09 10 import (#5)

* Added some debugging and formatting pages

* Source Update

.gitignore

@@ -2,4 +2,5 @@
 from_zendesk/cache/**
 from_zendesk/import_worktree/**
 public/*
+production/*
 **.pyc

SPECIFICATION.md

@@ -65,22 +65,34 @@ Not used for anything currently. Info imported from Zendesk Page.
 - `zendesk_article_id`:
 - `zendesk_section_id`:
 
-
 ## Formatting
 
 Most details about the extra markdown features can be found here.
 Will copy the specifics that apply to this site when I get time.
 
 https://squidfunk.github.io/mkdocs-material/reference/
 
-## Code Formatting
+### Admonation
 
-### Blocks
+!!! type
+    Something
 
-    import tensorflow as tf
-    import numpy as numpy
+Where 'type' is one of these https://squidfunk.github.io/mkdocs-material/reference/admonitions/#type:note
 
-Preferably
+### Content Tabs
+
+Look like this
+
+```
+=== "Tab One"
+    someting in the tab
+=== "Tab two"
+    something else
+```
+
+## Code Formatting
+
+### Blocks
 
 ```py
 import tensorflow as tf

docs/General/Announcements/Māui_upgrade_is_complete.md

@@ -28,7 +28,7 @@ possible and will do our best to assist you.
 
 This upgrade brings Māui's operating environment up to the latest
 supported release available for Cray's XC50 supercomputing platforms,
-with performance, reliability, and security benefits. This includes more
+with performance, reliability, and security benefits. This ../../../ more
 up-to-date tooling and libraries with associated features and
 performance benefits. This work also enables further upgrades to NeSI's
 shared HPC storage system.

docs/General/FAQs/How_to_replace_my_2FA_token.md

@@ -23,23 +23,23 @@ Log in to [my.nesi.org.nz](https://my.nesi.org.nz) and select the option
 Once you've created a token, you should see the 'Manage Two-Factor
 token' option.
 
-![image2018-10-26\_15-36-10.png](../includes/image2018-10-26_15-36-10.png)
+![image2018-10-26\_15-36-10.png](../../includes/images/image2018-10-26_15-36-10.png)
 
 ## Delete the Two-Factor token
 
 Select the option 'Manage Two-Factor token' under 'Account'.
 
 You should see the confirmation of the previous token.
 
-![](../includes/mceclip0_13.png)
+![](../../includes/images/mceclip0_13.png)
 
 After 'Delete Token' has been selected:
 
-![](../includes/mceclip1_2.png)
+![](../../includes/images/mceclip1_2.png)
 
 You will also receive an email confirmation:
 
-![](../includes/mceclip3.png)
+![](../../includes/images/mceclip3.png)
 
 ## Related content
 

docs/General/FAQs/How_to_submit_feedback_or_a_new_idea_using_a_product_portal?.md

@@ -26,7 +26,7 @@ provide feedback on. Each idea/feature on the Portal is represented as a
 Select a card, choose the importance and add let us know why this is
 important to you as well as your email address.
 
-![card\_feedback.gif](../includes/card_feedback.gif)
+![card\_feedback.gif](../../includes/images/card_feedback.gif)
 
 When users provide feedback on features/ideas in this way, their
 feedback is routed back to our Insights board.
@@ -39,7 +39,7 @@ You can also submit brand new ideas on the Portal. These will be routed
 to our Insights board as well and reviewed by the product management
 team.
 
-![submit\_idea.gif](../includes/submit_idea.gif)
+![submit\_idea.gif](../../includes/images/submit_idea.gif)
 
 ### What happens to the feedback?
 

docs/General/FAQs/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science?.md

@@ -47,7 +47,7 @@ As pictured in the screenshot below, you can type keywords into the
 catalogue's search field to browse by a specific software name or using
 more broad terms such as "machine learning". 
 
-![MachineLearningSoftwareEnvironments-May2021.png](../includes/MachineLearningSoftwareEnvironments-May2021.png)
+![MachineLearningSoftwareEnvironments-May2021.png](../../includes/images/MachineLearningSoftwareEnvironments-May2021.png)
 
 For more information on NeSI's model and approach to application
 support, refer to our [policy for the management of scientific

