Merge pull request #445 from tkphd/epcc-cirrus-slurm

EPCC Cirrus (slurm)

.github/workflows/test_and_build.yml

@@ -62,7 +62,7 @@ jobs:
         HPC_JEKYLL_CONFIG:
           - Birmingham_Baskerville_slurm
           - ComputeCanada_Graham_slurm
-          - EPCC_Cirrus_pbs
+          - EPCC_Cirrus_slurm
           - HPCC_MagicCastle_slurm
           - Magic_Castle_EESSI_slurm
           - NIST_CTCMS_slurm

_config.yml

@@ -11,9 +11,9 @@
 # `_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
+# Slurm, we could replace the options below with those from
 # 
-# _includes/snippets_library/EPCC_Cirrus_pbs/_config_options.yml
+# _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
@@ -74,6 +74,7 @@ sched:
   info: "sinfo"
   comment: "#SBATCH"
   hist: "sacct -u yourUsername"
+  hist_filter: ""
 
 episode_order:
   - 10-hpc-intro

_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 Software compiled against a newer version of the C libraries and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 +195,10 @@ Let's examine the output of `module avail` more closely.
 > >
 > > ```
 > > {{ 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
+> > 
 > > module load {{ site.remote.module_python3 }}
 > >
 > > python3 --version

_includes/snippets_library/Birmingham_Baskerville_slurm/_config_options.yml

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

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

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

_includes/snippets_library/ComputeCanada_Graham_slurm/_config_options.yml

@@ -8,9 +8,9 @@
 # `_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
+# Slurm, we could replace the options below with those from
 # 
-# _includes/snippets_library/EPCC_Cirrus_pbs/_config_options.yml
+# _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
@@ -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}