \"Ryan\", role = \"ctb\", email = \"dpryan79@gmail.com\", comment = c(ORCID = \"0000-0002-8549-0971\")), person(\"Ethan\", \"Heinzen\", role = \"ctb\"), person(\"Fernando\", \"Cagua\", role = \"ctb\"), person() )",
+      "Description": "Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.",
+      "Imports": [
+        "xfun (>= 0.29)"
       ],
-      "Hash": "9db859e8aabbb474293dde3097839420"
+      "Suggests": [
+        "testit",
+        "rstudioapi"
+      ],
+      "License": "MIT + file LICENSE",
+      "URL": "https://github.com/rstudio/tinytex",
+      "BugReports": "https://github.com/rstudio/tinytex/issues",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "NeedsCompilation": "no",
+      "Author": "Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>), Ethan Heinzen [ctb], Fernando Cagua [ctb]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
     },
     "xfun": {
       "Package": "xfun",
       "Version": "0.47",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
+      "Type": "Package",
+      "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'",
+      "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person() )",
+      "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.",
+      "Depends": [
+        "R (>= 3.2.0)"
+      ],
+      "Imports": [
         "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "36ab21660e2d095fef0d83f689e0477c"
+      "Suggests": [
+        "testit",
+        "parallel",
+        "codetools",
+        "methods",
+        "rstudioapi",
+        "tinytex (>= 0.30)",
+        "mime",
+        "markdown (>= 1.5)",
+        "knitr (>= 1.47)",
+        "htmltools",
+        "remotes",
+        "pak",
+        "rhub",
+        "renv",
+        "curl",
+        "xml2",
+        "jsonlite",
+        "magick",
+        "yaml",
+        "qs",
+        "rmarkdown"
+      ],
+      "License": "MIT + file LICENSE",
+      "URL": "https://github.com/yihui/xfun",
+      "BugReports": "https://github.com/yihui/xfun/issues",
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.2",
+      "VignetteBuilder": "knitr",
+      "NeedsCompilation": "yes",
+      "Author": "Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>), Christophe Dervieux [ctb], Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Yihui Xie <xie@yihui.name>",
+      "Repository": "CRAN"
     },
     "yaml": {
       "Package": "yaml",
       "Version": "2.3.10",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
+      "Type": "Package",
+      "Title": "Methods to Convert R Data to YAML and Back",
+      "Date": "2024-07-22",
+      "Suggests": [
+        "RUnit"
+      ],
+      "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]",
+      "Maintainer": "Shawn Garbett <shawn.garbett@vumc.org>",
+      "License": "BSD_3_clause + file LICENSE",
+      "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter (<https://pyyaml.org/wiki/LibYAML>) for R.",
+      "URL": "https://github.com/vubiostat/r-yaml/",
+      "BugReports": "https://github.com/vubiostat/r-yaml/issues",
+      "NeedsCompilation": "yes",
+      "Repository": "CRAN"
     }
   }
 }
diff --git a/renv/settings.json b/renv/settings.json
new file mode 100644
index 00000000..ffdbb320
--- /dev/null
+++ b/renv/settings.json
@@ -0,0 +1,19 @@
+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.type": "implicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}

From 93b261db62fb40a6fd45960259de2245089a680c Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 14:06:43 -0400
Subject: [PATCH 19/33] Workbenched Ep. 12

---
 config.yaml                                   |   3 +-
 episodes/11-connecting.Rmd                    |  34 +-
 .../{12-epcc-cluster.Rmd => 12-cluster.Rmd}   |  52 +--
 episodes/12-cluster.md                        | 379 ------------------
 .../{queue-info.snip => queue-info.Rmd}       |   2 +-
 .../cluster/specific-node-info.Rmd            |   5 +-
 .../{queue-info.snip => queue-info.Rmd}       |   3 +-
 .../cluster/specific-node-info.Rmd            |   7 +-
 .../cluster/specific-node-info.snip           |  11 -
 9 files changed, 53 insertions(+), 443 deletions(-)
 rename episodes/{12-epcc-cluster.Rmd => 12-cluster.Rmd} (95%)
 delete mode 100644 episodes/12-cluster.md
 rename episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/{queue-info.snip => queue-info.Rmd} (99%)
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/{queue-info.snip => queue-info.Rmd} (94%)
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.snip

diff --git a/config.yaml b/config.yaml
index 4b045ef6..e0f40424 100644
--- a/config.yaml
+++ b/config.yaml
@@ -67,8 +67,7 @@ contact: 'team@carpentries.org'
 episodes: 
 - 10-hpc-intro.md
 - 11-connecting.Rmd
-- 12-cluster.md
-- 12-epcc-cluster.Rmd
+- 12-cluster.Rmd
 - 13-scheduler.md
 - 13-hpcc-scheduler.Rmd
 - 13-epcc-scheduler.Rmd
diff --git a/episodes/11-connecting.Rmd b/episodes/11-connecting.Rmd
index 83f22c08..a6635d74 100644
--- a/episodes/11-connecting.Rmd
+++ b/episodes/11-connecting.Rmd
@@ -85,16 +85,18 @@ In this section you will create a pair of SSH keys:
 - a private key which you keep on your own computer, and
 - a public key which can be placed on any remote system you will access.
 
-> ## Private keys are your secure digital passport
-> 
-> A private key that is visible to anyone but you should be considered
-> compromised, and must be destroyed. This includes having improper permissions
-> on the directory it (or a copy) is stored in, traversing any network that is
-> not secure (encrypted), attachment on unencrypted email, and even displaying
-> the key on your terminal window.
-> 
-> Protect this key as if it unlocks your front door. In many ways, it does.
-> {: .caution}
+:::::::::::::::::::::::::::::::::::::::::  caution
+
+## Private keys are your secure digital passport
+
+A private key that is visible to anyone but you should be considered
+compromised, and must be destroyed. This includes having improper permissions
+on the directory it (or a copy) is stored in, traversing any network that is
+not secure (encrypted), attachment on unencrypted email, and even displaying
+the key on your terminal window.
+
+Protect this key as if it unlocks your front door. In many ways, it does.
+::::::::::::::::::::::::::::::::::::::::::::::::::
 
 Regardless of the software or operating system you use, *please* choose a
 strong password or passphrase to act as another layer of protection for your
@@ -116,8 +118,6 @@ common approaches to this:
 3. Nothing is *less* secure than a private key with no password. If you
   skipped password entry by accident, go back and generate a new key pair
   *with* a strong password.
-  
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 #### SSH Keys on Linux, Mac, MobaXterm, and Windows Subsystem for Linux
@@ -432,8 +432,6 @@ Policies and practices for handling SSH keys vary between HPC clusters:
 follow any guidance provided by the cluster administrators or
 documentation. In particular, if there is an online portal for managing SSH
 keys, use that instead of the directions outlined here.
-
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 If you transferred your SSH public key with `scp`, you should see
@@ -475,14 +473,12 @@ password for your SSH key.
 [ssh-agent]: https://www.ssh.com/academy/ssh/agent
 [putty-agent]: https://tartarus.org/~simon/putty-prerel-snapshots/htmldoc/Chapter9.html#pageant
 
-
 :::::::::::::::::::::::::::::::::::::::: keypoints
 
 - An HPC system is a set of networked machines.
 - HPC systems typically provide login nodes and a set of worker nodes.
-- The resources found on independent (worker) nodes can vary in volume and type (amount of RAM, processor architecture, availability of network mounted filesystems, etc.).
+- The resources found on independent (worker) nodes can vary in volume and type
+  (amount of RAM, processor architecture, availability of network mounted
+  filesystems, etc.).
 - Files saved on one node are available on all nodes.
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
-
-
diff --git a/episodes/12-epcc-cluster.Rmd b/episodes/12-cluster.Rmd
similarity index 95%
rename from episodes/12-epcc-cluster.Rmd
rename to episodes/12-cluster.Rmd
index 91a80fb2..8a6d7e66 100644
--- a/episodes/12-epcc-cluster.Rmd
+++ b/episodes/12-cluster.Rmd
@@ -1,24 +1,23 @@
 ---
-title: "EPCC version - Working on a remote HPC system"
+title: "Working on a remote HPC system"
 teaching: 25
 exercises: 10
 ---
 
-```{r load_config, include=FALSE}
-library(yaml)
-config <- yaml.load_file("epcc_config.yaml")
-snippets <- paste('files/snippets/', config$snippets, sep='')
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
 ```
 
 ::: questions
- - "What is an HPC system?"
- - "How does an HPC system work?"
- - "How do I log on to a remote HPC system?"
+- "What is an HPC system?"
+- "How does an HPC system work?"
+- "How do I log on to a remote HPC system?"
 :::
 
 ::: objectives
- - "Connect to a remote HPC system."
- - "Understand the general HPC system architecture."
+- "Connect to a remote HPC system."
+- "Understand the general HPC system architecture."
 :::
 
 ## What Is an HPC System?
@@ -114,7 +113,7 @@ may also notice that the current hostname is also part of our prompt!)
 `r config$remote$prompt` hostname
 ```
 
-```bash
+```output
 `r config$remote$host`
 ```
 
@@ -129,7 +128,7 @@ other filesystems. Take a look around and see what you can find.
 Home directory contents vary from user to user. Please discuss any
 differences you spot with your neighbors.
 
-::: solution
+:::: solution
 
 ## It's a Beautiful Day in the Neighborhood
 
@@ -140,7 +139,6 @@ If both of you have empty directories, they will look identical. If you
 or your neighbor has used the system before, there may be differences. What
 are you working on?
 
-
 Use `pwd` to **p**rint the **w**orking **d**irectory path:
 
 ```bash
@@ -158,7 +156,7 @@ use the `-a` flag to show hidden files, too.
 At a minimum, this will show the current directory as `.`, and the parent
 directory as `..`.
 
-:::
+::::
 :::
 
 ## Nodes
@@ -178,7 +176,9 @@ what is and isn't allowed. In these lessons, we will avoid running jobs on the
 head node.
 
 ::: callout
+
 ## Dedicated Transfer Nodes
+
 If you want to transfer larger amounts of data to or from the cluster, some
 systems offer dedicated nodes for data transfers only. The motivation for
 this lies in the fact that larger data transfers should not obstruct
@@ -206,7 +206,7 @@ For example, we can view all of the worker nodes by running the command
 `r config$remote$prompt` `r config$sched$info`
 ```
 
-```{r, child=paste(snippets, '/cluster/queue-info.snip', sep=''), eval=TRUE}
+```{r, child=paste(snippets, '/cluster/queue-info.Rmd', sep='')}
 ```
 
 There are also specialized machines used for managing disk storage, user
@@ -232,6 +232,7 @@ connect to a shared, remote fileserver or cluster of servers.
 ::: challenge
 
 ## Explore Your Computer
+
 Try to find out the number of CPUs and amount of memory available on your
 personal computer.
 Note that, if you're logged in to the remote computer cluster, you need to
@@ -242,40 +243,43 @@ log out first. To do so, type `Ctrl+d` or `exit`:
 `r config$local$prompt`
 ```
 
-::: solution
+:::: solution
 
 There are several ways to do this. Most operating systems have a graphical
-system monitor, like the Windows Task Manager. More detailed information
-can sometimes be found on the command line. For example, some of the commands used on 
-a Linux system are:
+system monitor, like the Windows Task Manager. More detailed information can
+sometimes be found on the command line. For example, some of the commands used
+on a Linux system are:
 
 Run system utilities
+
 ```bash
 `r config$local$prompt` nproc --all
 `r config$local$prompt` free -m
 ```
 
 Read from `/proc`
+
 ```bash
 `r config$local$prompt` cat /proc/cpuinfo
 `r config$local$prompt` cat /proc/meminfo
 ```
 
-Run system monitor
+Use a system monitor
+
 ```bash
 `r config$local$prompt` htop
 ```
 
-:::
+::::
 :::
 
-
 ::: challenge
+
 ## Explore the login node
 
 Now compare the resources of your computer with those of the head node.
 
-::: solution
+:::: solution
 
 ```bash
 `r config$local$prompt` ssh `r config$remote$user`@`r config$remote$login`
@@ -298,7 +302,7 @@ each resource is.
 ```bash
 `r config$remote$prompt` df -Th
 ```
-:::
+::::
 :::
 
 ::: discussion
diff --git a/episodes/12-cluster.md b/episodes/12-cluster.md
deleted file mode 100644
index c83dad32..00000000
--- a/episodes/12-cluster.md
+++ /dev/null
@@ -1,379 +0,0 @@
----
-title: Exploring Remote Resources
-teaching: 25
-exercises: 10
----
-
-::::::::::::::::::::::::::::::::::::::: objectives
-
-- Survey system resources using `nproc`, `free`, and the queuing system
-- Compare \& contrast resources on the local machine, login node, and worker nodes
-- Learn about the various filesystems on the cluster using `df`
-- Find out `who` else is logged in
-- Assess the number of idle and occupied nodes
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-:::::::::::::::::::::::::::::::::::::::: questions
-
-- How does my local computer compare to the remote systems?
-- How does the login node compare to the compute nodes?
-- Are all compute nodes alike?
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-## Look Around the Remote System
-
-If you have not already connected to {{ site.remote.name }}, please do so now:
-
-```bash
-{{ site.local.prompt }}  ssh {{ site.remote.user }}@{{ site.remote.login }}
-```
-
-Take a look at your home directory on the remote system:
-
-```bash
-{{ site.remote.prompt }} ls
-```
-
-::::::::::::::::::::::::::::::::::::::  challenge
-
-## What's different between your machine and the remote?
-
-Open a second terminal window on your local computer and run the `ls` command
-(without logging in to {{ site.remote.name }}). What differences do you see?
-
-:::::::::::::::  solution
-
-## Solution
-
-You would likely see something more like this:
-
-```bash
-{{ site.local.prompt }} ls
-```
-
-```output
-Applications Documents    Library      Music        Public
-Desktop      Downloads    Movies       Pictures
-```
-
-The remote computer's home directory shares almost nothing in common with
-the local computer: they are completely separate systems!
-
-
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-Most high-performance computing systems run the Linux operating system, which
-is built around the UNIX [Filesystem Hierarchy Standard][fshs]. Instead of
-having a separate root for each hard drive or storage medium, all files and
-devices are anchored to the "root" directory, which is `/`:
-
-```bash
-{{ site.remote.prompt }} ls /
-```
-
-```output
-bin   etc   lib64  proc  sbin     sys  var
-boot  {{ site.remote.homedir | replace: "/", "" }}  mnt    root  scratch  tmp  working
-dev   lib   opt    run   srv      usr
-```
-
-The "{{ site.remote.homedir | replace: "/", "" }}" directory is the one where
-we generally want to keep all of our files. Other folders on a UNIX OS contain
-system files and change as you install new software or upgrade your OS.
-
-:::::::::::::::::::::::::::::::::::::::::  callout
-
-## Using HPC filesystems
-
-On HPC systems, you have a number of places where you can store your files.
-These differ in both the amount of space allocated and whether or not they
-are backed up.
-
-- **Home** -- often a *network filesystem*, data stored here is available
-  throughout the HPC system, and often backed up periodically. Files stored
-  here are typically slower to access, the data is actually stored on another
-  computer and is being transmitted and made available over the network!
-- **Scratch** -- typically faster than the networked Home directory, but not
-  usually backed up, and should not be used for long term storage.
-- **Work** -- sometimes provided as an alternative to Scratch space, Work is
-  a fast file system accessed over the network. Typically, this will have
-  higher performance than your home directory, but lower performance than
-  Scratch; it may not be backed up. It differs from Scratch space in that
-  files in a work file system are not automatically deleted for you: you must
-  manage the space yourself.
-  
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-## Nodes
-
-Individual computers that compose a cluster are typically called *nodes*
-(although you will also hear people call them *servers*, *computers* and
-*machines*). On a cluster, there are different types of nodes for different
-types of tasks. The node where you are right now is called the *login node*,
-*head node*, *landing pad*, or *submit node*. A login node serves as an access
-point to the cluster.
-
-As a gateway, the login node should not be used for time-consuming or
-resource-intensive tasks. You should be alert to this, and check with your
-site's operators or documentation for details of what is and isn't allowed. It
-is well suited for uploading and downloading files, setting up software, and
-running tests. Generally speaking, in these lessons, we will avoid running jobs
-on the login node.
-
-Who else is logged in to the login node?
-
-```bash
-{{ site.remote.prompt }} who
-```
-
-This may show only your user ID, but there are likely several other people
-(including fellow learners) connected right now.
-
-:::::::::::::::::::::::::::::::::::::::::  callout
-
-## Dedicated Transfer Nodes
-
-If you want to transfer larger amounts of data to or from the cluster, some
-systems offer dedicated nodes for data transfers only. The motivation for
-this lies in the fact that larger data transfers should not obstruct
-operation of the login node for anybody else. Check with your cluster's
-documentation or its support team if such a transfer node is available. As a
-rule of thumb, consider all transfers of a volume larger than 500 MB to 1 GB
-as large. But these numbers change, e.g., depending on the network connection
-of yourself and of your cluster or other factors.
-
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-The real work on a cluster gets done by the *compute* (or *worker*) *nodes*.
-compute nodes come in many shapes and sizes, but generally are dedicated to long
-or hard tasks that require a lot of computational resources.
-
-All interaction with the compute nodes is handled by a specialized piece of
-software called a scheduler (the scheduler used in this lesson is called
-{{ site.sched.name }}). We'll learn more about how to use the
-scheduler to submit jobs next, but for now, it can also tell us more
-information about the compute nodes.
-
-For example, we can view all of the compute nodes by running the command
-`{{ site.sched.info }}`.
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.info }}
-```
-
-```output
-PARTITION          AVAIL  TIMELIMIT  NODES  STATE NODELIST
-cpubase_bycore_b1*    up   infinite      4   idle node[1-2],smnode[1-2]
-node                  up   infinite      2   idle node[1-2]
-smnode                up   infinite      2   idle smnode[1-2]
-```
-
-A lot of the nodes are busy running work for other users: we are not alone
-here!
-
-There are also specialized machines used for managing disk storage, user
-authentication, and other infrastructure-related tasks. Although we do not
-typically logon to or interact with these machines directly, they enable a
-number of key features like ensuring our user account and files are available
-throughout the HPC system.
-
-## What's in a Node?
-
-All of the nodes in an HPC system have the same components as your own laptop
-or desktop: *CPUs* (sometimes also called *processors* or *cores*), *memory*
-(or *RAM*), and *disk* space. CPUs are a computer's tool for actually running
-programs and calculations. Information about a current task is stored in the
-computer's memory. Disk refers to all storage that can be accessed like a file
-system. This is generally storage that can hold data permanently, i.e. data is
-still there even if the computer has been restarted. While this storage can be
-local (a hard drive installed inside of it), it is more common for nodes to
-connect to a shared, remote fileserver or cluster of servers.
-
-![](/fig/node\_anatomy.png){max-width="40%" alt="Node anatomy"}
-
-:::::::::::::::::::::::::::::::::::::::  challenge
-
-## Explore Your Computer
-
-Try to find out the number of CPUs and amount of memory available on your
-personal computer.
-
-Note that, if you're logged in to the remote computer cluster, you need to
-log out first. To do so, type `Ctrl+d` or `exit`:
-
-```bash
-{{ site.remote.prompt }} exit
-{{ site.local.prompt }}
-```
-
-:::::::::::::::  solution
-
-## Solution
-
-There are several ways to do this. Most operating systems have a graphical
-system monitor, like the Windows Task Manager. More detailed information
-can be found on the command line:
-
-- Run system utilities
-  
-  ```bash
-  {{ site.local.prompt }} nproc --all
-  {{ site.local.prompt }} free -m
-  ```
-
-- Read from `/proc`
-  
-  ```bash
-  {{ site.local.prompt }} cat /proc/cpuinfo
-  {{ site.local.prompt }} cat /proc/meminfo
-  ```
-
-- Run system monitor
-  
-  ```bash
-  {{ site.local.prompt }} htop
-  ```
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-:::::::::::::::::::::::::::::::::::::::  challenge
-
-## Explore the Login Node
-
-Now compare the resources of your computer with those of the login node.
-
-:::::::::::::::  solution
-
-## Solution
-
-```bash
-{{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }}
-{{ site.remote.prompt }} nproc --all
-{{ site.remote.prompt }} free -m
-```
-
-You can get more information about the processors using `lscpu`,
-and a lot of detail about the memory by reading the file `/proc/meminfo`:
-
-```bash
-{{ site.remote.prompt }} less /proc/meminfo
-```
-
-You can also explore the available filesystems using `df` to show **d**isk
-**f**ree space. The `-h` flag renders the sizes in a human-friendly format,
-i.e., GB instead of B. The **t**ype flag `-T` shows what kind of filesystem
-each resource is.
-
-```bash
-{{ site.remote.prompt }} df -Th
-```
-
-::::::::::::::::::::::::::::::::::::::  discussion
-
-## Different results from `df`
-
-- The local filesystems (ext, tmp, xfs, zfs) will depend on whether
-  you're on the same login node (or compute node, later on).
-- Networked filesystems (beegfs, cifs, gpfs, nfs, pvfs) will be similar
-  \-- but may include {{ site.remote.user }}, depending on how it
-  is [mounted][mount].
-  
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-:::::::::::::::::::::::::::::::::::::::::  callout
-
-## Shared Filesystems
-
-This is an important point to remember: files saved on one node
-(computer) are often available everywhere on the cluster!
-
-
-
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-:::::::::::::::::::::::::::::::::::::::  challenge
-
-## Explore a Worker Node
-
-Finally, let's look at the resources available on the worker nodes where your
-jobs will actually run. Try running this command to see the name, CPUs and
-memory available on the worker nodes:
-
-```bash
-{{ site.remote.prompt }} sinfo -o "%n %c %m" | column -t
-```
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::  challenge
-
-## Compare Your Computer, the Login Node and the Compute Node
-
-Compare your laptop's number of processors and memory with the numbers you
-see on the cluster login node and compute node. What implications do
-you think the differences might have on running your research work on the
-different systems and nodes?
-
-:::::::::::::::  solution
-
-## Solution
-
-Compute nodes are usually built with processors that have *higher
-core-counts* than the login node or personal computers in order to support
-highly parallel tasks. Compute nodes usually also have substantially *more
-memory (RAM)* installed than a personal computer. More cores tends to help
-jobs that depend on some work that is easy to perform in *parallel*, and
-more, faster memory is key for large or *complex numerical tasks*.
-
-
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-:::::::::::::::::::::::::::::::::::::::::  callout
-
-## Differences Between Nodes
-
-Many HPC clusters have a variety of nodes optimized for particular workloads.
-Some nodes may have larger amount of memory, or specialized resources such as
-Graphics Processing Units (GPUs or "video cards").
-
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-With all of this in mind, we will now cover how to talk to the cluster's
-scheduler, and use it to start running our scripts and programs!
-
-
-
-[fshs]: https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
-[mount]: https://en.wikipedia.org/wiki/Mount_\(computing\)
-
-
-:::::::::::::::::::::::::::::::::::::::: keypoints
-
-- An HPC system is a set of networked machines.
-- HPC systems typically provide login nodes and a set of compute nodes.
-- The resources found on independent (worker) nodes can vary in volume and type (amount of RAM, processor architecture, availability of network mounted filesystems, etc.).
-- Files saved on shared storage are available on all nodes.
-- The login node is a shared machine: be considerate of other users.
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.Rmd
similarity index 99%
rename from episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.snip
rename to episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.Rmd
index bdc94879..b9573160 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.snip
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.Rmd
@@ -5,4 +5,4 @@ standard     up 1-00:00:00      5  down* nid[001024,001026,001064,001239,001898]
 standard     up 1-00:00:00      8  drain nid[001002,001028,001030-001031,001360-001362,001745] 
 standard     up 1-00:00:00    945  alloc nid[001000-001001,001003-001023,001025,001027,001032-001037,001040-001049,001051-001063,001065-001108,001110-001145,001147,001150-001238,001240-001264,001266-001271,001274-001334,001337-001359,001364-001365,001367-001390,001392-001551,001553-001567,001569-001619,001621-001637,001639-001641,001643-001668,001670-001671,001676,001679-001687,001692-001734,001736-001744,001746,001748-001750,001752-001782,001784-001792,001794-001811,001813-001824,001826-001831,001836-001890,001892-001897,001899-001918,001920,001923-001934,001936-001945,001947-001965,001967-001981,001984-001991,002006-002023] 
 standard     up 1-00:00:00     37   resv nid[001038-001039,001109,001146,001148,001265,001272-001273,001335-001336,001638,001677-001678,001735,001891,001919,001921-001922,001935,001946,001966,001982-001983,001992-002005] 
-```
\ No newline at end of file
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
index dee005a4..54a94855 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
@@ -1,8 +1,9 @@
 ::: challenge
 ## Explore a Worker Node
 
-Finally, let's look at the resources available on the worker nodes where your jobs will actually
-run. Try running this command to see the name, CPUs and memory available on one of the worker nodes:
+Finally, let's look at the resources available on the worker nodes
+where your jobs will actually run. Try running this command to see
+the name, CPUs and memory available on one of the worker nodes:
 
 ```bash
 `r config$remote$prompt` sinfo -n nid001053 -o "%n %c %m"
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.Rmd
similarity index 94%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.Rmd
index decfc331..2487fc02 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/queue-info.Rmd
@@ -1,7 +1,6 @@
-```
+```output
 PARTITION          AVAIL  TIMELIMIT  NODES  STATE NODELIST
 cpubase_bycore_b1*    up   infinite      4   idle node[1-2],smnode[1-2]
 node                  up   infinite      2   idle node[1-2]
 smnode                up   infinite      2   idle smnode[1-2]
 ```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.Rmd
index 3a86da2c..b9f6c8dc 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.Rmd
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.Rmd
@@ -1,11 +1,12 @@
 ::: challenge
+
 ## Explore a Worker Node
 
-Finally, let's look at the resources available on the worker nodes where your jobs will actually
-run. Try running this command to see the name, CPUs and memory available on one of the worker nodes:
+Finally, let's look at the resources available on the worker nodes
+where your jobs will actually run. Try running this command to see
+the name, CPUs and memory available on one of the worker nodes:
 
 ```bash
 `r config$remote$prompt` sinfo -o "%n %c %m" | column -t
 ```
 :::
-
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.snip
deleted file mode 100644
index b70845bd..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/cluster/specific-node-info.snip
+++ /dev/null
@@ -1,11 +0,0 @@
-> ## Explore a Worker Node
->
-> Finally, let's look at the resources available on the worker nodes where your
-> jobs will actually run. Try running this command to see the name, CPUs and
-> memory available on the worker nodes:
->
-> ```
-> {{ site.remote.prompt }} sinfo -o "%n %c %m" | column -t
-> ```
-> {: .language-bash}
-{: .challenge}

From b077bd71e18422dc13d154be6a6335bcb2029878 Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 15:01:48 -0400
Subject: [PATCH 20/33] Workbenched Ep. 13

---
 config.yaml                                   |  32 +-
 episodes/13-epcc-scheduler.Rmd                | 434 ----------------
 episodes/13-hpcc-scheduler/hpcc/section1.rmd  |   6 -
 .../13-hpcc-scheduler/hpcc_test/section1.rmd  |   1 -
 ...13-hpcc-scheduler.Rmd => 13-scheduler.Rmd} |  85 ++--
 episodes/13-scheduler.md                      | 478 ------------------
 .../EPCC_ARCHER2_slurm/_config_options.yml    |   2 -
 .../scheduler/basic-job-script.Rmd            |   2 +-
 .../EPCC_ARCHER2_slurm/scheduler/del_job.Rmd  |   3 +
 .../EPCC_ARCHER2_slurm/scheduler/del_job.snip |   1 -
 .../scheduler/filesystem_issues.Rmd           |  23 +
 .../scheduler/filesystem_issues.snip          |  20 -
 .../scheduler/job-with-name-status.Rmd        |   2 +-
 .../scheduler/{long_job.snip => long_job.Rmd} |   2 +
 .../{ls-pgm-output.snip => ls-pgm-output.Rmd} |   2 +
 .../scheduler/parallel-challenge.Rmd          |   6 +-
 .../scheduler/parallel-challenge2.Rmd         |   6 +-
 .../scheduler/parallel-launch-desc.Rmd        |  16 +-
 .../scheduler/parallel-script.Rmd             |   2 +-
 .../scheduler/print-sched-variables.Rmd       |  11 +-
 .../scheduler/runtime-exceeded-job.Rmd        |   2 +-
 .../scheduler/runtime-exceeded-output.Rmd     |   2 +-
 .../scheduler/squeue_pending.Rmd              |   4 +
 .../scheduler/squeue_pending.snip             |   2 -
 ...squeue_running.snip => squeue_running.Rmd} |   0
 .../scheduler/terminate-multiple-jobs.Rmd     |  11 +-
 .../scheduler/using-nodes-interactively.Rmd   |   1 +
 .../scheduler/basic-job-script.snip           |   4 -
 ...c-job-status.snip => basic-job-status.Rmd} |   3 +-
 ...e-status.snip => job-with-name-status.Rmd} |   3 +-
 ...-flags-list.snip => option-flags-list.Rmd} |   0
 .../scheduler/print-sched-variables.Rmd       |  32 ++
 .../scheduler/print-sched-variables.snip      |  30 --
 .../scheduler/runtime-exceeded-job.Rmd        |   3 +
 .../scheduler/runtime-exceeded-job.snip       |   4 -
 ...utput.snip => runtime-exceeded-output.Rmd} |   3 +-
 ...job-begin.snip => terminate-job-begin.Rmd} |   3 +-
 ...b-cancel.snip => terminate-job-cancel.Rmd} |   3 +-
 .../scheduler/terminate-multiple-jobs.Rmd     |  29 ++
 .../scheduler/terminate-multiple-jobs.snip    |  27 -
 .../scheduler/using-nodes-interactively.Rmd   |  66 +++
 .../scheduler/using-nodes-interactively.snip  |  69 ---
 42 files changed, 256 insertions(+), 1179 deletions(-)
 delete mode 100644 episodes/13-epcc-scheduler.Rmd
 delete mode 100644 episodes/13-hpcc-scheduler/hpcc/section1.rmd
 delete mode 100644 episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
 rename episodes/{13-hpcc-scheduler.Rmd => 13-scheduler.Rmd} (83%)
 delete mode 100644 episodes/13-scheduler.md
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.snip
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.snip
 rename episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/{long_job.snip => long_job.Rmd} (92%)
 rename episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/{ls-pgm-output.snip => ls-pgm-output.Rmd} (89%)
 create mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.snip
 rename episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/{squeue_running.snip => squeue_running.Rmd} (100%)
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.snip
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/{basic-job-status.snip => basic-job-status.Rmd} (95%)
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/{job-with-name-status.snip => job-with-name-status.Rmd} (89%)
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/{option-flags-list.snip => option-flags-list.Rmd} (100%)
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.Rmd
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.Rmd
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.snip
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/{runtime-exceeded-output.snip => runtime-exceeded-output.Rmd} (88%)
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/{terminate-job-begin.snip => terminate-job-begin.Rmd} (90%)
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/{terminate-job-cancel.snip => terminate-job-cancel.Rmd} (82%)
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.Rmd
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.Rmd
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.snip

diff --git a/config.yaml b/config.yaml
index e0f40424..1f60cd16 100644
--- a/config.yaml
+++ b/config.yaml
@@ -20,7 +20,7 @@ carpentry: 'cp'
 title: 'Introduction to High-Performance Computing'
 
 # Date the lesson was created (YYYY-MM-DD, this is empty by default)
-created: 2017-03-24 
+created: 2017-03-24
 
 # Comma-separated list of keywords for the lesson
 keywords: 'software, data, lesson, The Carpentries'
@@ -64,28 +64,26 @@ contact: 'team@carpentries.org'
 # - another-learner.md
 
 # Order of episodes in your lesson
-episodes: 
-- 10-hpc-intro.md
-- 11-connecting.Rmd
-- 12-cluster.Rmd
-- 13-scheduler.md
-- 13-hpcc-scheduler.Rmd
-- 13-epcc-scheduler.Rmd
-- 14-environment-variables.md
-- 15-modules.md
-- 16-transferring-files.md
-- 17-parallel.md
-- 18-resources.md
-- 19-responsibility.md
+episodes:
+  - 10-hpc-intro.md
+  - 11-connecting.Rmd
+  - 12-cluster.Rmd
+  - 13-scheduler.Rmd
+  - 14-environment-variables.md
+  - 15-modules.md
+  - 16-transferring-files.md
+  - 17-parallel.md
+  - 18-resources.md
+  - 19-responsibility.md
 