docs/General/FAQs/When_does_CPU_efficiency_matter_more_than_speed?.md

@@ -21,6 +21,6 @@ efficiency rather than speed, and running on a single CPU is almost
 always more efficient than any form of parallelisation. 
 
 ![*Four serial tasks run concurrently will finish faster than for
-parallel 4cpu tasks CPUs one after another. *](../includes/4tasks.png)
+parallel 4cpu tasks CPUs one after another. *](../../includes/images/4tasks.png)
 
 </figure>

docs/General/FAQs/Why_am_I_seeing_'Account_is_not_ready'?.md

@@ -21,4 +21,4 @@ please email
 and wait for a member of our support team to confirm your account and
 group membership.
 
-![mceclip0.png](../includes/mceclip0_14.png)
+![mceclip0.png](../../includes/images/mceclip0_14.png)

docs/General/NeSI_Knowledge_Base/Formatting.md

@@ -65,7 +65,7 @@ This is a [Link](https://www.w3schools.com/html/html_links.asp)
 
 Image
 
-![redirects-and-pipes.png](../includes/6014468037775)
+![redirects-and-pipes.png](../../includes/images/6014468037775)
 
 ------------------------------------------------------------------------
 

docs/General/NeSI_Policies/Account_Requests_for_non-Tuakiri_Members.md

@@ -23,7 +23,7 @@ affiliated with an organisation supported by the
 federation, you can request access via
 [my.nesi.org.nz/register](https://my.nesi.org.nz/register).
 
-![mceclip0.png](../includes/mceclip0_15.png)
+![mceclip0.png](../../includes/images/mceclip0_15.png)
 
 > ### Warning
 >

docs/General/NeSI_Policies/NeSI_Application_Support_Model.md

@@ -30,7 +30,7 @@ three-tier model.
 
 ## Tier 1
 
-Includes applications (meaning tools, libraries and science
+../../../ applications (meaning tools, libraries and science
 applications) which:
 
 1.  Have a wide user base among users of the NeSI Compute and Analytics
@@ -48,7 +48,7 @@ applications) which:
 
 ## Tier 2
 
-Includes applications (meaning tools, libraries and science
+../../../ applications (meaning tools, libraries and science
 applications) which:
 
 1.  Have a small but important user base, meaning they are used by
@@ -63,7 +63,7 @@ applications) which:
 
 ## Tier 3
 
-Includes applications (meaning tools, libraries and science
+../../../ applications (meaning tools, libraries and science
 applications) that are required by one user, or have very limited use,
 in which case:
 

docs/Getting_Started/Accessing_the_HPCs/Choosing_and_Configuring_Software_for_Connecting_to_the_Clusters.md

@@ -92,7 +92,7 @@ different options, listed in order of preference.
 
 -   ## MobaXterm
 
-    In addition to being a terminal emulator, MobaXterm also includes
+    In addition to being a terminal emulator, MobaXterm also ../../../
     several useful features like multiplexing, X11 forwarding and a file
     transfer GUI.
 

docs/Getting_Started/Accessing_the_HPCs/Port_Forwarding.md

@@ -128,20 +128,20 @@ method described above. This is the recommended method.
 You can tell if MobaXterm is using WSL as it will appear in the banner
 when starting a new terminal session. 
 
-![mceclip0.png](../includes/360004708596)
+![mceclip0.png](../../includes/images/360004708596)
 
 You can also set up port forwarding using the MobaXterm tunnelling
 interface.
 
-![mceclip1.png](../includes/360004708616)
+![mceclip1.png](../../includes/images/360004708616)
 
 You will need to create **two** tunnels. One from lander to mahuika. And
 another from mahuika to itself. (This is what using an alias in the
 first two examples allows us to avoid).
 
 The two tunnels should look like this.
 
-![mobakey.png](../includes/360004580035)
+![mobakey.png](../../includes/images/360004580035)
 
 <span class="wysiwyg-color-green110">■</span> local port  
 <span class="wysiwyg-color-orange90">■</span> remote port  

docs/Getting_Started/Accessing_the_HPCs/Setting_Up_Two-Factor_Authentication.md

@@ -45,10 +45,10 @@ If you some reason you can't do this, please contact NeSI support.
 2.  Click **My HPC Account** on left hand panel  and then **Setup
     Two-Factor Authentication device**
 
