Update contents for Cirrus-EX machine

.github/workflows/sphinx.yml

@@ -27,7 +27,7 @@ jobs:
       # https://docs.github.com/en/actions/guides/building-and-testing-python#caching-dependencies
       # ^-- How to set up caching for pip on Ubuntu
       - name: Cache pip
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}

content/Part0_Introduction/contents.md

@@ -41,7 +41,7 @@ You will have been given instructions on how to obtain an ARCHER2 or Cirrus acco
 To connect to the EPCC systems for the practicals, participants must use a Mac, Linux, or Windows system (not a tablet, Chromebook, etc.). All attendees are also required to abide by the ARCHER2 Training [Code of Conduct](https://www.archer2.ac.uk/about/policies/code-of-conduct.html).
 
 Full instructions on how to log in to ARCHER2 are available in the [online ARCHER2 documentation](https://docs.archer2.ac.uk/user-guide/connecting/). If you have any problems connecting then please contact the ARCHER2 helpdesk (support@archer2.ac.uk).
-Full instructions on how to log in to Cirrus are available in the online [Cirrus documentation](https://cirrus.readthedocs.io/en/main/user-guide/connecting.html). If you have any problems connecting then please contact the Cirrus helpdesk (support@cirrus.ac.uk).
+Full instructions on how to log in to Cirrus are available in the online [Cirrus documentation](https://docs.cirrus.ac.uk/user-guide/connecting/). If you have any problems connecting then please contact the Cirrus helpdesk (support@cirrus.ac.uk).
 
 
 ## Questionnaires

content/Part1_Message_Passing_Overview_and_Introduction_to_MPI/contents.md

@@ -88,12 +88,15 @@ This subsection introduces MPI programming and several core functions ([slides](
 <iframe width="700" height="400" src="https://cdnapisec.kaltura.com/html5/html5lib/v2.101/mwEmbedFrame.php/p/2010292/uiconf_id/32599141/entry_id/0_c21vap59?wid=_2010292&iframeembed=true&playerId=kaltura_player&entry_id=0_c21vap59&flashvars[streamerType]=auto&flashvars[localizationCode]=en&flashvars[leadWithHTML5]=true&flashvars[sideBarContainer.plugin]=true&flashvars[sideBarContainer.position]=left&flashvars[sideBarContainer.clickToClose]=true&flashvars[chapters.plugin]=true&flashvars[chapters.layout]=vertical&flashvars[chapters.thumbnailRotator]=false&flashvars[streamSelector.plugin]=true&flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&flashvars[dualScreen.plugin]=true&flashvars[Kaltura.addCrossoriginToIframe]=true&&wid=1_uqd00t6i#" title="Kaltura video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe><br><br>
 ```
 
-Next videos cover running MPI programs on ARCHER2 and Cirrus ([slides](../slides/L03-archer2-cirrus-mpi.pdf), [ARCHER2 notes](../exercises/ARCHER2-MPI-online-cribsheet.pdf), [Cirrus notes]../exercises/Cirrus-MPI-online-cribsheet.pdf)) and the first exercise ([exercise slides](../exercises/MPP-exercises.pdf), [code archive](../exercises/MPP-templates.tar)).
+For running MPI programs on ARCHER2 and Cirrus, see the ([slides](../slides/L03-archer2-cirrus-mpi.pdf), [ARCHER2 notes](../exercises/ARCHER2-MPI-online-cribsheet.pdf), [Cirrus notes](../exercises/Cirrus-MPI-online-cribsheet.pdf)) 
 
 
-```{raw} html
+<!-- ```{raw} html
 <iframe width="700" height="400" src="https://cdnapisec.kaltura.com/html5/html5lib/v2.101/mwEmbedFrame.php/p/2010292/uiconf_id/32599141/entry_id/1_umfdoth2?wid=_2010292&iframeembed=true&playerId=kaltura_player&entry_id=1_umfdoth2&flashvars[streamerType]=auto&flashvars[localizationCode]=en&flashvars[leadWithHTML5]=true&flashvars[sideBarContainer.plugin]=true&flashvars[sideBarContainer.position]=left&flashvars[sideBarContainer.clickToClose]=true&flashvars[chapters.plugin]=true&flashvars[chapters.layout]=vertical&flashvars[chapters.thumbnailRotator]=false&flashvars[streamSelector.plugin]=true&flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&flashvars[dualScreen.plugin]=true&flashvars[Kaltura.addCrossoriginToIframe]=true&&wid=1_4tgdelpv#" title="Kaltura video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe><br><br>
-```
+``` -->
+
+
+Next video covers the first exercise ([exercise slides](../exercises/MPP-exercises.pdf), [code archive](../exercises/MPP-templates.tar)).
 
 
 ```{raw} html
@@ -109,9 +112,9 @@ The next short video shows how to log on to ARCHER2, transfer files, and compile
 <iframe width="700" height="400" src="https://cdnapisec.kaltura.com/html5/html5lib/v2.101/mwEmbedFrame.php/p/2010292/uiconf_id/32599141/entry_id/1_slrvujkg?wid=_2010292&iframeembed=true&playerId=kaltura_player&entry_id=1_slrvujkg&flashvars[streamerType]=auto&flashvars[localizationCode]=en&flashvars[leadWithHTML5]=true&flashvars[sideBarContainer.plugin]=true&flashvars[sideBarContainer.position]=left&flashvars[sideBarContainer.clickToClose]=true&flashvars[chapters.plugin]=true&flashvars[chapters.layout]=vertical&flashvars[chapters.thumbnailRotator]=false&flashvars[streamSelector.plugin]=true&flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&flashvars[dualScreen.plugin]=true&flashvars[Kaltura.addCrossoriginToIframe]=true&&wid=1_lo305y3c#" title="Kaltura video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe><br><br>
 ```
 
-The following short video shows how to log on to Cirrus, transfer files, and compile and run parallel programs.
-
+For instructions on logging on to Cirrus, transferring files, and compiling and running parallel programs, see the [Cirrus notes](../exercises/Cirrus-MPI-online-cribsheet.pdf).
 
+<!-- 
 ```{raw} html
 <iframe width="700" height="400" src="https://cdnapisec.kaltura.com/html5/html5lib/v2.101/mwEmbedFrame.php/p/2010292/uiconf_id/32599141/entry_id/1_4vv745wp?wid=_2010292&iframeembed=true&playerId=kaltura_player&entry_id=1_4vv745wp&flashvars[streamerType]=auto&flashvars[localizationCode]=en&flashvars[leadWithHTML5]=true&flashvars[sideBarContainer.plugin]=true&flashvars[sideBarContainer.position]=left&flashvars[sideBarContainer.clickToClose]=true&flashvars[chapters.plugin]=true&flashvars[chapters.layout]=vertical&flashvars[chapters.thumbnailRotator]=false&flashvars[streamSelector.plugin]=true&flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&flashvars[dualScreen.plugin]=true&flashvars[Kaltura.addCrossoriginToIframe]=true&&wid=1_570vnzcb#" title="Kaltura video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe><br><br>
-```
+``` -->