 # Information for Learners
-learners: 
+learners:
 
 # Information for Instructors
-instructors: 
+instructors:
 
 # Learner Profiles
-profiles: 
+profiles:
 
 # Customisation ---------------------------------------------
 #
diff --git a/episodes/13-epcc-scheduler.Rmd b/episodes/13-epcc-scheduler.Rmd
deleted file mode 100644
index 08b62b22..00000000
--- a/episodes/13-epcc-scheduler.Rmd
+++ /dev/null
@@ -1,434 +0,0 @@
----
-title: "EPCC version - Working with the scheduler"
-teaching: 50
-exercises: 30
----
-
-```{r load_config, include=FALSE}
-library(yaml)
-config <- yaml.load_file("epcc_config.yaml")
-snippets <- paste('files/snippets/', config$snippets, sep='')
-```
-
-::: questions
- - "What is a scheduler and why are they used?"
- - "How do I launch a program to run on any one node in the cluster?"
- - "How do I capture the output of a program that is run on a node in the
-   cluster?"
-:::
-
-::: objectives
- - "Run a simple Hello World style program on the cluster."
- - "Submit a simple Hello World style script to the cluster."
- - "Use the batch system command line tools to monitor the execution of your
-   job."
- - "Inspect the output and error files of your jobs."
-:::
-
-## Job Scheduler
-
-An HPC system might have thousands of nodes and thousands of users. How do we
-decide who gets what and when? How do we ensure that a task is run with the
-resources it needs? This job is handled by a special piece of software called
-the scheduler. On an HPC system, the scheduler manages which jobs run where and
-when.
-
-The following illustration compares these tasks of a job scheduler to a waiter
-in a restaurant. If you can relate to an instance where you had to wait for a
-while in a queue to get in to a popular restaurant, then you may now understand
-why sometimes your job do not start instantly as in your laptop.
-
-![The waiter scheduler](fig/restaurant_queue_manager.svg){caption="" alt="Compare a job scheduler to a waiter in a restaurant"}
-
-The scheduler used in this lesson is `r config$sched$name`. Although
-`r config$sched$name` is not used everywhere, running jobs is quite similar
-regardless of what software is being used. The exact syntax might change, but
-the concepts remain the same.
-
-## Running a Batch Job
-
-The most basic use of the scheduler is to run a command non-interactively. Any
-command (or series of commands) that you want to run on the cluster is called a
-*job*, and the process of using a scheduler to run the job is called *batch job
-submission*.
-
-In this case, the job we want to run is just a shell script. Let's create a
-demo shell script to run as a test. The landing pad will have a number of
-terminal-based text editors installed. Use whichever you prefer. Unsure? `nano`
-is a pretty good, basic choice.
-
-```bash
-`r config$remote$prompt` nano example-job.sh
-`r config$remote$prompt` chmod +x example-job.sh
-`r config$remote$prompt` cat example-job.sh
-```
-
-```output
-`r config$remote$bash_shebang`
-
-echo -n "This script is running on "
-hostname
-```
-
-::: challenge
-## Creating Our Test Job
-
-Run the script. Does it execute on the cluster or just our login node?
-
-```bash
-`r config$remote$prompt` ./example-job.sh
-```
-
-::: solution
-
-```output
-This script is running on `r config$remote$host`
-```
-This job runs on the login node.
-:::
-:::
-
-If you completed the previous challenge successfully, you probably realise that
-there is a distinction between running the job through the scheduler and just
-"running it". To submit this job to the scheduler, we use the
-``r config$sched$submit$name`` command.
-
-```bash
-`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
-```
-
-```output
-sbatch: Warning: Your job has no time specification (--time=) and the default time is short. You can cancel your job with 'scancel <JOB_ID>' if you wish to resubmit.
-sbatch: Warning: It appears your working directory may be on the home filesystem. It is /home2/home/ta114/ta114/userid. This is not available from the compute nodes - please check that this is what you intended. You can cancel your job with 'scancel <JOBID>' if you wish to resubmit.
-Submitted batch job 286949
-```
-
-Ah! What went wrong here? Slurm is telling us that the file system we are currently on, `/home`, is not available
-on the compute nodes and that we are getting the default, short runtime. We will deal with the runtime 
-later, but we need to move to a different file system to submit the job and have it visible to the 
-compute nodes. On ARCHER2, this is the `/work` file system. The path is similar to home but with 
-`/work` at the start. Lets move there now, copy our job script across and resubmit:
-
-```bash
-`r config$remote$prompt` cd /work/ta114/ta114/userid
-`r config$remote$prompt_work` cp ~/example-job.sh .
-`r config$remote$prompt_work` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
-```
-```{r, child=paste(snippets, '/scheduler/basic-job-script.Rmd', sep=''), eval=TRUE}
-```
-
-That's better! And that's all we need to do to submit a job. Our work is done --- now the
-scheduler takes over and tries to run the job for us. While the job is waiting
-to run, it goes into a list of jobs called the *queue*. To check on our job's
-status, we check the queue using the command
-``r config$sched$status` `r config$sched$flag$user``.
-
-```bash
-`r config$remote$prompt_work` `r config$sched$status` `r config$sched$flag$user`
-```
-
-```{r, child=paste(snippets, '/scheduler/basic-job-status.Rmd', sep=''), eval=TRUE}
-```
-
-The best way to check our job's status is with ``r config$sched$status``. Of
-course, running ``r config$sched$status`` repeatedly to check on things can be
-a little tiresome. To see a real-time view of our jobs, we can use the `watch`
-command. `watch` reruns a given command at 2-second intervals. This is too
-frequent, and will likely upset your system administrator. You can change the
-interval to a more reasonable value, for example 15 seconds, with the `-n 15`
-parameter. Let's try using it to monitor another job.
-
-```bash
-`r config$remote$prompt_work` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
-`r config$remote$prompt_work` watch -n 15 `r config$sched$status` `r config$sched$flag$user`
-```
-
-You should see an auto-updating display of your job's status. When it finishes,
-it will disappear from the queue. Press `Ctrl-c` when you want to stop the
-`watch` command.
-
-::: discussion
-## Where's the Output?
-On the login node, this script printed output to the terminal --- but
-when we exit `watch`, there's nothing. Where'd it go?
-HPC job output is typically redirected to a file in the directory you
-launched it from. Use `ls` to find and read the file.
-:::
-
-## Customising a Job
-
-The job we just ran used some of the scheduler's default options. In a
-real-world scenario, that's probably not what we want. The default options
-represent a reasonable minimum. Chances are, we will need more cores, more
-memory, more time, among other special considerations. To get access to these
-resources we must customize our job script.
-
-Comments in UNIX shell scripts (denoted by `#`) are typically ignored, but
-there are exceptions. For instance the special `#!` comment at the beginning of
-scripts specifies what program should be used to run it (you'll typically see
-``r config$local$bash_shebang``). Schedulers like `r config$sched$name` also
-have a special comment used to denote special scheduler-specific options.
-Though these comments differ from scheduler to scheduler,
-`r config$sched$name`'s special comment is ``r config$sched$comment``. Anything
-following the ``r config$sched$comment`` comment is interpreted as an
-instruction to the scheduler.
-
-Let's illustrate this by example. By default, a job's name is the name of the
-script, but the ``r config$sched$flag$name`` option can be used to change the
-name of a job. Add an option to the script:
-
-```bash
-`r config$remote$prompt_work` cat example-job.sh
-```
-
-```output
-`r config$remote$bash_shebang`
-`r config$sched$comment` `r config$sched$flag$name` new_name
-
-echo -n "This script is running on "
-hostname
-echo "This script has finished successfully."
-```
-
-Submit the job and monitor its status:
-
-```bash
-`r config$remote$prompt_work` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
-`r config$remote$prompt_work` `r config$sched$status` `r config$sched$flag$user`
-```
-
-```{r, child=paste(snippets, '/scheduler/job-with-name-status.Rmd', sep=''), eval=TRUE}
-```
-
-Fantastic, we've successfully changed the name of our job!
-
-### Resource Requests
-
-But what about more important changes, such as the number of cores and memory
-for our jobs? One thing that is absolutely critical when working on an HPC
-system is specifying the resources required to run a job. This allows the
-scheduler to find the right time and place to schedule our job. If you do not
-specify requirements (such as the amount of time you need), you will likely be
-stuck with your site's default resources, which is probably not what you want.
-
-The following are several key resource requests:
-
-```{r, child=paste(snippets, '/scheduler/option-flags-list.Rmd', sep=''), eval=TRUE}
-```
-
-Note that just *requesting* these resources does not make your job run faster,
-nor does it necessarily mean that you will consume all of these resources. It
-only means that these are made available to you. Your job may end up using less
-memory, or less time, or fewer tasks or nodes, than you have requested, and it
-will still run.
-
-It's best if your requests accurately reflect your job's requirements. We'll
-talk more about how to make sure that you're using resources effectively in a
-later episode of this lesson.
-
-::: callout
-## Command line options or job script options?
-All of the options we specify can be supplied on the command line (as we
-do here for `--partition=standard`) or in the job script (as we have done
-for the job name above). These are interchangeable. It is often more convenient
-to put the options in the job script as it avoids lots of typing at the command
-line.
-:::
-
-::: challenge
-## Submitting Resource Requests
-Modify our `hostname` script so that it runs for a minute, then submit a job
-for it on the cluster. You should also move all the options we have been specifying
-on the command line (e.g. `--partition`) into the script at this point.
-
-::: solution
-
-```bash
-`r config$remote$prompt_work` cat example-job.sh
-```
-
-```output
-`r config$remote$bash_shebang`
-`r config$sched$comment` `r config$sched$flag$time` 00:01:15
-`r config$sched$comment` --partition=standard
-`r config$sched$comment` --qos=`r config$sched$qos`
-`r config$sched$comment` --reservation=`r config$sched$reservation`
-echo -n "This script is running on "
-sleep 60 # time in seconds
-hostname
-echo "This script has finished successfully."
-```
-
-```bash
-`r config$remote$prompt` `r config$sched$submit$name` example-job.sh
-```
-
-Why are the `r config$sched$name` runtime and `sleep` time not identical?
-:::
-:::
-
-
-```{r, child=paste(snippets, '/scheduler/print-sched-variables.Rmd', sep=''), eval=TRUE}
-```
-
-Resource requests are typically binding. If you exceed them, your job will be
-killed. Let's use walltime as an example. We will request 30 seconds of
-walltime, and attempt to run a job for two minutes.
-
-```bash
-`r config$remote$prompt_work` cat example-job.sh
-```
-
-```output
-`r config$remote$bash_shebang`
-`r config$sched$comment` `r config$sched$flag$name` long_job
-`r config$sched$comment` `r config$sched$flag$time` 00:00:30
-`r config$sched$comment` --partition=`r config$sched$partition`
-`r config$sched$comment` --qos=`r config$sched$qos`
-`r config$sched$comment` --reservation=`r config$sched$reservation`
-
-echo "This script is running on ... "
-sleep 120 # time in seconds
-hostname
-echo "This script has finished successfully."
-```
-
-Submit the job and wait for it to finish. Once it is has finished, check the
-log file.
-
-```bash
-`r config$remote$prompt_work` `r config$sched$submit$name` example-job.sh
-`r config$remote$prompt_work` watch -n 15 `r config$sched$status` `r config$sched$flag$user`
-```
-
-```{r, child=paste(snippets, '/scheduler/runtime-exceeded-job.Rmd', sep=''), eval=TRUE}
-```
-```{r, child=paste(snippets, '/scheduler/runtime-exceeded-output.Rmd', sep=''), eval=TRUE}
-```
-
-Our job was killed for exceeding the amount of resources it requested. Although
-this appears harsh, this is actually a feature. Strict adherence to resource
-requests allows the scheduler to find the best possible place for your jobs.
-Even more importantly, it ensures that another user cannot use more resources
-than they've been given. If another user messes up and accidentally attempts to
-use all of the cores or memory on a node, `r config$sched$name` will either
-restrain their job to the requested resources or kill the job outright. Other
-jobs on the node will be unaffected. This means that one user cannot mess up
-the experience of others, the only jobs affected by a mistake in scheduling
-will be their own.
-
-::: callout
-## But how much does it cost?
-Although your job will be killed if it exceeds the selected runtime,
-a job that completes within the time limit is only charged for the
-time it actually used. However, you should always try and specify a
-wallclock limit that is close to (but greater than!) the expected
-runtime as this will enable your job to be scheduled more
-quickly.
-If you say your job will run for an hour, the scheduler has
-to wait until a full hour becomes free on the machine. If it only ever
-runs for 5 minutes, you could have set a limit of 10 minutes and it
-might have been run earlier in the gaps between other users' jobs.
-:::
-
-## Cancelling a Job
-
-Sometimes we'll make a mistake and need to cancel a job. This can be done with
-the ``r config$sched$del`` command. Let's submit a job and then cancel it using
-its job number (remember to change the walltime so that it runs long enough for
-you to cancel it before it is killed!).
-
-```bash
-`r config$remote$prompt_work` `r config$sched$submit$name` example-job.sh
-`r config$remote$prompt_work` `r config$sched$status` `r config$sched$flag$user`
-```
-
-```{r, child=paste(snippets, '/scheduler/terminate-job-begin.Rmd', sep=''), eval=TRUE}
-```
-
-Now cancel the job with its job number (printed in your terminal). Absence of any
-job info indicates that the job has been successfully cancelled.
-
-```bash
-`r config$remote$prompt_work` `r config$sched$del` 38759
-# It might take a minute for the job to disappear from the queue...
-`r config$remote$prompt_work` `r config$sched$status` `r config$sched$flag$user`
-```
-
-```{r, child=paste(snippets, '/scheduler/terminate-job-cancel.Rmd', sep=''), eval=TRUE}
-```
-
-```{r, child=paste(snippets, '/scheduler/terminate-multiple-jobs.Rmd', sep=''), eval=TRUE}
-```
-
-## Other Types of Jobs
-
-Up to this point, we've focused on running jobs in batch mode.
-`r config$sched$name` also provides the ability to start an interactive session.
-
-There are very frequently tasks that need to be done interactively. Creating an
-entire job script might be overkill, but the amount of resources required is
-too much for a login node to handle. A good example of this might be building a
-genome index for alignment with a tool like
-[HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml). Fortunately, we can
-run these types of tasks as a one-off with ``r config$sched$interactive``.
-
-```{r, child=paste(snippets, '/scheduler/using-nodes-interactively.Rmd', sep=''), eval=TRUE}
-```
-
-## Running parallel jobs using MPI
-
-As we have already seen, the power of HPC systems comes from *parallelism*, i.e. having lots of
-processors/disks etc. connected together rather than having more powerful components than your
-laptop or workstation. Often, when running research programs on HPC you will need to run a
-program that has been built to use the MPI (Message Passing Interface) parallel library. The MPI
-library allows programs to exploit multiple processing cores in parallel to allow researchers
-to model or simulate faster on larger problem sizes. The details of how MPI work are not important
-for this course or even to use programs that have been built using MPI; however, MPI programs 
-typically have to be launched in job submission scripts in a different way to serial programs and
-users of parallel programs on HPC systems need to know how to do this. Specifically, launching
-parallel MPI programs typically requires four things:
-
-  - A special parallel launch program such as `mpirun`, `mpiexec`, `srun` or `aprun`.
-  - A specification of how many processes to use in parallel. For example, our parallel program
-    may use 256 processes in parallel.
-  - A specification of how many parallel processes to use per compute node. For example, if our
-    compute nodes each have 32 cores we often want to specify 32 parallel processes per node.
-  - The command and arguments for our parallel program.
-
-```{r, child=paste(snippets, '/resources/pi-mpi-details.Rmd', sep=''), eval=TRUE}
-```
-
-To illustrate this process, we will use a simple MPI parallel program that estimates the value of Pi.
-(We will meet this example program in more detail in a later episode.) Here is a job submission
-script that runs the program across two compute nodes on the cluster. Create a file
-(e.g. called: `run-pi-mpi.slurm`) with the contents of this script in it.
-
-```{r, child=paste(snippets, '/scheduler/parallel-script.Rmd', sep=''), eval=TRUE}
-```
-
-The parallel launch line for the sharpen program can be seen towards the bottom of the script:
-
-```{r, child=paste(snippets, '/scheduler/parallel-launch-desc.Rmd', sep=''), eval=TRUE}
-```
-
-As for our other jobs, we launch using the ``r config$sched$submit$name`` command.
-
-```bash
-`r config$remote$prompt_work` `r config$sched$submit$name` run-pi-mpi.slurm
-```
-
-The program generates no output with all details printed to the job log.
-
-```{r, child=paste(snippets, '/scheduler/parallel-challenge.Rmd', sep=''), eval=TRUE}
-```
-
-```{r, child=paste(snippets, '/scheduler/parallel-challenge2.Rmd', sep=''), eval=TRUE}
-```
-
-::: keypoints
- - "The scheduler handles how compute resources are shared between users."
- - "Everything you do should be run through the scheduler."
- - "A job is just a shell script."
- - "If in doubt, request more resources than you will need."
-:::
diff --git a/episodes/13-hpcc-scheduler/hpcc/section1.rmd b/episodes/13-hpcc-scheduler/hpcc/section1.rmd
deleted file mode 100644
index 7c419e3a..00000000
--- a/episodes/13-hpcc-scheduler/hpcc/section1.rmd
+++ /dev/null
@@ -1,6 +0,0 @@
----
-layout: page
-author: Alan O'Cais
-comment: Snippet test
----
-I was hoping this would appear.
diff --git a/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd b/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
deleted file mode 100644
index 673021ac..00000000
--- a/episodes/13-hpcc-scheduler/hpcc_test/section1.rmd
+++ /dev/null
@@ -1 +0,0 @@
-I was hoping this would appear first.
diff --git a/episodes/13-hpcc-scheduler.Rmd b/episodes/13-scheduler.Rmd
similarity index 83%
rename from episodes/13-hpcc-scheduler.Rmd
rename to episodes/13-scheduler.Rmd
index d5ca99e2..d74d1b83 100644
--- a/episodes/13-hpcc-scheduler.Rmd
+++ b/episodes/13-scheduler.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "HPCC version - Scheduler Fundamentals"
+title: "Scheduler Fundamentals"
 teaching: 45
 exercises: 30
 ---
@@ -26,15 +26,6 @@ source("load_config.R")
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-### Section 1
-
-We are testing the snippet library mechanism, stay tuned!
-
-```{r child=choose_doc("section1.rmd")}
-```
-
-How does spacing look?
-
 ## Job Scheduler
 
 An HPC system might have thousands of nodes and thousands of users. How do we
@@ -83,7 +74,7 @@ manner. Our shell script will have three parts:
 `r config$remote$prompt` nano example-job.sh
 ```
 
-```output
+```bash
 `r config$remote$bash_shebang`
 
 echo -n "This script is running on "
@@ -117,14 +108,13 @@ the compute nodes: we need the scheduler to queue up `example-job.sh`
 to run on a compute node.
 
 To submit this task to the scheduler, we use the
-``r config$sched$flag$submit$name`` command.
+``r config$sched$submit$name`` command.
 This creates a *job* which will run the *script* when *dispatched* to
 a compute node which the queuing system has identified as being
 available to perform the work.
 
 ```bash
-# `r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
-`r config$remote$prompt``r config$sched$submit$name`r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
 ```
 
 ```{r, child=paste(snippets, '/scheduler/basic-job-script.Rmd', sep=''), eval=TRUE}
@@ -137,7 +127,7 @@ status, we check the queue using the command
 ``r config$sched$status` `r config$sched$flag$user``.
 
 ```bash
-`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+`r config$remote$prompt` `r config$sched$status` `r config$sched$flag$user`
 ```
 
 ```output
@@ -160,7 +150,6 @@ nothing was printed to the terminal.
 Cluster job output is typically redirected to a file in the directory you
 launched it from. Use `ls` to find and `cat` to read the file.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 ## Customising a Job
@@ -186,12 +175,12 @@ script, but the ``r config$sched$flag$name`` option can be used to change the
 name of a job. Add an option to the script:
 
 ```bash
-`r config$remote$prompt`cat example-job.sh
+`r config$remote$prompt` cat example-job.sh
 ```
 
-```output
+```bash
 `r config$remote$bash_shebang`
-`r config$sched$comment``r config$sched$flag$name`hello-world
+`r config$sched$comment` `r config$sched$flag$name` hello-world
 
 echo -n "This script is running on "
 hostname
@@ -200,8 +189,8 @@ hostname
 Submit the job and monitor its status:
 
 ```bash
-`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
-`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$status` `r config$sched$flag$user`
 ```
 
 ```output
@@ -260,12 +249,12 @@ for it on the cluster.
 ## Solution
 
 ```bash
-`r config$remote$prompt`cat example-job.sh
+`r config$remote$prompt` cat example-job.sh
 ```
 
-```output
+```bash
 `r config$remote$bash_shebang`
-`r config$sched$comment``r config$sched$flag$time`00:01 # timeout in HH:MM
+`r config$sched$comment` `r config$sched$flag$time` 00:01 # timeout in HH:MM
 
 echo -n "This script is running on "
 sleep 20 # time in seconds
@@ -273,7 +262,7 @@ hostname
 ```
 
 ```bash
-`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
 ```
 
 Why are the `r config$sched$name` runtime and `sleep` time not identical?
@@ -289,13 +278,13 @@ killed. Let's use wall time as an example. We will request 1 minute of
 wall time, and attempt to run a job for two minutes.
 
 ```bash
-`r config$remote$prompt`cat example-job.sh
+`r config$remote$prompt` cat example-job.sh
 ```
 
-```output
+```bash
 `r config$remote$bash_shebang`
-`r config$sched$comment``r config$sched$flag$name`long_job
-`r config$sched$comment``r config$sched$flag$time`00:01 # timeout in HH:MM
+`r config$sched$comment` `r config$sched$flag$name` long_job
+`r config$sched$comment` `r config$sched$flag$time` 00:01 # timeout in HH:MM
 
 echo "This script is running on ... "
 sleep 240 # time in seconds
@@ -306,12 +295,12 @@ Submit the job and wait for it to finish. Once it is has finished, check the
 log file.
 
 ```bash
-`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
-`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$status` `r config$sched$flag$user`
 ```
 
 ```bash
-`r config$remote$prompt`cat slurm-12.out
+`r config$remote$prompt` cat slurm-12.out
 ```
 
 ```output
@@ -339,8 +328,8 @@ its job number (remember to change the walltime so that it runs long enough for
 you to cancel it before it is killed!).
 
 ```bash
-`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
-`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$status` `r config$sched$flag$user`
 ```
 
 ```output
@@ -355,9 +344,9 @@ return of your command prompt indicates that the request to cancel the job was
 successful.
 
 ```bash
-`r config$remote$prompt`{{site.sched.del }} 38759
+`r config$remote$prompt` `r config$sched$del` 38759
 # It might take a minute for the job to disappear from the queue...
-`r config$remote$prompt``r config$sched$status` `r config$sched$flag$user`
+`r config$remote$prompt` `r config$sched$status` `r config$sched$flag$user`
 ```
 
 ```output
@@ -381,15 +370,15 @@ Try submitting multiple jobs and then cancelling them all.
 First, submit a trio of jobs:
 
 ```bash
-`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
-`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
-`r config$remote$prompt``r config$sched$submit$name`{% if site.sched.submit.options != '' %}`r config$sched$submit$options` {% endif %}example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
 ```
 
 Then, cancel them all:
 
 ```bash
-`r config$remote$prompt``r config$sched$del` -u `r config$remote$user`
+`r config$remote$prompt` `r config$sched$del` -u `r config$remote$user`
 ```
 
 :::::::::::::::::::::::::
@@ -399,7 +388,7 @@ Then, cancel them all:
 ## Other Types of Jobs
 
 Up to this point, we've focused on running jobs in batch mode.
-`r config$sched$name` also provides the ability to start an interactive session.
+``r config$sched$name`` also provides the ability to start an interactive session.
 
 There are very frequently tasks that need to be done interactively. Creating an
 entire job script might be overkill, but the amount of resources required is
@@ -413,7 +402,7 @@ exits. Let's demonstrate this by running the `hostname` command with
 job with `Ctrl-c`.)
 
 ```bash
-`r config$remote$prompt``r config$sched$interactive` hostname
+`r config$remote$prompt` `r config$sched$interactive` hostname
 ```
 
 ```output
@@ -421,12 +410,12 @@ job with `Ctrl-c`.)
 ```
 
 ``r config$sched$interactive`` accepts all of the same options as
-``r config$sched$flag$submit$name``. However, instead of specifying these in a script,
+``r config$sched$submit$name``. However, instead of specifying these in a script,
 these options are specified on the command-line when starting a job. To submit
 a job that uses 2 CPUs for instance, we could use the following command:
 
 ```bash
-`r config$remote$prompt``r config$sched$interactive` -n 2 echo "This job will use 2 CPUs."
+`r config$remote$prompt` `r config$sched$interactive` -n 2 echo "This job will use 2 CPUs."
 ```
 
 ```output
@@ -435,7 +424,7 @@ This job will use 2 CPUs.
 ```
 
 Typically, the resulting shell environment will be the same as that for
-``r config$sched$flag$submit$name``.
+``r config$sched$submit$name``.
 
 ### Interactive jobs
 
@@ -445,7 +434,7 @@ went wrong with a previous job. Fortunately, `r config$sched$name` makes it
 easy to start an interactive job with ``r config$sched$interactive``:
 
 ```bash
-`r config$remote$prompt``r config$sched$interactive` --pty bash
+`r config$remote$prompt` `r config$sched$interactive` --pty bash
 ```
 
 You should be presented with a bash prompt. Note that the prompt will likely
@@ -471,16 +460,12 @@ installed, you can ensure X11 forwarding within interactive jobs by using the
 `--x11` option for ``r config$sched$interactive`` with the command
 ``r config$sched$interactive` --x11 --pty bash`.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 When you are done with the interactive job, type `exit` to quit your session.
 
-
-
 [hisat]: https://daehwankimlab.github.io/hisat2/
 
-
 :::::::::::::::::::::::::::::::::::::::: keypoints
 
 - The scheduler handles how compute resources are shared between users.
diff --git a/episodes/13-scheduler.md b/episodes/13-scheduler.md
deleted file mode 100644
index 69889dcb..00000000
--- a/episodes/13-scheduler.md
+++ /dev/null
@@ -1,478 +0,0 @@
----
-title: Scheduler Fundamentals
-teaching: 45
-exercises: 30
----
-
-::::::::::::::::::::::::::::::::::::::: objectives
-
-- Submit a simple script to the cluster.
-- Monitor the execution of jobs using command line tools.
-- Inspect the output and error files of your jobs.
-- Find the right place to put large datasets on the cluster.
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-:::::::::::::::::::::::::::::::::::::::: questions
-
-- What is a scheduler and why does a cluster need one?
-- How do I launch a program to run on a compute node in the cluster?
-- How do I capture the output of a program that is run on a node in the cluster?
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-## Job Scheduler
-
-An HPC system might have thousands of nodes and thousands of users. How do we
-decide who gets what and when? How do we ensure that a task is run with the
-resources it needs? This job is handled by a special piece of software called
-the *scheduler*. On an HPC system, the scheduler manages which jobs run where
-and when.
-
-The following illustration compares these tasks of a job scheduler to a waiter
-in a restaurant. If you can relate to an instance where you had to wait for a
-while in a queue to get in to a popular restaurant, then you may now understand
-why sometimes your job do not start instantly as in your laptop.
-
-![](/fig/restaurant_queue_manager.svg){alt="Compare a job scheduler to a waiter in a restaurant" max-width="75%"}
-
-The scheduler used in this lesson is {{ site.sched.name }}. Although
-{{ site.sched.name }} is not used everywhere, running jobs is quite similar
-regardless of what software is being used. The exact syntax might change, but
-the concepts remain the same.
-
-## Running a Batch Job
-
-The most basic use of the scheduler is to run a command non-interactively. Any
-command (or series of commands) that you want to run on the cluster is called a
-*job*, and the process of using a scheduler to run the job is called *batch job
-submission*.
-
-In this case, the job we want to run is a shell script -- essentially a
-text file containing a list of UNIX commands to be executed in a sequential
-manner. Our shell script will have three parts:
-
-- On the very first line, add `{{ site.remote.bash_shebang }}`. The `#!`
-  (pronounced "hash-bang" or "shebang") tells the computer what program is
-  meant to process the contents of this file. In this case, we are telling it
-  that the commands that follow are written for the command-line shell (what
-  we've been doing everything in so far).
-- Anywhere below the first line, we'll add an `echo` command with a friendly
-  greeting. When run, the shell script will print whatever comes after `echo`
-  in the terminal.
-  - `echo -n` will print everything that follows, *without* ending
-    the line by printing the new-line character.
-- On the last line, we'll invoke the `hostname` command, which will print the
-  name of the machine the script is run on.
-
-```bash
-{{ site.remote.prompt }} nano example-job.sh
-```
-
-```output
-{{ site.remote.bash_shebang }}
-
-echo -n "This script is running on "
-hostname
-```
-
-:::::::::::::::::::::::::::::::::::::::  challenge
-
-## Creating Our Test Job
-
-Run the script. Does it execute on the cluster or just our login node?
-
-:::::::::::::::  solution
-
-## Solution
-
-```bash
-{{ site.remote.prompt }} bash example-job.sh
-```
-
-```output
-This script is running on {{ site.remote.host }}
-```
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-This script ran on the login node, but we want to take advantage of
-the compute nodes: we need the scheduler to queue up `example-job.sh`
-to run on a compute node.
-
-To submit this task to the scheduler, we use the
-`{{ site.sched.submit.name }}` command.
-This creates a *job* which will run the *script* when *dispatched* to
-a compute node which the queuing system has identified as being
-available to perform the work.
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-```
-
-```output
-Submitted batch job 9
-```
-
-And that's all we need to do to submit a job. Our work is done -- now the
-scheduler takes over and tries to run the job for us. While the job is waiting
-to run, it goes into a list of jobs called the *queue*. To check on our job's
-status, we check the queue using the command
-`{{ site.sched.status }} {{ site.sched.flag.user }}`.
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.status }} {{ site.sched.flag.user }}
-```
-
-```output
-JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-    9 cpubase_b example-   user01  R       0:05      1 node1
-```
-
-We can see all the details of our job, most importantly that it is in the `R`
-or `RUNNING` state. Sometimes our jobs might need to wait in a queue
-(`PENDING`) or have an error (`E`).
-
-::::::::::::::::::::::::::::::::::::::  discussion
-
-## Where's the Output?
-
-On the login node, this script printed output to the terminal -- but
-now, when `{{ site.sched.status }}` shows the job has finished,
-nothing was printed to the terminal.
-
-Cluster job output is typically redirected to a file in the directory you
-launched it from. Use `ls` to find and `cat` to read the file.
-
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-## Customising a Job
-
-The job we just ran used all of the scheduler's default options. In a
-real-world scenario, that's probably not what we want. The default options
-represent a reasonable minimum. Chances are, we will need more cores, more
-memory, more time, among other special considerations. To get access to these
-resources we must customize our job script.
-
-Comments in UNIX shell scripts (denoted by `#`) are typically ignored, but
-there are exceptions. For instance the special `#!` comment at the beginning of
-scripts specifies what program should be used to run it (you'll typically see
-`{{ site.local.bash_shebang }}`). Schedulers like {{ site.sched.name }} also
-have a special comment used to denote special scheduler-specific options.
-Though these comments differ from scheduler to scheduler,
-{{ site.sched.name }}'s special comment is `{{ site.sched.comment }}`. Anything
-following the `{{ site.sched.comment }}` comment is interpreted as an
-instruction to the scheduler.
-
-Let's illustrate this by example. By default, a job's name is the name of the
-script, but the `{{ site.sched.flag.name }}` option can be used to change the
-name of a job. Add an option to the script:
-
-```bash
-{{ site.remote.prompt }} cat example-job.sh
-```
-
-```output
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} hello-world
-
-echo -n "This script is running on "
-hostname
-```
-
-Submit the job and monitor its status:
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-{{ site.remote.prompt }} {{ site.sched.status }} {{ site.sched.flag.user }}
-```
-
-```output
-JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-   10 cpubase_b hello-wo   user01  R       0:02      1 node1
-```
-
-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
-our jobs? One thing that is absolutely critical when working on an HPC system
-is specifying the resources required to run a job. This allows the scheduler to
-find the right time and place to schedule our job. If you do not specify
-requirements (such as the amount of time you need), you will likely be stuck
-with your site's default resources, which is probably not what you want.
-
-The following are several key resource requests:
-
-- `--ntasks=<ntasks>` or `-n <ntasks>`: How many CPU cores does your job need,
-  in total?
-
-- `--time <days-hours:minutes:seconds>` or `-t <days-hours:minutes:seconds>`:
-  How much real-world time (walltime) will your job take to run? The `<days>`
-  part can be omitted.
-
-- `--mem=<megabytes>`: How much memory on a node does your job need in
-  megabytes? You can also specify gigabytes using by adding a little "g"
-  afterwards (example: `--mem=5g`)
-
-- `--nodes=<nnodes>` or `-N <nnodes>`: How many separate machines does your job
-  need to run on? Note that if you set `ntasks` to a number greater than what
-  one machine can offer, {{ site.sched.name }} will set this value
-  automatically.
-
-Note that just *requesting* these resources does not make your job run faster,
-nor does it necessarily mean that you will consume all of these resources. It
-only means that these are made available to you. Your job may end up using less
-memory, or less time, or fewer nodes than you have requested, and it will still
-run.
-
-It's best if your requests accurately reflect your job's requirements. We'll
-talk more about how to make sure that you're using resources effectively in a
-later episode of this lesson.
-
-:::::::::::::::::::::::::::::::::::::::  challenge
-
-## Submitting Resource Requests
-
-Modify our `hostname` script so that it runs for a minute, then submit a job
-for it on the cluster.
-
-:::::::::::::::  solution
-
-## Solution
-
-```bash
-{{ site.remote.prompt }} cat example-job.sh
-```
-
-```output
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.time }} 00:01 # timeout in HH:MM
-
-echo -n "This script is running on "
-sleep 20 # time in seconds
-hostname
-```
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-```
-
-Why are the {{ site.sched.name }} runtime and `sleep` time not identical?
-
-
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-Resource requests are typically binding. If you exceed them, your job will be
-killed. Let's use wall time as an example. We will request 1 minute of
-wall time, and attempt to run a job for two minutes.
-
-```bash
-{{ site.remote.prompt }} cat example-job.sh
-```
-
-```output
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} long_job
-{{ site.sched.comment }} {{ site.sched.flag.time }} 00:01 # timeout in HH:MM
-
-echo "This script is running on ... "
-sleep 240 # time in seconds
-hostname
-```
-
-Submit the job and wait for it to finish. Once it is has finished, check the
-log file.
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-{{ site.remote.prompt }} {{ site.sched.status }} {{ site.sched.flag.user }}
-```
-
-```bash
-{{ site.remote.prompt }} cat slurm-12.out
-```
-
-```output
-This script is running on ...
-slurmstepd: error: *** JOB 12 ON node1 CANCELLED AT 2021-02-19T13:55:57
-DUE TO TIME LIMIT ***
-```
-
-Our job was killed for exceeding the amount of resources it requested. Although
-this appears harsh, this is actually a feature. Strict adherence to resource
-requests allows the scheduler to find the best possible place for your jobs.
-Even more importantly, it ensures that another user cannot use more resources
-than they've been given. If another user messes up and accidentally attempts to
-use all of the cores or memory on a node, {{ site.sched.name }} will either
-restrain their job to the requested resources or kill the job outright. Other
-jobs on the node will be unaffected. This means that one user cannot mess up
-the experience of others, the only jobs affected by a mistake in scheduling
-will be their own.
-
-## Cancelling a Job
-
-Sometimes we'll make a mistake and need to cancel a job. This can be done with
-the `{{ site.sched.del }}` command. Let's submit a job and then cancel it using
-its job number (remember to change the walltime so that it runs long enough for
-you to cancel it before it is killed!).
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-{{ site.remote.prompt }} {{ site.sched.status }} {{ site.sched.flag.user }}
-```
-
-```output
-Submitted batch job 13
-
-JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-   13 cpubase_b long_job   user01  R       0:02      1 node1
-```
-
-Now cancel the job with its job number (printed in your terminal). A clean
-return of your command prompt indicates that the request to cancel the job was
-successful.
-
-```bash
-{{ site.remote.prompt }} {{site.sched.del }} 38759
-# It might take a minute for the job to disappear from the queue...
-{{ site.remote.prompt }} {{ site.sched.status }} {{ site.sched.flag.user }}
-```
-
-```output
-JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-```
-
-:::::::::::::::::::::::::::::::::::::::  challenge
-
-## Cancelling multiple jobs
-
-We can also cancel all of our jobs at once using the `-u` option. This will
-delete all jobs for a specific user (in this case, yourself). Note that you
-can only delete your own jobs.
-
-Try submitting multiple jobs and then cancelling them all.
-
-:::::::::::::::  solution
-
-## Solution
-
-First, submit a trio of jobs:
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-```
-
-Then, cancel them all:
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.del }} -u {{ site.remote.user }}
-```
-
-:::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-## Other Types of Jobs
-
-Up to this point, we've focused on running jobs in batch mode.
-{{ site.sched.name }} also provides the ability to start an interactive session.
-
-There are very frequently tasks that need to be done interactively. Creating an
-entire job script might be overkill, but the amount of resources required is
-too much for a login node to handle. A good example of this might be building a
-genome index for alignment with a tool like [HISAT2][hisat]. Fortunately, we
-can run these types of tasks as a one-off with `{{ site.sched.interactive }}`.
-
-`{{ site.sched.interactive }}` runs a single command on the cluster and then
-exits. Let's demonstrate this by running the `hostname` command with
-`{{ site.sched.interactive }}`. (We can cancel an `{{ site.sched.interactive }}`
-job with `Ctrl-c`.)
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.interactive }} hostname
-```
-
-```output
-{{ site.remote.node }}
-```
-
-`{{ site.sched.interactive }}` accepts all of the same options as
-`{{ site.sched.submit.name }}`. However, instead of specifying these in a script,
-these options are specified on the command-line when starting a job. To submit
-a job that uses 2 CPUs for instance, we could use the following command:
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.interactive }} -n 2 echo "This job will use 2 CPUs."
-```
-
-```output
-This job will use 2 CPUs.
-This job will use 2 CPUs.
-```
-
-Typically, the resulting shell environment will be the same as that for
-`{{ site.sched.submit.name }}`.
-
-### Interactive jobs
-
-Sometimes, you will need a lot of resources for interactive use. Perhaps it's
-our first time running an analysis or we are attempting to debug something that
-went wrong with a previous job. Fortunately, {{ site.sched.name }} makes it
-easy to start an interactive job with `{{ site.sched.interactive }}`:
-
-```bash
-{{ site.remote.prompt }} {{ site.sched.interactive }} --pty bash
-```
-
-You should be presented with a bash prompt. Note that the prompt will likely
-change to reflect your new location, in this case the compute node we are
-logged on. You can also verify this with `hostname`.
-
-:::::::::::::::::::::::::::::::::::::::::  callout
-
-## Creating remote graphics
-
-To see graphical output inside your jobs, you need to use X11 forwarding. To
-connect with this feature enabled, use the `-Y` option when you login with
-the `ssh` command, e.g., `ssh -Y {{ site.remote.user }}@{{ site.remote.login }}`.
-
-To demonstrate what happens when you create a graphics window on the remote
-node, use the `xeyes` command. A relatively adorable pair of eyes should pop
-up (press `Ctrl-C` to stop). If you are using a Mac, you must have installed
-XQuartz (and restarted your computer) for this to work.
-
-If your cluster has the
-[slurm-spank-x11](https://github.com/hautreux/slurm-spank-x11) plugin
-installed, you can ensure X11 forwarding within interactive jobs by using the
-`--x11` option for `{{ site.sched.interactive }}` with the command
-`{{ site.sched.interactive }} --x11 --pty bash`.
-
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-When you are done with the interactive job, type `exit` to quit your session.
-
-
-
-[hisat]: https://daehwankimlab.github.io/hisat2/
-
-
-:::::::::::::::::::::::::::::::::::::::: keypoints
-
-- The scheduler handles how compute resources are shared between users.
-- A job is just a shell script.
-- Request *slightly* more resources than you will need.
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
-
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml b/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
index 8d176a4e..694a44a9 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
@@ -61,5 +61,3 @@ sched:
   info: "sinfo"
   comment: "#SBATCH"
   hist: "sacct"
-
-
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
index 2e12f1d8..0c2eb8fa 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
@@ -1,3 +1,3 @@
 ```output
 Submitted batch job 36855
-```
\ No newline at end of file
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.Rmd
new file mode 100644
index 00000000..6906426a
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.Rmd
@@ -0,0 +1,3 @@
+```bash
+`r config$remote$prompt` scancel 38759
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.snip
deleted file mode 100644
index 950788df..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.snip
+++ /dev/null
@@ -1 +0,0 @@
-{{ site.host_prompt }} scancel 38759
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.Rmd
new file mode 100644
index 00000000..708dfe2e
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.Rmd
@@ -0,0 +1,23 @@
+::: callout
+
+## Filesystem on ARCHER2
+
+At this point it is important to remember that ARCHER2  has two *separate*
+filesystems: `/home` and `/work`.
+
+* `/home` is meant for small files such as source code, and is the
+  filesystem that you are on when you log in
+* `/work` is a much larger and faster filesystem, meant for production
+  runs and storing large datasets
+
+The `/home` filesystem **is not mounted on the compute nodes**
+meaning that programs run in the batch queues cannot read from or
+write to files in your home directory. This has not been a problem
+so far as none of our programs have done file input or
+output. However, the parallel program we will run here reads and
+writes large images.
+
+* When you log in, you will be in your home directory, ``r config$remote$homedir``.
+* Before you run real programs on ARCHER2, you **must change directory** to
+  `/work`.
+:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.snip
deleted file mode 100644
index 1bc94d83..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.snip
+++ /dev/null
@@ -1,20 +0,0 @@
-> ## Filesystem on ARCHER2
-> At this point it is important to remember that ARCHER2  has two *separate*
-> filesystems: `/home` and `/work`.
->
-> * `/home` is meant for small files such as source code, and is the
->    filesystem that you are on when you log in
-> *  `/work` is a much larger and faster filesystem, meant for production
->    runs and storing large datasets
->
-> The `/home` filesystem **is not mounted on the compute nodes**
-> meaning that programs run in the batch queues cannot read from or
-> write to files in your home directory. This has not been a problem
-> so far as none of our programs have done file input or
-> output. However, the parallel program we will run here reads and
-> writes large images.
->
-> * When you log in, you will be in your home directory {{ site.host_homedir }}
-> * Before you run real programs on ARCHER2, you **must change directory** to
->   {{ site.host_workdir }}
-{: .callout}
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
index fcd8ee25..c7657ef5 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
@@ -1,4 +1,4 @@
 ```output
 JOBID USER         ACCOUNT     NAME     ST REASON   START_TIME TIME TIME_LEFT NODES CPUS
 38191 yourUsername yourAccount new_name PD Priority N/A        0:00 1:00:00   1     1
-```
\ No newline at end of file
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.Rmd
similarity index 92%
rename from episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.snip
rename to episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.Rmd
index 5a7eafae..ddd0d12f 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.snip
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.Rmd
@@ -1,3 +1,4 @@
+```bash
 #!/bin/bash
 
 #SBATCH --partition=standard
@@ -7,3 +8,4 @@
 echo 'This script is running on:'
 hostname
 sleep 120
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.Rmd
similarity index 89%
rename from episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.snip
rename to episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.Rmd
index f67c18fd..6e0886a7 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.snip
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.Rmd
@@ -1,2 +1,4 @@
+```output
 -rw-r--r-- 1 userid ta028 1762743 Jun 26 17:29 fuzzy.pgm
 -rw------- 1 userid ta028 1678630 Jun 26 17:33 sharpened.pgm
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
index 7205ade4..205f15ff 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
@@ -1,10 +1,12 @@
 ::: challenge
+
 ## Running parallel jobs
+
 Modify the pi-mpi-run script that you used above to use all 128 cores on
 one node.  Check the output to confirm that it used the correct number
 of cores in parallel for the calculation.
 
-::: solution
+:::: solution
 Here is a modified script
 
 ```bash
@@ -21,5 +23,5 @@ Here is a modified script
 module load cray-python
 srun python pi-mpi.py 10000000
 ```
+::::
 :::
-:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
index 328b62d6..2ec4d28f 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
@@ -1,5 +1,7 @@
 ::: challenge
+
 ## Configuring parallel jobs
+
 You will see in the job output that information is displayed about
 where each MPI process is running, in particular which node it is
 on.
@@ -9,7 +11,7 @@ but to use only 8 tasks on each of two nodes.
 Check the output file to ensure that you understand the job
 distribution.
 
