Added all changes associated with EPCC_Cirrus_slurm.

_episodes/14-modules.md

@@ -27,16 +27,16 @@ understand the reasoning behind this approach. The three biggest factors are:
 
 Software incompatibility is a major headache for programmers. Sometimes the
 presence (or absence) of a software package will break others that depend on
-it. Two of the most famous examples are Python 2 and 3 and C compiler versions.
+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 Software compiled against a newer version of the C libraries and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 used when they are not present will result in a nasty `'GLIBCXX_3.4.20'
-not found` error, for instance.
+then run on a machine that has older C libraries installed will result in a
+nasty `'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
 change (for instance, if a package was updated), it might affect their results.
-Having access to multiple software versions allow a set of researchers to
+Having access to multiple software versions allows a set of researchers to
 prevent software versioning issues from affecting their results.
 
 Dependencies are where a particular software package (or even a particular
@@ -89,10 +89,7 @@ message telling you so
 ```
 {: .language-bash}
 
-```
-No Modulefiles Currently Loaded.
-```
-{: .output}
+{% include {{ site.snippets }}/modules/default-modules.snip %}
 
 ## Loading and Unloading Software
 
@@ -198,7 +195,9 @@ Let's examine the output of `module avail` more closely.
 > >
 > > ```
 > > {{ site.remote.bash_shebang }}
-> >
+> > {% include {{ site.snippets }}/scheduler/sbatch-options.snip %}
+> > {{ site.sched.comment }} {{ site.sched.flag.time }} 00:00:30
+> > 
 > > module load {{ site.remote.module_python3 }}
 > >
 > > python3 --version
@@ -212,4 +211,4 @@ Let's examine the output of `module avail` more closely.
 > {: .solution}
 {: .challenge}
 
-{% include links.md %}
+{% include links.md %}

_includes/snippets_library/ComputeCanada_Graham_slurm/_config_options.yml

@@ -55,6 +55,7 @@ sched:
   info: "sinfo"
   comment: "#SBATCH"
   hist: "sacct -u yourUsername"
+  hist_filter: ""
 
 episode_order:
   - 10-hpc-intro

_includes/snippets_library/ComputeCanada_Graham_slurm/cluster/root-folders.snip

@@ -0,0 +1,6 @@
+```
+bin   etc   lib64  proc  sbin     sys  var
+boot  {{ site.remote.homedir | replace: "/", "" }}  mnt    root  scratch  tmp  working
+dev   lib   opt    run   srv      usr
+```
+{: .output}

_includes/snippets_library/ComputeCanada_Graham_slurm/modules/default-modules.snip

@@ -0,0 +1,4 @@
+```
+No Modulefiles Currently Loaded.
+```
+{: .output}

_includes/snippets_library/ComputeCanada_Graham_slurm/resources/hist-fields.snip

@@ -0,0 +1,6 @@
+* **Hostname**: Where did your job run?
+* **MaxRSS**: What was the maximum amount of memory used?
+* **Elapsed**: How long did the job take?
+* **State**: What is the job currently doing/what happened to it?
+* **MaxDiskRead**: Amount of data read from disk.
+* **MaxDiskWrite**: Amount of data written to disk.

_includes/snippets_library/ComputeCanada_Graham_slurm/scheduler/email-notifications.snip

@@ -0,0 +1,19 @@
+> Jobs on an HPC system might run for days or even weeks. We probably have
+> better things to do than constantly check on the status of our job with
+> `{{ site.sched.status }}`. Looking at the manual page for
+> `{{ site.sched.submit.name }}`, can you set up our test job to send you an email
+> when it finishes?
+>
+> > ## Hint
+> >
+> > You can use the *manual pages* for {{ site.sched.name }} utilities to find
+> > more about their capabilities. On the command line, these are accessed
+> > through the `man` utility: run `man <program-name>`. You can find the same
+> > information online by searching > "man <program-name>".
+> >
+> > ```
+> > {{ site.remote.prompt }} man {{ site.sched.submit.name }}
+> > ```
+> > {: .language-bash}
+> {: .solution}
+{: .challenge}

_includes/snippets_library/EPCC_Cirrus_slurm/_config_options.yml

@@ -0,0 +1,74 @@
+#------------------------------------------------------------
+# EPCC, The University of Edinburgh: Cirrus + PBS Pro
+#------------------------------------------------------------
+
+# 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
+# Slurm, we could replace the options below with those from
+# 
+# _includes/snippets_library/EPCC_Cirrus_slurm/_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_Cirrus_slurm"
+
+local:
+  prompt: "[auser@laptop ~]$"
+  bash_shebang: "#!/bin/bash"
+
+remote:
+  name: "Cirrus"
+  login: "login.cirrus.ac.uk"
+  host: "cirrus-login1"
+  node: "r1i0n32"
+  location: "EPCC, The University of Edinburgh"
+  homedir: "/lustre/home/tc001"
+  user: "auser"
+  group: "tc001"
+  prompt: "[auser@cirrus-login1 ~]$"
+  bash_shebang: "#!/bin/bash"
+  module_python3: "anaconda/python3-2021.11"
+
+sched:
+  name: "Slurm"
+  submit:
+    name: "sbatch"
+    options: "--partition=standard --qos=standard --time=00:02:00"
+  queue:
+    debug: "debug"
+    testing: "testing"
+  status: "squeue"
+  flag:
+    user: "-u auser"
+    interactive: "--time=00:20:00 --partition=standard --qos=standard --pty /usr/bin/bash --login"
+    histdetail: "-l -j"
+    name: "-J"
+    partition: "-p standard"
+    qos: "-q standard"
+    time: "-t"
+    queue: "-p"
+    nodes: "-N"
+    tasks: "-n"
+  del: "scancel"
+  interactive: "srun"
+  info: "sinfo"
+  comment: "#SBATCH"
+  hist: "sacct"
+  hist_filter: "--format=JobID,JobName,State,Elapsed,NodeList,MaxRSS,MaxDiskRead,MaxDiskWrite"
+
+episode_order:
+  - 11-hpc-intro
+  - 12-cluster
+  - 13-scheduler
+  - 14-modules
+  - 15-transferring-files
+  - 16-parallel
+  - 17-resources
+  - 18-responsibility