content/substitutions/substitutions_ARCHER2/ssh_login.md

@@ -1,4 +1,4 @@
 ## Connecting to ARCHER2
 
 ### Sign up for an account on ARCHER2 through SAFE
 
@@ -28,6 +28,9 @@
 
 The public SSH key part will now be added to your login account on the ARCHER2 system.
 
+### Time-based one-time passcode (TOTP code)
+
+Remember, you will need to use both an SSH key and time-based one-time passcode to log into ARCHER2 so you will also need to [set up a method for generating a TOTP code](https://epcced.github.io/safe-docs/safe-for-users/#how-to-turn-on-mfa-on-your-machine-account) before you can log into ARCHER2.
 
 ### Log into ARCHER2
 

content/substitutions/substitutions_Cirrus/ssh_login.md

@@ -1,4 +1,4 @@
 ## Connecting to Cirrus
 
 ### Sign up for an account on Cirrus through SAFE
 
@@ -15,7 +15,7 @@
 ### Generate an SSH key pair and upload it to SAFE
 
 In addition to your password, you will need an SSH key pair to access Cirrus. There is useful guidance on how
-to generate SSH key pairs in [the Cirrus documentation](https://cirrus.readthedocs.io/en/master/user-guide/connecting.html).
+to generate SSH key pairs in [the Cirrus documentation]https://docs.cirrus.ac.uk/user-guide/connecting/#ssh-key-pairs).
 
 Once you have generated your key pair, you need to add the public part to your Cirrus account in SAFE:
 
@@ -28,7 +28,31 @@
 
 The public SSH key part will now be added to your login account on the Cirrus system.
 
+### Time-based one-time passcode (TOTP code)
+
+Remember, you will need to use both an SSH key and time-based one-time passcode (TOTP code) to log into Cirrus so you will also need to [set up a method for generating a TOTP code](https://epcced.github.io/safe-docs/safe-for-users/#how-to-turn-on-mfa-on-your-machine-account) before you can log into Cirrus.
 
 ### Log into Cirrus
 
-You should now be able to log into Cirrus by following the [login instructions in the Cirrus documentation](https://cirrus.readthedocs.io/en/master/user-guide/connecting.html).
+You should now be able to log into Cirrus by following the [login instructions in the Cirrus documentation](https://docs.cirrus.ac.uk/user-guide/connecting/#ssh-clients).
+
+E.g:
+
+```bash
+ssh username@login.cirrus.ac.uk
+```
+
+
+`````{note}
+
+If you are using Cirrus before you download the files you should move to the ``/work`` filesystem:
+
+```bash
+cd /work/[project code]/[group code]/[username]
+```
+
+The `/work` filesystem is a high performance parallel file system that can be accessed by both the frontend login nodes and the compute nodes. All jobs on Cirrus should be run from the `/work` file system. Cirrus compute nodes cannot access the `/home` file system at all. Any jobs attempting to use `/home` will fail with an error. 
+
+For more information the Cirrus documentation: https://docs.cirrus.ac.uk/user-guide/data/#cirrus-file-systems-and-storage](https://docs.cirrus.ac.uk/user-guide/data/#cirrus-file-systems-and-storage)
+
+``````