-::: solution
+:::: solution
 ```bash
 #!/bin/bash
 
@@ -23,5 +25,5 @@ distribution.
 module load cray-python
 srun python pi-mpi.py 10000000
 ```
+::::
 :::
-:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
index d6a797d8..98cbb455 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
@@ -4,10 +4,12 @@ srun python pi-mpi.py 10000000
 
 And this corresponds to the four required items we described above:
 
-  1. Parallel launch program: in this case the parallel launch program is
-     called `srun`; the additional argument controls which cores are used.
-  2. Number of parallel processes per node: in this case this is 16,
-     and is specified by the option `--ntasks-per-node=16` option.
-  2. Total number of parallel processes: in this case this is also 16, because
-     we specified 1 node and 16 parallel processes per node.
-  4. Our program and arguments: in this case this is `python pi-mpi.py 10000000`.
+1. Parallel launch program: in this case the parallel launch program
+   is called `srun`; the additional argument controls which cores are
+   used.
+2. Number of parallel processes per node: in this case this is 16,
+   and is specified by the option `--ntasks-per-node=16` option.
+3. Total number of parallel processes: in this case this is also 16,
+   because we specified 1 node and 16 parallel processes per node.
+4. Our program and arguments: in this case this is 
+   `python pi-mpi.py 10000000`.
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
index 983799c3..cb09f254 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
@@ -12,4 +12,4 @@
 module load cray-python
 
 srun python pi-mpi.py 10000000
-```
\ No newline at end of file
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
index b2009095..0d1e07e3 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
@@ -1,9 +1,12 @@
 ::: challenge
+
 ## Job environment variables
 
-When Slurm runs a job, it sets a number of environment variables for the job. One of these will
-let us check our work from the last problem. The `SLURM_CPUS_PER_TASK` variable is set to the
-number of CPUs we requested with `-c`. Using the `SLURM_CPUS_PER_TASK` variable, modify your job
-so that it prints how many CPUs have been allocated.
+When Slurm runs a job, it sets a number of environment variables for
+the job. One of these will let us check our work from the last
+problem. The `SLURM_CPUS_PER_TASK` variable is set to the number of
+CPUs we requested with `-c`. Using the `SLURM_CPUS_PER_TASK`
+variable, modify your job so that it prints how many CPUs have been
+allocated.
 
 :::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
index 86f57113..43bd23a5 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
@@ -1,3 +1,3 @@
 ```bash
 `r config$remote$prompt_work` cat slurm-38193.out
-```
\ No newline at end of file
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
index 617e03e9..9f277a14 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
@@ -2,4 +2,4 @@
 This job is running on:
 nid001147
 slurmstepd: error: *** JOB 38193 ON cn01 CANCELLED AT 2017-07-02T16:35:48 DUE TO TIME LIMIT ***
-```
\ No newline at end of file
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.Rmd
new file mode 100644
index 00000000..f040e903
--- /dev/null
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.Rmd
@@ -0,0 +1,4 @@
+```output
+ JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+119867  standard    myjob   userid PD       0:00      1 (Resources) 
+```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.snip
deleted file mode 100644
index 46997eb0..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.snip
+++ /dev/null
@@ -1,2 +0,0 @@
-        JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-       119867  standard    myjob   userid PD       0:00      1 (Resources) 
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.Rmd
similarity index 100%
rename from episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.snip
rename to episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.Rmd
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
index c8d76a27..ec27cd39 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
@@ -1,6 +1,9 @@
 ::: challenge
+
 ## Cancelling multiple jobs
-We can also cancel all of our jobs at once using the `-u` option. This will delete all jobs for a
-specific user (in this case us). Note that you can only delete your own jobs.
-Try submitting multiple jobs and then cancelling them all with `scancel -u yourUsername`.
-:::
\ No newline at end of file
+
+We can also cancel all of our jobs at once using the `-u` option. This will
+delete all jobs for a specific user (in this case us). Note that you can only
+delete your own jobs.  Try submitting multiple jobs and then cancelling them
+all with `scancel -u yourUsername`.
+:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
index 9b303a0d..2d93dd78 100644
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
+++ b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
@@ -5,6 +5,7 @@ Let's demonstrate this by running the
 ```bash
 `r config$host_prompt_work` srun `r config$sched$submit$options` --time=00:01:00 hostname
 ```
+
 ```output
 nid001976
 ```
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.snip
deleted file mode 100644
index 06b7fc91..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-script.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-Submitted batch job 7
-```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.Rmd
similarity index 95%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.Rmd
index 6bb1b93e..9011f5b4 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/basic-job-status.Rmd
@@ -1,8 +1,7 @@
-```
+```output
 JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
     9 cpubase_b example-   user01  R       0:05      1 node1
 ```
-{: .output}
 
 We can see all the details of our job, most importantly that it is in the `R`
 or `RUNNING` state. Sometimes our jobs might need to wait in a queue
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.Rmd
similarity index 89%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.Rmd
index 838c5464..815f3b9d 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/job-with-name-status.Rmd
@@ -1,5 +1,4 @@
-```
+```output
 JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
    10 cpubase_b hello-wo   user01  R       0:02      1 node1
 ```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/option-flags-list.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/option-flags-list.Rmd
similarity index 100%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/option-flags-list.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/option-flags-list.Rmd
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.Rmd
new file mode 100644
index 00000000..21fec883
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.Rmd
@@ -0,0 +1,32 @@
+::: challenge
+
+## Job environment variables
+
+When {{ site.sched.name }} runs a job, it sets a number of environment
+variables for the job. One of these will let us check what directory our job
+script was submitted from. The `SLURM_SUBMIT_DIR` variable is set to the
+directory from which our job was submitted. Using the `SLURM_SUBMIT_DIR`
+variable, modify your job so that it prints out the location from which the
+job was submitted.
+
+:::: solution
+
+## Solution
+
+```bash
+{{ site.remote.prompt }} nano example-job.sh
+{{ site.remote.prompt }} cat example-job.sh
+```
+
+```bash
+`r site$remote$bash_shebang`
+#SBATCH -t 00:00:30
+
+echo -n "This script is running on "
+hostname
+
+echo "This job was launched in the following directory:"
+echo ${SLURM_SUBMIT_DIR}
+```
+::::
+:::
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.snip
deleted file mode 100644
index 5234a4ed..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/print-sched-variables.snip
+++ /dev/null
@@ -1,30 +0,0 @@
-> ## Job environment variables
->
-> When {{ site.sched.name }} runs a job, it sets a number of environment
-> variables for the job. One of these will let us check what directory our job
-> script was submitted from. The `SLURM_SUBMIT_DIR` variable is set to the
-> directory from which our job was submitted. Using the `SLURM_SUBMIT_DIR`
-> variable, modify your job so that it prints out the location from which the
-> job was submitted.
->
-> > ## Solution
-> >
-> > ```
-> > {{ site.remote.prompt }} nano example-job.sh
-> > {{ site.remote.prompt }} cat example-job.sh
-> > ```
-> > {: .language-bash}
-> >
-> > ```
-> > {{ site.remote.bash_shebang }}
-> > #SBATCH -t 00:00:30
-> >
-> > echo -n "This script is running on "
-> > hostname
-> >
-> > echo "This job was launched in the following directory:"
-> > echo ${SLURM_SUBMIT_DIR}
-> > ```
-> > {: .output}
-> {: .solution}
-{: .challenge}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.Rmd
new file mode 100644
index 00000000..7dde2ada
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.Rmd
@@ -0,0 +1,3 @@
+```bash
+`r config$remote$prompt` cat slurm-12.out
+```
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.snip
deleted file mode 100644
index a9eae8de..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-job.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-{{ site.remote.prompt }} cat slurm-12.out
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.Rmd
similarity index 88%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.Rmd
index 180d3ea4..106d9ecc 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/runtime-exceeded-output.Rmd
@@ -1,6 +1,5 @@
-```
+```output
 This script is running on ...
 slurmstepd: error: *** JOB 12 ON node1 CANCELLED AT 2021-02-19T13:55:57
 DUE TO TIME LIMIT ***
 ```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.Rmd
similarity index 90%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.Rmd
index c7af2eef..3cfb8c95 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-begin.Rmd
@@ -1,7 +1,6 @@
-```
+```output
 Submitted batch job 13
 
 JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
    13 cpubase_b long_job   user01  R       0:02      1 node1
 ```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.Rmd
similarity index 82%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.Rmd
index 5429787d..ccb9cd24 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-job-cancel.Rmd
@@ -1,4 +1,3 @@
-```
+```output
 JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
 ```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.Rmd
new file mode 100644
index 00000000..5ee30f8d
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.Rmd
@@ -0,0 +1,29 @@
+::: challenge
+## Cancelling multiple jobs
+
+We can also cancel all of our jobs at once using the `-u` option. This will
+delete all jobs for a specific user (in this case, yourself). Note that you
+can only delete your own jobs.
+
+Try submitting multiple jobs and then cancelling them all.
+
+:::: solution
+
+## Solution
+
+First, submit a trio of jobs:
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+```
+
+Then, cancel them all:
+
+```bash
+`r config$remote$prompt` `r config$sched$del` -u `r config$remote$user`
+```
+
+::::
+:::
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.snip
deleted file mode 100644
index 3a229b55..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/terminate-multiple-jobs.snip
+++ /dev/null
@@ -1,27 +0,0 @@
-> ## Cancelling multiple jobs
->
-> We can also cancel all of our jobs at once using the `-u` option. This will
-> delete all jobs for a specific user (in this case, yourself). Note that you
-> can only delete your own jobs.
->
-> Try submitting multiple jobs and then cancelling them all.
->
-> > ## Solution
-> >
-> > First, submit a trio of jobs:
-> >
-> > ```
-> > {{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-> > {{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-> > {{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}example-job.sh
-> > ```
-> > {: .language-bash}
-> >
-> > Then, cancel them all:
-> >
-> > ```
-> > {{ site.remote.prompt }} {{ site.sched.del }} -u {{ site.remote.user }}
-> > ```
-> > {: .language-bash}
-> {: .solution}
-{: .challenge}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.Rmd
new file mode 100644
index 00000000..0a305412
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.Rmd
@@ -0,0 +1,66 @@
+The `r config$sched$interactive` command runs a single command on the cluster
+and then exits. Let's demonstrate this by running the `hostname` command with
+`r config$sched$interactive`. (We can cancel an `r config$sched$interactive`
+job with `Ctrl-c`.)
+
+```bash
+`r config$remote.prompt` `r config$sched$interactive` hostname
+```
+
+```output
+{{ config$remote.node`
+```
+
+`r config$sched$interactive` accepts all of the same options as
+`r config$sched$submit.name`. However, instead of specifying these in a script,
+these options are specified on the command-line when starting a job. To submit
+a job that uses 2 CPUs for instance, we could use the following command:
+
+```bash
+`r config$remote.prompt` `r config$sched$interactive` -n 2 echo "This job will use 2 CPUs."
+```
+
+```output
+This job will use 2 CPUs.
+This job will use 2 CPUs.
+```
+
+Typically, the resulting shell environment will be the same as that for
+`r config$sched$submit.name`.
+
+### Interactive jobs
+
+Sometimes, you will need a lot of resources for interactive use. Perhaps it's
+our first time running an analysis or we are attempting to debug something that
+went wrong with a previous job. Fortunately, {{ config$sched$name` makes it
+easy to start an interactive job with `r config$sched$interactive`:
+
+```bash
+`r config$remote.prompt` `r config$sched$interactive` --pty bash
+```
+
+You should be presented with a bash prompt. Note that the prompt will likely
+change to reflect your new location, in this case the compute node we are
+logged on. You can also verify this with `hostname`.
+
+::: callout
+
+## Creating remote graphics
+
+To see graphical output inside your jobs, you need to use X11 forwarding. To
+connect with this feature enabled, use the `-Y` option when you login with
+the `ssh` command, e.g., `r paste("ssh -Y ", config$remote$user, "@", config$remote$login, sep="")`.
+
+To demonstrate what happens when you create a graphics window on the remote
+node, use the `xeyes` command. A relatively adorable pair of eyes should pop
+up (press `Ctrl-C` to stop). If you are using a Mac, you must have installed
+XQuartz (and restarted your computer) for this to work.
+
+If your cluster has the
+[slurm-spank-x11](https://github.com/hautreux/slurm-spank-x11) plugin
+installed, you can ensure X11 forwarding within interactive jobs by using the
+`--x11` option for `r config$sched$interactive` with the command
+`r paste(config$sched$interactive, " --x11", " --pty bash", sep="")`.
+:::
+
+When you are done with the interactive job, type `exit` to quit your session.
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.snip
deleted file mode 100644
index 40b11437..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/scheduler/using-nodes-interactively.snip
+++ /dev/null
@@ -1,69 +0,0 @@
-`{{ site.sched.interactive }}` runs a single command on the cluster and then
-exits. Let's demonstrate this by running the `hostname` command with
-`{{ site.sched.interactive }}`. (We can cancel an `{{ site.sched.interactive }}`
-job with `Ctrl-c`.)
-
-```
-{{ site.remote.prompt }} {{ site.sched.interactive }} hostname
-```
-{: .language-bash}
-
-```
-{{ site.remote.node }}
-```
-{: .output}
-
-`{{ site.sched.interactive }}` accepts all of the same options as
-`{{ site.sched.submit.name }}`. However, instead of specifying these in a script,
-these options are specified on the command-line when starting a job. To submit
-a job that uses 2 CPUs for instance, we could use the following command:
-
-```
-{{ site.remote.prompt }} {{ site.sched.interactive }} -n 2 echo "This job will use 2 CPUs."
-```
-{: .language-bash}
-
-```
-This job will use 2 CPUs.
-This job will use 2 CPUs.
-```
-{: .output}
-
-Typically, the resulting shell environment will be the same as that for
-`{{ site.sched.submit.name }}`.
-
-### Interactive jobs
-
-Sometimes, you will need a lot of resources for interactive use. Perhaps it's
-our first time running an analysis or we are attempting to debug something that
-went wrong with a previous job. Fortunately, {{ site.sched.name }} makes it
-easy to start an interactive job with `{{ site.sched.interactive }}`:
-
-```
-{{ site.remote.prompt }} {{ site.sched.interactive }} --pty bash
-```
-{: .language-bash}
-
-You should be presented with a bash prompt. Note that the prompt will likely
-change to reflect your new location, in this case the compute node we are
-logged on. You can also verify this with `hostname`.
-
-> ## Creating remote graphics
->
-> To see graphical output inside your jobs, you need to use X11 forwarding. To
-> connect with this feature enabled, use the `-Y` option when you login with
-> the `ssh` command, e.g., `ssh -Y {{ site.remote.user }}@{{ site.remote.login }}`.
->
-> To demonstrate what happens when you create a graphics window on the remote
-> node, use the `xeyes` command. A relatively adorable pair of eyes should pop
-> up (press `Ctrl-C` to stop). If you are using a Mac, you must have installed
-> XQuartz (and restarted your computer) for this to work.
->
-> If your cluster has the
-> [slurm-spank-x11](https://github.com/hautreux/slurm-spank-x11) plugin
-> installed, you can ensure X11 forwarding within interactive jobs by using the
-> `--x11` option for `{{ site.sched.interactive }}` with the command
-> `{{ site.sched.interactive }} --x11 --pty bash`.
-{: .callout}
-
-When you are done with the interactive job, type `exit` to quit your session.

From 4f4fb85b25ba0d2edaa53c598874f2a603e22b3e Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 15:14:37 -0400
Subject: [PATCH 21/33] Workbenched Ep. 14

---
 config.yaml                                   |  2 +-
 ...iables.md => 14-environment-variables.Rmd} | 22 +++++++++----------
 2 files changed, 12 insertions(+), 12 deletions(-)
 rename episodes/{14-environment-variables.md => 14-environment-variables.Rmd} (95%)

diff --git a/config.yaml b/config.yaml
index 1f60cd16..41716f0f 100644
--- a/config.yaml
+++ b/config.yaml
@@ -69,7 +69,7 @@ episodes:
   - 11-connecting.Rmd
   - 12-cluster.Rmd
   - 13-scheduler.Rmd
-  - 14-environment-variables.md
+  - 14-environment-variables.Rmd
   - 15-modules.md
   - 16-transferring-files.md
   - 17-parallel.md
diff --git a/episodes/14-environment-variables.md b/episodes/14-environment-variables.Rmd
similarity index 95%
rename from episodes/14-environment-variables.md
rename to episodes/14-environment-variables.Rmd
index 84ccdec9..2c150b5d 100644
--- a/episodes/14-environment-variables.md
+++ b/episodes/14-environment-variables.Rmd
@@ -4,6 +4,11 @@ teaching: 10
 exercises: 5
 ---
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Understand how variables are implemented in the shell
@@ -27,8 +32,7 @@ exercises: 5
 
 This episode has been remixed from the
 [Shell Extras episode on Shell Variables](https://github.com/carpentries-incubator/shell-extras/blob/gh-pages/_episodes/08-environment-variables.md)
-and the [HPC Shell episode on scripts](https://github.com/hpc-carpentry/hpc-shell/blob/gh-pages/_episodes/05-scripts.md)
-
+and the [HPC Shell episode on scripts](https://github.com/hpc-carpentry/hpc-shell/blob/gh-pages/_episodes/05-scripts.md).
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -191,7 +195,7 @@ run**.
 
 ## Job environment variables
 
-When {{ site.sched.name }} runs a job, it sets a number of environment
+When ``r config$sched$name`` runs a job, it sets a number of environment
 variables for the job. One of these will let us check what directory our job
 script was submitted from. The `SLURM_SUBMIT_DIR` variable is set to the
 directory from which our job was submitted. Using the `SLURM_SUBMIT_DIR`
@@ -203,13 +207,13 @@ job was submitted.
 ## Solution
 
 ```bash
-{{ site.remote.prompt }} nano example-job.sh
-{{ site.remote.prompt }} cat example-job.sh
+`r config$remote$prompt` nano example-job.sh
+`r config$remote$prompt` cat example-job.sh
 ```
 
 ```output
-{{ site.remote.bash_shebang }}
-#SBATCH -t 00:00:30
+`r config$remote$bash_shebang`
+`r config$sched$comment` `r config$sched$flag$time` 00:00:30
 
 echo -n "This script is running on "
 hostname
@@ -285,8 +289,6 @@ runtime environment to make that possible without us needing to do a lot of
 bookkeeping on what the value of `PATH` (and other important environment
 variables) is or should be.
 
-
-
 :::::::::::::::::::::::::::::::::::::::: keypoints
 
 - Shell variables are by default treated as strings
@@ -295,5 +297,3 @@ variables) is or should be.
 - The `PATH` variable defines the shell's search path
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
-
-

From 5098d86025f7f77ceb8bb2ec6991ec6f22360d0c Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 15:32:31 -0400
Subject: [PATCH 22/33] Workbenched Ep. 15, without snippets

---
 config.yaml                                |  2 +-
 episodes/{15-modules.md => 15-modules.Rmd} | 60 +++++++++++-----------
 2 files changed, 32 insertions(+), 30 deletions(-)
 rename episodes/{15-modules.md => 15-modules.Rmd} (91%)

diff --git a/config.yaml b/config.yaml
index 41716f0f..316500ab 100644
--- a/config.yaml
+++ b/config.yaml
@@ -70,7 +70,7 @@ episodes:
   - 12-cluster.Rmd
   - 13-scheduler.Rmd
   - 14-environment-variables.Rmd
-  - 15-modules.md
+  - 15-modules.Rmd
   - 16-transferring-files.md
   - 17-parallel.md
   - 18-resources.md
diff --git a/episodes/15-modules.md b/episodes/15-modules.Rmd
similarity index 91%
rename from episodes/15-modules.md
rename to episodes/15-modules.Rmd
index 4b77091d..1bb42a48 100644
--- a/episodes/15-modules.md
+++ b/episodes/15-modules.Rmd
@@ -4,6 +4,11 @@ teaching: 30
 exercises: 15
 ---
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Load and use a software package.
@@ -75,7 +80,7 @@ you are using.
 To see available software modules, use `module avail`:
 
 ```bash
-{{ site.remote.prompt }} module avail
+`r config$remote$prompt` module avail
 ```
 
 ```output
@@ -106,7 +111,7 @@ loaded in your environment. If you have no modules loaded, you will see a
 message telling you so
 
 ```bash
-{{ site.remote.prompt }} module list
+`r config$remote$prompt` module list
 ```
 
 ```output
@@ -123,13 +128,13 @@ command. `which` looks for programs the same way that Bash does, so we can use
 it to tell us where a particular piece of software is stored.
 
 ```bash
-{{ site.remote.prompt }} which python3
+`r config$remote$prompt` which python3
 ```
 
 If the `python3` command was unavailable, we would see output like
 
 ```output
-/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/{{site.remote.user}}/.local/bin:/home/{{site.remote.user}}/bin)
+/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/`r config$remote$user`/.local/bin:/home/`r config$remote$user`/bin)
 ```
 
 Note that this wall of text is really a list, with values separated
@@ -144,8 +149,8 @@ searched the following directories for `python3`, without success:
 /usr/local/sbin
 /usr/sbin
 /opt/puppetlabs/bin
-/home/{{site.remote.user}}/.local/bin
-/home/{{site.remote.user}}/bin
+/home/`r config$remote$user`/.local/bin
+/home/`r config$remote$user`/bin
 ```
 
 However, in our case we do have an existing `python3` available so we see
@@ -160,8 +165,8 @@ a module to access it.
 We can load the `python3` command with `module load`:
 
 ```bash
-{{ site.remote.prompt }} module load {{ site.remote.module_python3 }}
-{{ site.remote.prompt }} which python3
+`r config$remote$prompt` module load `r config$remote$module_python3`
+`r config$remote$prompt` which python3
 ```
 
 ```output
@@ -178,7 +183,7 @@ before giving up and telling us it can't find it. As with all environment
 variables we can print it out using `echo`.
 
 ```bash
-{{ site.remote.prompt }} echo $PATH
+`r config$remote$prompt` echo $PATH
 ```
 
 ```output
@@ -191,7 +196,7 @@ ran the `module load` command, it added a directory to the beginning of our
 `$PATH`. Let's examine what's there:
 
 ```bash
-{{ site.remote.prompt }} ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
+`r config$remote$prompt` ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
 ```
 
 ```output
@@ -219,7 +224,7 @@ To demonstrate, let's use `module list`. `module list` shows all loaded
 software modules.
 
 ```bash
-{{ site.remote.prompt }} module list
+`r config$remote$prompt` module list
 ```
 
 ```output
@@ -230,8 +235,8 @@ Currently Loaded Modules:
 ```
 
 ```bash
-{{ site.remote.prompt }} module load GROMACS
-{{ site.remote.prompt }} module list
+`r config$remote$prompt` module load GROMACS
+`r config$remote$prompt` module list
 ```
 
 ```output
@@ -257,8 +262,8 @@ package), also loaded `GMP/6.2.0-GCCcore-x.y.z` and
 `GROMACS` package.
 
 ```bash
-{{ site.remote.prompt }} module unload GROMACS
-{{ site.remote.prompt }} module list
+`r config$remote$prompt` module unload GROMACS
+`r config$remote$prompt` module list
 ```
 
 ```output
@@ -283,8 +288,8 @@ not). If we wanted to unload everything at once, we could run `module purge`
 (unloads everything).
 
 ```bash
-{{ site.remote.prompt }} module purge
-{{ site.remote.prompt }} module list
+`r config$remote$prompt` module purge
+`r config$remote$prompt` module list
 ```
 
 ```output
@@ -320,7 +325,7 @@ software is loaded.
 Let's examine the output of `module avail` more closely.
 
 ```bash
-{{ site.remote.prompt }} module avail
+`r config$remote$prompt` module avail
 ```
 
 ```output
@@ -358,23 +363,23 @@ compute node).
 ## Solution
 
 ```bash
-{{ site.remote.prompt }} nano python-module.sh
-{{ site.remote.prompt }} cat python-module.sh
+`r config$remote$prompt` nano python-module.sh
+`r config$remote$prompt` cat python-module.sh
 ```
 
 ```output
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.partition }}{% if site.sched.flag.qos %}
-{{ site.sched.comment }} {{ site.sched.flag.qos }}
-{% endif %}{{ site.sched.comment }} {{ site.sched.flag.time }} 00:00:30
+`r config$remote$bash_shebang`
+`r config$sched$comment` `r config$sched$flag$partition`
+`r if (!is.null(config$sched$flag$qos)) {print(paste(config$sched$comment,config$sched$flag$qos))}
+`r config$sched$comment` `r config$sched$flag$time` 00:00:30
 
-module load {{ site.remote.module_python3 }}
+module load `r config$remote$module_python3`
 
 python3 --version
 ```
 
 ```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} {% if site.sched.submit.options != '' %}{{ site.sched.submit.options }} {% endif %}python-module.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` python-module.sh
 ```
 
 :::::::::::::::::::::::::
@@ -382,7 +387,6 @@ python3 --version
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 
-
 :::::::::::::::::::::::::::::::::::::::: keypoints
 
 - Load software with `module load softwareName`.
@@ -390,5 +394,3 @@ python3 --version
 - The module system handles software versioning and package conflicts for you automatically.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
-
-

From 2140d2f57614de8477bfdae0cc4ea12b13cf0ff8 Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 15:47:18 -0400
Subject: [PATCH 23/33] Workbenched Ep. 16, without snippets

---
 config.yaml                                   |  2 +-
 ...ing-files.md => 16-transferring-files.Rmd} | 58 +++++++++----------
 2 files changed, 30 insertions(+), 30 deletions(-)
 rename episodes/{16-transferring-files.md => 16-transferring-files.Rmd} (90%)

diff --git a/config.yaml b/config.yaml
index 316500ab..fa65d1b9 100644
--- a/config.yaml
+++ b/config.yaml
@@ -71,7 +71,7 @@ episodes:
   - 13-scheduler.Rmd
   - 14-environment-variables.Rmd
   - 15-modules.Rmd
-  - 16-transferring-files.md
+  - 16-transferring-files.Rmd
   - 17-parallel.md
   - 18-resources.md
   - 19-responsibility.md
diff --git a/episodes/16-transferring-files.md b/episodes/16-transferring-files.Rmd
similarity index 90%
rename from episodes/16-transferring-files.md
rename to episodes/16-transferring-files.Rmd
index 824489f0..2108df8a 100644
--- a/episodes/16-transferring-files.md
+++ b/episodes/16-transferring-files.Rmd
@@ -4,6 +4,11 @@ teaching: 15
 exercises: 15
 ---
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Transfer files to and from a computing cluster.
@@ -62,9 +67,9 @@ Use one of the above commands to save the tarball as `amdahl.tar.gz`.
 ## `wget` and `curl` Commands
 
 ```bash
-{{ site.local.prompt }} wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
+`r config$local$prompt` wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
 # or
-{{ site.local.prompt }} curl -o amdahl.tar.gz -L https://github.com/hpc-carpentry/amdahl/tarball/main
+`r config$local$prompt` curl -o amdahl.tar.gz -L https://github.com/hpc-carpentry/amdahl/tarball/main
 ```
 
 The `-L` option to `curl` tells it to follow URL redirects (which `wget` does by default).
@@ -78,7 +83,7 @@ The `-L` option to `curl` tells it to follow URL redirects (which `wget` does by
 After downloading the file, use `ls` to see it in your working directory:
 
 ```bash
-{{ site.local.prompt }} ls
+`r config$local$prompt` ls
 ```
 
 ## Archiving Files
@@ -115,7 +120,7 @@ However, the argument following `-f` must be a filename, so writing `-ft` will
 *not* work.
 
 ```bash
-{{ site.local.prompt }} tar -tf amdahl.tar.gz
+`r config$local$prompt` tar -tf amdahl.tar.gz
 hpc-carpentry-amdahl-46c9b4b/
 hpc-carpentry-amdahl-46c9b4b/.github/
 hpc-carpentry-amdahl-46c9b4b/.github/workflows/
@@ -150,7 +155,7 @@ Using the flags above, unpack the source code tarball into a new
 directory named "amdahl" using `tar`.
 
 ```bash
-{{ site.local.prompt }} tar -xvzf amdahl.tar.gz
+`r config$local$prompt` tar -xvzf amdahl.tar.gz
 ```
 
 ```output
@@ -181,16 +186,16 @@ The folder has an unfortunate name, so let's change that to something more
 convenient.
 
 ```bash
-{{ site.local.prompt }} mv hpc-carpentry-amdahl-46c9b4b amdahl
+`r config$local$prompt` mv hpc-carpentry-amdahl-46c9b4b amdahl
 ```
 
 Check the size of the extracted directory and compare to the compressed
 file size, using `du` for "**d**isk **u**sage".
 
 ```bash
-{{ site.local.prompt }} du -sh amdahl.tar.gz
+`r config$local$prompt` du -sh amdahl.tar.gz
 8.0K     amdahl.tar.gz
-{{ site.local.prompt }} du -sh amdahl
+`r config$local$prompt` du -sh amdahl
 48K    amdahl
 ```
 
@@ -202,7 +207,7 @@ extracting it -- set a `c` flag instead of `x`, set the archive filename,
 then provide a directory to compress:
 
 ```bash
-{{ site.local.prompt }} tar -cvzf compressed_code.tar.gz amdahl
+`r config$local$prompt` tar -cvzf compressed_code.tar.gz amdahl
 ```
 
 ```output
@@ -264,7 +269,7 @@ mechanism.
 To *upload to* another computer, the template command is
 
 ```bash
-{{ site.local.prompt }} scp local_file {{ site.remote.user }}@{{ site.remote.login }}:remote_destination
+`r config$local$prompt` scp local_file `r config$remote$user`@`r config$remote$login`:remote_destination
 ```
 
 in which `@` and `:` are field separators and `remote_destination` is a path
@@ -283,12 +288,12 @@ for `local_file`.
 Upload the lesson material to your remote home directory like so:
 
 ```bash
-{{ site.local.prompt }} scp amdahl.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:
+`r config$local$prompt` scp amdahl.tar.gz `r config$remote$user`@`r config$remote$login`:
 ```
 
 :::::::::::::::::::::::::::::::::::::::  challenge
 
-## Why Not Download on {{ site.remote.name }} Directly?
+## Why Not Download on `r config$remote$name` Directly?
 
 Most computer clusters are protected from the open internet by a *firewall*.
 For enhanced security, some are configured to allow traffic *inbound*, but
@@ -305,10 +310,10 @@ OK!
 ## Commands
 
 ```bash
-{{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }}
-{{ site.remote.prompt }} wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
+`r config$local$prompt` ssh `r config$remote$user`@`r config$remote$login`
+`r config$remote$prompt` wget -O amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
 # or
-{{ site.remote.prompt }} curl -o amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
+`r config$remote$prompt` curl -o amdahl.tar.gz https://github.com/hpc-carpentry/amdahl/tarball/main
 ```
 
 :::::::::::::::::::::::::
@@ -327,7 +332,7 @@ until it reaches the bottom of the directory tree rooted at the folder name you
 provided.
 
 ```bash
-{{ site.local.prompt }} scp -r amdahl {{ site.remote.user }}@{{ site.remote.login }}:
+`r config$local$prompt` scp -r amdahl `r config$remote$user`@`r config$remote$login`:
 ```
 
 :::::::::::::::::::::::::::::::::::::::::  callout
@@ -378,7 +383,7 @@ The syntax is similar to `scp`. To transfer *to* another computer with
 commonly used options:
 
 ```bash
-{{ site.local.prompt }} rsync -avP amdahl.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:
+`r config$local$prompt` rsync -avP amdahl.tar.gz `r config$remote$user`@`r config$remote$login`:
 ```
 
 The options are:
@@ -392,7 +397,7 @@ The options are:
 To recursively copy a directory, we can use the same options:
 
 ```bash
-{{ site.local.prompt }} rsync -avP amdahl {{ site.remote.user }}@{{ site.remote.login }}:~/
+`r config$local$prompt` rsync -avP amdahl `r config$remote$user`@`r config$remote$login`:~/
 ```
 
 As written, this will place the local directory and its contents under your
@@ -404,7 +409,7 @@ copied directly into the destination directory.
 To download a file, we simply change the source and destination:
 
 ```bash
-{{ site.local.prompt }} rsync -avP {{ site.remote.user }}@{{ site.remote.login }}:amdahl ./
+`r config$local$prompt` rsync -avP `r config$remote$user`@`r config$remote$login`:amdahl ./
 ```
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -423,7 +428,7 @@ Say we have to connect `rsync` through port 768 instead of 22. How would we
 modify this command?
 
 ```bash
-{{ site.local.prompt }} rsync amdahl.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:
+`r config$local$prompt` rsync amdahl.tar.gz `r config$remote$user`@`r config$remote$login`:
 ```
 
 *Hint:* check the `man` page or "help" for `rsync`.
@@ -433,11 +438,11 @@ modify this command?
 ## Solution
 
 ```bash
-{{ site.local.prompt }} man rsync
-{{ site.local.prompt }} rsync --help | grep port
+`r config$local$prompt` man rsync
+`r config$local$prompt` rsync --help | grep port
      --port=PORT             specify double-colon alternate port number
 See http://rsync.samba.org/ for updates, bug reports, and answers
-{{ site.local.prompt }} rsync --port=768 amdahl.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:
+`r config$local$prompt` rsync --port=768 amdahl.tar.gz `r config$remote$user`@`r config$remote$login`:
 ```
 
 (Note that this command will fail, as the correct port in this case is the
@@ -466,7 +471,7 @@ side.
 To connect to the cluster, we'll just need to enter our credentials at the top
 of the screen:
 
-- Host: `sftp://{{ site.remote.login }}`
+- Host: `sftp://`r config$remote$login``
 - User: Your cluster username
 - Password: Your cluster password
 - Port: (leave blank to use the default port)
@@ -482,12 +487,9 @@ will be more efficient than using FileZilla (or related applications) that
 would copy from the source to your local machine, then to the destination
 machine.
 
-
-
 [git-swc]: https://swcarpentry.github.io/git-novice/
 [rsync]: https://rsync.samba.org/
 
-
 :::::::::::::::::::::::::::::::::::::::: keypoints
 
 - `wget` and `curl -O` download a file from the internet.
@@ -495,5 +497,3 @@ machine.
 - You can use an SFTP client like FileZilla to transfer files through a GUI.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
-
-

From f29cda2b004b835afc44328ffca1d0bbd950a73b Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 16:18:16 -0400
Subject: [PATCH 24/33] Workbenched Ep. 17, without snippets

---
 config.yaml                                  |   2 +-
 episodes/{17-parallel.md => 17-parallel.Rmd} | 177 ++++++++++---------
 2 files changed, 92 insertions(+), 87 deletions(-)
 rename episodes/{17-parallel.md => 17-parallel.Rmd} (76%)

diff --git a/config.yaml b/config.yaml
index fa65d1b9..8340971b 100644
--- a/config.yaml
+++ b/config.yaml
@@ -72,7 +72,7 @@ episodes:
   - 14-environment-variables.Rmd
   - 15-modules.Rmd
   - 16-transferring-files.Rmd
-  - 17-parallel.md
+  - 17-parallel.Rmd
   - 18-resources.md
   - 19-responsibility.md
 
diff --git a/episodes/17-parallel.md b/episodes/17-parallel.Rmd
similarity index 76%
rename from episodes/17-parallel.md
rename to episodes/17-parallel.Rmd
index 7d587c36..9f05f34c 100644
--- a/episodes/17-parallel.md
+++ b/episodes/17-parallel.Rmd
@@ -4,6 +4,11 @@ teaching: 30
 exercises: 60
 ---
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Install a Python package using `pip`
@@ -29,7 +34,7 @@ we have to improve the performance of computational tasks.
 If you disconnected, log back in to the cluster.
 
 ```bash
-{{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }}
+`r config$local$prompt` ssh `r config$remote$user`@`r config$remote$login`
 ```
 
 ## Install the Amdahl Program
@@ -40,8 +45,8 @@ Move into the extracted directory, then use the Package Installer for Python,
 or `pip`, to install it in your ("user") home directory:
 
 ```bash
-{{ site.remote.prompt }} cd amdahl
-{{ site.remote.prompt }} python3 -m pip install --user .
+`r config$remote$prompt` cd amdahl
+`r config$remote$prompt` python3 -m pip install --user .
 ```
 
 :::::::::::::::::::::::::::::::::::::::::  callout
@@ -73,20 +78,20 @@ retrieve the tarball from <https://github.com/mpi4py/mpi4py/tarball/master>
 then `rsync` it to the cluster, extract, and install:
 
 ```bash
-{{ site.local.prompt }} wget -O mpi4py.tar.gz https://github.com/mpi4py/mpi4py/releases/download/3.1.4/mpi4py-3.1.4.tar.gz
-{{ site.local.prompt }} scp mpi4py.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:
+`r config$local$prompt` wget -O mpi4py.tar.gz https://github.com/mpi4py/mpi4py/releases/download/3.1.4/mpi4py-3.1.4.tar.gz
+`r config$local$prompt` scp mpi4py.tar.gz `r config$remote$user`@`r config$remote$login`:
 # or
-{{ site.local.prompt }} rsync -avP mpi4py.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:
+`r config$local$prompt` rsync -avP mpi4py.tar.gz `r config$remote$user`@`r config$remote$login`:
 ```
 
 ```bash
-{{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }}
-{{ site.remote.prompt }} tar -xvzf mpi4py.tar.gz  # extract the archive
-{{ site.remote.prompt }} mv mpi4py* mpi4py        # rename the directory
-{{ site.remote.prompt }} cd mpi4py
-{{ site.remote.prompt }} python3 -m pip install --user .
-{{ site.remote.prompt }} cd ../amdahl
-{{ site.remote.prompt }} python3 -m pip install --user .
+`r config$local$prompt` ssh `r config$remote$user`@`r config$remote$login`
+`r config$remote$prompt` tar -xvzf mpi4py.tar.gz  # extract the archive
+`r config$remote$prompt` mv mpi4py* mpi4py        # rename the directory
+`r config$remote$prompt` cd mpi4py
+`r config$remote$prompt` python3 -m pip install --user .
+`r config$remote$prompt` cd ../amdahl
+`r config$remote$prompt` python3 -m pip install --user .
 ```
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -107,7 +112,7 @@ To check whether this warning is a problem, use `which` to search for the
 `amdahl` program:
 
 ```bash
-{{ site.remote.prompt }} which amdahl
+`r config$remote$prompt` which amdahl
 ```
 
 If the command returns no output, displaying a new prompt, it means the file
@@ -117,15 +122,15 @@ Edit your shell configuration file as follows, then log off the cluster and
 back on again so it takes effect.
 
 ```bash
-{{ site.remote.prompt }} nano ~/.bashrc
-{{ site.remote.prompt }} tail ~/.bashrc
+`r config$remote$prompt` nano ~/.bashrc
+`r config$remote$prompt` tail ~/.bashrc
 ```
 
 ```output
 export PATH=${PATH}:${HOME}/.local/bin
 ```
 
-After logging back in to {{ site.remote.login }}, `which` should be able to
+After logging back in to `r config$remote$login`, `which` should be able to
 find `amdahl` without difficulties.
 If you had to load a Python module, load it again.
 
@@ -137,7 +142,7 @@ If you had to load a Python module, load it again.
 Many command-line programs include a "help" message. Try it with `amdahl`:
 
 ```bash
-{{ site.remote.prompt }} amdahl --help
+`r config$remote$prompt` amdahl --help
 ```
 
 ```output
@@ -163,33 +168,33 @@ tell us the important flags we might want to use when launching it.
 Create a submission file, requesting one task on a single node, then launch it.
 
 ```bash
-{{ site.remote.prompt }} nano serial-job.sh
-{{ site.remote.prompt }} cat serial-job.sh
+`r config$remote$prompt` nano serial-job.sh
+`r config$remote$prompt` cat serial-job.sh
 ```
 
 ```bash
-{{ 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
+`r config$remote$bash_shebang`
+`r config$sched$comment` `r config$sched$flag$name` solo-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 1
 
 # Load the computing environment we need
-module load {{ site.remote.module_python3 }}
+module load `r config$remote$module_python3`
 
 # Execute the task
 amdahl
 ```
 
 ```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} serial-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` serial-job.sh
 ```
 
-As before, use the {{ site.sched.name }} status commands to check whether your job
+As before, use the `r config$sched$name` status commands to check whether your job
 is running and when it ends:
 
 ```bash
-{{ site.remote.prompt }} {{ site.sched.status }} {{ site.sched.flag.user }}
+`r config$remote$prompt` `r config$sched$status` `r config$sched$flag$user`
 ```
 
 Use `ls` to locate the output file. The `-t` flag sorts in
@@ -203,7 +208,7 @@ The cluster output should be written to a file in the folder you launched the
 job from. For example,
 
 ```bash
-{{ site.remote.prompt }} ls -t
+`r config$remote$prompt` ls -t
 ```
 
 ```output
@@ -211,15 +216,15 @@ slurm-347087.out  serial-job.sh  amdahl  README.md  LICENSE.txt
 ```
 
 ```bash
-{{ site.remote.prompt }} cat slurm-347087.out
+`r config$remote$prompt` cat slurm-347087.out
 ```
 
 ```output
 Doing 30.000 seconds of 'work' on 1 processor,
 which should take 30.000 seconds with 0.850 parallel proportion of the workload.
 
-  Hello, World! I am process 0 of 1 on {{ site.remote.node }}. I will do all the serial 'work' for 4.500 seconds.
-  Hello, World! I am process 0 of 1 on {{ site.remote.node }}. I will do parallel 'work' for 25.500 seconds.
+  Hello, World! I am process 0 of 1 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
+  Hello, World! I am process 0 of 1 on `r config$remote$node`. I will do parallel 'work' for 25.500 seconds.
 
 Total execution time (according to rank 0): 30.033 seconds
 ```
@@ -278,27 +283,26 @@ In the context of a queuing system, however, it is frequently the case that
 MPI run-time will obtain the necessary parameters from the queuing system,
 by examining the environment variables set when the job is launched.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 Let's modify the job script to request more cores and use the MPI run-time.
 
-```bash, bash
-{{ site.remote.prompt }} cp serial-job.sh parallel-job.sh
-{{ site.remote.prompt }} nano parallel-job.sh
-{{ site.remote.prompt }} cat parallel-job.sh
+```bash
+`r config$remote$prompt` cp serial-job.sh parallel-job.sh
+`r config$remote$prompt` nano parallel-job.sh
+`r config$remote$prompt` cat parallel-job.sh
 ```
 
 ```bash
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
-{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
-{{ site.sched.comment }} -N 1
-{{ site.sched.comment }} -n 4
+`r config$remote$bash_shebang`
+`r config$sched$comment` `r config$sched$flag$name` parallel-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 4
 
 # Load the computing environment we need
 # (mpi4py and numpy are in SciPy-bundle)
-module load {{ site.remote.module_python3 }}
+module load `r config$remote$module_python3`
 module load SciPy-bundle
 
 # Execute the task
@@ -310,13 +314,13 @@ from how we submitted the serial job: all the parallel settings are in the
 batch file rather than the command line.
 
 ```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} parallel-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` parallel-job.sh
 ```
 
 As before, use the status commands to check when your job runs.
 
 ```bash
-{{ site.remote.prompt }} ls -t
+`r config$remote$prompt` ls -t
 ```
 
 ```output
@@ -324,18 +328,18 @@ slurm-347178.out  parallel-job.sh  slurm-347087.out  serial-job.sh  amdahl  READ
 ```
 
 ```bash
-{{ site.remote.prompt }} cat slurm-347178.out
+`r config$remote$prompt` cat slurm-347178.out
 ```
 
 ```output
 Doing 30.000 seconds of 'work' on 4 processors,
 which should take 10.875 seconds with 0.850 parallel proportion of the workload.
 
-  Hello, World! I am process 0 of 4 on {{ site.remote.node }}. I will do all the serial 'work' for 4.500 seconds.
-  Hello, World! I am process 2 of 4 on {{ site.remote.node }}. I will do parallel 'work' for 6.375 seconds.
-  Hello, World! I am process 1 of 4 on {{ site.remote.node }}. I will do parallel 'work' for 6.375 seconds.
-  Hello, World! I am process 3 of 4 on {{ site.remote.node }}. I will do parallel 'work' for 6.375 seconds.
-  Hello, World! I am process 0 of 4 on {{ site.remote.node }}. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 0 of 4 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
+  Hello, World! I am process 2 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 1 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 3 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 0 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
 
 Total execution time (according to rank 0): 10.888 seconds
 ```
@@ -403,20 +407,20 @@ Let's run one more job, so we can see how close to a straight line our `amdahl`
 code gets.
 
 ```bash
-{{ site.remote.prompt }} nano parallel-job.sh
-{{ site.remote.prompt }} cat parallel-job.sh
+`r config$remote$prompt` nano parallel-job.sh
+`r config$remote$prompt` cat parallel-job.sh
 ```
 
 ```bash
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
-{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
-{{ site.sched.comment }} -N 1
-{{ site.sched.comment }} -n 8
+`r config$remote$bash_shebang`
+`r config$sched$comment` `r config$sched$flag$name` parallel-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 8
 
 # Load the computing environment we need
 # (mpi4py and numpy are in SciPy-bundle)
-module load {{ site.remote.module_python3 }}
+module load `r config$remote$module_python3`
 module load SciPy-bundle
 
 # Execute the task
@@ -428,13 +432,13 @@ from how we submitted the serial job: all the parallel settings are in the
 batch file rather than the command line.
 
 ```bash
-{{ site.remote.prompt }} {{ site.sched.submit.name }} parallel-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` parallel-job.sh
 ```
 
 As before, use the status commands to check when your job runs.
 
 ```bash
-{{ site.remote.prompt }} ls -t
+`r config$remote$prompt` ls -t
 ```
 
 ```output
@@ -442,21 +446,21 @@ slurm-347271.out  parallel-job.sh  slurm-347178.out  slurm-347087.out  serial-jo
 ```
 
 ```bash
-{{ site.remote.prompt }} cat slurm-347178.out
+`r config$remote$prompt` cat slurm-347178.out
 ```
 
 ```output
 which should take 7.688 seconds with 0.850 parallel proportion of the workload.
 
-  Hello, World! I am process 4 of 8 on {{ site.remote.node }}. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 0 of 8 on {{ site.remote.node }}. I will do all the serial 'work' for 4.500 seconds.
-  Hello, World! I am process 2 of 8 on {{ site.remote.node }}. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 1 of 8 on {{ site.remote.node }}. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 3 of 8 on {{ site.remote.node }}. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 5 of 8 on {{ site.remote.node }}. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 6 of 8 on {{ site.remote.node }}. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 7 of 8 on {{ site.remote.node }}. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 0 of 8 on {{ site.remote.node }}. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 4 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 0 of 8 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
+  Hello, World! I am process 2 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 1 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 3 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 5 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 6 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 7 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 0 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
 
 Total execution time (according to rank 0): 7.697 seconds
 ```
@@ -473,28 +477,32 @@ With 8 workers, this is not the case: since the parallel workers take less
 time than the serial work, it is hard to say which process will write its
 output first, except that it will *not* be process 0!
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 Now, let's summarize the amount of time it took each job to run:
 
-| Number of CPUs | Runtime (sec) | 
+| Number of CPUs | Runtime (sec) |
 | -------------- | ------------- |
-| 1              | 30\.033        | 
-| 4              | 10\.888        | 
-| 8              | 7\.697         | 
+| 1              | 30\.033        |
+| 4              | 10\.888        |
+| 8              | 7\.697         |
 
-Then, use the first row to compute speedups *S*, using Python as a command-line calculator:
+Then, use the first row to compute speedups $S$, using Python as a command-line
+calculator and the formula
+
+$$
+S(t_{n}) = \frac{t_{1}}{t_{n}}
+$$
 
 ```bash
-{{ site.remote.prompt }} for n in 30.033 10.888 7.697; do python3 -c "print(30.033 / $n)"; done
+`r config$remote$prompt` for n in 30.033 10.888 7.697; do python3 -c "print(30.033 / $n)"; done
 ```
 
-| Number of CPUs | Speedup       | Ideal | 
+| Number of CPUs | Speedup       | Ideal |
 | -------------- | ------------- | ----- |
-| 1              | 1\.0           | 1     | 
-| 4              | 2\.75          | 4     | 
-| 8              | 3\.90          | 8     | 
+| 1              | 1\.0           | 1     |
+| 4              | 2\.75          | 4     |
+| 8              | 3\.90          | 8     |
 
 The job output files have been telling us that this program is performing 85%
 of its work in parallel, leaving 15% to run in serial. This seems reasonably
@@ -518,7 +526,6 @@ thousands of CPUs into solving a single problem. To learn more about
 parallelization, see the [parallel novice lesson][parallel-novice] lesson.
 
 
-
 [amdahl]: https://en.wikipedia.org/wiki/Amdahl\'s_law
 [parallel-novice]: https://www.hpc-carpentry.org/hpc-parallel-novice/
 
@@ -530,5 +537,3 @@ parallelization, see the [parallel novice lesson][parallel-novice] lesson.
 - Performance improvements from parallel execution do not scale linearly.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
-
-

From 94f77cb3ddc830d0f7763f526cd67efde158cff4 Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 16:24:33 -0400
Subject: [PATCH 25/33] Workbenched Ep. 18, without snippets

---
 config.yaml                                   |  2 +-
 .../{18-resources.md => 18-resources.Rmd}     | 27 ++++++++++---------
 2 files changed, 16 insertions(+), 13 deletions(-)
 rename episodes/{18-resources.md => 18-resources.Rmd} (88%)

diff --git a/config.yaml b/config.yaml
index 8340971b..9d8d13c1 100644
--- a/config.yaml
+++ b/config.yaml
@@ -73,7 +73,7 @@ episodes:
   - 15-modules.Rmd
   - 16-transferring-files.Rmd
   - 17-parallel.Rmd
-  - 18-resources.md
+  - 18-resources.Rmd
   - 19-responsibility.md
 
 # Information for Learners
diff --git a/episodes/18-resources.md b/episodes/18-resources.Rmd
similarity index 88%
rename from episodes/18-resources.md
rename to episodes/18-resources.Rmd
index 99d01e3b..8fe70605 100644
--- a/episodes/18-resources.md
+++ b/episodes/18-resources.Rmd
@@ -4,10 +4,16 @@ teaching: 10
 exercises: 20
 ---
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Look up job statistics.
-- Make more accurate resource requests in job scripts based on data describing past performance.
+- Make more accurate resource requests in job scripts based on data
+  describing past performance.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -40,12 +46,11 @@ document sent along when you register for an account. Take a look at these
 resources, and search for the software you plan to use: somebody might have
 written up guidance for getting the most out of it.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 A convenient way of figuring out the resources required for a job to run
 successfully is to submit a test job, and then ask the scheduler about its
-impact using `{{ site.sched.hist }}`. You can use this knowledge to set up the
+impact using ``r config$sched$hist``. You can use this knowledge to set up the
 next job with a closer estimate of its load on the system. A good general rule
 is to ask the scheduler for 20% to 30% more time and memory than you expect the
 job to need. This ensures that minor fluctuations in run time or memory use
@@ -58,10 +63,10 @@ finish and free up the resources needed to match what you asked for.
 
 Since we already submitted `amdahl` to run on the cluster, we can query the
 scheduler to see how long our job took and what resources were used. We will
-use `{{ site.sched.hist }}` to get statistics about `parallel-job.sh`.
+use ``r config$sched$hist`` to get statistics about `parallel-job.sh`.
 
 ```bash
-{{ site.remote.prompt }} {{ site.sched.hist }}
+`r config$remote$prompt` `r config$sched$hist`
 ```
 
 ```output
@@ -84,7 +89,7 @@ To get info about a specific job (for example, 347087), we change command
 slightly.
 
 ```bash
-{{ site.remote.prompt }} {{ site.sched.hist }} {{ site.sched.flag.histdetail }} 347087
+`r config$remote$prompt` `r config$sched$hist` `r config$sched$flag$histdetail` 347087
 ```
 
 It will show a lot of info; in fact, every single piece of info collected on
@@ -93,7 +98,7 @@ information to `less` to make it easier to view (use the left and right arrow
 keys to scroll through fields).
 
 ```bash
-{{ site.remote.prompt }} {{ site.sched.hist }} {{ site.sched.flag.histdetail }} 347087 | less -S
+`r config$remote$prompt` `r config$sched$hist` `r config$sched$flag$histdetail` 347087 | less -S
 ```
 
 ::::::::::::::::::::::::::::::::::::::  discussion
@@ -129,17 +134,17 @@ get your job dispatched earlier.
 Edit `parallel_job.sh` to set a better time estimate. How close can
 you get?
 
-Hint: use `{{ site.sched.flag.time }}`.
+Hint: use ``r config$sched$flag$time``.
 
 :::::::::::::::  solution
 
 ## Solution
 
-The following line tells {{ site.sched.name }} that our job should
+The following line tells `r config$sched$name` that our job should
 finish within 2 minutes:
 
 ```bash
-{{ site.sched.comment }} {{ site.sched.flag.time }}{% if site.sched.name == "Slurm" %} {% else %}={% endif %}00:02:00
+`r config$sched$comment` `r config$sched$flag$time` `r if(config$sched$name == "Slurm") {print(" ")} else {print("=")}`00:02:00
 ```
 
 :::::::::::::::::::::::::
@@ -147,11 +152,9 @@ finish within 2 minutes:
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 
-
 :::::::::::::::::::::::::::::::::::::::: keypoints
 
 - Accurate job scripts help the queuing system efficiently allocate shared resources.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-

From b91909dab676cec0c949e92f11c30c2e9ccf882d Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 20 Mar 2025 16:27:13 -0400
Subject: [PATCH 26/33] Workbenched Ep. 19, without snippets

---
 config.yaml                                   |  2 +-
 ...esponsibility.md => 19-responsibility.Rmd} | 42 +++++++------------
 2 files changed, 17 insertions(+), 27 deletions(-)
 rename episodes/{19-responsibility.md => 19-responsibility.Rmd} (94%)

diff --git a/config.yaml b/config.yaml
index 9d8d13c1..a117e923 100644
--- a/config.yaml
+++ b/config.yaml
@@ -74,7 +74,7 @@ episodes:
   - 16-transferring-files.Rmd
   - 17-parallel.Rmd
   - 18-resources.Rmd
-  - 19-responsibility.md
+  - 19-responsibility.Rmd
 
 # Information for Learners
 learners:
diff --git a/episodes/19-responsibility.md b/episodes/19-responsibility.Rmd
similarity index 94%
rename from episodes/19-responsibility.md
rename to episodes/19-responsibility.Rmd
index e214fd19..72252418 100644
--- a/episodes/19-responsibility.md
+++ b/episodes/19-responsibility.Rmd
@@ -4,6 +4,11 @@ teaching: 15
 exercises: 5
 ---
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Describe how the actions of a single user can affect the experience of others on a shared system.
@@ -262,30 +267,17 @@ data.
 
 Say you have a "data" folder containing 10,000 or so files, a healthy mix of
 small and large ASCII and binary data. Which of the following would be the
-best way to transfer them to {{ site.remote.name }}?
-
-1. 
-  ```bash
-  {{ site.local.prompt }} scp -r data {{ site.remote.user }}@{{ site.remote.login }}:~/
-  ```
-2. 
-  ```bash
-  {{ site.local.prompt }} rsync -ra data {{ site.remote.user }}@{{ site.remote.login }}:~/
-  ```
-3. 
-  ```bash
-  {{ site.local.prompt }} rsync -raz data {{ site.remote.user }}@{{ site.remote.login }}:~/
-  ```
-4. 
-  ```bash
-  {{ site.local.prompt }} tar -cvf data.tar data
-  {{ site.local.prompt }} rsync -raz data.tar {{ site.remote.user }}@{{ site.remote.login }}:~/
-  ```
-5. 
-  ```bash
-  {{ site.local.prompt }} tar -cvzf data.tar.gz data
-  {{ site.local.prompt }} rsync -ra data.tar.gz {{ site.remote.user }}@{{ site.remote.login }}:~/
-  ```
+best way to transfer them to `r config$remote$name`?
+
+1. `scp -r data `r config$remote$user`@`r config$remote$login`:~/`
+2. `rsync -ra data `r config$remote$user`@`r config$remote$login`:~/`
+3. `rsync -raz data `r config$remote$user`@`r config$remote$login`:~/`
+4. `tar -cvf data.tar data;`
+
+   `rsync -raz data.tar `r config$remote$user`@`r config$remote$login`:~/`
+5. `tar -cvzf data.tar.gz data;`
+
+   `rsync -ra data.tar.gz `r config$remote$user`@`r config$remote$login`:~/`
 
 :::::::::::::::  solution
 
@@ -306,8 +298,6 @@ best way to transfer them to {{ site.remote.name }}?
   transfer it. This may perform similarly to #4, but in most cases (for
   large datasets), it's the best combination of high throughput and low
   latency (making the most of your time and network connection).
-  
-  
 
 :::::::::::::::::::::::::
 

From 34b46ad026edadc535b920b4adfa2778232ca07f Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 15 May 2025 07:41:12 -0400
Subject: [PATCH 27/33] Rmd conversion

---
 config.yaml                                   |  5 +-
 .../{10-hpc-intro.md => 10-hpc-intro.Rmd}     | 54 +++++++-------
 episodes/11-connecting.Rmd                    | 20 +++---
 episodes/13-hpcc-scheduler/hpcc/section2.rmd  |  8 ---
 episodes/load_config.R                        | 25 ++++---
 episodes/slurm_defaults.yaml                  | 70 +++++++++++++++++++
 ...structor-notes.md => instructor-notes.Rmd} |  0
 7 files changed, 122 insertions(+), 60 deletions(-)
 rename episodes/{10-hpc-intro.md => 10-hpc-intro.Rmd} (79%)
 delete mode 100644 episodes/13-hpcc-scheduler/hpcc/section2.rmd
 create mode 100644 episodes/slurm_defaults.yaml
 rename instructors/{instructor-notes.md => instructor-notes.Rmd} (100%)

diff --git a/config.yaml b/config.yaml
index a117e923..5aa74027 100644
--- a/config.yaml
+++ b/config.yaml
@@ -65,7 +65,7 @@ contact: 'team@carpentries.org'
 
 # Order of episodes in your lesson
 episodes:
-  - 10-hpc-intro.md
+  - 10-hpc-intro.Rmd
   - 11-connecting.Rmd
   - 12-cluster.Rmd
   - 13-scheduler.Rmd
@@ -78,12 +78,15 @@ episodes:
 
 # Information for Learners
 learners:
+  - setup.md
 
 # Information for Instructors
 instructors:
+  - instructor-notes.Rmd
 
 # Learner Profiles
 profiles:
+  - learner-profiles.md
 
 # Customisation ---------------------------------------------
 #
diff --git a/episodes/10-hpc-intro.md b/episodes/10-hpc-intro.Rmd
similarity index 79%
rename from episodes/10-hpc-intro.md
rename to episodes/10-hpc-intro.Rmd
index 4292cedc..6b7e88c9 100644
--- a/episodes/10-hpc-intro.md
+++ b/episodes/10-hpc-intro.Rmd
@@ -22,7 +22,7 @@ Frequently, research problems that use computing can outgrow the capabilities
 of the desktop or laptop computer where they started:
 
 - A statistics student wants to cross-validate a model. This involves running
-  the model 1000 times -- but each run takes an hour. Running the model on
+  the model 1000 times — but each run takes an hour. Running the model on
   a laptop will take over a month! In this research problem, final results are
   calculated after all 1000 models have run, but typically only one model is
   run at a time (in **serial**) on the laptop. Since each of the 1000 runs is
@@ -30,7 +30,7 @@ of the desktop or laptop computer where they started:
   possible to run them all at once (in **parallel**).
 - A genomics researcher has been using small datasets of sequence data, but
   soon will be receiving a new type of sequencing data that is 10 times as
-  large. It's already challenging to open the datasets on a computer --
+  large. It's already challenging to open the datasets on a computer —
   analyzing these larger datasets will probably crash it. In this research
   problem, the calculations required might be impossible to parallelize, but a
   computer with **more memory** would be required to analyze the much larger
@@ -54,7 +54,7 @@ problems in parallel**.
 
 ## Jargon Busting Presentation
 
-Open the [HPC Jargon Buster](../files/jargon#p1)
+Open the [HPC Jargon Buster](files/jargon.html#p1)
 in a new tab. To present the content, press `C` to open a **c**lone in a
 separate window, then press `P` to toggle **p**resentation mode.
 
@@ -71,48 +71,44 @@ results.
 ## Some Ideas
 
 - Checking email: your computer (possibly in your pocket) contacts a remote
-  machine, authenticates, and downloads a list of new messages; it also
-  uploads changes to message status, such as whether you read, marked as
-  junk, or deleted the message. Since yours is not the only account, the
-  mail server is probably one of many in a data center.
-- Searching for a phrase online involves comparing your search term against
-  a massive database of all known sites, looking for matches. This "query"
+  machine, authenticates, and downloads a list of new messages; it also uploads
+  changes to message status, such as whether you read, marked as junk, or
+  deleted the message. Since yours is not the only account, the mail server is
+  probably one of many in a data center.
+- Searching for a phrase online involves comparing your search term against a
+  massive database of all known sites, looking for matches. This "query"
   operation can be straightforward, but building that database is a
   [monumental task][mapreduce]! Servers are involved at every step.
-- Searching for directions on a mapping website involves connecting your
-  (A) starting and (B) end points by [traversing a graph][dijkstra] in
-  search of the "shortest" path by distance, time, expense, or another
-  metric. Converting a map into the right form is relatively simple, but
-  calculating all the possible routes between A and B is expensive.
+- Searching for directions on a mapping website involves connecting your (A)
+  starting and (B) end points by [traversing a graph][dijkstra] in search of
+  the "shortest" path by distance, time, expense, or another metric. Converting
+  a map into the right form is relatively simple, but calculating all the
+  possible routes between A and B is expensive.
 
 Checking email could be serial: your machine connects to one server and
 exchanges data. Searching by querying the database for your search term (or
-endpoints) could also be serial, in that one machine receives your query
-and returns the result. However, assembling and storing the full database
-is far beyond the capability of any one machine. Therefore, these functions
-are served in parallel by a large, ["hyperscale"][hyperscale] collection of
-servers working together.
-
-
+endpoints) could also be serial, in that one machine receives your query and
+returns the result. However, assembling and storing the full database is far
+beyond the capability of any one machine. Therefore, these functions are served
+in parallel by a large, ["hyperscale"][hyperscale] collection of servers
+working together.
 
 :::::::::::::::::::::::::
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-
-
 [mapreduce]: https://en.wikipedia.org/wiki/MapReduce
 [dijkstra]: https://en.wikipedia.org/wiki/Dijkstra%27s_algorithm
 [hyperscale]: https://en.wikipedia.org/wiki/Hyperscale_computing
 
-
 :::::::::::::::::::::::::::::::::::::::: keypoints
 
-- High Performance Computing (HPC) typically involves connecting to very large computing systems elsewhere in the world.
-- These other systems can be used to do work that would either be impossible or much slower on smaller systems.
+- High Performance Computing (HPC) typically involves connecting to very large
+  computing systems elsewhere in the world.
+- These other systems can be used to do work that would either be impossible or
+  much slower on smaller systems.
 - HPC resources are shared by multiple users.
-- The standard method of interacting with such systems is via a command line interface.
+- The standard method of interacting with such systems is via a command line
+  interface.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
-
-
diff --git a/episodes/11-connecting.Rmd b/episodes/11-connecting.Rmd
index a6635d74..3ef0dc90 100644
--- a/episodes/11-connecting.Rmd
+++ b/episodes/11-connecting.Rmd
@@ -38,15 +38,17 @@ results.
 If you have ever opened the Windows Command Prompt or macOS Terminal, you have
 seen a CLI. If you have already taken The Carpentries' courses on the UNIX
 Shell or Version Control, you have used the CLI on your *local machine*
-extensively. The only leap to be made here is to open a CLI on a *remote machine*,
-while taking some precautions so that other folks on the network can't see (or
-change) the commands you're running or the results the remote machine sends
-back. We will use the Secure SHell protocol (or SSH) to open an encrypted
-network connection between two machines, allowing you to send \& receive text
-and data without having to worry about prying eyes.
-
-![](/fig/connect-to-remote.svg){max-width="50%" alt="Connect to cluster"}
-
+extensively. The only leap to be made here is to open a CLI on a *remote
+machine*, while taking some precautions so that other folks on the network
+can't see (or change) the commands you're running or the results the remote
+machine sends back. We will use the Secure SHell protocol (or SSH) to open an
+encrypted network connection between two machines, allowing you to send \&
+receive text and data without having to worry about prying eyes.
+
+![connect-to-remote.svg](/fig/connect-to-remote.svg){
+  max-width="50%"
+  alt="Connect to cluster. "
+}
 
 SSH clients are usually command-line tools, where you provide the remote
 machine address as the only required argument. If your username on the remote
diff --git a/episodes/13-hpcc-scheduler/hpcc/section2.rmd b/episodes/13-hpcc-scheduler/hpcc/section2.rmd
deleted file mode 100644
index 48ec3cdb..00000000
--- a/episodes/13-hpcc-scheduler/hpcc/section2.rmd
+++ /dev/null
@@ -1,8 +0,0 @@
----
-layout: page
-author: Alan O'Cais
-comment: Snippet test
----
-::: discussion
-This is a second snippet that only appears in the backup.
-:::
diff --git a/episodes/load_config.R b/episodes/load_config.R
index 872489eb..b00ec7a1 100644
--- a/episodes/load_config.R
+++ b/episodes/load_config.R
@@ -1,30 +1,28 @@
+## R script to chain-load lesson configuration YAML files.
+## Top-level configuration is `/episodes/lesson_config.yml`
 
-# Function to merge two lists (with overrides)
-merge_lists <- function(base, override) {
-  modifyList(base, override)
-}
-
-# Load required package
 library(yaml)
-# Load primary configuration
+
+## Load primary configuration
 config <- yaml.load_file("lesson_config.yaml")
-# If 'config' key exists, load the second configuration and merge
+
+## If "config" key exists, load the second configuration and merge
 if (!is.null(config$main_config) && file.exists(config$main_config)) {
   override_config <- yaml.load_file(config$main_config)
-  config <- merge_lists(config, override_config)
+  config <- modifyList(config, override_config)
 }
 
-snippets <- paste('files/snippets/', config$snippets, sep='')
+snippets <- paste("files/snippets/", config$snippets, sep="")
 
 # Extract main and fallback paths from config
-main_snippets <- config$main_snippets
+main_snippets     <- config$main_snippets
 fallback_snippets <- config$fallback_snippets
 
 # Function to choose the correct document path (or return NULL if neither exists)
 choose_doc <- function(child_file) {
   # Get the current document name (without extension)
   current_doc <- tools::file_path_sans_ext(knitr::current_input(dir = TRUE))
-  
+
   # Build paths for the child document inside subdirectories
   doc_paths <- list(
     main = file.path(current_doc, main_snippets, child_file),
@@ -32,6 +30,7 @@ choose_doc <- function(child_file) {
   )
   print(doc_paths)
   print(getwd())
+
   # Return the valid path, or NULL if neither exists
   if (file.exists(doc_paths$main)) {
     print("Returning")
@@ -45,4 +44,4 @@ choose_doc <- function(child_file) {
     print("Returning NULL")
     return(NULL)  # Return NULL if neither path exists
   }
-}
\ No newline at end of file
+}
diff --git a/episodes/slurm_defaults.yaml b/episodes/slurm_defaults.yaml
new file mode 100644
index 00000000..fc550217
--- /dev/null
+++ b/episodes/slurm_defaults.yaml
@@ -0,0 +1,70 @@
+# Fail-safe defaults and implicit schema for lesson configuration files
+---
+snippets: slurm
+baseurl: "https://ocaisa.github.io/probable-pancake/"
+# main_config: "lesson_config.yaml"
+
+# about the Learner's laptop
+local:
+  prompt: "[you@laptop:~]$"                  # command-line prompt
+  shebang: "#!/bin/bash"                     # first line of every shell script
+
+# about the remote/cluster environment
+remote:
+  name: "Example Cluster"                    # Name of the cluster (proper noun)
+  login: "cluster.example.com"               # domain name of the login node
+  host: "head"                               # hostname of the login node
+  node: "node"                               # hostname of a compute node
+  location: "SchedMD"                        # institutional host of the cluster
+  homedir: "/home"                           # parent of home directories
+  user: "userid"                             # stand-in for the username
+  prompt: "[userid@head:~]"                  # command-line prompt
+  prompt_work: "[userid@head:/work/userid]"  # prompt under /work
+  module_python3: "Python"                   # name of the module providing py3
+  shebang: "#!/bin/bash"                     # first line of every shell script
+
+# Commands & flags for the scheduler environment
+sched:
+  name: "Slurm"                              # proper name of the scheduler
+  command:
+    batch:       "sbatch"                    # run later
+    interactive: "srun"                      # run now
+    cancel:      "scancel"                   # don't run
+  queue:
+    test: "debug"
+    prod: "batch"
+  status: "squeue"
+  flag:
+    user: "-u userid"
+    interactive: "--pty bash"
+    histdetail: "-l -j"
+    name: "-J"
+    time: "-t"
+    queue: "-p"
+    nodes: "-N"
+    tasks: "-n"
+  del: "scancel"
+  interactive:
+    command: "srun"
+  info:
+    command: "sinfo"
+  comment: "#SBATCH"
+  hist: "sacct -u userid"
+  hist_filter: ""
+  reservation: ""
+  qos: ""
+  budget: ""
+  project: ""
+
+# submit:
+#   salloc:   obtain a job allocation
+#   sbatch:   submit a batch script for later execution
+#   srun:     obtain an allocation and execute an application
+# account:
+#   sacct:    display accounting data
+# manage:
+#   sbcast:   transfer a file to a job's compute nodes
+#   scancel:  signal jobs/steps
+#   squeue:   view information about jobs
+#   sinfo:    view information about nodes & partitions
+#   scontrol: view & modify state
diff --git a/instructors/instructor-notes.md b/instructors/instructor-notes.Rmd
similarity index 100%
rename from instructors/instructor-notes.md
rename to instructors/instructor-notes.Rmd

From c287cd7d1cba22443e8e3ae4ac198c06612bca2f Mon Sep 17 00:00:00 2001
From: Trevor Keller <trevor.keller@nist.gov>
Date: Thu, 21 Aug 2025 16:26:24 -0400
Subject: [PATCH 28/33] Initialize a testing snippet library with clearly-wrong
 data

---
 .../Ghastly_Mistakes/_config_options.yml      | 65 ++++++++++++++
 .../Ghastly_Mistakes/cluster/queue-info.Rmd   |  5 ++
 .../cluster/specific-node-info.Rmd            | 12 +++
 .../modules/available-modules.snip            | 21 +++++
 .../modules/default-modules.snip              |  4 +
 .../modules/missing-python.snip               | 33 +++++++
 .../modules/module-load-python.snip           |  5 ++
 .../modules/python-executable-dir.snip        |  4 +
 .../modules/python-ls-dir-command.snip        |  4 +
 .../modules/python-ls-dir-output.snip         | 16 ++++
 .../modules/python-module-path.snip           |  4 +
 .../modules/software-dependencies.snip        | 87 +++++++++++++++++++
 .../modules/wrong-gcc-version.snip            |  5 ++
 .../parallel/eight-tasks-jobscript.snip       | 16 ++++
 .../parallel/four-tasks-jobscript.snip        | 16 ++++
 .../parallel/one-task-jobscript.snip          | 14 +++
 .../resources/account-history.snip            | 14 +++
 .../resources/monitor-processes-top.snip      | 19 ++++
 .../resources/system-memory-free.snip         |  6 ++
 .../scheduler/basic-job-script.Rmd            |  3 +
 .../scheduler/basic-job-status.Rmd            |  8 ++
 .../scheduler/job-with-name-status.Rmd        |  4 +
 .../scheduler/option-flags-list.Rmd           | 17 ++++
 .../scheduler/print-sched-variables.Rmd       | 32 +++++++
 .../scheduler/runtime-exceeded-job.Rmd        |  3 +
 .../scheduler/runtime-exceeded-output.Rmd     |  5 ++
 .../scheduler/terminate-job-begin.Rmd         |  6 ++
 .../scheduler/terminate-job-cancel.Rmd        |  3 +
 .../scheduler/terminate-multiple-jobs.Rmd     | 29 +++++++
 .../scheduler/using-nodes-interactively.Rmd   | 68 +++++++++++++++
 .../filezilla-ssh-tunnel-instructions.snip    |  0
 31 files changed, 528 insertions(+)
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/cluster/queue-info.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/cluster/specific-node-info.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/default-modules.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-command.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-output.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/python-module-path.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/wrong-gcc-version.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks-jobscript.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks-jobscript.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/one-task-jobscript.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/resources/account-history.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/resources/monitor-processes-top.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/resources/system-memory-free.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-script.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-status.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/job-with-name-status.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/option-flags-list.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/print-sched-variables.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-job.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-output.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-begin.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-cancel.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-multiple-jobs.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/scheduler/using-nodes-interactively.Rmd
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/transferring-files/filezilla-ssh-tunnel-instructions.snip

diff --git a/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml b/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
new file mode 100644
index 00000000..76eb0075
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
@@ -0,0 +1,65 @@
+# ------------------------
+# Ghastly Mistakes Cluster
+# ------------------------
+#
+# This is not a real cluster, and its options are meant to
+# highlight configuration changes while we develop the config
+# chain-loader, per @tobyhodges' suggestion.
+#
+# Compute irresponsibly.
+---
+
+snippets: "/snippets_library/Ghastly_Mistakes"
+
+local:
+  prompt: "luigi@mushroomkingdom:~$"
+  bash_shebang: "#!/bin/bash"
+
+remote:
+  name: "Bowser's Castle"
+  login: "castle.bowser.org"
+  portal: "https://pipe.bowser.org"
+  host: "castle"
+  node: "turtle"
+  location: "World 8-4"
+  homedir: "/darkland"
+  user: "luigi"
+  module_python3: "Boa"
+  prompt: "luigi@castle:~$"
+  bash_shebang: "#!/bin/no"
+
+sched:
+  name: "Slurp"
+  submit:
+    name: "smash"
+    options: ""
+  queue:
+    debug: "doom"
+    testing: "gloom"
+  status: "skew"
+  flag:
+    user: "-u luigi"
+    interactive: ""
+    histdetail: "-l -j"
+    name: "-J"
+    time: "-t"
+    queue: "-p"
+  del: "scandle"
+  interactive: "spun"
+  info: "sink"
+  comment: "#SMASH"
+  hist: "sacked -u luigi"
+  hist_filter: ""
+
+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
+ 
\ No newline at end of file
diff --git a/episodes/files/snippets/Ghastly_Mistakes/cluster/queue-info.Rmd b/episodes/files/snippets/Ghastly_Mistakes/cluster/queue-info.Rmd
new file mode 100644
index 00000000..29f69030
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/cluster/queue-info.Rmd
@@ -0,0 +1,5 @@
+```output
+PARTITION          AVAIL  TIMELIMIT  NODES  STATE NODELIST
+doom                 up   infinite      2   idle  doo[1-2]
+gloom                up   infinite      2   idle  glo[1-2]
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/cluster/specific-node-info.Rmd b/episodes/files/snippets/Ghastly_Mistakes/cluster/specific-node-info.Rmd
new file mode 100644
index 00000000..c38b377b
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/cluster/specific-node-info.Rmd
@@ -0,0 +1,12 @@
+::: challenge
+
+## Explore a Worker Node
+
+Finally, let's look at the resources available on the worker nodes
+where your jobs will actually run. Try running this command to see
+the name, CPUs and memory available on one of the worker nodes:
+
+```bash
+`r config$remote$prompt` `r config$sched$info` -o "%n %c %m" | column -t
+```
+:::
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.snip
new file mode 100644
index 00000000..f6f3f50b
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.snip
@@ -0,0 +1,21 @@
+```
+~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
+  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
+  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
+  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
+  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
+  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a
+
+[removed most of the output here for clarity]
+
+  Where:
+   L:        Module is loaded
+   Aliases:  Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
+             will load foo/1.2.3
+   D:        Default Module
+
+Use "module spider" to find all possible modules and extensions.
+Use "module keyword key1 key2 ..." to search for all possible modules matching
+any of the "keys".
+```
+{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/default-modules.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/default-modules.snip
new file mode 100644
index 00000000..a448dd96
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/default-modules.snip
@@ -0,0 +1,4 @@
+```
+No Modulefiles Currently Loaded.
+```
+{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.snip
new file mode 100644
index 00000000..89039d32
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.snip
@@ -0,0 +1,33 @@
+If the `python3` command was unavailable, we would see output like
+
+```
+/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/{{site.remote.user}}/.local/bin:/home/{{site.remote.user}}/bin)
+```
+{: .output}
+
+Note that this wall of text is really a list, with values separated
+by the `:` character. The output is telling us that the `which` command
+searched the following directories for `python3`, without success:
+
+```
+/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin
+/opt/software/slurm/bin
+/usr/local/bin
+/usr/bin
+/usr/local/sbin
+/usr/sbin
+/opt/puppetlabs/bin
+/home/{{site.remote.user}}/.local/bin
+/home/{{site.remote.user}}/bin
+```
+{: .output}
+
+However, in our case we do have an existing `python3` available so we see
+
+```
+/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin/python3
+```
+{: .output}
+
+We need a different Python than the system provided one though, so let us load
+a module to access it.
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.snip
new file mode 100644
index 00000000..d9bab7b4
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.snip
@@ -0,0 +1,5 @@
+```
+{{ site.remote.prompt }} module load {{ site.remote.module_python3 }}
+{{ site.remote.prompt }} which python3
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.snip
new file mode 100644
index 00000000..46dec092
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.snip
@@ -0,0 +1,4 @@
+```
+/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3
+```
+{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-command.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-command.snip
new file mode 100644
index 00000000..80319d0a
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-command.snip
@@ -0,0 +1,4 @@
+```
+{{ site.remote.prompt }} ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-output.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-output.snip
new file mode 100644
index 00000000..01d010ba
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-output.snip
@@ -0,0 +1,16 @@
+```
+2to3              nosetests-3.8  python                 rst2s5.py
+2to3-3.8          pasteurize     python3                rst2xetex.py
+chardetect        pbr            python3.8              rst2xml.py
+cygdb             pip            python3.8-config       rstpep2html.py
+cython            pip3           python3-config         runxlrd.py
+cythonize         pip3.8         rst2html4.py           sphinx-apidoc
+easy_install      pybabel        rst2html5.py           sphinx-autogen
+easy_install-3.8  __pycache__    rst2html.py            sphinx-build
+futurize          pydoc3         rst2latex.py           sphinx-quickstart
+idle3             pydoc3.8       rst2man.py             tabulate
+idle3.8           pygmentize     rst2odt_prepstyles.py  virtualenv
+netaddr           pytest         rst2odt.py             wheel
+nosetests         py.test        rst2pseudoxml.py
+```
+{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/python-module-path.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/python-module-path.snip
new file mode 100644
index 00000000..68e97df1
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/python-module-path.snip
@@ -0,0 +1,4 @@
+```
+/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/SQLite/3.31.1-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Tcl/8.6.10-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/GCCcore/x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/user01/.local/bin:/home/user01/bin
+```
+{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.snip
new file mode 100644
index 00000000..fe107f2e
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.snip
@@ -0,0 +1,87 @@
+To demonstrate, let's use `module list`. `module list` shows all loaded
+software modules.
+
+```
+{{ site.remote.prompt }} module list
+```
+{: .language-bash}
+
+```
+Currently Loaded Modules:
+  1) GCCcore/x.y.z                 4) GMP/6.2.0-GCCcore-x.y.z
+  2) Tcl/8.6.10-GCCcore-x.y.z      5) libffi/3.3-GCCcore-x.y.z
+  3) SQLite/3.31.1-GCCcore-x.y.z   6) Python/3.x.y-GCCcore-x.y.z
+```
+{: .output}
+
+```
+{{ site.remote.prompt }} module load GROMACS
+{{ site.remote.prompt }} module list
+```
+{: .language-bash}
+
+```
+Currently Loaded Modules:
+  1) GCCcore/x.y.z                    14) libfabric/1.11.0-GCCcore-x.y.z
+  2) Tcl/8.6.10-GCCcore-x.y.z         15) PMIx/3.1.5-GCCcore-x.y.z
+  3) SQLite/3.31.1-GCCcore-x.y.z      16) OpenMPI/4.0.3-GCC-x.y.z
+  4) GMP/6.2.0-GCCcore-x.y.z          17) OpenBLAS/0.3.9-GCC-x.y.z
+  5) libffi/3.3-GCCcore-x.y.z         18) gompi/2020a
+  6) Python/3.x.y-GCCcore-x.y.z       19) FFTW/3.3.8-gompi-2020a
+  7) GCC/x.y.z                        20) ScaLAPACK/2.1.0-gompi-2020a
+  8) numactl/2.0.13-GCCcore-x.y.z     21) foss/2020a
+  9) libxml2/2.9.10-GCCcore-x.y.z     22) pybind11/2.4.3-GCCcore-x.y.z-Pytho...
+ 10) libpciaccess/0.16-GCCcore-x.y.z  23) SciPy-bundle/2020.03-foss-2020a-Py...
+ 11) hwloc/2.2.0-GCCcore-x.y.z        24) networkx/2.4-foss-2020a-Python-3.8...
+ 12) libevent/2.1.11-GCCcore-x.y.z    25) GROMACS/2020.1-foss-2020a-Python-3...
+ 13) UCX/1.8.0-GCCcore-x.y.z
+```
+{: .output}
+
+So in this case, loading the `GROMACS` module (a bioinformatics software
+package), also loaded `GMP/6.2.0-GCCcore-x.y.z` and
+`SciPy-bundle/2020.03-foss-2020a-Python-3.x.y` as well. Let's try unloading the
+`GROMACS` package.
+
+```
+{{ site.remote.prompt }} module unload GROMACS
+{{ site.remote.prompt }} module list
+```
+{: .language-bash}
+
+```
+Currently Loaded Modules:
+  1) GCCcore/x.y.z                    13) UCX/1.8.0-GCCcore-x.y.z
+  2) Tcl/8.6.10-GCCcore-x.y.z         14) libfabric/1.11.0-GCCcore-x.y.z
+  3) SQLite/3.31.1-GCCcore-x.y.z      15) PMIx/3.1.5-GCCcore-x.y.z
+  4) GMP/6.2.0-GCCcore-x.y.z          16) OpenMPI/4.0.3-GCC-x.y.z
+  5) libffi/3.3-GCCcore-x.y.z         17) OpenBLAS/0.3.9-GCC-x.y.z
+  6) Python/3.x.y-GCCcore-x.y.z       18) gompi/2020a
+  7) GCC/x.y.z                        19) FFTW/3.3.8-gompi-2020a
+  8) numactl/2.0.13-GCCcore-x.y.z     20) ScaLAPACK/2.1.0-gompi-2020a
+  9) libxml2/2.9.10-GCCcore-x.y.z     21) foss/2020a
+ 10) libpciaccess/0.16-GCCcore-x.y.z  22) pybind11/2.4.3-GCCcore-x.y.z-Pytho...
+ 11) hwloc/2.2.0-GCCcore-x.y.z        23) SciPy-bundle/2020.03-foss-2020a-Py...
+ 12) libevent/2.1.11-GCCcore-x.y.z    24) networkx/2.4-foss-2020a-Python-3.x.y
+```
+{: .output}
+
+So using `module unload` "un-loads" a module, and depending on how a site is
+ configured it may also unload all of the dependencies (in our case it does
+ not). If we wanted to unload everything at once, we could run `module purge`
+ (unloads everything).
+
+```
+{{ site.remote.prompt }} module purge
+{{ site.remote.prompt }} module list
+```
+{: .language-bash}
+
+```
+No modules loaded
+```
+{: .output}
+
+Note that `module purge` is informative. It will also let us know if a default
+set of "sticky" packages cannot be unloaded (and how to actually unload these
+if we truly so desired).
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/wrong-gcc-version.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/wrong-gcc-version.snip
new file mode 100644
index 00000000..8fbd2825
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/wrong-gcc-version.snip
@@ -0,0 +1,5 @@
+<!--- There is a long additional section on some specific features of Lmod in
+snippets_library/ComputeCanada_Graham_slurm/modules/wrong-gcc-version.snip,
+particular covering the concept of a module hierarchy. While this is not
+relevant to the EESSI configuration right now, it may become so in the future
+if we change the default module naming scheme to hierarchical. -->
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks-jobscript.snip b/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks-jobscript.snip
new file mode 100644
index 00000000..2f643071
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks-jobscript.snip
@@ -0,0 +1,16 @@
+```
+{{ site.remote.bash_shebang }}
+{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
+{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
+{{ site.sched.comment }} -N 1
+{{ site.sched.comment }} -n 8
+
+# Load the computing environment we need
+# (mpi4py and numpy are in SciPy-bundle)
+module load {{ site.remote.module_python3 }}
+module load SciPy-bundle
+
+# Execute the task
+mpiexec amdahl
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks-jobscript.snip b/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks-jobscript.snip
new file mode 100644
index 00000000..19804d74
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks-jobscript.snip
@@ -0,0 +1,16 @@
+```
+{{ site.remote.bash_shebang }}
+{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
+{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
+{{ site.sched.comment }} -N 1
+{{ site.sched.comment }} -n 4
+
+# Load the computing environment we need
+# (mpi4py and numpy are in SciPy-bundle)
+module load {{ site.remote.module_python3 }}
+module load SciPy-bundle
+
+# Execute the task
+mpiexec amdahl
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task-jobscript.snip b/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task-jobscript.snip
new file mode 100644
index 00000000..1941ef04
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task-jobscript.snip
@@ -0,0 +1,14 @@
+```
+{{ 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
+
+# Load the computing environment we need
+module load {{ site.remote.module_python3 }}
+
+# Execute the task
+amdahl
+```
+{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/resources/account-history.snip b/episodes/files/snippets/Ghastly_Mistakes/resources/account-history.snip
new file mode 100644
index 00000000..d5a87620
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/resources/account-history.snip
@@ -0,0 +1,14 @@
+```
+       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
+------------ ---------- ---------- ---------- ---------- ---------- --------
+7               file.sh cpubase_b+ def-spons+          1  COMPLETED      0:0
+7.batch           batch            def-spons+          1  COMPLETED      0:0
+7.extern         extern            def-spons+          1  COMPLETED      0:0
+8               file.sh cpubase_b+ def-spons+          1  COMPLETED      0:0
+8.batch           batch            def-spons+          1  COMPLETED      0:0
+8.extern         extern            def-spons+          1  COMPLETED      0:0
+9            example-j+ cpubase_b+ def-spons+          1  COMPLETED      0:0
+9.batch           batch            def-spons+          1  COMPLETED      0:0
+9.extern         extern            def-spons+          1  COMPLETED      0:0
+```
+{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/resources/monitor-processes-top.snip b/episodes/files/snippets/Ghastly_Mistakes/resources/monitor-processes-top.snip
new file mode 100644
index 00000000..12685735
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/resources/monitor-processes-top.snip
@@ -0,0 +1,19 @@
+```
+top - 21:00:19 up  3:07,  1 user,  load average: 1.06, 1.05, 0.96
+Tasks: 311 total,   1 running, 222 sleeping,   0 stopped,   0 zombie
+%Cpu(s):  7.2 us,  3.2 sy,  0.0 ni, 89.0 id,  0.0 wa,  0.2 hi,  0.2 si,  0.0 st
+KiB Mem : 16303428 total,  8454704 free,  3194668 used,  4654056 buff/cache
+KiB Swap:  8220668 total,  8220668 free,        0 used. 11628168 avail Mem
+
+  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
+ 1693 jeff      20   0 4270580 346944 171372 S  29.8  2.1   9:31.89 gnome-shell
+ 3140 jeff      20   0 3142044 928972 389716 S  27.5  5.7  13:30.29 Web Content
+ 3057 jeff      20   0 3115900 521368 231288 S  18.9  3.2  10:27.71 firefox
+ 6007 jeff      20   0  813992 112336  75592 S   4.3  0.7   0:28.25 tilix
+ 1742 jeff      20   0  975080 164508 130624 S   2.0  1.0   3:29.83 Xwayland
+    1 root      20   0  230484  11924   7544 S   0.3  0.1   0:06.08 systemd
+   68 root      20   0       0      0      0 I   0.3  0.0   0:01.25 kworker/4:1
+ 2913 jeff      20   0  965620  47892  37432 S   0.3  0.3   0:11.76 code
+    2 root      20   0       0      0      0 S   0.0  0.0   0:00.02 kthreadd
+```
+{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/resources/system-memory-free.snip b/episodes/files/snippets/Ghastly_Mistakes/resources/system-memory-free.snip
new file mode 100644
index 00000000..ec4c0d3f
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/resources/system-memory-free.snip
@@ -0,0 +1,6 @@
+```
+total        used        free      shared  buff/cache   available
+Mem:           3.8G        1.5G        678M        327M        1.6G        1.6G
+Swap:          3.9G        170M        3.7G
+```
+{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-script.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-script.Rmd
new file mode 100644
index 00000000..5f76fb2c
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-script.Rmd
@@ -0,0 +1,3 @@
+```output
+Submitted batch job 7
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-status.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-status.Rmd
new file mode 100644
index 00000000..8873c7c1
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-status.Rmd
@@ -0,0 +1,8 @@
+```output
+JOBID PARTITION  NAME         USER   ST  TIME  NODES NODELIST(REASON)
+    9 doom       example-job  luigi  R   0:05  1     doo1
+```
+
+We can see all the details of our job, most importantly that it is in the `R`
+or `RUNNING` state. Sometimes our jobs might need to wait in a queue
+(`PENDING`) or have an error (`E`).
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/job-with-name-status.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/job-with-name-status.Rmd
new file mode 100644
index 00000000..aa8eab85
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/job-with-name-status.Rmd
@@ -0,0 +1,4 @@
+```output
+JOBID PARTITION  NAME         USER   ST  TIME  NODES  NODELIST(REASON)
+   10 doom       hello-world  luigi  R   0:02      1  doo1
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/option-flags-list.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/option-flags-list.Rmd
new file mode 100644
index 00000000..9bc993ff
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/option-flags-list.Rmd
@@ -0,0 +1,17 @@
+> option-flag-list.Rmd is constant for all snippet libraries
+
+* `--ntasks=<ntasks>` or `-n <ntasks>`: How many CPU cores does your job need,
+  in total?
+
+* `--time <days-hours:minutes:seconds>` or `-t <days-hours:minutes:seconds>`:
+  How much real-world time (walltime) will your job take to run? The `<days>`
+  part can be omitted.
+
+* `--mem=<megabytes>`: How much memory on a node does your job need in
+  megabytes? You can also specify gigabytes using by adding a little "g"
+  afterwards (example: `--mem=5g`)
+
+* `--nodes=<nnodes>` or `-N <nnodes>`: How many separate machines does your job
+  need to run on? Note that if you set `ntasks` to a number greater than what
+  one machine can offer, {{ site.sched.name }} will set this value
+  automatically.
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/print-sched-variables.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/print-sched-variables.Rmd
new file mode 100644
index 00000000..659cefae
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/print-sched-variables.Rmd
@@ -0,0 +1,32 @@
+::: challenge
+
+## Job environment variables
+
+When ``r config$sched$name`` runs a job, it sets a number of environment
+variables for the job. One of these will let us check what directory our job
+script was submitted from. The `SLURM_SUBMIT_DIR` variable is set to the
+directory from which our job was submitted. Using the `SLURM_SUBMIT_DIR`
+variable, modify your job so that it prints out the location from which the
+job was submitted.
+
+:::: solution
+
+## Solution
+
+```bash
+`r config$remote$prompt` nano example-job.sh
+`r config$remote$prompt` cat example-job.sh
+```
+
+```bash
+`r config$remote$bash_shebang`
+`r config$sched$comment` -t 00:00:30
+
+echo -n "This script is running on "
+hostname
+
+echo "This job was launched in the following directory:"
+echo ${SLURM_SUBMIT_DIR}
+```
+::::
+:::
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-job.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-job.Rmd
new file mode 100644
index 00000000..7dde2ada
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-job.Rmd
@@ -0,0 +1,3 @@
+```bash
+`r config$remote$prompt` cat slurm-12.out
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-output.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-output.Rmd
new file mode 100644
index 00000000..fa1b19ea
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-output.Rmd
@@ -0,0 +1,5 @@
+```output
+This script is running on ...
+slurmstepd: error: *** JOB 12 ON doo1 CANCELLED AT 2021-02-19T13:55:57
+DUE TO TIME LIMIT ***
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-begin.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-begin.Rmd
new file mode 100644
index 00000000..d5a03bfb
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-begin.Rmd
@@ -0,0 +1,6 @@
+```output
+Submitted batch job 13
+
+JOBID PARTITION  NAME      USER   ST  TIME  NODES NODELIST(REASON)
+   13 doom       long_job  luigi  R   0:02  1     doo1
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-cancel.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-cancel.Rmd
new file mode 100644
index 00000000..ccb9cd24
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-cancel.Rmd
@@ -0,0 +1,3 @@
+```output
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-multiple-jobs.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-multiple-jobs.Rmd
new file mode 100644
index 00000000..5ee30f8d
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-multiple-jobs.Rmd
@@ -0,0 +1,29 @@
+::: challenge
+## Cancelling multiple jobs
+
+We can also cancel all of our jobs at once using the `-u` option. This will
+delete all jobs for a specific user (in this case, yourself). Note that you
+can only delete your own jobs.
+
+Try submitting multiple jobs and then cancelling them all.
+
+:::: solution
+
+## Solution
+
+First, submit a trio of jobs:
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+`r config$remote$prompt` `r config$sched$submit$name` `r config$sched$submit$options` example-job.sh
+```
+
+Then, cancel them all:
+
+```bash
+`r config$remote$prompt` `r config$sched$del` -u `r config$remote$user`
+```
+
+::::
+:::
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/using-nodes-interactively.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/using-nodes-interactively.Rmd
new file mode 100644
index 00000000..80834a8f
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/using-nodes-interactively.Rmd
@@ -0,0 +1,68 @@
+> using-nodes-interactively.Rmd is constant across snippets
+
+The `r config$sched$interactive` command runs a single command on the cluster
+and then exits. Let's demonstrate this by running the `hostname` command with
+`r config$sched$interactive`. (We can cancel an `r config$sched$interactive`
+job with `Ctrl-c`.)
+
+```bash
+`r config$remote.prompt` `r config$sched$interactive` hostname
+```
+
+```output
+`r config$remote$node`
+```
+
+`r config$sched$interactive` accepts all of the same options as
+`r config$sched$submit.name`. However, instead of specifying these in a script,
+these options are specified on the command-line when starting a job. To submit
+a job that uses 2 CPUs for instance, we could use the following command:
+
+```bash
+`r config$remote.prompt` `r config$sched$interactive` -n 2 echo "This job will use 2 CPUs."
+```
+
+```output
+This job will use 2 CPUs.
+This job will use 2 CPUs.
+```
+
+Typically, the resulting shell environment will be the same as that for
+`r config$sched$submit$name`.
+
+### Interactive jobs
+
+Sometimes, you will need a lot of resources for interactive use. Perhaps it's
+our first time running an analysis or we are attempting to debug something that
+went wrong with a previous job. Fortunately, {{ config$sched$name` makes it
+easy to start an interactive job with `r config$sched$interactive`:
+
+```bash
+`r config$remote$prompt` `r config$sched$interactive` --pty bash
+```
+
+You should be presented with a bash prompt. Note that the prompt will likely
+change to reflect your new location, in this case the compute node we are
+logged on. You can also verify this with `hostname`.
+
+::: callout
+
+## Creating remote graphics
+
+To see graphical output inside your jobs, you need to use X11 forwarding. To
+connect with this feature enabled, use the `-Y` option when you login with
+the `ssh` command, e.g., `r paste("ssh -Y ", config$remote$user, "@", config$remote$login, sep="")`.
+
+To demonstrate what happens when you create a graphics window on the remote
+node, use the `xeyes` command. A relatively adorable pair of eyes should pop
+up (press `Ctrl-C` to stop). If you are using a Mac, you must have installed
+XQuartz (and restarted your computer) for this to work.
+
+If your cluster has the
+[slurm-spank-x11](https://github.com/hautreux/slurm-spank-x11) plugin
+installed, you can ensure X11 forwarding within interactive jobs by using the
+`--x11` option for `r config$sched$interactive` with the command
+`r paste(config$sched$interactive, " --x11", " --pty bash", sep="")`.
+:::
+
+When you are done with the interactive job, type `exit` to quit your session.
diff --git a/episodes/files/snippets/Ghastly_Mistakes/transferring-files/filezilla-ssh-tunnel-instructions.snip b/episodes/files/snippets/Ghastly_Mistakes/transferring-files/filezilla-ssh-tunnel-instructions.snip
new file mode 100644
index 00000000..e69de29b

From 5067601226114b8d299b523aa78ee45f11a4370d Mon Sep 17 00:00:00 2001
From: Trevor Keller <tkellerphd@gmail.com>
Date: Wed, 5 Nov 2025 14:13:19 -0500
Subject: [PATCH 29/33] Snippetized Ep. 15

---
 episodes/11-connecting.Rmd                    |   2 +-
 episodes/14-environment-variables.Rmd         |   2 +-
 episodes/15-modules.Rmd                       | 209 ++----------------
 .../Ghastly_Mistakes/_config_options.yml      |   2 +-
 .../modules/available-modules.Rmd             |  13 ++
 .../_config_options.yml                       |   3 +
 .../modules/available-modules.Rmd}            |  11 +-
 .../modules/available-modules.snip            |  21 --
 .../modules/default-modules.snip              |   4 -
 ...missing-python.snip => missing-python.Rmd} |  15 +-
 .../modules/module-load-python.Rmd            |   8 +
 .../modules/module-load-python.snip           |   5 -
 ...-output.snip => python-executable-dir.Rmd} |   5 +-
 .../modules/python-executable-dir.snip        |   4 -
 .../modules/python-ls-dir-command.snip        |   4 -
 .../modules/software-dependencies.snip        |  44 ++--
 episodes/lesson_config.yaml                   |  53 +----
 episodes/load_config.R                        |   3 +-
 18 files changed, 87 insertions(+), 321 deletions(-)
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.Rmd
 rename episodes/files/snippets/{Ghastly_Mistakes/modules/available-modules.snip => HPCC_MagicCastle_slurm/modules/available-modules.Rmd} (81%)
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.snip
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/default-modules.snip
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/modules/{missing-python.snip => missing-python.Rmd} (82%)
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.Rmd
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.snip
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/modules/{python-ls-dir-output.snip => python-executable-dir.Rmd} (85%)
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.snip
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-command.snip

diff --git a/episodes/11-connecting.Rmd b/episodes/11-connecting.Rmd
index 3ef0dc90..103d0379 100644
--- a/episodes/11-connecting.Rmd
+++ b/episodes/11-connecting.Rmd
@@ -45,7 +45,7 @@ machine sends back. We will use the Secure SHell protocol (or SSH) to open an
 encrypted network connection between two machines, allowing you to send \&
 receive text and data without having to worry about prying eyes.
 
-![connect-to-remote.svg](/fig/connect-to-remote.svg){
+![connect-to-remote.svg](fig/connect-to-remote.svg){
   max-width="50%"
   alt="Connect to cluster. "
 }
diff --git a/episodes/14-environment-variables.Rmd b/episodes/14-environment-variables.Rmd
index 2c150b5d..3e4c6977 100644
--- a/episodes/14-environment-variables.Rmd
+++ b/episodes/14-environment-variables.Rmd
@@ -279,7 +279,7 @@ unless we type in the full path to the program,
 since the directory `/users/vlad` isn't in `PATH`.
 
 This means that I can have executables in lots of different places as long as
-I remember that I need to to update my `PATH` so that my shell can find them.
+I remember that I need to update my `PATH` so that my shell can find them.
 
 What if I want to run two different versions of the same program?
 Since they share the same name, if I add them both to my `PATH` the first one
diff --git a/episodes/15-modules.Rmd b/episodes/15-modules.Rmd
index 1bb42a48..db1d387e 100644
--- a/episodes/15-modules.Rmd
+++ b/episodes/15-modules.Rmd
@@ -38,11 +38,11 @@ presence (or absence) of a software package will break others that depend on
 it. Two well known examples are Python and C compiler versions.
 Python 3 famously provides a `python` command that conflicts with that provided
 by Python 2. Software compiled against a newer version of the C libraries and
-then run on a machine that has older C libraries installed will result in a
-nasty `'GLIBCXX_3.4.20' not found` error.
+then run on a machine that has older C libraries installed will result in an
+opaque `'GLIBCXX_3.4.20' not found` error.
 
 Software versioning is another common issue. A team might depend on a certain
-package version for their research project - if the software version was to
+package version for their research project -- if the software version was to
 change (for instance, if a package was updated), it might affect their results.
 Having access to multiple software versions allows a set of researchers to
 prevent software versioning issues from affecting their results.
@@ -50,7 +50,7 @@ prevent software versioning issues from affecting their results.
 Dependencies are where a particular software package (or even a particular
 version) depends on having access to another software package (or even a
 particular version of another software package). For example, the VASP
-materials science software may depend on having a particular version of the
+materials science software may require a particular version of the
 FFTW (Fastest Fourier Transform in the West) software library available for it
 to work.
 
@@ -79,36 +79,14 @@ you are using.
 
 To see available software modules, use `module avail`:
 
-```bash
-`r config$remote$prompt` module avail
-```
-
-```output
-~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
-  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
-  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
-  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
-  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
-  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a
-
-[removed most of the output here for clarity]
-
-  Where:
-   L:        Module is loaded
-   Aliases:  Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
-             will load foo/1.2.3
-   D:        Default Module
-
-Use "module spider" to find all possible modules and extensions.
-Use "module keyword key1 key2 ..." to search for all possible modules matching
-any of the "keys".
+```{r, child=paste(snippets, '/modules/available-modules.Rmd', sep=''), eval=TRUE}
 ```
 
 ### Listing Currently Loaded Modules
 
 You can use the `module list` command to see which modules you currently have
 loaded in your environment. If you have no modules loaded, you will see a
-message telling you so
+message telling you so.
 
 ```bash
 `r config$remote$prompt` module list
@@ -120,57 +98,23 @@ No Modulefiles Currently Loaded.
 
 ## Loading and Unloading Software
 
-To load a software module, use `module load`. In this example we will use
-Python 3.
+To load a software module, use `module load`.
 
-Initially, Python 3 is not loaded. We can test this by using the `which`
-command. `which` looks for programs the same way that Bash does, so we can use
-it to tell us where a particular piece of software is stored.
+In this example we will use Python 3. Initially, it is not loaded.
+We can test this by using the `which` command. `which` looks for
+programs the same way that Bash does, so we can use it to tell us
+where a particular piece of software is stored.
 
 ```bash
 `r config$remote$prompt` which python3
 ```
 
-If the `python3` command was unavailable, we would see output like
-
-```output
-/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/`r config$remote$user`/.local/bin:/home/`r config$remote$user`/bin)
-```
-
-Note that this wall of text is really a list, with values separated
-by the `:` character. The output is telling us that the `which` command
-searched the following directories for `python3`, without success:
-
-```output
-/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin
-/opt/software/slurm/bin
-/usr/local/bin
-/usr/bin
-/usr/local/sbin
-/usr/sbin
-/opt/puppetlabs/bin
-/home/`r config$remote$user`/.local/bin
-/home/`r config$remote$user`/bin
-```
-
-However, in our case we do have an existing `python3` available so we see
-
-```output
-/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin/python3
+```{r, child=paste(snippets, '/modules/missing-python.Rmd', sep=''), eval=TRUE}
 ```
 
-We need a different Python than the system provided one though, so let us load
-a module to access it.
-
 We can load the `python3` command with `module load`:
 
-```bash
-`r config$remote$prompt` module load `r config$remote$module_python3`
-`r config$remote$prompt` which python3
-```
-
-```output
-/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3
+```{r, child=paste(snippets, '/modules/module-load-python.Rmd', sep=''), eval=TRUE}
 ```
 
 So, what just happened?
@@ -193,26 +137,9 @@ variables we can print it out using `echo`.
 You'll notice a similarity to the output of the `which` command. In this case,
 there's only one difference: the different directory at the beginning. When we
 ran the `module load` command, it added a directory to the beginning of our
-`$PATH`. Let's examine what's there:
-
-```bash
-`r config$remote$prompt` ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
-```
+`$PATH` -- or "prepended to PATH". Let's examine what's there:
 
-```output
-2to3              nosetests-3.8  python                 rst2s5.py
-2to3-3.8          pasteurize     python3                rst2xetex.py
-chardetect        pbr            python3.8              rst2xml.py
-cygdb             pip            python3.8-config       rstpep2html.py
-cython            pip3           python3-config         runxlrd.py
-cythonize         pip3.8         rst2html4.py           sphinx-apidoc
-easy_install      pybabel        rst2html5.py           sphinx-autogen
-easy_install-3.8  __pycache__    rst2html.py            sphinx-build
-futurize          pydoc3         rst2latex.py           sphinx-quickstart
-idle3             pydoc3.8       rst2man.py             tabulate
-idle3.8           pygmentize     rst2odt_prepstyles.py  virtualenv
-netaddr           pytest         rst2odt.py             wheel
-nosetests         py.test        rst2pseudoxml.py
+```{r, child=paste(snippets, '/modules/python-executable-dir.Rmd', sep=''), eval=TRUE}
 ```
 
 Taking this to its conclusion, `module load` will add software to your `$PATH`.
@@ -220,86 +147,9 @@ It "loads" software. A special note on this - depending on which version of the
 `module` program that is installed at your site, `module load` will also load
 required software dependencies.
 
-To demonstrate, let's use `module list`. `module list` shows all loaded
-software modules.
-
-```bash
-`r config$remote$prompt` module list
+```{r, child=paste(snippets, '/modules/software-dependencies.Rmd', sep=''), eval=TRUE}
 ```
 
-```output
-Currently Loaded Modules:
-  1) GCCcore/x.y.z                 4) GMP/6.2.0-GCCcore-x.y.z
-  2) Tcl/8.6.10-GCCcore-x.y.z      5) libffi/3.3-GCCcore-x.y.z
-  3) SQLite/3.31.1-GCCcore-x.y.z   6) Python/3.x.y-GCCcore-x.y.z
-```
-
-```bash
-`r config$remote$prompt` module load GROMACS
-`r config$remote$prompt` module list
-```
-
-```output
-Currently Loaded Modules:
-  1) GCCcore/x.y.z                    14) libfabric/1.11.0-GCCcore-x.y.z
-  2) Tcl/8.6.10-GCCcore-x.y.z         15) PMIx/3.1.5-GCCcore-x.y.z
-  3) SQLite/3.31.1-GCCcore-x.y.z      16) OpenMPI/4.0.3-GCC-x.y.z
-  4) GMP/6.2.0-GCCcore-x.y.z          17) OpenBLAS/0.3.9-GCC-x.y.z
-  5) libffi/3.3-GCCcore-x.y.z         18) gompi/2020a
-  6) Python/3.x.y-GCCcore-x.y.z       19) FFTW/3.3.8-gompi-2020a
-  7) GCC/x.y.z                        20) ScaLAPACK/2.1.0-gompi-2020a
-  8) numactl/2.0.13-GCCcore-x.y.z     21) foss/2020a
-  9) libxml2/2.9.10-GCCcore-x.y.z     22) pybind11/2.4.3-GCCcore-x.y.z-Pytho...
- 10) libpciaccess/0.16-GCCcore-x.y.z  23) SciPy-bundle/2020.03-foss-2020a-Py...
- 11) hwloc/2.2.0-GCCcore-x.y.z        24) networkx/2.4-foss-2020a-Python-3.8...
- 12) libevent/2.1.11-GCCcore-x.y.z    25) GROMACS/2020.1-foss-2020a-Python-3...
- 13) UCX/1.8.0-GCCcore-x.y.z
-```
-
-So in this case, loading the `GROMACS` module (a bioinformatics software
-package), also loaded `GMP/6.2.0-GCCcore-x.y.z` and
-`SciPy-bundle/2020.03-foss-2020a-Python-3.x.y` as well. Let's try unloading the
-`GROMACS` package.
-
-```bash
-`r config$remote$prompt` module unload GROMACS
-`r config$remote$prompt` module list
-```
-
-```output
-Currently Loaded Modules:
-  1) GCCcore/x.y.z                    13) UCX/1.8.0-GCCcore-x.y.z
-  2) Tcl/8.6.10-GCCcore-x.y.z         14) libfabric/1.11.0-GCCcore-x.y.z
-  3) SQLite/3.31.1-GCCcore-x.y.z      15) PMIx/3.1.5-GCCcore-x.y.z
-  4) GMP/6.2.0-GCCcore-x.y.z          16) OpenMPI/4.0.3-GCC-x.y.z
-  5) libffi/3.3-GCCcore-x.y.z         17) OpenBLAS/0.3.9-GCC-x.y.z
-  6) Python/3.x.y-GCCcore-x.y.z       18) gompi/2020a
-  7) GCC/x.y.z                        19) FFTW/3.3.8-gompi-2020a
-  8) numactl/2.0.13-GCCcore-x.y.z     20) ScaLAPACK/2.1.0-gompi-2020a
-  9) libxml2/2.9.10-GCCcore-x.y.z     21) foss/2020a
- 10) libpciaccess/0.16-GCCcore-x.y.z  22) pybind11/2.4.3-GCCcore-x.y.z-Pytho...
- 11) hwloc/2.2.0-GCCcore-x.y.z        23) SciPy-bundle/2020.03-foss-2020a-Py...
- 12) libevent/2.1.11-GCCcore-x.y.z    24) networkx/2.4-foss-2020a-Python-3.x.y
-```
-
-So using `module unload` "un-loads" a module, and depending on how a site is
-configured it may also unload all of the dependencies (in our case it does
-not). If we wanted to unload everything at once, we could run `module purge`
-(unloads everything).
-
-```bash
-`r config$remote$prompt` module purge
-`r config$remote$prompt` module list
-```
-
-```output
-No modules loaded
-```
-
-Note that `module purge` is informative. It will also let us know if a default
-set of "sticky" packages cannot be unloaded (and how to actually unload these
-if we truly so desired).
-
 Note that this module loading process happens principally through
 the manipulation of environment variables like `$PATH`. There
 is usually little or no data transfer involved.
@@ -322,31 +172,14 @@ certain version, or version X broke compatibility with a file format you use.
 In either of these example cases, it helps to be very specific about what
 software is loaded.
 
-Let's examine the output of `module avail` more closely.
+Let's examine the output of `module avail` more closely, using the pager since
+there may be reams of output:
 
 ```bash
-`r config$remote$prompt` module avail
+`r config$remote$prompt` module avail | less
 ```
 
-```output
-~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
-  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
-  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
-  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
-  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
-  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a
-
-[removed most of the output here for clarity]
-
-  Where:
-   L:        Module is loaded
-   Aliases:  Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
-             will load foo/1.2.3
-   D:        Default Module
-
-Use "module spider" to find all possible modules and extensions.
-Use "module keyword key1 key2 ..." to search for all possible modules matching
-any of the "keys".
+```{r, child=paste(snippets, '/modules/available-modules.Rmd', sep=''), eval=TRUE}
 ```
 
 :::::::::::::::::::::::::::::::::::::::  challenge
@@ -373,7 +206,7 @@ compute node).
 `r if (!is.null(config$sched$flag$qos)) {print(paste(config$sched$comment,config$sched$flag$qos))}
 `r config$sched$comment` `r config$sched$flag$time` 00:00:30
 
-module load `r config$remote$module_python3`
+module load `r config$remote$modules$python`
 
 python3 --version
 ```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml b/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
index 76eb0075..54b76da6 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
+++ b/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
@@ -9,7 +9,7 @@
 # Compute irresponsibly.
 ---
 
-snippets: "/snippets_library/Ghastly_Mistakes"
+snippets: "Ghastly_Mistakes"
 
 local:
   prompt: "luigi@mushroomkingdom:~$"
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.Rmd b/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.Rmd
new file mode 100644
index 00000000..e7fc4eb2
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.Rmd
@@ -0,0 +1,13 @@
+```output
+~~~ /usr/local/modules ~~~
+  amdahl/0.0.1 (D)      python/2.7.1 (O)
+
+  Where:
+   L:        Module is loaded
+   D:        Default Module
+   O:        Module is obsolete
+
+Use "module spider" to find all possible modules and extensions.
+Use "module keyword key1 key2 ..." to search for all possible modules matching
+any of the "keys".
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml b/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
index 45f7a367..1995b6cb 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
@@ -29,6 +29,9 @@ remote:
   module_python3: "Python"
   prompt: "[yourUsername@login1 ~]$"
   bash_shebang: "#!/bin/bash"
+  modules:
+    python: "Python"
+
 
 sched:
   name: "Slurm"
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.Rmd
similarity index 81%
rename from episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.Rmd
index f6f3f50b..2c48235a 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.Rmd
@@ -1,4 +1,8 @@
+```bash
+`r config$remote$prompt` module avail
 ```
+
+```output
 ~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
   Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
   Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
@@ -10,12 +14,11 @@
 
   Where:
    L:        Module is loaded
-   Aliases:  Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
-             will load foo/1.2.3
    D:        Default Module
+   Aliases exist: foo/1.2.3 (1.2) means that
+             "module load foo/1.2" will load foo/1.2.3
 
 Use "module spider" to find all possible modules and extensions.
 Use "module keyword key1 key2 ..." to search for all possible modules matching
 any of the "keys".
-```
-{: .output}
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.snip
deleted file mode 100644
index f6f3f50b..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.snip
+++ /dev/null
@@ -1,21 +0,0 @@
-```
-~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
-  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
-  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
-  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
-  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
-  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a
-
-[removed most of the output here for clarity]
-
-  Where:
-   L:        Module is loaded
-   Aliases:  Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
-             will load foo/1.2.3
-   D:        Default Module
-
-Use "module spider" to find all possible modules and extensions.
-Use "module keyword key1 key2 ..." to search for all possible modules matching
-any of the "keys".
-```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/default-modules.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/default-modules.snip
deleted file mode 100644
index a448dd96..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/default-modules.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-No Modulefiles Currently Loaded.
-```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.Rmd
similarity index 82%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.Rmd
index 89039d32..f06ed919 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/missing-python.Rmd
@@ -1,15 +1,14 @@
 If the `python3` command was unavailable, we would see output like
 
+```output
+/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/`r config$remote$user`/.local/bin:/home/`r config$remote$user`/bin)
 ```
-/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/{{site.remote.user}}/.local/bin:/home/{{site.remote.user}}/bin)
-```
-{: .output}
 
 Note that this wall of text is really a list, with values separated
 by the `:` character. The output is telling us that the `which` command
 searched the following directories for `python3`, without success:
 
-```
+```output
 /cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin
 /opt/software/slurm/bin
 /usr/local/bin
@@ -17,17 +16,15 @@ searched the following directories for `python3`, without success:
 /usr/local/sbin
 /usr/sbin
 /opt/puppetlabs/bin
-/home/{{site.remote.user}}/.local/bin
-/home/{{site.remote.user}}/bin
+/home/`r config$remote$user`/.local/bin
+/home/`r config$remote$user`/bin
 ```
-{: .output}
 
 However, in our case we do have an existing `python3` available so we see
 
-```
+```output
 /cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin/python3
 ```
-{: .output}
 
 We need a different Python than the system provided one though, so let us load
 a module to access it.
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.Rmd
new file mode 100644
index 00000000..81d3be34
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.Rmd
@@ -0,0 +1,8 @@
+```bash
+`r config$remote$prompt` module load `r config$remote$modules$python`
+`r config$remote$prompt` which python3
+```
+
+```output
+/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.snip
deleted file mode 100644
index d9bab7b4..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/module-load-python.snip
+++ /dev/null
@@ -1,5 +0,0 @@
-```
-{{ site.remote.prompt }} module load {{ site.remote.module_python3 }}
-{{ site.remote.prompt }} which python3
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-output.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.Rmd
similarity index 85%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-output.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.Rmd
index 01d010ba..13031bf9 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-output.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.Rmd
@@ -1,4 +1,8 @@
+```bash
+`r config$remote$prompt` ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
 ```
+
+```output
 2to3              nosetests-3.8  python                 rst2s5.py
 2to3-3.8          pasteurize     python3                rst2xetex.py
 chardetect        pbr            python3.8              rst2xml.py
@@ -13,4 +17,3 @@ idle3.8           pygmentize     rst2odt_prepstyles.py  virtualenv
 netaddr           pytest         rst2odt.py             wheel
 nosetests         py.test        rst2pseudoxml.py
 ```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.snip
deleted file mode 100644
index 46dec092..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-executable-dir.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3
-```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-command.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-command.snip
deleted file mode 100644
index 80319d0a..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-ls-dir-command.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-{{ site.remote.prompt }} ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip
index fe107f2e..01234436 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip
@@ -1,26 +1,23 @@
 To demonstrate, let's use `module list`. `module list` shows all loaded
 software modules.
 
+```bash
+`r config$remote$prompt` module list
 ```
-{{ site.remote.prompt }} module list
-```
-{: .language-bash}
 
-```
+```output
 Currently Loaded Modules:
   1) GCCcore/x.y.z                 4) GMP/6.2.0-GCCcore-x.y.z
   2) Tcl/8.6.10-GCCcore-x.y.z      5) libffi/3.3-GCCcore-x.y.z
   3) SQLite/3.31.1-GCCcore-x.y.z   6) Python/3.x.y-GCCcore-x.y.z
 ```
-{: .output}
 
+```bash
+`r config$remote$prompt` module load GROMACS
+`r config$remote$prompt` module list
 ```
-{{ site.remote.prompt }} module load GROMACS
-{{ site.remote.prompt }} module list
-```
-{: .language-bash}
 
-```
+```output
 Currently Loaded Modules:
   1) GCCcore/x.y.z                    14) libfabric/1.11.0-GCCcore-x.y.z
   2) Tcl/8.6.10-GCCcore-x.y.z         15) PMIx/3.1.5-GCCcore-x.y.z
@@ -36,20 +33,18 @@ Currently Loaded Modules:
  12) libevent/2.1.11-GCCcore-x.y.z    25) GROMACS/2020.1-foss-2020a-Python-3...
  13) UCX/1.8.0-GCCcore-x.y.z
 ```
-{: .output}
 
 So in this case, loading the `GROMACS` module (a bioinformatics software
 package), also loaded `GMP/6.2.0-GCCcore-x.y.z` and
 `SciPy-bundle/2020.03-foss-2020a-Python-3.x.y` as well. Let's try unloading the
 `GROMACS` package.
 
+```bash
+`r config$remote$prompt` module unload GROMACS
+`r config$remote$prompt` module list
 ```
-{{ site.remote.prompt }} module unload GROMACS
-{{ site.remote.prompt }} module list
-```
-{: .language-bash}
 
-```
+```output
 Currently Loaded Modules:
   1) GCCcore/x.y.z                    13) UCX/1.8.0-GCCcore-x.y.z
   2) Tcl/8.6.10-GCCcore-x.y.z         14) libfabric/1.11.0-GCCcore-x.y.z
@@ -64,23 +59,20 @@ Currently Loaded Modules:
  11) hwloc/2.2.0-GCCcore-x.y.z        23) SciPy-bundle/2020.03-foss-2020a-Py...
  12) libevent/2.1.11-GCCcore-x.y.z    24) networkx/2.4-foss-2020a-Python-3.x.y
 ```
-{: .output}
 
 So using `module unload` "un-loads" a module, and depending on how a site is
- configured it may also unload all of the dependencies (in our case it does
- not). If we wanted to unload everything at once, we could run `module purge`
- (unloads everything).
+configured it may also unload all of the dependencies (in our case it does
+not). If we wanted to unload everything at once, we could run `module purge`
+(unloads everything).
 
+```bash
+`r config$remote$prompt` module purge
+`r config$remote$prompt` module list
 ```
-{{ site.remote.prompt }} module purge
-{{ site.remote.prompt }} module list
-```
-{: .language-bash}
 
-```
+```output
 No modules loaded
 ```
-{: .output}
 
 Note that `module purge` is informative. It will also let us know if a default
 set of "sticky" packages cannot be unloaded (and how to actually unload these
diff --git a/episodes/lesson_config.yaml b/episodes/lesson_config.yaml
index 52f0a9d7..39ae49a6 100644
--- a/episodes/lesson_config.yaml
+++ b/episodes/lesson_config.yaml
@@ -1,52 +1,3 @@
 ---
-local:
-  prompt: "[you@laptop:~]$"
-  bash_shebang: "#!/usr/bin/env bash"
-
-snippets: HPCC_MagicCastle_slurm
-baseurl: "https://ocaisa.github.io/probable-pancake/"
-
-remote:
-  name: "HPC Carpentry's Cloud Cluster"
-  host_id: #"EPCC_ARCHER2"
-  login: "cluster.hpc-carpentry.org"
-  host: "login1"
-  node: "smnode1"
-  location: "cluster.hpc-carpentry.org"
-  homedir: "/home"
-  user: "yourUsername"
-  prompt: '[yourUsername@login1 ~]'
-  prompt_work: #"userid@uan01:/work/ta114/ta114/userid>"
-  module_python3: "Python"
-  bash_shebang: "#!/bin/bash"
-
-sched:
-  name: "Slurm"
-  submit:
-    name: "sbatch"
-    options: ""
-  queue:
-    debug: "smnode"
-    testing: "cpubase_bycore_b1"
-  status: "squeue"
-  flag:
-    user: "-u yourUsername"
-    interactive: ""
-    histdetail: "-l -j"
-    name: "-J"
-    time: "-t"
-    queue: "-p"
-    nodes: ""
-    tasks: ""
-  del: "scancel"
-  interactive: "srun"
-  info: "sinfo"
-  comment: "#SBATCH"
-  hist: "sacct -u yourUsername"
-  hist_filter: ""
-  partition: "standard"
-  reservation: "shortqos"
-  qos: "short"
-  budget: "short"
-  project: ""
-main_config: "lesson_config_hpcc.yaml"
+main_config: files/snippets/Ghastly_Mistakes/_config_options.yml
+snippets: Ghastly_Mistakes
\ No newline at end of file
diff --git a/episodes/load_config.R b/episodes/load_config.R
index b00ec7a1..dce81aa6 100644
--- a/episodes/load_config.R
+++ b/episodes/load_config.R
@@ -6,7 +6,8 @@ library(yaml)
 ## Load primary configuration
 config <- yaml.load_file("lesson_config.yaml")
 
-## If "config" key exists, load the second configuration and merge
+## If "main_config" key exists, load the second configuration and merge
+print(paste("Loading ", config$main_config))
 if (!is.null(config$main_config) && file.exists(config$main_config)) {
   override_config <- yaml.load_file(config$main_config)
   config <- modifyList(config, override_config)

From 8b9e0e004c53ae0e81cf82183e134af5cedc2f86 Mon Sep 17 00:00:00 2001
From: Trevor Keller <tkellerphd@gmail.com>
Date: Wed, 5 Nov 2025 14:35:26 -0500
Subject: [PATCH 30/33] Snippetized Ep. 17

---
 episodes/17-parallel.Rmd                      | 140 +-----------------
 .../_config_options.yml                       |   4 +-
 .../parallel/eight-tasks-jobscript.snip       |  16 --
 .../parallel/eight-tasks.Rmd                  |  58 ++++++++
 .../parallel/four-tasks-jobscript.snip        |  16 --
 .../parallel/four-tasks.Rmd                   |  56 +++++++
 .../parallel/one-task-jobscript.snip          |  14 --
 .../parallel/one-task.Rmd                     |  22 +++
 .../filezilla-ssh-tunnel-instructions.snip    |   0
 episodes/slurm_defaults.yaml                  |   3 +-
 10 files changed, 144 insertions(+), 185 deletions(-)
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks-jobscript.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks.Rmd
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks-jobscript.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks.Rmd
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task-jobscript.snip
 create mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task.Rmd
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/transferring-files/filezilla-ssh-tunnel-instructions.snip

diff --git a/episodes/17-parallel.Rmd b/episodes/17-parallel.Rmd
index 9f05f34c..f12ebe49 100644
--- a/episodes/17-parallel.Rmd
+++ b/episodes/17-parallel.Rmd
@@ -167,27 +167,7 @@ tell us the important flags we might want to use when launching it.
 
 Create a submission file, requesting one task on a single node, then launch it.
 
-```bash
-`r config$remote$prompt` nano serial-job.sh
-`r config$remote$prompt` cat serial-job.sh
-```
-
-```bash
-`r config$remote$bash_shebang`
-`r config$sched$comment` `r config$sched$flag$name` solo-job
-`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
-`r config$sched$comment` -N 1
-`r config$sched$comment` -n 1
-
-# Load the computing environment we need
-module load `r config$remote$module_python3`
-
-# Execute the task
-amdahl
-```
-
-```bash
-`r config$remote$prompt` `r config$sched$submit$name` serial-job.sh
+```{r, child=paste(snippets, '/parallel/one-task.Rmd', sep=''), eval=TRUE}
 ```
 
 As before, use the `r config$sched$name` status commands to check whether your job
@@ -244,7 +224,7 @@ for 25.5 seconds, and no time was saved. The cluster can do better, if we ask.
 ## Running the Parallel Job
 
 The `amdahl` program uses the Message Passing Interface (MPI) for parallelism
-\-- this is a common tool on HPC systems.
+-- this is a common tool on HPC systems.
 
 :::::::::::::::::::::::::::::::::::::::::  callout
 
@@ -287,61 +267,7 @@ by examining the environment variables set when the job is launched.
 
 Let's modify the job script to request more cores and use the MPI run-time.
 
-```bash
-`r config$remote$prompt` cp serial-job.sh parallel-job.sh
-`r config$remote$prompt` nano parallel-job.sh
-`r config$remote$prompt` cat parallel-job.sh
-```
-
-```bash
-`r config$remote$bash_shebang`
-`r config$sched$comment` `r config$sched$flag$name` parallel-job
-`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
-`r config$sched$comment` -N 1
-`r config$sched$comment` -n 4
-
-# Load the computing environment we need
-# (mpi4py and numpy are in SciPy-bundle)
-module load `r config$remote$module_python3`
-module load SciPy-bundle
-
-# Execute the task
-mpiexec amdahl
-```
-
-Then submit your job. Note that the submission command has not really changed
-from how we submitted the serial job: all the parallel settings are in the
-batch file rather than the command line.
-
-```bash
-`r config$remote$prompt` `r config$sched$submit$name` parallel-job.sh
-```
-
-As before, use the status commands to check when your job runs.
-
-```bash
-`r config$remote$prompt` ls -t
-```
-
-```output
-slurm-347178.out  parallel-job.sh  slurm-347087.out  serial-job.sh  amdahl  README.md  LICENSE.txt
-```
-
-```bash
-`r config$remote$prompt` cat slurm-347178.out
-```
-
-```output
-Doing 30.000 seconds of 'work' on 4 processors,
-which should take 10.875 seconds with 0.850 parallel proportion of the workload.
-
-  Hello, World! I am process 0 of 4 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
-  Hello, World! I am process 2 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
-  Hello, World! I am process 1 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
-  Hello, World! I am process 3 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
-  Hello, World! I am process 0 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
-
-Total execution time (according to rank 0): 10.888 seconds
+```{r, child=paste(snippets, '/parallel/four-tasks.Rmd', sep=''), eval=TRUE}
 ```
 
 :::::::::::::::::::::::::::::::::::::::  challenge
@@ -373,8 +299,6 @@ This is the basic principle behind [Amdahl's Law][amdahl], which is one way
 of predicting improvements in execution time for a **fixed** workload that
 can be subdivided and run in parallel to some extent.
 
-
-
 :::::::::::::::::::::::::
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -406,63 +330,7 @@ versus the number of CPUs *n* would give a straight line, *S* = *n*.
 Let's run one more job, so we can see how close to a straight line our `amdahl`
 code gets.
 
-```bash
-`r config$remote$prompt` nano parallel-job.sh
-`r config$remote$prompt` cat parallel-job.sh
-```
-
-```bash
-`r config$remote$bash_shebang`
-`r config$sched$comment` `r config$sched$flag$name` parallel-job
-`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
-`r config$sched$comment` -N 1
-`r config$sched$comment` -n 8
-
-# Load the computing environment we need
-# (mpi4py and numpy are in SciPy-bundle)
-module load `r config$remote$module_python3`
-module load SciPy-bundle
-
-# Execute the task
-mpiexec amdahl
-```
-
-Then submit your job. Note that the submission command has not really changed
-from how we submitted the serial job: all the parallel settings are in the
-batch file rather than the command line.
-
-```bash
-`r config$remote$prompt` `r config$sched$submit$name` parallel-job.sh
-```
-
-As before, use the status commands to check when your job runs.
-
-```bash
-`r config$remote$prompt` ls -t
-```
-
-```output
-slurm-347271.out  parallel-job.sh  slurm-347178.out  slurm-347087.out  serial-job.sh  amdahl  README.md  LICENSE.txt
-```
-
-```bash
-`r config$remote$prompt` cat slurm-347178.out
-```
-
-```output
-which should take 7.688 seconds with 0.850 parallel proportion of the workload.
-
-  Hello, World! I am process 4 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 0 of 8 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
-  Hello, World! I am process 2 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 1 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 3 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 5 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 6 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 7 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
-  Hello, World! I am process 0 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
-
-Total execution time (according to rank 0): 7.697 seconds
+```{r, child=paste(snippets, '/parallel/eight-tasks.Rmd', sep=''), eval=TRUE}
 ```
 
 ::::::::::::::::::::::::::::::::::::::  discussion
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml b/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
index 1995b6cb..71c8b924 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
@@ -15,7 +15,7 @@ snippets: "/snippets_library/HPCC_MagicCastle_slurm"
 
 local:
   prompt: "[you@laptop:~]$"
-  bash_shebang: "#!/usr/bin/env bash"
+  shebang: "#!/bin/bash"
 
 remote:
   name: "HPC Carpentry's Cloud Cluster"
@@ -28,7 +28,7 @@ remote:
   user: "yourUsername"
   module_python3: "Python"
   prompt: "[yourUsername@login1 ~]$"
-  bash_shebang: "#!/bin/bash"
+  shebang: "#!/bin/bash"
   modules:
     python: "Python"
 
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks-jobscript.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks-jobscript.snip
deleted file mode 100644
index 2f643071..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks-jobscript.snip
+++ /dev/null
@@ -1,16 +0,0 @@
-```
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
-{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
-{{ site.sched.comment }} -N 1
-{{ site.sched.comment }} -n 8
-
-# Load the computing environment we need
-# (mpi4py and numpy are in SciPy-bundle)
-module load {{ site.remote.module_python3 }}
-module load SciPy-bundle
-
-# Execute the task
-mpiexec amdahl
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks.Rmd
new file mode 100644
index 00000000..dcbe379a
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/eight-tasks.Rmd
@@ -0,0 +1,58 @@
+```bash
+`r config$remote$prompt` nano parallel-job.sh
+`r config$remote$prompt` cat parallel-job.sh
+```
+
+```bash
+`r config$remote$shebang`
+`r config$sched$comment` `r config$sched$flag$name` parallel-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 8
+
+# Load the computing environment we need
+# (mpi4py and numpy are in SciPy-bundle)
+module load `r config$remote$modules$python`
+module load SciPy-bundle
+
+# Execute the task
+mpiexec amdahl
+```
+
+Then submit your job. Note that the submission command has not really changed
+from how we submitted the serial job: all the parallel settings are in the
+batch file rather than the command line.
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` parallel-job.sh
+```
+
+As before, use the status commands to check when your job runs.
+
+```bash
+`r config$remote$prompt` ls -t
+```
+
+```output
+slurm-347271.out  parallel-job.sh  slurm-347178.out  slurm-347087.out  serial-job.sh  amdahl  README.md  LICENSE.txt
+```
+
+```bash
+`r config$remote$prompt` cat slurm-347178.out
+```
+
+```output
+which should take 7.688 seconds with 0.850 parallel proportion of the workload.
+
+  Hello, World! I am process 4 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 0 of 8 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
+  Hello, World! I am process 2 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 1 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 3 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 5 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 6 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 7 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 0 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+
+Total execution time (according to rank 0): 7.697 seconds
+```
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks-jobscript.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks-jobscript.snip
deleted file mode 100644
index 19804d74..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks-jobscript.snip
+++ /dev/null
@@ -1,16 +0,0 @@
-```
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
-{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
-{{ site.sched.comment }} -N 1
-{{ site.sched.comment }} -n 4
-
-# Load the computing environment we need
-# (mpi4py and numpy are in SciPy-bundle)
-module load {{ site.remote.module_python3 }}
-module load SciPy-bundle
-
-# Execute the task
-mpiexec amdahl
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks.Rmd
new file mode 100644
index 00000000..2e885505
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/four-tasks.Rmd
@@ -0,0 +1,56 @@
+```bash
+`r config$remote$prompt` cp serial-job.sh parallel-job.sh
+`r config$remote$prompt` nano parallel-job.sh
+`r config$remote$prompt` cat parallel-job.sh
+```
+
+```bash
+`r config$remote$shebang`
+`r config$sched$comment` `r config$sched$flag$name` parallel-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 4
+
+# Load the computing environment we need
+# (mpi4py and numpy are in SciPy-bundle)
+module load `r config$remote$modules$python`
+module load SciPy-bundle
+
+# Execute the task
+mpiexec amdahl
+```
+
+Then submit your job. Note that the submission command has not really changed
+from how we submitted the serial job: all the parallel settings are in the
+batch file rather than the command line.
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` parallel-job.sh
+```
+
+As before, use the status commands to check when your job runs.
+
+```bash
+`r config$remote$prompt` ls -t
+```
+
+```output
+slurm-347178.out  parallel-job.sh  slurm-347087.out  serial-job.sh  amdahl  README.md  LICENSE.txt
+```
+
+```bash
+`r config$remote$prompt` cat slurm-347178.out
+```
+
+```output
+Doing 30.000 seconds of 'work' on 4 processors,
+which should take 10.875 seconds with 0.850 parallel proportion of the workload.
+
+  Hello, World! I am process 0 of 4 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
+  Hello, World! I am process 2 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 1 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 3 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 0 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+
+Total execution time (according to rank 0): 10.888 seconds
+```
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task-jobscript.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task-jobscript.snip
deleted file mode 100644
index 1941ef04..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task-jobscript.snip
+++ /dev/null
@@ -1,14 +0,0 @@
-```
-{{ 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
-
-# Load the computing environment we need
-module load {{ site.remote.module_python3 }}
-
-# Execute the task
-amdahl
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task.Rmd
new file mode 100644
index 00000000..ceefdfdb
--- /dev/null
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/parallel/one-task.Rmd
@@ -0,0 +1,22 @@
+```bash
+`r config$remote$prompt` nano serial-job.sh
+`r config$remote$prompt` cat serial-job.sh
+```
+
+```bash
+`r config$remote$shebang`
+`r config$sched$comment` `r config$sched$flag$name` solo-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 1
+
+# Load the computing environment we need
+module load `r config$remote$modules$python`
+
+# Execute the task
+amdahl
+```
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` serial-job.sh
+```
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/transferring-files/filezilla-ssh-tunnel-instructions.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/transferring-files/filezilla-ssh-tunnel-instructions.snip
deleted file mode 100644
index e69de29b..00000000
diff --git a/episodes/slurm_defaults.yaml b/episodes/slurm_defaults.yaml
index fc550217..6372be9c 100644
--- a/episodes/slurm_defaults.yaml
+++ b/episodes/slurm_defaults.yaml
@@ -20,7 +20,8 @@ remote:
   user: "userid"                             # stand-in for the username
   prompt: "[userid@head:~]"                  # command-line prompt
   prompt_work: "[userid@head:/work/userid]"  # prompt under /work
-  module_python3: "Python"                   # name of the module providing py3
+  modules:
+    python: "Python"                         # name of the module providing Python v3
   shebang: "#!/bin/bash"                     # first line of every shell script
 
 # Commands & flags for the scheduler environment

From 2c924f8f419a14c2e41b4f9c34530e4089683149 Mon Sep 17 00:00:00 2001
From: Trevor Keller <tkellerphd@gmail.com>
Date: Wed, 5 Nov 2025 14:41:42 -0500
Subject: [PATCH 31/33] Snippetized Ep. 18

---
 episodes/18-resources.Rmd                     | 13 +------------
 ...count-history.snip => account-history.Rmd} |  5 ++---
 .../resources/monitor-processes-top.snip      | 19 -------------------
 .../resources/system-memory-free.snip         |  6 ------
 4 files changed, 3 insertions(+), 40 deletions(-)
 rename episodes/files/snippets/HPCC_MagicCastle_slurm/resources/{account-history.snip => account-history.Rmd} (97%)
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/resources/monitor-processes-top.snip
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/resources/system-memory-free.snip

diff --git a/episodes/18-resources.Rmd b/episodes/18-resources.Rmd
index 8fe70605..d95d8b53 100644
--- a/episodes/18-resources.Rmd
+++ b/episodes/18-resources.Rmd
@@ -69,18 +69,7 @@ use ``r config$sched$hist`` to get statistics about `parallel-job.sh`.
 `r config$remote$prompt` `r config$sched$hist`
 ```
 
-```output
-       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
------------- ---------- ---------- ---------- ---------- ---------- --------
-7               file.sh cpubase_b+ def-spons+          1  COMPLETED      0:0
-7.batch           batch            def-spons+          1  COMPLETED      0:0
-7.extern         extern            def-spons+          1  COMPLETED      0:0
-8               file.sh cpubase_b+ def-spons+          1  COMPLETED      0:0
-8.batch           batch            def-spons+          1  COMPLETED      0:0
-8.extern         extern            def-spons+          1  COMPLETED      0:0
-9            example-j+ cpubase_b+ def-spons+          1  COMPLETED      0:0
-9.batch           batch            def-spons+          1  COMPLETED      0:0
-9.extern         extern            def-spons+          1  COMPLETED      0:0
+```{r, child=paste(snippets, '/resources/account-history.Rmd', sep=''), eval=TRUE}
 ```
 
 This shows all the jobs we ran today (note that there are multiple entries per
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.Rmd
similarity index 97%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.Rmd
index d5a87620..5e8a53f2 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/account-history.Rmd
@@ -1,4 +1,4 @@
-```
+```output
        JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
 ------------ ---------- ---------- ---------- ---------- ---------- --------
 7               file.sh cpubase_b+ def-spons+          1  COMPLETED      0:0
@@ -10,5 +10,4 @@
 9            example-j+ cpubase_b+ def-spons+          1  COMPLETED      0:0
 9.batch           batch            def-spons+          1  COMPLETED      0:0
 9.extern         extern            def-spons+          1  COMPLETED      0:0
-```
-{: .output}
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/monitor-processes-top.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/monitor-processes-top.snip
deleted file mode 100644
index 12685735..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/monitor-processes-top.snip
+++ /dev/null
@@ -1,19 +0,0 @@
-```
-top - 21:00:19 up  3:07,  1 user,  load average: 1.06, 1.05, 0.96
-Tasks: 311 total,   1 running, 222 sleeping,   0 stopped,   0 zombie
-%Cpu(s):  7.2 us,  3.2 sy,  0.0 ni, 89.0 id,  0.0 wa,  0.2 hi,  0.2 si,  0.0 st
-KiB Mem : 16303428 total,  8454704 free,  3194668 used,  4654056 buff/cache
-KiB Swap:  8220668 total,  8220668 free,        0 used. 11628168 avail Mem
-
-  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
- 1693 jeff      20   0 4270580 346944 171372 S  29.8  2.1   9:31.89 gnome-shell
- 3140 jeff      20   0 3142044 928972 389716 S  27.5  5.7  13:30.29 Web Content
- 3057 jeff      20   0 3115900 521368 231288 S  18.9  3.2  10:27.71 firefox
- 6007 jeff      20   0  813992 112336  75592 S   4.3  0.7   0:28.25 tilix
- 1742 jeff      20   0  975080 164508 130624 S   2.0  1.0   3:29.83 Xwayland
-    1 root      20   0  230484  11924   7544 S   0.3  0.1   0:06.08 systemd
-   68 root      20   0       0      0      0 I   0.3  0.0   0:01.25 kworker/4:1
- 2913 jeff      20   0  965620  47892  37432 S   0.3  0.3   0:11.76 code
-    2 root      20   0       0      0      0 S   0.0  0.0   0:00.02 kthreadd
-```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/system-memory-free.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/system-memory-free.snip
deleted file mode 100644
index ec4c0d3f..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/resources/system-memory-free.snip
+++ /dev/null
@@ -1,6 +0,0 @@
-```
-total        used        free      shared  buff/cache   available
-Mem:           3.8G        1.5G        678M        327M        1.6G        1.6G
-Swap:          3.9G        170M        3.7G
-```
-{: .output}

From f91826fb8dd3614fc6b78871d1a661df2dc68cdf Mon Sep 17 00:00:00 2001
From: Trevor Keller <tkellerphd@gmail.com>
Date: Wed, 5 Nov 2025 15:45:33 -0500
Subject: [PATCH 32/33] Ghastly Mistakes appears to work

---
 episodes/10-hpc-intro.Rmd                     |  5 ++
 episodes/11-connecting.Rmd                    | 10 +--
 episodes/15-modules.Rmd                       | 11 ++-
 episodes/18-resources.Rmd                     |  4 +-
 .../EPCC_ARCHER2_slurm/_config_options.yml    | 63 -------------
 .../EPCC_ARCHER2_slurm/cluster/queue-info.Rmd |  8 --
 .../cluster/specific-node-info.Rmd            | 11 ---
 .../EPCC_ARCHER2_slurm/login_output.Rmd       | 26 ------
 .../modules/available-modules.Rmd             | 26 ------
 .../modules/missing-python.snip               |  1 -
 .../modules/module-load-python.snip           |  2 -
 .../modules/module_list.snip                  | 16 ----
 .../modules/python-executable-dir.snip        |  1 -
 .../modules/python-ls-dir-command.snip        |  1 -
 .../modules/python-ls-dir-output.snip         |  2 -
 .../modules/python-module-path.snip           |  1 -
 .../modules/software-dependencies.snip        | 80 -----------------
 .../modules/wrong-gcc-version.snip            | 73 ---------------
 .../resources/job-detail.Rmd                  |  2 -
 .../resources/perf-exercise.Rmd               | 67 --------------
 .../resources/pi-mpi-details.Rmd              | 16 ----
 .../resources/runtime-exercise.Rmd            | 47 ----------
 .../resources/serial-submit.Rmd               | 25 ------
 .../resources/sharpen-details.snip            | 18 ----
 .../resources/view-output.snip                | 12 ---
 .../scheduler/basic-job-script.Rmd            |  3 -
 .../scheduler/basic-job-status.Rmd            |  8 --
 .../EPCC_ARCHER2_slurm/scheduler/del_job.Rmd  |  3 -
 .../scheduler/filesystem_issues.Rmd           | 23 -----
 .../scheduler/job-with-name-status.Rmd        |  4 -
 .../EPCC_ARCHER2_slurm/scheduler/long_job.Rmd | 11 ---
 .../scheduler/ls-pgm-output.Rmd               |  4 -
 .../scheduler/option-flags-list.Rmd           |  5 --
 .../scheduler/parallel-challenge.Rmd          | 27 ------
 .../scheduler/parallel-challenge2.Rmd         | 29 ------
 .../scheduler/parallel-launch-desc.Rmd        | 15 ----
 .../scheduler/parallel-script.Rmd             | 15 ----
 .../scheduler/print-sched-variables.Rmd       | 12 ---
 .../scheduler/runtime-exceeded-job.Rmd        |  3 -
 .../scheduler/runtime-exceeded-output.Rmd     |  5 --
 .../scheduler/squeue_pending.Rmd              |  4 -
 .../scheduler/squeue_running.Rmd              |  2 -
 .../scheduler/terminate-job-begin.Rmd         |  6 --
 .../scheduler/terminate-job-cancel.Rmd        |  3 -
 .../scheduler/terminate-multiple-jobs.Rmd     |  9 --
 .../scheduler/using-nodes-interactively.Rmd   | 33 -------
 .../Ghastly_Mistakes/_config_options.yml      |  3 +-
 .../Ghastly_Mistakes/cluster/queue-info.Rmd   |  5 +-
 .../cluster/specific-node-info.Rmd            |  2 +-
 .../modules/available-modules.Rmd             | 17 +++-
 .../modules/default-modules.snip              |  4 -
 ...missing-python.snip => missing-python.Rmd} | 15 ++--
 .../modules/module-load-python.Rmd            |  8 ++
 .../modules/module-load-python.snip           |  5 --
 ...-output.snip => python-executable-dir.Rmd} |  5 +-
 .../modules/python-executable-dir.snip        |  4 -
 .../modules/python-ls-dir-command.snip        |  4 -
 .../modules/python-module-path.snip           |  4 -
 .../modules/software-dependencies.Rmd}        |  0
 .../modules/wrong-gcc-version.snip            |  5 --
 .../parallel/eight-tasks-jobscript.snip       | 16 ----
 .../Ghastly_Mistakes/parallel/eight-tasks.Rmd | 58 ++++++++++++
 .../parallel/four-tasks-jobscript.snip        | 16 ----
 .../Ghastly_Mistakes/parallel/four-tasks.Rmd  | 56 ++++++++++++
 .../parallel/one-task-jobscript.snip          | 14 ---
 .../Ghastly_Mistakes/parallel/one-task.Rmd    | 22 +++++
 ...count-history.snip => account-history.Rmd} |  5 +-
 .../resources/monitor-processes-top.snip      | 19 ----
 .../resources/system-memory-free.snip         |  6 --
 .../scheduler/basic-job-status.Rmd            |  4 +-
 .../scheduler/job-with-name-status.Rmd        |  4 +-
 .../scheduler/option-flags-list.Rmd           |  2 -
 .../scheduler/print-sched-variables.Rmd       | 10 +--
 .../scheduler/runtime-exceeded-output.Rmd     |  2 +-
 .../scheduler/terminate-job-begin.Rmd         |  4 +-
 .../scheduler/using-nodes-interactively.Rmd   |  8 +-
 .../filezilla-ssh-tunnel-instructions.snip    |  0
 .../modules/available-modules.Rmd             |  2 +-
 .../modules/python-module-path.snip           |  4 -
 .../modules/software-dependencies.Rmd}        | 44 ++++-----
 .../modules/wrong-gcc-version.snip            |  5 --
 episodes/files/snippets/rename-snippets.sh    | 89 -------------------
 episodes/lesson_config.yaml                   |  3 +-
 episodes/load_config.R                        | 10 +--
 site/README.md                                |  2 +-
 85 files changed, 236 insertions(+), 1002 deletions(-)
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/login_output.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/available-modules.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/missing-python.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module-load-python.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module_list.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-executable-dir.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-command.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-output.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-module-path.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/software-dependencies.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/modules/wrong-gcc-version.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/job-detail.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/perf-exercise.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/pi-mpi-details.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/runtime-exercise.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/serial-submit.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/sharpen-details.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/resources/view-output.snip
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-status.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/option-flags-list.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-begin.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-cancel.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
 delete mode 100644 episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/default-modules.snip
 rename episodes/files/snippets/Ghastly_Mistakes/modules/{missing-python.snip => missing-python.Rmd} (82%)
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.Rmd
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.snip
 rename episodes/files/snippets/Ghastly_Mistakes/modules/{python-ls-dir-output.snip => python-executable-dir.Rmd} (85%)
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.snip
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-command.snip
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/python-module-path.snip
 rename episodes/files/snippets/{HPCC_MagicCastle_slurm/modules/software-dependencies.snip => Ghastly_Mistakes/modules/software-dependencies.Rmd} (100%)
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/modules/wrong-gcc-version.snip
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks-jobscript.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks.Rmd
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks-jobscript.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks.Rmd
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/one-task-jobscript.snip
 create mode 100644 episodes/files/snippets/Ghastly_Mistakes/parallel/one-task.Rmd
 rename episodes/files/snippets/Ghastly_Mistakes/resources/{account-history.snip => account-history.Rmd} (97%)
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/resources/monitor-processes-top.snip
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/resources/system-memory-free.snip
 delete mode 100644 episodes/files/snippets/Ghastly_Mistakes/transferring-files/filezilla-ssh-tunnel-instructions.snip
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-module-path.snip
 rename episodes/files/snippets/{Ghastly_Mistakes/modules/software-dependencies.snip => HPCC_MagicCastle_slurm/modules/software-dependencies.Rmd} (80%)
 delete mode 100644 episodes/files/snippets/HPCC_MagicCastle_slurm/modules/wrong-gcc-version.snip
 delete mode 100755 episodes/files/snippets/rename-snippets.sh

diff --git a/episodes/10-hpc-intro.Rmd b/episodes/10-hpc-intro.Rmd
index 6b7e88c9..6059c5a7 100644
--- a/episodes/10-hpc-intro.Rmd
+++ b/episodes/10-hpc-intro.Rmd
@@ -4,6 +4,11 @@ teaching: 15
 exercises: 5
 ---
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Describe what an HPC system is
diff --git a/episodes/11-connecting.Rmd b/episodes/11-connecting.Rmd
index 103d0379..428ac5e6 100644
--- a/episodes/11-connecting.Rmd
+++ b/episodes/11-connecting.Rmd
@@ -4,6 +4,11 @@ teaching: 25
 exercises: 10
 ---
 
+```{r, echo=FALSE}
+# Source the external configuration script
+source("load_config.R")
+```
+
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Configure secure access to a remote HPC system.
@@ -17,11 +22,6 @@ exercises: 10
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-```{r, echo=FALSE}
-# Source the external configuration script
-source("load_config.R")
-```
-
 ## Secure Connections
 
 The first step in using a cluster is to establish a connection from our laptop
diff --git a/episodes/15-modules.Rmd b/episodes/15-modules.Rmd
index db1d387e..fc044cfa 100644
--- a/episodes/15-modules.Rmd
+++ b/episodes/15-modules.Rmd
@@ -82,6 +82,8 @@ To see available software modules, use `module avail`:
 ```{r, child=paste(snippets, '/modules/available-modules.Rmd', sep=''), eval=TRUE}
 ```
 
+Note that piping the output through `less` allows us to search within the output using the <kbd>/</kbd> key.
+
 ### Listing Currently Loaded Modules
 
 You can use the `module list` command to see which modules you currently have
@@ -175,13 +177,14 @@ software is loaded.
 Let's examine the output of `module avail` more closely, using the pager since
 there may be reams of output:
 
-```bash
-`r config$remote$prompt` module avail | less
-```
-
 ```{r, child=paste(snippets, '/modules/available-modules.Rmd', sep=''), eval=TRUE}
 ```
 
+If the software your Slurm script runs requires on a specific version
+of a dependency, make sure you use the full name of the module, rather
+than the _default_ loaded when you give only its name (up to the first
+slash).
+
 :::::::::::::::::::::::::::::::::::::::  challenge
 
 ## Using Software Modules in Scripts
diff --git a/episodes/18-resources.Rmd b/episodes/18-resources.Rmd
index d95d8b53..86901f40 100644
--- a/episodes/18-resources.Rmd
+++ b/episodes/18-resources.Rmd
@@ -31,8 +31,8 @@ might matter.
 
 ## Estimating Required Resources Using the Scheduler
 
-Although we covered requesting resources from the scheduler earlier with the
-π code, how do we know what type of resources the software will need in
+Although we covered requesting resources from the scheduler earlier,
+how do we know what type of resources the software will need in
 the first place, and its demand for each? In general, unless the software
 documentation or user testimonials provide some idea, we won't know how much
 memory or compute time a program will need.
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml b/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
deleted file mode 100644
index 694a44a9..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/_config_options.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-#------------------------------------------------------------
-# ComputeCanada: Graham + Slurm
-#------------------------------------------------------------
-
-# Cluster host and scheduler options: the defaults come from
-# Graham at Compute Canada, running Slurm. Other options can
-# be found in the library of snippets,
-# `_includes/snippets_library`. To use one, replace options
-# below with those in `_config_options.yml` from the
-# library. E.g, to customise for Cirrus at EPCC, running
-# PBS, we could replace the options below with those from
-# 
-# _includes/snippets_library/EPCC_Cirrus_pbs/_config_options.yml
-# 
-# If your cluster is not represented in the library, please
-# copy an existing folder, rename it, and customize for your
-# installation. Remember to keep the leading slash on the
-# `snippets` variable below!
-
-snippets: "/snippets_library/EPCC_ARCHER2_slurm"
-
-local:
-  prompt: "[user@laptop ~]$"
-  bash_shebang: "#!/bin/bash"
-
-remote:
-  name: "ARCHER2"
-  login: "login.archer2.ac.uk"
-  host: "ln03"
-  node: "nid001053"
-  location: "EPCC, The University of Edinburgh"
-  homedir: "/home/ta076/ta076/"
-  user: "userid"
-  prompt: "userid@ln03:~>"
-  prompt-work: "userid@ln03:/work/ta076/ta076/userid>"
-  module_python3: "cray-python"
-  bash_shebang: "#!/bin/bash"
-
-sched:
-  name: "Slurm"
-  reservation: "shortqos"
-  budget: "short"
-  submit:
-    name: "sbatch"
-    options: "--partition=standard --qos=short"
-  queue:
-    debug: ""
-    testing: ""
-  status: "squeue"
-  flag:
-    user: "-u userid"
-    interactive: ""
-    histdetail: "-l -j"
-    name: "--job-name"
-    time: "--time"
-    queue: "--partition"
-    nodes: "--nodes"
-    tasks: ""
-  del: "scancel"
-  interactive: "srun"
-  info: "sinfo"
-  comment: "#SBATCH"
-  hist: "sacct"
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.Rmd
deleted file mode 100644
index b9573160..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/queue-info.Rmd
+++ /dev/null
@@ -1,8 +0,0 @@
-```output
-PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST 
-standard     up 1-00:00:00     27 drain* nid[001029,001050,001149,001363,001366,001391,001552,001568,001620,001642,001669,001672-001675,001688,001690-001691,001747,001751,001783,001793,001812,001832-001835] 
-standard     up 1-00:00:00      5  down* nid[001024,001026,001064,001239,001898] 
-standard     up 1-00:00:00      8  drain nid[001002,001028,001030-001031,001360-001362,001745] 
-standard     up 1-00:00:00    945  alloc nid[001000-001001,001003-001023,001025,001027,001032-001037,001040-001049,001051-001063,001065-001108,001110-001145,001147,001150-001238,001240-001264,001266-001271,001274-001334,001337-001359,001364-001365,001367-001390,001392-001551,001553-001567,001569-001619,001621-001637,001639-001641,001643-001668,001670-001671,001676,001679-001687,001692-001734,001736-001744,001746,001748-001750,001752-001782,001784-001792,001794-001811,001813-001824,001826-001831,001836-001890,001892-001897,001899-001918,001920,001923-001934,001936-001945,001947-001965,001967-001981,001984-001991,002006-002023] 
-standard     up 1-00:00:00     37   resv nid[001038-001039,001109,001146,001148,001265,001272-001273,001335-001336,001638,001677-001678,001735,001891,001919,001921-001922,001935,001946,001966,001982-001983,001992-002005] 
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
deleted file mode 100644
index 54a94855..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/cluster/specific-node-info.Rmd
+++ /dev/null
@@ -1,11 +0,0 @@
-::: challenge
-## Explore a Worker Node
-
-Finally, let's look at the resources available on the worker nodes
-where your jobs will actually run. Try running this command to see
-the name, CPUs and memory available on one of the worker nodes:
-
-```bash
-`r config$remote$prompt` sinfo -n nid001053 -o "%n %c %m"
-```
-:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/login_output.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/login_output.Rmd
deleted file mode 100644
index dbba457f..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/login_output.Rmd
+++ /dev/null
@@ -1,26 +0,0 @@
-```output
-This node is running Cray's Linux Environment version 1.3.2
-
-#######################################################################################
-
-        @@@@@@@@@
-     @@@         @@@            _      ____     ____   _   _   _____   ____    ____
-   @@@    @@@@@    @@@         / \    |  _ \   / ___| | | | | | ____| |  _ \  |___ \
-  @@@   @@     @@   @@@       / _ \   | |_) | | |     | |_| | |  _|   | |_) |   __) |
-  @@   @@  @@@  @@   @@      / ___ \  |  _ <  | |___  |  _  | | |___  |  _ <   / __/
-  @@   @@  @@@  @@   @@     /_/   \_\ |_| \_\  \____| |_| |_| |_____| |_| \_\ |_____|
-  @@@   @@     @@   @@@
-   @@@    @@@@@    @@@       https://www.archer2.ac.uk/support-access/
-     @@@         @@@
-        @@@@@@@@@
-
- -         U K R I         -        E P C C        -         H P E   C r a y         -
-
-Hostname:     uan01
-Distribution: SLES 15.1 1
-CPUS:         256
-Memory:       257.4GB
-Configured:   2021-04-27
-
-######################################################################################
-```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/available-modules.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/available-modules.Rmd
deleted file mode 100644
index 132ecf1f..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/available-modules.Rmd
+++ /dev/null
@@ -1,26 +0,0 @@
-```output
------------ /work/y07/shared/archer2-modules/modulefiles-cse-pyvenvs -----------
-tensorflow/2.3.1-py38  torch/1.6.0-py38  
-
------------ /work/y07/shared/archer2-modules/modulefiles-cse-pymods ------------
-python-netCDF4/1.5.5.1  
-
------------- /work/y07/shared/archer2-modules/modulefiles-cse-utils ------------
-bolt/0.7                  ncview/ncview-2.1.7-gcc-10.1.0  vmd/1.9.3-mpi-gcc10  
-cmake/3.18.4              reframe/3.2                     xios/2.5-gcc10       
-ed/1.16-gcc10             tcl/8.4.20-gcc10                xthi/1.0             
-epcc-job-env              tcl/8.5.0-gcc10                 xthi/1.0-gcc10       
-epcc-reframe/0.1          tcl/8.6.0-gcc10                 
-genmaskcpu/1.0            tcl/8.6.10-gcc10(default)       
-gnuplot/5.4.1-gcc-10.1.0  tk/8.5.6-gcc10                  
-lzip/1.20-gcc10           tk/8.6.10-gcc10(default)        
-nco/4.9.6                 visidata/2.1                    
-nco/4.9.6-gcc-10.1.0      vmd/1.9.3-gcc10(default)        
-
------------- /work/y07/shared/archer2-modules/modulefiles-cse-libs -------------
-adios/1.13.1     hypre/2.18.0             mumps/5.2.1     superlu-dist/6.1.1  
-boost/1.72.0     libxml2/2.9.7-gcc-9.3.0  parmetis/4.0.3  superlu/5.2.1       
-glm/0.9.9.6      matio/1.5.18             petsc/3.13.3    trilinos/12.18.1    
-gmp/6.1.2-gcc10  metis/5.1.0              scotch/6.0.10   
-...
-```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/missing-python.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/missing-python.snip
deleted file mode 100644
index 381142dc..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/missing-python.snip
+++ /dev/null
@@ -1 +0,0 @@
-/usr/bin/python3
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module-load-python.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module-load-python.snip
deleted file mode 100644
index d0e214d5..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module-load-python.snip
+++ /dev/null
@@ -1,2 +0,0 @@
-{{ site.host_prompt-work }} module load cray-python
-{{ site.host_prompt-work }} which python3
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module_list.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module_list.snip
deleted file mode 100644
index c180fda5..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/module_list.snip
+++ /dev/null
@@ -1,16 +0,0 @@
-Currently Loaded Modulefiles:
- 1) cpe-cray                                                                 
- 2) cce/10.0.4(default)                                                      
- 3) craype/2.7.2(default)                                                    
- 4) craype-x86-rome                                                          
- 5) libfabric/1.11.0.0.233(default)                                          
- 6) craype-network-ofi                                                       
- 7) cray-dsmml/0.1.2(default)                                                
- 8) perftools-base/20.10.0(default)                                          
- 9) xpmem/2.2.35-7.0.1.0_1.9__gd50fabf.shasta(default)                       
-10) cray-mpich/8.0.16(default)                                               
-11) cray-libsci/20.10.1.2(default)                                           
-12) bolt/0.7                                                                 
-13) /work/y07/shared/archer2-modules/modulefiles-cse/epcc-setup-env          
-14) /usr/local/share/epcc-module/epcc-module-loader                          
-15) /work/y07/shared/archer2-modules/modulefiles-cse/epcc-setup-env-profile
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-executable-dir.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-executable-dir.snip
deleted file mode 100644
index b9f4b294..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-executable-dir.snip
+++ /dev/null
@@ -1 +0,0 @@
-/opt/cray/pe/python/3.8.5.0/bin/python3
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-command.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-command.snip
deleted file mode 100644
index f87667f8..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-command.snip
+++ /dev/null
@@ -1 +0,0 @@
-{{ site.host_prompt-work }} ls /opt/cray/pe/python/3.8.5.0/bin
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-output.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-output.snip
deleted file mode 100644
index b8411602..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-ls-dir-output.snip
+++ /dev/null
@@ -1,2 +0,0 @@
-2to3	  cygdb   cythonize	easy_install-3.8  f2py3    idle3    nosetests	   pip	 pip3.8  pydoc3.8  py.test  python3    python3.8-config
-2to3-3.8  cython  easy_install	f2py		  f2py3.8  idle3.8  nosetests-3.8  pip3  pydoc3  pytest    python   python3.8  python3-config
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-module-path.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-module-path.snip
deleted file mode 100644
index b8480b0e..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/python-module-path.snip
+++ /dev/null
@@ -1 +0,0 @@
-/opt/cray/pe/python/3.8.5.0/bin:/lus/cls01095/work/z19/z19/aturner/.local/bin:/lus/cls01095/work/y07/shared/bolt/0.7/bin:/work/y07/shared/utils/bin:/usr/local/maven/bin:/opt/cray/pe/perftools/20.10.0/bin:/opt/cray/pe/papi/6.0.0.4/bin:/opt/cray/libfabric/1.11.0.0.233/bin:/opt/cray/pe/craype/2.7.2/bin:/opt/cray/pe/cce/10.0.4/cce-clang/x86_64/bin:/opt/cray/pe/cce/10.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin:/opt/cray/pe/cce/10.0.4/binutils/cross/x86_64-aarch64/aarch64-linux-gnu/../bin:/opt/cray/pe/cce/10.0.4/utils/x86_64/bin:/usr/local/Modules/bin:/home/z19/z19/aturner/bin:/usr/local/bin:/usr/bin:/bin:/opt/cray/pe/bin:/usr/lib/mit/bin
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/software-dependencies.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/software-dependencies.snip
deleted file mode 100644
index f555f415..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/software-dependencies.snip
+++ /dev/null
@@ -1,80 +0,0 @@
-To demonstrate, let's use `module list`. `module list` shows all loaded software modules.
-
-```
-{{ site.host_prompt }} module list
-```
-{: .language-bash}
-```
-Currently Loaded Modules:
-  1) nixpkgs/.16.09  (H,S)   3) gcccore/.5.4.0    (H)   5) intel/2016.4  (t)   7) StdEnv/2016.4 (S)
-  2) icc/.2016.4.258 (H)     4) ifort/.2016.4.258 (H)   6) openmpi/2.1.1 (m)   8) python/3.5.2  (t)
-
-  Where:
-   S:  Module is Sticky, requires --force to unload or purge
-   m:  MPI implementations / Implémentations MPI
-   t:  Tools for development / Outils de développement
-   H:             Hidden Module
-```
-{: .output}
-
-```
-{{ site.host_prompt }} module load beast
-{{ site.host_prompt }} module list
-```
-{: .language-bash}
-```
-Currently Loaded Modules:
-  1) nixpkgs/.16.09    (H,S)   5) intel/2016.4  (t)   9) java/1.8.0_121   (t)
-  2) icc/.2016.4.258   (H)     6) openmpi/2.1.1 (m)  10) beagle-lib/2.1.2 (bio)
-  3) gcccore/.5.4.0    (H)     7) StdEnv/2016.4 (S)  11) beast/2.4.0      (chem)
-  4) ifort/.2016.4.258 (H)     8) python/3.5.2  (t)
-
-  Where:
-   S:     Module is Sticky, requires --force to unload or purge
-   bio:   Bioinformatic libraries/apps / Logiciels de bioinformatique
-   m:     MPI implementations / Implémentations MPI
-   t:     Tools for development / Outils de développement
-   chem:  Chemistry libraries/apps / Logiciels de chimie
-   H:                Hidden Module
-```
-{: .output}
-
-So in this case, loading the `beast` module (a bioinformatics software package), also loaded
-`java/1.8.0_121` and `beagle-lib/2.1.2` as well. Let's try unloading the `beast` package.
-
-```
-{{ site.host_prompt }} module unload beast
-{{ site.host_prompt }} module list
-```
-{: .language-bash}
-```
-Currently Loaded Modules:
-  1) nixpkgs/.16.09  (H,S)   3) gcccore/.5.4.0    (H)   5) intel/2016.4  (t)   7) StdEnv/2016.4 (S)
-  2) icc/.2016.4.258 (H)     4) ifort/.2016.4.258 (H)   6) openmpi/2.1.1 (m)   8) python/3.5.2  (t)
-
-  Where:
-   S:  Module is Sticky, requires --force to unload or purge
-   m:  MPI implementations / Implémentations MPI
-   t:  Tools for development / Outils de développement
-   H:             Hidden Module
-```
-{: .output}
-
-So using `module unload` "un-loads" a module along with its dependencies.
-If we wanted to unload everything at once, we could run `module purge` (unloads everything).
-
-```
-{{ site.host_prompt }} module purge
-```
-{: .language-bash}
-```
-The following modules were not unloaded:
-  (Use "module --force purge" to unload all):
-
-  1) StdEnv/2016.4    3) icc/.2016.4.258   5) ifort/.2016.4.258   7) imkl/11.3.4.258
-  2) nixpkgs/.16.09   4) gcccore/.5.4.0    6) intel/2016.4        8) openmpi/2.1.1
-```
-{: .output}
-
-Note that `module purge` is informative. It lets us know that all but a default set of packages 
-have been unloaded (and how to actually unload these if we truly so desired).
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/wrong-gcc-version.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/wrong-gcc-version.snip
deleted file mode 100644
index 9e0f7666..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/modules/wrong-gcc-version.snip
+++ /dev/null
@@ -1,73 +0,0 @@
-Let's take a closer look at the `gcc` module. GCC is an extremely widely used 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 two different versions: `gcc/4.8.5` and
-`gcc/5.4.0`. How do we load each copy and which copy is the default?
-
-In this case, `gcc/5.4.0` has a `(D)` next to it. This indicates that it is the default - if we type
-`module load gcc`, this is the copy that will be loaded.
-
-```
-{{ site.host_prompt }} module load gcc
-{{ site.host_prompt }} gcc --version
-```
-{: .language-bash}
-```
-Lmod is automatically replacing "intel/2016.4" with "gcc/5.4.0".
-
-
-Due to MODULEPATH changes, the following have been reloaded:
-  1) openmpi/2.1.1
-
-gcc (GCC) 5.4.0
-Copyright (C) 2015 Free Software Foundation, Inc.
-This is free software; see the source for copying conditions.  There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-```
-{: .output}
-
-Note that three things happened: the default copy of GCC was loaded (version 5.4.0), the Intel
-compilers (which conflict with GCC) were unloaded, and software that is dependent on compiler
-(OpenMPI) was reloaded. The `module` system turned what might be a super-complex operation into a
-single command.
-
-So how do we load the non-default copy of a software package? In this case, the only change we need
-to make is be more specific about the module we are loading. There are two GCC modules: `gcc/5.4.0`
-and `gcc/4.8.5`. To load a non-default module, the only change we need to make to our `module load`
-command is to leave in the version number after the `/`.
-
-```
-{{ site.host_prompt }} module load gcc/4.8.5
-{{ site.host_prompt }} gcc --version
-```
-{: .language-bash}
-```
-Inactive Modules:
-  1) openmpi
-
-The following have been reloaded with a version change:
-  1) gcc/5.4.0 => gcc/4.8.5
-
-gcc (GCC) 4.8.5
-Copyright (C) 2015 Free Software Foundation, Inc.
-This is free software; see the source for copying conditions.  There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-```
-{: .output}
-
-We now have successfully switched from GCC 5.4.0 to GCC 4.8.5. It is also important to note that
-there was no compatible OpenMPI module available for GCC 4.8.5. Because of this, the `module`
-program has "inactivated" the module. All this means for us is that if we re-load GCC 5.4.0,
-`module` will remember OpenMPI used to be loaded and load that module as well.
-
-```
-{{ site.host_prompt }} module load gcc/5.4.0
-```
-{: .language-bash}
-```
-Activating Modules:
-  1) openmpi/2.1.1
-
-The following have been reloaded with a version change:
-  1) gcc/4.8.5 => gcc/5.4.0
-```
-{: .output}
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/job-detail.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/job-detail.Rmd
deleted file mode 100644
index 880b8421..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/job-detail.Rmd
+++ /dev/null
@@ -1,2 +0,0 @@
-JOBID USER         ACCOUNT     NAME           ST REASON START_TIME         T...
-36856 yourUsername yourAccount example-job.sh R  None   2017-07-01T16:47:02 ...
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/perf-exercise.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/perf-exercise.Rmd
deleted file mode 100644
index f79772f7..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/perf-exercise.Rmd
+++ /dev/null
@@ -1,67 +0,0 @@
-::: challenge
-## Computing the speedup and parallel efficiency
-Use your *Overall run times* from above to fill in a table like the one below.
-
-| Cores      | Overall run time (s) | Ideal speedup | Actual speedup | Parallel efficiency |
-|------------|----------------------|---------------|----------------|---------------------|
-| 1 (serial) |                      |               |                |                     |
-| 2          |                      |               |                |                     |
-| 4          |                      |               |                |                     |                   
-| 8          |                      |               |                |                     | 
-| 16         |                      |               |                |                     |
-| 32         |                      |               |                |                     |
-| 64         |                      |               |                |                     |             
-| 128        |                      |               |                |                     |
-| 256        |                      |               |                |                     |
-
-Given your results, try to answer the following questions:
-
-1. What is the core count where you get the **most** efficient use of resources, irrespective
-  of run time?
-2. What is the core count where you get the fastest solution, irrespective of efficiency?
-3. What do you think a good core count choice would be for this application that balances
-   time to solution and efficiency? Why did you choose this option?
-
-::: solution
-
-The table below gives example results for `r config$remote$name` based on the example 
-runtimes given in the solution above.
-
-| Cores      | Overall run time (s) | Ideal speedup | Actual speedup | Parallel efficiency |
-|-----------:|---------------------:|--------------:|---------------:|--------------------:|
-|          1 |                3.931 |         1.000 |          1.000 |               1.000 |
-|          2 |                2.002 |         2.000 |          1.963 |               0.982 |
-|          4 |                1.048 |         4.000 |          3.751 |               0.938 |
-|          8 |                0.572 |         8.000 |          6.872 |               0.859 |
-|         16 |                0.613 |        16.000 |          6.408 |               0.401 |
-|         32 |                0.360 |        32.000 |         10.928 |               0.342 |
-|         64 |                0.249 |        64.000 |         15.767 |               0.246 |
-|        128 |                0.170 |       128.000 |         23.122 |               0.181 |
-|        256 |                0.187 |       256.000 |         21.077 |               0.082 |
-
-### What is the core count where you get the **most** efficient use of resources?
-Just using a single core is the cheapest (and always will be unless your speedup is better
-than perfect – “super-linear” speedup). However, it may not be possible to run on small
-numbers of cores depending on how much memory you need or other technical constraints.
-**Note:** on most high-end systems, nodes are not shared between users. This means you are
-charged for all the CPU-cores on a node regardless of whether you actually use them. Typically
-we would be running on many hundreds of CPU-cores not a few tens, so the real question in
-practice is: what is the optimal number of nodes to use?
-### What is the core count where you get the fastest solution, irrespective of efficiency?
-256 cores gives the fastest time to solution.
-The fastest time to solution does not often make the most efficient use of resources so 
-to use this option, you may end up wasting your resources. Sometimes, when there is 
-time pressure to run the calculations, this may be a valid approach to running 
-applications.
-### What do you think a good core count choice would be for this application to use?
-
-8 cores is probably a good number of cores to use with a parallel efficiency of 86%.
-Usually, the best choice is one that delivers good parallel efficiency with an acceptable
-time to solution. Note that *acceptable time to solution* differs depending on circumstances
-so this is something that the individual researcher will have to assess. Good parallel
-efficiency is often considered to be 70% or greater though many researchers will be happy
-to run in a regime with parallel efficiency greater than 60%. As noted above, running with
-worse parallel efficiency may also be useful if the time to solution is an overriding factor.
-
-:::
-:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/pi-mpi-details.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/pi-mpi-details.Rmd
deleted file mode 100644
index 086f90e8..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/pi-mpi-details.Rmd
+++ /dev/null
@@ -1,16 +0,0 @@
-::: prereq
-
-## Required Files
-
-The program used in this example can be retrieved using wget or a browser and copied to the remote.
-
-**Using wget**: 
-```bash
-`r config$remote$prompt` wget `r config$url``r config$baseurl`/files/pi-mpi.py
-```
-
-**Using a web browser**:
-
-[`r config$url``r config$baseurl`/files/pi-mpi.py](`r config$url``r config$baseurl`/files/pi-mpi.py)
-
-:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/runtime-exercise.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/runtime-exercise.Rmd
deleted file mode 100644
index 4977a00e..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/runtime-exercise.Rmd
+++ /dev/null
@@ -1,47 +0,0 @@
-::: challenge
-## Benchmarking the parallel performance
-Modify your job script to run on multiple cores and evaluate the performance of `pi-mpi.py`
-on a variety of different core counts and use multiple runs to complete a table like the one
-below.
-If you examine the log file you will see that it contains two timings: the total time taken by the
-entire program and the time taken solely by the calculation. The calculation of Pi from the Monte-Carlo counts
-is not parallelised so this is a serial overhead, performed by a single processor.
-The calculation part is, in theory, perfectly parallel (each processor operates on independent sets of unique random numbers
-) so this should get faster on more cores. The Calculation core seconds is the
-*calculation time* multiplied by the number of cores.
-
-| Cores      | Overall run time (s) | Calculation time (s) | Calculation core seconds |
-|------------|----------------------|----------------------|--------------------------|
-| 1 (serial) |                      |                      |                          |
-| 2          |                      |                      |                          |
-| 4          |                      |                      |                          |                    
-| 8          |                      |                      |                          | 
-| 16         |                      |                      |                          | 
-| 32         |                      |                      |                          | 
-| 64         |                      |                      |                          |              
-| 128        |                      |                      |                          | 
-| 256        |                      |                      |                          |
-
-Look at your results – do they make sense? Given the structure of the code, you would
-expect the performance of the calculation to increase
-linearly with the number of cores: this would give a roughly constant figure for the Calculation core
-seconds. Is this what you observe?
-
-::: solution
-
-The table below shows example timings for runs on `r config$remote$name`
-
-| Cores      | Overall run time (s) | Calculation time (s) |       Calculation core seconds |
-|-----------:|---------------------:|---------------------:|-------------------------------:|
-|          1 |                3.931 |                3.854 |                          3.854 |
-|          2 |                2.002 |                1.930 |                          3.859 |
-|          4 |                1.048 |                0.972 |                          3.888 |
-|          8 |                0.572 |                0.495 |                          3.958 |
-|         16 |                0.613 |                0.536 |                          8.574 |
-|         32 |                0.360 |                0.278 |                          8.880 |
-|         64 |                0.249 |                0.163 |                         10.400 |
-|        128 |                0.170 |                0.083 |                         10.624 |
-|        256 |                0.187 |                0.135 |                         34.560 |
-
-:::
-:::
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/serial-submit.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/serial-submit.Rmd
deleted file mode 100644
index b7f68819..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/serial-submit.Rmd
+++ /dev/null
@@ -1,25 +0,0 @@
-Creating a file called `submit-pi-mpi.slurm`:
-
-```bash
-#!/bin/bash
-#SBATCH --partition=`r config$sched$partition`
-#SBATCH --qos=`r config$sched$qos`
-#SBATCH --reservation=`r config$sched$reservation`
-
-#SBATCH --job-name=pi-mpi
-#SBATCH --nodes=1
-#SBATCH --tasks-per-node=1
-#SBATCH --time=00:15:00
-srun python pi-mpi.py 10000000
-```
-
-Run application using a single process (i.e. in serial) with a blocking `srun` command:
-```bash
-srun python pi-mpi.py 10000000
-```
-
-Submit with to the batch queue with:
-
-```bash
-`r config$sched$prompt_work` `r config$sched$submit.name` submit-pi-mpi.slurm
-```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/sharpen-details.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/sharpen-details.snip
deleted file mode 100644
index 08172fbe..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/sharpen-details.snip
+++ /dev/null
@@ -1,18 +0,0 @@
-The `sharpen` program has been precompiled on {{ site.remote.name }}, you can add it to your `PATH` variable with the commands:
-
-```
-export PATH=/work/{{ site.sched.project }}/{{ site.sched.project }}/shared/bin:$PATH
-export FUZZY_INPUT=/work/{{ site.sched.project }}/{{ site.sched.project }}/shared/fuzzy.pgm
-``````
-{: .language-bash}
-
-Once you have set the required environment variables, you can access the program as `sharpen-mpi`.
-You will also need to get a copy of the input file for this application.
-To do this, copy it from the 
-central install location to your directory with (note you must have loaded the 
-sharpen module as described above for this to work):
-
-```
-{{ site.host_prompt }} cp $FUZZY_INPUT .
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/view-output.snip b/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/view-output.snip
deleted file mode 100644
index 5b2a572b..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/resources/view-output.snip
+++ /dev/null
@@ -1,12 +0,0 @@
-> ## Viewing the sharpened output image
-> To see the effect of the sharpening algorithm, you can view the images using the display
-> program from the ImageMagick suite.
-> ```
-> display sharpened.pgm
-> ```
-> Type `q` in the image window to close the program. To view the image you will need an X
-> window client installed and you will have to have logged into {{ site.host_name }} with the `ssh -Y`
-> option to export the display back to your local system. If you are using Windows, the 
-> MobaXterm program provides a login shell with X capability. If you are using macOS, then
-> you will need to install XQuartz. If you are using Linux then X should just work!
-{: .callout}
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
deleted file mode 100644
index 0c2eb8fa..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-script.Rmd
+++ /dev/null
@@ -1,3 +0,0 @@
-```output
-Submitted batch job 36855
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-status.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-status.Rmd
deleted file mode 100644
index e98253bd..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/basic-job-status.Rmd
+++ /dev/null
@@ -1,8 +0,0 @@
-```output
-JOBID USER         ACCOUNT     NAME           ST REASON START_TIME         T...
-36856 yourUsername yourAccount example-job.sh R  None   2017-07-01T16:47:02 ...
-```
-
-We can see all the details of our job, most importantly that it is in the `R`
-or `RUNNING` state. Sometimes our jobs might need to wait in a queue
-(`PENDING`) or have an error (`E`).
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.Rmd
deleted file mode 100644
index 6906426a..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/del_job.Rmd
+++ /dev/null
@@ -1,3 +0,0 @@
-```bash
-`r config$remote$prompt` scancel 38759
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.Rmd
deleted file mode 100644
index 708dfe2e..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/filesystem_issues.Rmd
+++ /dev/null
@@ -1,23 +0,0 @@
-::: callout
-
-## Filesystem on ARCHER2
-
-At this point it is important to remember that ARCHER2  has two *separate*
-filesystems: `/home` and `/work`.
-
-* `/home` is meant for small files such as source code, and is the
-  filesystem that you are on when you log in
-* `/work` is a much larger and faster filesystem, meant for production
-  runs and storing large datasets
-
-The `/home` filesystem **is not mounted on the compute nodes**
-meaning that programs run in the batch queues cannot read from or
-write to files in your home directory. This has not been a problem
-so far as none of our programs have done file input or
-output. However, the parallel program we will run here reads and
-writes large images.
-
-* When you log in, you will be in your home directory, ``r config$remote$homedir``.
-* Before you run real programs on ARCHER2, you **must change directory** to
-  `/work`.
-:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
deleted file mode 100644
index c7657ef5..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/job-with-name-status.Rmd
+++ /dev/null
@@ -1,4 +0,0 @@
-```output
-JOBID USER         ACCOUNT     NAME     ST REASON   START_TIME TIME TIME_LEFT NODES CPUS
-38191 yourUsername yourAccount new_name PD Priority N/A        0:00 1:00:00   1     1
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.Rmd
deleted file mode 100644
index ddd0d12f..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/long_job.Rmd
+++ /dev/null
@@ -1,11 +0,0 @@
-```bash
-#!/bin/bash
-
-#SBATCH --partition=standard
-#SBATCH --qos=short
-#SBATCH --time=00:00:30
-
-echo 'This script is running on:'
-hostname
-sleep 120
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.Rmd
deleted file mode 100644
index 6e0886a7..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/ls-pgm-output.Rmd
+++ /dev/null
@@ -1,4 +0,0 @@
-```output
--rw-r--r-- 1 userid ta028 1762743 Jun 26 17:29 fuzzy.pgm
--rw------- 1 userid ta028 1678630 Jun 26 17:33 sharpened.pgm
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/option-flags-list.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/option-flags-list.Rmd
deleted file mode 100644
index 626c6eab..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/option-flags-list.Rmd
+++ /dev/null
@@ -1,5 +0,0 @@
-* `--nodes=<nodes>` - Number of nodes to use
-* `--ntasks-per-node=<tasks-per-node>` - Number of parallel processes per node
-* `--cpus-per-task=<cpus-per-task>` - Number of cores to assign to each parallel process
-* `--time=<days-hours:minutes:seconds>` - Maximum real-world time (walltime)
-your job will be allowed to run. The `<days>` part can be omitted.
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
deleted file mode 100644
index 205f15ff..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge.Rmd
+++ /dev/null
@@ -1,27 +0,0 @@
-::: challenge
-
-## Running parallel jobs
-
-Modify the pi-mpi-run script that you used above to use all 128 cores on
-one node.  Check the output to confirm that it used the correct number
-of cores in parallel for the calculation.
-
-:::: solution
-Here is a modified script
-
-```bash
-#!/bin/bash
-
-#SBATCH --partition=`r config$sched$partition`
-#SBATCH --qos=`r config$sched$qos`
-#SBATCH --reservation=`r config$sched$reservation`
-#SBATCH --time=00:00:30
-
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=128
-
-module load cray-python
-srun python pi-mpi.py 10000000
-```
-::::
-:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
deleted file mode 100644
index 2ec4d28f..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-challenge2.Rmd
+++ /dev/null
@@ -1,29 +0,0 @@
-::: challenge
-
-## Configuring parallel jobs
-
-You will see in the job output that information is displayed about
-where each MPI process is running, in particular which node it is
-on.
-
-Modify the pi-mpi-run script that you run a total of 2 nodes and 16 processes;
-but to use only 8 tasks on each of two nodes.
-Check the output file to ensure that you understand the job
-distribution.
-
-:::: solution
-```bash
-#!/bin/bash
-
-#SBATCH --partition=`r config$sched$partition`
-#SBATCH --qos=`r config$sched$qos`
-#SBATCH --time=00:00:30
-
-#SBATCH --nodes=2
-#SBATCH --ntasks-per-node=8
-
-module load cray-python
-srun python pi-mpi.py 10000000
-```
-::::
-:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
deleted file mode 100644
index 98cbb455..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-launch-desc.Rmd
+++ /dev/null
@@ -1,15 +0,0 @@
-```bash
-srun python pi-mpi.py 10000000
-```
-
-And this corresponds to the four required items we described above:
-
-1. Parallel launch program: in this case the parallel launch program
-   is called `srun`; the additional argument controls which cores are
-   used.
-2. Number of parallel processes per node: in this case this is 16,
-   and is specified by the option `--ntasks-per-node=16` option.
-3. Total number of parallel processes: in this case this is also 16,
-   because we specified 1 node and 16 parallel processes per node.
-4. Our program and arguments: in this case this is 
-   `python pi-mpi.py 10000000`.
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
deleted file mode 100644
index cb09f254..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/parallel-script.Rmd
+++ /dev/null
@@ -1,15 +0,0 @@
-```bash
-#!/bin/bash
-
-#SBATCH --partition=`r config$sched$partition`
-#SBATCH --qos=`r config$sched$qos`
-#SBATCH --reservation=`r config$sched$reservation`
-#SBATCH --time=00:05:00
-
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=16
-
-module load cray-python
-
-srun python pi-mpi.py 10000000
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
deleted file mode 100644
index 0d1e07e3..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/print-sched-variables.Rmd
+++ /dev/null
@@ -1,12 +0,0 @@
-::: challenge
-
-## Job environment variables
-
-When Slurm runs a job, it sets a number of environment variables for
-the job. One of these will let us check our work from the last
-problem. The `SLURM_CPUS_PER_TASK` variable is set to the number of
-CPUs we requested with `-c`. Using the `SLURM_CPUS_PER_TASK`
-variable, modify your job so that it prints how many CPUs have been
-allocated.
-
-:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
deleted file mode 100644
index 43bd23a5..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-job.Rmd
+++ /dev/null
@@ -1,3 +0,0 @@
-```bash
-`r config$remote$prompt_work` cat slurm-38193.out
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
deleted file mode 100644
index 9f277a14..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/runtime-exceeded-output.Rmd
+++ /dev/null
@@ -1,5 +0,0 @@
-```output
-This job is running on:
-nid001147
-slurmstepd: error: *** JOB 38193 ON cn01 CANCELLED AT 2017-07-02T16:35:48 DUE TO TIME LIMIT ***
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.Rmd
deleted file mode 100644
index f040e903..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_pending.Rmd
+++ /dev/null
@@ -1,4 +0,0 @@
-```output
- JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-119867  standard    myjob   userid PD       0:00      1 (Resources) 
-```
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.Rmd
deleted file mode 100644
index 3233cdb7..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/squeue_running.Rmd
+++ /dev/null
@@ -1,2 +0,0 @@
-        JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
-       119867  standard example-   userid  R    0:00:06      1 nid001609 
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-begin.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-begin.Rmd
deleted file mode 100644
index 214a8756..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-begin.Rmd
+++ /dev/null
@@ -1,6 +0,0 @@
-```output
-Submitted batch job 38759
-
-JOBID USER         ACCOUNT     NAME           ST REASON   START_TIME TIME TIME_LEFT NODES CPUS
-38759 yourUsername yourAccount example-job.sh PD Priority N/A        0:00 1:00      1     1
-```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-cancel.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-cancel.Rmd
deleted file mode 100644
index 695180ff..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-job-cancel.Rmd
+++ /dev/null
@@ -1,3 +0,0 @@
-```output
-JOBID  USER  ACCOUNT  NAME  ST  REASON  START_TIME  TIME  TIME_LEFT  NODES  CPUS
-```
\ No newline at end of file
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
deleted file mode 100644
index ec27cd39..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/terminate-multiple-jobs.Rmd
+++ /dev/null
@@ -1,9 +0,0 @@
-::: challenge
-
-## Cancelling multiple jobs
-
-We can also cancel all of our jobs at once using the `-u` option. This will
-delete all jobs for a specific user (in this case us). Note that you can only
-delete your own jobs.  Try submitting multiple jobs and then cancelling them
-all with `scancel -u yourUsername`.
-:::
diff --git a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd b/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
deleted file mode 100644
index 2d93dd78..00000000
--- a/episodes/files/snippets/EPCC_ARCHER2_slurm/scheduler/using-nodes-interactively.Rmd
+++ /dev/null
@@ -1,33 +0,0 @@
-`srun` runs a single command in the queue system and then exits.
-Let's demonstrate this by running the
-`hostname` command with `srun`. (We can cancel an `srun` job with `Ctrl-c`.)
-
-```bash
-`r config$host_prompt_work` srun `r config$sched$submit$options` --time=00:01:00 hostname
-```
-
-```output
-nid001976
-```
-
-`srun` accepts all of the same options as `sbatch`. However, instead of specifying these in a
-script, these options are specified on the command-line when starting a job.
-
-Typically, the resulting shell environment will be the same as that for
-`sbatch`.
-
-### Interactive jobs
-
-Sometimes, you will need a lot of resource for interactive use. Perhaps it's our first time running
-an analysis or we are attempting to debug something that went wrong with a previous job.
-Fortunately, SLURM makes it easy to start an interactive job with `srun`:
-
-```bash
-`r config$host_prompt_work` srun `r config$sched$submit$options` --pty /bin/bash
-```
-
-You should be presented with a bash prompt. Note that the prompt may change
-to reflect your new location, in this case the compute node we are logged on.
-You can also verify this with `hostname`.
-
-When you are done with the interactive job, type `exit` to quit your session.
diff --git a/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml b/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
index 54b76da6..a6d78a72 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
+++ b/episodes/files/snippets/Ghastly_Mistakes/_config_options.yml
@@ -62,4 +62,5 @@ episode_order:
   - 17-parallel
   - 18-resources
   - 19-responsibility
- 
\ No newline at end of file
+
+...
diff --git a/episodes/files/snippets/Ghastly_Mistakes/cluster/queue-info.Rmd b/episodes/files/snippets/Ghastly_Mistakes/cluster/queue-info.Rmd
index 29f69030..2487fc02 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/cluster/queue-info.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/cluster/queue-info.Rmd
@@ -1,5 +1,6 @@
 ```output
 PARTITION          AVAIL  TIMELIMIT  NODES  STATE NODELIST
-doom                 up   infinite      2   idle  doo[1-2]
-gloom                up   infinite      2   idle  glo[1-2]
+cpubase_bycore_b1*    up   infinite      4   idle node[1-2],smnode[1-2]
+node                  up   infinite      2   idle node[1-2]
+smnode                up   infinite      2   idle smnode[1-2]
 ```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/cluster/specific-node-info.Rmd b/episodes/files/snippets/Ghastly_Mistakes/cluster/specific-node-info.Rmd
index c38b377b..b9f6c8dc 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/cluster/specific-node-info.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/cluster/specific-node-info.Rmd
@@ -7,6 +7,6 @@ where your jobs will actually run. Try running this command to see
 the name, CPUs and memory available on one of the worker nodes:
 
 ```bash
-`r config$remote$prompt` `r config$sched$info` -o "%n %c %m" | column -t
+`r config$remote$prompt` sinfo -o "%n %c %m" | column -t
 ```
 :::
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.Rmd b/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.Rmd
index e7fc4eb2..8402eaa0 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/available-modules.Rmd
@@ -1,11 +1,22 @@
+```bash
+`r config$remote$prompt` module avail | less
+```
+
 ```output
-~~~ /usr/local/modules ~~~
-  amdahl/0.0.1 (D)      python/2.7.1 (O)
+~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
+  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
+  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
+  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
+  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
+  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a
+
+[removed most of the output here for clarity]
 
   Where:
    L:        Module is loaded
    D:        Default Module
-   O:        Module is obsolete
+   Aliases exist: foo/1.2.3 (1.2) means that
+             "module load foo/1.2" will load foo/1.2.3
 
 Use "module spider" to find all possible modules and extensions.
 Use "module keyword key1 key2 ..." to search for all possible modules matching
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/default-modules.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/default-modules.snip
deleted file mode 100644
index a448dd96..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/default-modules.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-No Modulefiles Currently Loaded.
-```
-{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.Rmd
similarity index 82%
rename from episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.snip
rename to episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.Rmd
index 89039d32..f06ed919 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.snip
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/missing-python.Rmd
@@ -1,15 +1,14 @@
 If the `python3` command was unavailable, we would see output like
 
+```output
+/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/`r config$remote$user`/.local/bin:/home/`r config$remote$user`/bin)
 ```
-/usr/bin/which: no python3 in (/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/{{site.remote.user}}/.local/bin:/home/{{site.remote.user}}/bin)
-```
-{: .output}
 
 Note that this wall of text is really a list, with values separated
 by the `:` character. The output is telling us that the `which` command
 searched the following directories for `python3`, without success:
 
-```
+```output
 /cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin
 /opt/software/slurm/bin
 /usr/local/bin
@@ -17,17 +16,15 @@ searched the following directories for `python3`, without success:
 /usr/local/sbin
 /usr/sbin
 /opt/puppetlabs/bin
-/home/{{site.remote.user}}/.local/bin
-/home/{{site.remote.user}}/bin
+/home/`r config$remote$user`/.local/bin
+/home/`r config$remote$user`/bin
 ```
-{: .output}
 
 However, in our case we do have an existing `python3` available so we see
 
-```
+```output
 /cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin/python3
 ```
-{: .output}
 
 We need a different Python than the system provided one though, so let us load
 a module to access it.
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.Rmd b/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.Rmd
new file mode 100644
index 00000000..81d3be34
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.Rmd
@@ -0,0 +1,8 @@
+```bash
+`r config$remote$prompt` module load `r config$remote$modules$python`
+`r config$remote$prompt` which python3
+```
+
+```output
+/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.snip
deleted file mode 100644
index d9bab7b4..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/module-load-python.snip
+++ /dev/null
@@ -1,5 +0,0 @@
-```
-{{ site.remote.prompt }} module load {{ site.remote.module_python3 }}
-{{ site.remote.prompt }} which python3
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-output.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.Rmd
similarity index 85%
rename from episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-output.snip
rename to episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.Rmd
index 01d010ba..13031bf9 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-output.snip
+++ b/episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.Rmd
@@ -1,4 +1,8 @@
+```bash
+`r config$remote$prompt` ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
 ```
+
+```output
 2to3              nosetests-3.8  python                 rst2s5.py
 2to3-3.8          pasteurize     python3                rst2xetex.py
 chardetect        pbr            python3.8              rst2xml.py
@@ -13,4 +17,3 @@ idle3.8           pygmentize     rst2odt_prepstyles.py  virtualenv
 netaddr           pytest         rst2odt.py             wheel
 nosetests         py.test        rst2pseudoxml.py
 ```
-{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.snip
deleted file mode 100644
index 46dec092..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/python-executable-dir.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin/python3
-```
-{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-command.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-command.snip
deleted file mode 100644
index 80319d0a..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/python-ls-dir-command.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-{{ site.remote.prompt }} ls /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/python-module-path.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/python-module-path.snip
deleted file mode 100644
index 68e97df1..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/python-module-path.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/SQLite/3.31.1-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Tcl/8.6.10-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/GCCcore/x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/user01/.local/bin:/home/user01/bin
-```
-{: .output}
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.Rmd
similarity index 100%
rename from episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.snip
rename to episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.Rmd
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/wrong-gcc-version.snip b/episodes/files/snippets/Ghastly_Mistakes/modules/wrong-gcc-version.snip
deleted file mode 100644
index 8fbd2825..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/wrong-gcc-version.snip
+++ /dev/null
@@ -1,5 +0,0 @@
-<!--- There is a long additional section on some specific features of Lmod in
-snippets_library/ComputeCanada_Graham_slurm/modules/wrong-gcc-version.snip,
-particular covering the concept of a module hierarchy. While this is not
-relevant to the EESSI configuration right now, it may become so in the future
-if we change the default module naming scheme to hierarchical. -->
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks-jobscript.snip b/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks-jobscript.snip
deleted file mode 100644
index 2f643071..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks-jobscript.snip
+++ /dev/null
@@ -1,16 +0,0 @@
-```
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
-{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
-{{ site.sched.comment }} -N 1
-{{ site.sched.comment }} -n 8
-
-# Load the computing environment we need
-# (mpi4py and numpy are in SciPy-bundle)
-module load {{ site.remote.module_python3 }}
-module load SciPy-bundle
-
-# Execute the task
-mpiexec amdahl
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks.Rmd b/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks.Rmd
new file mode 100644
index 00000000..dcbe379a
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/parallel/eight-tasks.Rmd
@@ -0,0 +1,58 @@
+```bash
+`r config$remote$prompt` nano parallel-job.sh
+`r config$remote$prompt` cat parallel-job.sh
+```
+
+```bash
+`r config$remote$shebang`
+`r config$sched$comment` `r config$sched$flag$name` parallel-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 8
+
+# Load the computing environment we need
+# (mpi4py and numpy are in SciPy-bundle)
+module load `r config$remote$modules$python`
+module load SciPy-bundle
+
+# Execute the task
+mpiexec amdahl
+```
+
+Then submit your job. Note that the submission command has not really changed
+from how we submitted the serial job: all the parallel settings are in the
+batch file rather than the command line.
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` parallel-job.sh
+```
+
+As before, use the status commands to check when your job runs.
+
+```bash
+`r config$remote$prompt` ls -t
+```
+
+```output
+slurm-347271.out  parallel-job.sh  slurm-347178.out  slurm-347087.out  serial-job.sh  amdahl  README.md  LICENSE.txt
+```
+
+```bash
+`r config$remote$prompt` cat slurm-347178.out
+```
+
+```output
+which should take 7.688 seconds with 0.850 parallel proportion of the workload.
+
+  Hello, World! I am process 4 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 0 of 8 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
+  Hello, World! I am process 2 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 1 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 3 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 5 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 6 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 7 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+  Hello, World! I am process 0 of 8 on `r config$remote$node`. I will do parallel 'work' for 3.188 seconds.
+
+Total execution time (according to rank 0): 7.697 seconds
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks-jobscript.snip b/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks-jobscript.snip
deleted file mode 100644
index 19804d74..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks-jobscript.snip
+++ /dev/null
@@ -1,16 +0,0 @@
-```
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-job
-{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
-{{ site.sched.comment }} -N 1
-{{ site.sched.comment }} -n 4
-
-# Load the computing environment we need
-# (mpi4py and numpy are in SciPy-bundle)
-module load {{ site.remote.module_python3 }}
-module load SciPy-bundle
-
-# Execute the task
-mpiexec amdahl
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks.Rmd b/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks.Rmd
new file mode 100644
index 00000000..2e885505
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/parallel/four-tasks.Rmd
@@ -0,0 +1,56 @@
+```bash
+`r config$remote$prompt` cp serial-job.sh parallel-job.sh
+`r config$remote$prompt` nano parallel-job.sh
+`r config$remote$prompt` cat parallel-job.sh
+```
+
+```bash
+`r config$remote$shebang`
+`r config$sched$comment` `r config$sched$flag$name` parallel-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 4
+
+# Load the computing environment we need
+# (mpi4py and numpy are in SciPy-bundle)
+module load `r config$remote$modules$python`
+module load SciPy-bundle
+
+# Execute the task
+mpiexec amdahl
+```
+
+Then submit your job. Note that the submission command has not really changed
+from how we submitted the serial job: all the parallel settings are in the
+batch file rather than the command line.
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` parallel-job.sh
+```
+
+As before, use the status commands to check when your job runs.
+
+```bash
+`r config$remote$prompt` ls -t
+```
+
+```output
+slurm-347178.out  parallel-job.sh  slurm-347087.out  serial-job.sh  amdahl  README.md  LICENSE.txt
+```
+
+```bash
+`r config$remote$prompt` cat slurm-347178.out
+```
+
+```output
+Doing 30.000 seconds of 'work' on 4 processors,
+which should take 10.875 seconds with 0.850 parallel proportion of the workload.
+
+  Hello, World! I am process 0 of 4 on `r config$remote$node`. I will do all the serial 'work' for 4.500 seconds.
+  Hello, World! I am process 2 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 1 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 3 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+  Hello, World! I am process 0 of 4 on `r config$remote$node`. I will do parallel 'work' for 6.375 seconds.
+
+Total execution time (according to rank 0): 10.888 seconds
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task-jobscript.snip b/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task-jobscript.snip
deleted file mode 100644
index 1941ef04..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task-jobscript.snip
+++ /dev/null
@@ -1,14 +0,0 @@
-```
-{{ site.remote.bash_shebang }}
-{{ site.sched.comment }} {{ site.sched.flag.name }} solo-job
-{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }}
-{{ site.sched.comment }} -N 1
-{{ site.sched.comment }} -n 1
-
-# Load the computing environment we need
-module load {{ site.remote.module_python3 }}
-
-# Execute the task
-amdahl
-```
-{: .language-bash}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task.Rmd b/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task.Rmd
new file mode 100644
index 00000000..ceefdfdb
--- /dev/null
+++ b/episodes/files/snippets/Ghastly_Mistakes/parallel/one-task.Rmd
@@ -0,0 +1,22 @@
+```bash
+`r config$remote$prompt` nano serial-job.sh
+`r config$remote$prompt` cat serial-job.sh
+```
+
+```bash
+`r config$remote$shebang`
+`r config$sched$comment` `r config$sched$flag$name` solo-job
+`r config$sched$comment` `r config$sched$flag$queue` `r config$sched$queue$testing`
+`r config$sched$comment` -N 1
+`r config$sched$comment` -n 1
+
+# Load the computing environment we need
+module load `r config$remote$modules$python`
+
+# Execute the task
+amdahl
+```
+
+```bash
+`r config$remote$prompt` `r config$sched$submit$name` serial-job.sh
+```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/resources/account-history.snip b/episodes/files/snippets/Ghastly_Mistakes/resources/account-history.Rmd
similarity index 97%
rename from episodes/files/snippets/Ghastly_Mistakes/resources/account-history.snip
rename to episodes/files/snippets/Ghastly_Mistakes/resources/account-history.Rmd
index d5a87620..5e8a53f2 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/resources/account-history.snip
+++ b/episodes/files/snippets/Ghastly_Mistakes/resources/account-history.Rmd
@@ -1,4 +1,4 @@
-```
+```output
        JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
 ------------ ---------- ---------- ---------- ---------- ---------- --------
 7               file.sh cpubase_b+ def-spons+          1  COMPLETED      0:0
@@ -10,5 +10,4 @@
 9            example-j+ cpubase_b+ def-spons+          1  COMPLETED      0:0
 9.batch           batch            def-spons+          1  COMPLETED      0:0
 9.extern         extern            def-spons+          1  COMPLETED      0:0
-```
-{: .output}
+```
\ No newline at end of file
diff --git a/episodes/files/snippets/Ghastly_Mistakes/resources/monitor-processes-top.snip b/episodes/files/snippets/Ghastly_Mistakes/resources/monitor-processes-top.snip
deleted file mode 100644
index 12685735..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/resources/monitor-processes-top.snip
+++ /dev/null
@@ -1,19 +0,0 @@
-```
-top - 21:00:19 up  3:07,  1 user,  load average: 1.06, 1.05, 0.96
-Tasks: 311 total,   1 running, 222 sleeping,   0 stopped,   0 zombie
-%Cpu(s):  7.2 us,  3.2 sy,  0.0 ni, 89.0 id,  0.0 wa,  0.2 hi,  0.2 si,  0.0 st
-KiB Mem : 16303428 total,  8454704 free,  3194668 used,  4654056 buff/cache
-KiB Swap:  8220668 total,  8220668 free,        0 used. 11628168 avail Mem
-
-  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
- 1693 jeff      20   0 4270580 346944 171372 S  29.8  2.1   9:31.89 gnome-shell
- 3140 jeff      20   0 3142044 928972 389716 S  27.5  5.7  13:30.29 Web Content
- 3057 jeff      20   0 3115900 521368 231288 S  18.9  3.2  10:27.71 firefox
- 6007 jeff      20   0  813992 112336  75592 S   4.3  0.7   0:28.25 tilix
- 1742 jeff      20   0  975080 164508 130624 S   2.0  1.0   3:29.83 Xwayland
-    1 root      20   0  230484  11924   7544 S   0.3  0.1   0:06.08 systemd
-   68 root      20   0       0      0      0 I   0.3  0.0   0:01.25 kworker/4:1
- 2913 jeff      20   0  965620  47892  37432 S   0.3  0.3   0:11.76 code
-    2 root      20   0       0      0      0 S   0.0  0.0   0:00.02 kthreadd
-```
-{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/resources/system-memory-free.snip b/episodes/files/snippets/Ghastly_Mistakes/resources/system-memory-free.snip
deleted file mode 100644
index ec4c0d3f..00000000
--- a/episodes/files/snippets/Ghastly_Mistakes/resources/system-memory-free.snip
+++ /dev/null
@@ -1,6 +0,0 @@
-```
-total        used        free      shared  buff/cache   available
-Mem:           3.8G        1.5G        678M        327M        1.6G        1.6G
-Swap:          3.9G        170M        3.7G
-```
-{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-status.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-status.Rmd
index 8873c7c1..9011f5b4 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-status.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/basic-job-status.Rmd
@@ -1,6 +1,6 @@
 ```output
-JOBID PARTITION  NAME         USER   ST  TIME  NODES NODELIST(REASON)
-    9 doom       example-job  luigi  R   0:05  1     doo1
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+    9 cpubase_b example-   user01  R       0:05      1 node1
 ```
 
 We can see all the details of our job, most importantly that it is in the `R`
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/job-with-name-status.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/job-with-name-status.Rmd
index aa8eab85..815f3b9d 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/scheduler/job-with-name-status.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/job-with-name-status.Rmd
@@ -1,4 +1,4 @@
 ```output
-JOBID PARTITION  NAME         USER   ST  TIME  NODES  NODELIST(REASON)
-   10 doom       hello-world  luigi  R   0:02      1  doo1
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+   10 cpubase_b hello-wo   user01  R       0:02      1 node1
 ```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/option-flags-list.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/option-flags-list.Rmd
index 9bc993ff..5e80b164 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/scheduler/option-flags-list.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/option-flags-list.Rmd
@@ -1,5 +1,3 @@
-> option-flag-list.Rmd is constant for all snippet libraries
-
 * `--ntasks=<ntasks>` or `-n <ntasks>`: How many CPU cores does your job need,
   in total?
 
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/print-sched-variables.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/print-sched-variables.Rmd
index 659cefae..21fec883 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/scheduler/print-sched-variables.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/print-sched-variables.Rmd
@@ -2,7 +2,7 @@
 
 ## Job environment variables
 
-When ``r config$sched$name`` runs a job, it sets a number of environment
+When {{ site.sched.name }} runs a job, it sets a number of environment
 variables for the job. One of these will let us check what directory our job
 script was submitted from. The `SLURM_SUBMIT_DIR` variable is set to the
 directory from which our job was submitted. Using the `SLURM_SUBMIT_DIR`
@@ -14,13 +14,13 @@ job was submitted.
 ## Solution
 
 ```bash
-`r config$remote$prompt` nano example-job.sh
-`r config$remote$prompt` cat example-job.sh
+{{ site.remote.prompt }} nano example-job.sh
+{{ site.remote.prompt }} cat example-job.sh
 ```
 
 ```bash
-`r config$remote$bash_shebang`
-`r config$sched$comment` -t 00:00:30
+`r site$remote$bash_shebang`
+#SBATCH -t 00:00:30
 
 echo -n "This script is running on "
 hostname
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-output.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-output.Rmd
index fa1b19ea..106d9ecc 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-output.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/runtime-exceeded-output.Rmd
@@ -1,5 +1,5 @@
 ```output
 This script is running on ...
-slurmstepd: error: *** JOB 12 ON doo1 CANCELLED AT 2021-02-19T13:55:57
+slurmstepd: error: *** JOB 12 ON node1 CANCELLED AT 2021-02-19T13:55:57
 DUE TO TIME LIMIT ***
 ```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-begin.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-begin.Rmd
index d5a03bfb..3cfb8c95 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-begin.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/terminate-job-begin.Rmd
@@ -1,6 +1,6 @@
 ```output
 Submitted batch job 13
 
-JOBID PARTITION  NAME      USER   ST  TIME  NODES NODELIST(REASON)
-   13 doom       long_job  luigi  R   0:02  1     doo1
+JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+   13 cpubase_b long_job   user01  R       0:02      1 node1
 ```
diff --git a/episodes/files/snippets/Ghastly_Mistakes/scheduler/using-nodes-interactively.Rmd b/episodes/files/snippets/Ghastly_Mistakes/scheduler/using-nodes-interactively.Rmd
index 80834a8f..0a305412 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/scheduler/using-nodes-interactively.Rmd
+++ b/episodes/files/snippets/Ghastly_Mistakes/scheduler/using-nodes-interactively.Rmd
@@ -1,5 +1,3 @@
-> using-nodes-interactively.Rmd is constant across snippets
-
 The `r config$sched$interactive` command runs a single command on the cluster
 and then exits. Let's demonstrate this by running the `hostname` command with
 `r config$sched$interactive`. (We can cancel an `r config$sched$interactive`
@@ -10,7 +8,7 @@ job with `Ctrl-c`.)
 ```
 
 ```output
-`r config$remote$node`
+{{ config$remote.node`
 ```
 
 `r config$sched$interactive` accepts all of the same options as
@@ -28,7 +26,7 @@ This job will use 2 CPUs.
 ```
 
 Typically, the resulting shell environment will be the same as that for
-`r config$sched$submit$name`.
+`r config$sched$submit.name`.
 
 ### Interactive jobs
 
@@ -38,7 +36,7 @@ went wrong with a previous job. Fortunately, {{ config$sched$name` makes it
 easy to start an interactive job with `r config$sched$interactive`:
 
 ```bash
-`r config$remote$prompt` `r config$sched$interactive` --pty bash
+`r config$remote.prompt` `r config$sched$interactive` --pty bash
 ```
 
 You should be presented with a bash prompt. Note that the prompt will likely
diff --git a/episodes/files/snippets/Ghastly_Mistakes/transferring-files/filezilla-ssh-tunnel-instructions.snip b/episodes/files/snippets/Ghastly_Mistakes/transferring-files/filezilla-ssh-tunnel-instructions.snip
deleted file mode 100644
index e69de29b..00000000
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.Rmd b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.Rmd
index 2c48235a..8402eaa0 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.Rmd
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/available-modules.Rmd
@@ -1,5 +1,5 @@
 ```bash
-`r config$remote$prompt` module avail
+`r config$remote$prompt` module avail | less
 ```
 
 ```output
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-module-path.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-module-path.snip
deleted file mode 100644
index 68e97df1..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/python-module-path.snip
+++ /dev/null
@@ -1,4 +0,0 @@
-```
-/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Python/3.x.y-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/SQLite/3.31.1-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/Tcl/8.6.10-GCCcore-x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/software/GCCcore/x.y.z/bin:/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/x86_64/usr/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/user01/.local/bin:/home/user01/bin
-```
-{: .output}
diff --git a/episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.Rmd
similarity index 80%
rename from episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.snip
rename to episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.Rmd
index fe107f2e..01234436 100644
--- a/episodes/files/snippets/Ghastly_Mistakes/modules/software-dependencies.snip
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/software-dependencies.Rmd
@@ -1,26 +1,23 @@
 To demonstrate, let's use `module list`. `module list` shows all loaded
 software modules.
 
+```bash
+`r config$remote$prompt` module list
 ```
-{{ site.remote.prompt }} module list
-```
-{: .language-bash}
 
-```
+```output
 Currently Loaded Modules:
   1) GCCcore/x.y.z                 4) GMP/6.2.0-GCCcore-x.y.z
   2) Tcl/8.6.10-GCCcore-x.y.z      5) libffi/3.3-GCCcore-x.y.z
   3) SQLite/3.31.1-GCCcore-x.y.z   6) Python/3.x.y-GCCcore-x.y.z
 ```
-{: .output}
 
+```bash
+`r config$remote$prompt` module load GROMACS
+`r config$remote$prompt` module list
 ```
-{{ site.remote.prompt }} module load GROMACS
-{{ site.remote.prompt }} module list
-```
-{: .language-bash}
 
-```
+```output
 Currently Loaded Modules:
   1) GCCcore/x.y.z                    14) libfabric/1.11.0-GCCcore-x.y.z
   2) Tcl/8.6.10-GCCcore-x.y.z         15) PMIx/3.1.5-GCCcore-x.y.z
@@ -36,20 +33,18 @@ Currently Loaded Modules:
  12) libevent/2.1.11-GCCcore-x.y.z    25) GROMACS/2020.1-foss-2020a-Python-3...
  13) UCX/1.8.0-GCCcore-x.y.z
 ```
-{: .output}
 
 So in this case, loading the `GROMACS` module (a bioinformatics software
 package), also loaded `GMP/6.2.0-GCCcore-x.y.z` and
 `SciPy-bundle/2020.03-foss-2020a-Python-3.x.y` as well. Let's try unloading the
 `GROMACS` package.
 
+```bash
+`r config$remote$prompt` module unload GROMACS
+`r config$remote$prompt` module list
 ```
-{{ site.remote.prompt }} module unload GROMACS
-{{ site.remote.prompt }} module list
-```
-{: .language-bash}
 
-```
+```output
 Currently Loaded Modules:
   1) GCCcore/x.y.z                    13) UCX/1.8.0-GCCcore-x.y.z
   2) Tcl/8.6.10-GCCcore-x.y.z         14) libfabric/1.11.0-GCCcore-x.y.z
@@ -64,23 +59,20 @@ Currently Loaded Modules:
  11) hwloc/2.2.0-GCCcore-x.y.z        23) SciPy-bundle/2020.03-foss-2020a-Py...
  12) libevent/2.1.11-GCCcore-x.y.z    24) networkx/2.4-foss-2020a-Python-3.x.y
 ```
-{: .output}
 
 So using `module unload` "un-loads" a module, and depending on how a site is
- configured it may also unload all of the dependencies (in our case it does
- not). If we wanted to unload everything at once, we could run `module purge`
- (unloads everything).
+configured it may also unload all of the dependencies (in our case it does
+not). If we wanted to unload everything at once, we could run `module purge`
+(unloads everything).
 
+```bash
+`r config$remote$prompt` module purge
+`r config$remote$prompt` module list
 ```
-{{ site.remote.prompt }} module purge
-{{ site.remote.prompt }} module list
-```
-{: .language-bash}
 
-```
+```output
 No modules loaded
 ```
-{: .output}
 
 Note that `module purge` is informative. It will also let us know if a default
 set of "sticky" packages cannot be unloaded (and how to actually unload these
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/wrong-gcc-version.snip b/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/wrong-gcc-version.snip
deleted file mode 100644
index 8fbd2825..00000000
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/modules/wrong-gcc-version.snip
+++ /dev/null
@@ -1,5 +0,0 @@
-<!--- There is a long additional section on some specific features of Lmod in
-snippets_library/ComputeCanada_Graham_slurm/modules/wrong-gcc-version.snip,
-particular covering the concept of a module hierarchy. While this is not
-relevant to the EESSI configuration right now, it may become so in the future
-if we change the default module naming scheme to hierarchical. -->
diff --git a/episodes/files/snippets/rename-snippets.sh b/episodes/files/snippets/rename-snippets.sh
deleted file mode 100755
index 85dd5711..00000000
--- a/episodes/files/snippets/rename-snippets.sh
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/bin/bash
-
-# This script renames snippets from the argument directory in an effort
-# to make the names more meaningful, thereby simplifying the process of
-# porting to a new site.
-
-if [[ $# != 1 ]] || [[ $1 == "-h" ]] || [[ $1 == "--help" ]]; then
-    echo "Please supply a folder name containing snippets for your site. This"
-    echo "script will rename those snippets based on the script activity. E.g.,"
-    echo "    $0 ComputeCanada_Graham_slurm"
-    exit 1
-fi
-
-if [[ $(which git) == "" ]]; then
-    echo "Error: This script requires git. Please install it and try again."
-    exit 1
-fi
-
-PREFIX=$1
-
-function rename_snip {
-    mv $1 $2
-}
-
-## Episode 12: Working on a remote HPC system
-
-#$ {{ site.sched.info }}
-rename_snip  ${PREFIX}/12/info.snip     ${PREFIX}/12/queue-info.snip
-#$ sinfo -n {{ site.remote.node }} -o "%n %c %m"
-rename_snip  ${PREFIX}/12/explore.snip  ${PREFIX}/12/specific-node-info.snip
-
-## Episode 13: Scheduling jobs
-
-# {{ site.sched.submit.name }} {{ site.sched.submit.options }} example-job.sh
-rename_snip  ${PREFIX}/13/submit_output.snip           ${PREFIX}/13/basic-job-script.snip
-#$ {{ site.sched.status }} {{ site.sched.flag.user }}
-rename_snip  ${PREFIX}/13/statu_output.snip            ${PREFIX}/13/basic-job-status.snip
-#$ {{ site.sched.status }} {{ site.sched.flag.user }}
-rename_snip  ${PREFIX}/13/statu_name_output.snip       ${PREFIX}/13/job-with-name-status.snip
-## The following are several key resource requests:
-rename_snip  ${PREFIX}/13/stat_options.snip            ${PREFIX}/13/option-flags-list.snip
-## Print SLURM_CPUS_PER_TASK, PBS_O_WORKDIR, or similar
-rename_snip  ${PREFIX}/13/env_challenge.snip           ${PREFIX}/13/print-sched-variables.snip
-#$ {{ site.sched.submit.name }} {{ site.sched.submit.options }} example-job.sh
-rename_snip  ${PREFIX}/13/long_job_cat.snip            ${PREFIX}/13/runtime-exceeded-job.snip
-#$ {{ site.sched.status }} {{ site.sched.flag.user }}
-rename_snip  ${PREFIX}/13/long_job_err.snip            ${PREFIX}/13/runtime-exceeded-output.snip
-#$ {{ site.sched.submit.name }} {{ site.sched.submit.options }} example-job.sh
-#$ {{ site.sched.status }} {{ site.sched.flag.user }}
-rename_snip  ${PREFIX}/13/del_job_output1.snip         ${PREFIX}/13/terminate-job-begin.snip
-#$ {{site.sched.del }} 38759
-rename_snip  ${PREFIX}/13/del_job_output2.snip         ${PREFIX}/13/terminate-job-cancel.snip
-#$ {{site.sched.del }} {{ site.sched.flag.user }}
-rename_snip  ${PREFIX}/13/del_multiple_challenge.snip  ${PREFIX}/13/terminate-multiple-jobs.snip
-## use the compute node resources interactively
-rename_snip  ${PREFIX}/13/interactive_example.snip     ${PREFIX}/13/using-nodes-interactively.snip
-
-## Episode 14: Accessing software
-
-#$ module avail
-rename_snip  ${PREFIX}/14/module_avail.snip   ${PREFIX}/14/available-modules.snip
-#$ which python
-rename_snip  ${PREFIX}/14/which_missing.snip  ${PREFIX}/14/missing-python.snip
-#$ module load python[3]
-rename_snip  ${PREFIX}/14/load_python.snip    ${PREFIX}/14/module-load-python.snip
-#$ which python
-rename_snip  ${PREFIX}/14/which_python.snip   ${PREFIX}/14/python-executable-dir.snip
-#$ echo $PATH
-rename_snip  ${PREFIX}/14/path.snip           ${PREFIX}/14/python-module-path.snip
-#$ ls $(dirname $(which python))
-rename_snip  ${PREFIX}/14/ls_dir.snip         ${PREFIX}/14/python-ls-dir-command.snip
-rename_snip  ${PREFIX}/14/ls_dir_output.snip  ${PREFIX}/14/python-ls-dir-output.snip
-## Loading & unloading software and dependencies
-rename_snip  ${PREFIX}/14/depend_demo.snip    ${PREFIX}/14/software-dependencies.snip
-## gcc example
-rename_snip  ${PREFIX}/14/gcc_example.snip    ${PREFIX}/14/wrong-gcc-version.snip
-
-## Episode 15: Transferring files
-
-## Episode 16: Using resources effectively
-
-#$ {{ site.sched.hist }}
-rename_snip  ${PREFIX}/16/stat_output.snip  ${PREFIX}/16/account-history.snip
-#$ top
-rename_snip  ${PREFIX}/16/top_output.snip   ${PREFIX}/16/monitor-processes-top.snip
-#$ free -h
-rename_snip  ${PREFIX}/16/free_output.snip  ${PREFIX}/16/system-memory-free.snip
-
-## Episode 17: Using shared resources responsibly
diff --git a/episodes/lesson_config.yaml b/episodes/lesson_config.yaml
index 39ae49a6..da2ae88d 100644
--- a/episodes/lesson_config.yaml
+++ b/episodes/lesson_config.yaml
@@ -1,3 +1,4 @@
 ---
 main_config: files/snippets/Ghastly_Mistakes/_config_options.yml
-snippets: Ghastly_Mistakes
\ No newline at end of file
+snippets: Ghastly_Mistakes
+...
diff --git a/episodes/load_config.R b/episodes/load_config.R
index dce81aa6..f6506897 100644
--- a/episodes/load_config.R
+++ b/episodes/load_config.R
@@ -7,7 +7,7 @@ library(yaml)
 config <- yaml.load_file("lesson_config.yaml")
 
 ## If "main_config" key exists, load the second configuration and merge
-print(paste("Loading ", config$main_config))
+### print(paste("Loading ", config$main_config))
 if (!is.null(config$main_config) && file.exists(config$main_config)) {
   override_config <- yaml.load_file(config$main_config)
   config <- modifyList(config, override_config)
@@ -30,16 +30,14 @@ choose_doc <- function(child_file) {
     fallback = file.path(current_doc, fallback_snippets, child_file)
   )
   print(doc_paths)
-  print(getwd())
+  ### print(getwd())
 
   # Return the valid path, or NULL if neither exists
   if (file.exists(doc_paths$main)) {
-    print("Returning")
-    print(doc_paths$main)
+    print(paste("Returning", doc_paths$main))
     return(doc_paths$main)
   } else if (file.exists(doc_paths$fallback)) {
-    print("Returning")
-    print(doc_paths$fallback)
+    print(paste("Returning", doc_paths$fallback))
     return(doc_paths$fallback)
   } else {
     print("Returning NULL")
diff --git a/site/README.md b/site/README.md
index 42997e3d..0a00291c 100644
--- a/site/README.md
+++ b/site/README.md
@@ -1,2 +1,2 @@
 This directory contains rendered lesson materials. Please do not edit files
-here.  
+here.

From 2bfd247c66789db240570fb410ecf6abd30608b9 Mon Sep 17 00:00:00 2001
From: Trevor Keller <tkellerphd@gmail.com>
Date: Wed, 5 Nov 2025 16:44:35 -0500
Subject: [PATCH 33/33] Working snippetized version.

---
 episodes/13-scheduler.Rmd                     | 12 ++--
 episodes/14-environment-variables.Rmd         |  2 +-
 episodes/15-modules.Rmd                       |  2 +-
 episodes/epcc_config.yaml                     | 50 -------------
 .../_config_options.yml                       |  2 +-
 episodes/lesson_config.yaml                   |  4 +-
 episodes/lesson_config_hpcc.yaml              |  2 -
 episodes/slurm_defaults.yaml                  | 71 -------------------
 8 files changed, 11 insertions(+), 134 deletions(-)
 delete mode 100644 episodes/epcc_config.yaml
 delete mode 100644 episodes/lesson_config_hpcc.yaml
 delete mode 100644 episodes/slurm_defaults.yaml

diff --git a/episodes/13-scheduler.Rmd b/episodes/13-scheduler.Rmd
index d74d1b83..1d8bc45d 100644
--- a/episodes/13-scheduler.Rmd
+++ b/episodes/13-scheduler.Rmd
@@ -57,7 +57,7 @@ In this case, the job we want to run is a shell script -- essentially a
 text file containing a list of UNIX commands to be executed in a sequential
 manner. Our shell script will have three parts:
 
-- On the very first line, add ``r config$remote$bash_shebang``. The `#!`
+- On the very first line, add ``r config$remote$shebang``. The `#!`
   (pronounced "hash-bang" or "shebang") tells the computer what program is
   meant to process the contents of this file. In this case, we are telling it
   that the commands that follow are written for the command-line shell (what
@@ -75,7 +75,7 @@ manner. Our shell script will have three parts:
 ```
 
 ```bash
-`r config$remote$bash_shebang`
+`r config$remote$shebang`
 
 echo -n "This script is running on "
 hostname
@@ -163,7 +163,7 @@ resources we must customize our job script.
 Comments in UNIX shell scripts (denoted by `#`) are typically ignored, but
 there are exceptions. For instance the special `#!` comment at the beginning of
 scripts specifies what program should be used to run it (you'll typically see
-``r config$local$bash_shebang``). Schedulers like `r config$sched$name` also
+``r config$local$shebang``). Schedulers like `r config$sched$name` also
 have a special comment used to denote special scheduler-specific options.
 Though these comments differ from scheduler to scheduler,
 `r config$sched$name`'s special comment is ``r config$sched$comment``. Anything
@@ -179,7 +179,7 @@ name of a job. Add an option to the script:
 ```
 
 ```bash
-`r config$remote$bash_shebang`
+`r config$remote$shebang`
 `r config$sched$comment` `r config$sched$flag$name` hello-world
 
 echo -n "This script is running on "
@@ -253,7 +253,7 @@ for it on the cluster.
 ```
 
 ```bash
-`r config$remote$bash_shebang`
+`r config$remote$shebang`
 `r config$sched$comment` `r config$sched$flag$time` 00:01 # timeout in HH:MM
 
 echo -n "This script is running on "
@@ -282,7 +282,7 @@ wall time, and attempt to run a job for two minutes.
 ```
 
 ```bash
-`r config$remote$bash_shebang`
+`r config$remote$shebang`
 `r config$sched$comment` `r config$sched$flag$name` long_job
 `r config$sched$comment` `r config$sched$flag$time` 00:01 # timeout in HH:MM
 
diff --git a/episodes/14-environment-variables.Rmd b/episodes/14-environment-variables.Rmd
index 3e4c6977..39bc80d3 100644
--- a/episodes/14-environment-variables.Rmd
+++ b/episodes/14-environment-variables.Rmd
@@ -212,7 +212,7 @@ job was submitted.
 ```
 
 ```output
-`r config$remote$bash_shebang`
+`r config$remote$shebang`
 `r config$sched$comment` `r config$sched$flag$time` 00:00:30
 
 echo -n "This script is running on "
diff --git a/episodes/15-modules.Rmd b/episodes/15-modules.Rmd
index fc044cfa..f02b43a7 100644
--- a/episodes/15-modules.Rmd
+++ b/episodes/15-modules.Rmd
@@ -204,7 +204,7 @@ compute node).
 ```
 
 ```output
-`r config$remote$bash_shebang`
+`r config$remote$shebang`
 `r config$sched$comment` `r config$sched$flag$partition`
 `r if (!is.null(config$sched$flag$qos)) {print(paste(config$sched$comment,config$sched$flag$qos))}
 `r config$sched$comment` `r config$sched$flag$time` 00:00:30
diff --git a/episodes/epcc_config.yaml b/episodes/epcc_config.yaml
deleted file mode 100644
index 5425d7b1..00000000
--- a/episodes/epcc_config.yaml
+++ /dev/null
@@ -1,50 +0,0 @@
----
-local:
-  prompt: "[user@laptop ~]$"
-  bash_shebang: "#!/bin/bash"
-
-snippets: EPCC_ARCHER2_slurm
-baseurl: "https://epcced.github.io/2023-06-28-uoe-hpcintro"
-
-remote:
-  name: "ARCHER2"
-  host_id: "EPCC_ARCHER2"
-  login: "login.archer2.ac.uk"
-  host: "ln03"
-  node: "nid001053"
-  location: "EPCC, The University of Edinburgh"
-  homedir: "/home/ta114/ta114/"
-  user: "userid"
-  prompt: "userid@ln03:~>"
-  prompt_work: "userid@uan01:/work/ta114/ta114/userid>"
-  module_python3: "cray-python"
-  bash_shebang: "#!/bin/bash"
-
-sched:
-  name: "Slurm"
-  partition: "standard"
-  reservation: "shortqos"
-  qos: "short"
-  budget: "short"
-  submit:
-    name: "sbatch"
-    options: "--partition=standard --qos=short"
-  queue:
-    debug: ""
-    testing: ""
-  status: "squeue"
-  flag:
-    user: "-u userid"
-    interactive: ""
-    histdetail: "-l -j"
-    name: "--job-name"
-    time: "--time"
-    queue: "--partition"
-    nodes: "--nodes"
-    tasks: ""
-  del: "scancel"
-  interactive: "srun"
-  info: "sinfo"
-  comment: "#SBATCH"
-  hist: "sacct"
-  project: ta114
diff --git a/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml b/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
index 71c8b924..524b6807 100644
--- a/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
+++ b/episodes/files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
@@ -11,7 +11,7 @@
 # Compute responsibly.
 ---
 
-snippets: "/snippets_library/HPCC_MagicCastle_slurm"
+snippets: "HPCC_MagicCastle_slurm"
 
 local:
   prompt: "[you@laptop:~]$"
diff --git a/episodes/lesson_config.yaml b/episodes/lesson_config.yaml
index da2ae88d..af0b8166 100644
--- a/episodes/lesson_config.yaml
+++ b/episodes/lesson_config.yaml
@@ -1,4 +1,4 @@
 ---
-main_config: files/snippets/Ghastly_Mistakes/_config_options.yml
-snippets: Ghastly_Mistakes
+main_config: files/snippets/HPCC_MagicCastle_slurm/_config_options.yml
+snippets: HPCC_MagicCastle_slurm
 ...
diff --git a/episodes/lesson_config_hpcc.yaml b/episodes/lesson_config_hpcc.yaml
deleted file mode 100644
index f2044649..00000000
--- a/episodes/lesson_config_hpcc.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-main_snippets: "hpcc_test"
-fallback_snippets: "hpcc"
diff --git a/episodes/slurm_defaults.yaml b/episodes/slurm_defaults.yaml
deleted file mode 100644
index 6372be9c..00000000
--- a/episodes/slurm_defaults.yaml
+++ /dev/null
@@ -1,71 +0,0 @@
-# Fail-safe defaults and implicit schema for lesson configuration files
----
-snippets: slurm
-baseurl: "https://ocaisa.github.io/probable-pancake/"
-# main_config: "lesson_config.yaml"
-
-# about the Learner's laptop
-local:
-  prompt: "[you@laptop:~]$"                  # command-line prompt
-  shebang: "#!/bin/bash"                     # first line of every shell script
-
-# about the remote/cluster environment
-remote:
-  name: "Example Cluster"                    # Name of the cluster (proper noun)
-  login: "cluster.example.com"               # domain name of the login node
-  host: "head"                               # hostname of the login node
-  node: "node"                               # hostname of a compute node
-  location: "SchedMD"                        # institutional host of the cluster
-  homedir: "/home"                           # parent of home directories
-  user: "userid"                             # stand-in for the username
-  prompt: "[userid@head:~]"                  # command-line prompt
-  prompt_work: "[userid@head:/work/userid]"  # prompt under /work
-  modules:
-    python: "Python"                         # name of the module providing Python v3
-  shebang: "#!/bin/bash"                     # first line of every shell script
-
-# Commands & flags for the scheduler environment
-sched:
-  name: "Slurm"                              # proper name of the scheduler
-  command:
-    batch:       "sbatch"                    # run later
-    interactive: "srun"                      # run now
-    cancel:      "scancel"                   # don't run
-  queue:
-    test: "debug"
-    prod: "batch"
-  status: "squeue"
-  flag:
-    user: "-u userid"
-    interactive: "--pty bash"
-    histdetail: "-l -j"
-    name: "-J"
-    time: "-t"
-    queue: "-p"
-    nodes: "-N"
-    tasks: "-n"
-  del: "scancel"
-  interactive:
-    command: "srun"
-  info:
-    command: "sinfo"
-  comment: "#SBATCH"
-  hist: "sacct -u userid"
-  hist_filter: ""
-  reservation: ""
-  qos: ""
-  budget: ""
-  project: ""
-
-# submit:
-#   salloc:   obtain a job allocation
-#   sbatch:   submit a batch script for later execution
-#   srun:     obtain an allocation and execute an application
-# account:
-#   sacct:    display accounting data
-# manage:
-#   sbcast:   transfer a file to a job's compute nodes
-#   scancel:  signal jobs/steps
-#   squeue:   view information about jobs
-#   sinfo:    view information about nodes & partitions
-#   scontrol: view & modify state