-    <img src="../includes/4414700806543" alt="authentication_factor_setup.png" width="560" height="210" />
+    <img src="../../includes/images/4414700806543" alt="authentication_factor_setup.png" width="560" height="210" />
 
 3.  Click the "**Setup Two-Factor Authentication device**" link.  
-    ![](../includes/360001267755)
+    ![](../../includes/images/360001267755)
 4.  After clicking on "Continue" you will retrieve the QR code.
 
 5.  Open your Authy or Google Authenticator app and click on the add

docs/Getting_Started/Accessing_the_HPCs/Setting_Up_and_Resetting_Your_Password.md

@@ -36,22 +36,22 @@ zendesk_section_id: 360000034315
     Password** (If you are resetting your password this will read
     **Reset Password**).  
     Note your** Username.  
-    <img src="../includes/authentication_factor_setup.png" alt="authentication_factor_setup.png" width="442" height="166" />  
+    <img src="../../includes/images/authentication_factor_setup.png" alt="authentication_factor_setup.png" width="442" height="166" />  
     **
 3.  Enter and verify your new password, making sure it follows the
     [password
     policy](https://support.nesi.org.nz/hc/en-gb/articles/360000336015).  
 
 
-    #### <img src="../includes/SetNeSIaccountPassword.png" alt="SetNeSIaccountPassword.png" width="628" height="314" />
+    #### <img src="../../includes/images/SetNeSIaccountPassword.png" alt="SetNeSIaccountPassword.png" width="628" height="314" />
 
 4.  If the password set was successful, following confirmation label
     will appear on the same page within few seconds  
 
-    ![change\_success.png](../includes/5662974048911)
+    ![change\_success.png](../../includes/images/5662974048911)
 5.  Followed by an email confirmation similar to below
 
-<img src="../includes/password_set_confirmation.png" alt="password_set_confirmation.png" width="440" height="285" />
+<img src="../../includes/images/password_set_confirmation.png" alt="password_set_confirmation.png" width="440" height="285" />
 
 
 
@@ -77,13 +77,13 @@ zendesk_section_id: 360000034315
 
 4.  If the password **reset** was successful, following confirmation
     label will appear on the same page within few seconds  
-    1.  -   ![change\_success.png](../includes/5662974048911_0.name_me)
+    1.  -   ![change\_success.png](../../includes/images/5662974048911_0.name_me)
 
 5.  Followed by an email confirmation similar to below  
 
 
 
-<img src="../includes/password_set_confirmation_0.png" alt="password_set_confirmation.png" width="440" height="285" />
+<img src="../../includes/images/password_set_confirmation_0.png" alt="password_set_confirmation.png" width="440" height="285" />
 
 
 

docs/Getting_Started/Accounts,_Projects_and_Allocations/Quarterly_allocation_periods.md

@@ -26,15 +26,15 @@ Allocations will start on the first day of the next month and run for
 one year. The diagram below illustrates how these quarterly call periods
 are scheduled during the year:
 
-![Quarterly\_Allocation\_Periods\_2021\_\_1\_.png](../includes/Quarterly_Allocation_Periods_2021__1_.png)
+![Quarterly\_Allocation\_Periods\_2021\_\_1\_.png](../../includes/images/Quarterly_Allocation_Periods_2021__1_.png)
 
 For example, if you apply for a new allocation on your existing project
 in the month of October, we will review your application in October or
 early November, you will be notified of your allocation by the end of
 November, and your allocation will start on 1 December (as shown in the
 graphic below).
 
-![Blank\_Diagram\_\_1\_.png](../includes/Blank_Diagram__1_.png)
+![Blank\_Diagram\_\_1\_.png](../../includes/images/Blank_Diagram__1_.png)
 
 ## Existing allocations
 

docs/Getting_Started/Accounts,_Projects_and_Allocations/What_is_an_allocation?.md

@@ -100,7 +100,7 @@ supercomputer is allocated by node-hours. Though some Māui nodes have
 more RAM than others, we do not currently distinguish between low-memory
 and high-memory nodes for allocation, billing or Fair Share purposes.
 
-Each allocation on Māui includes an entitlement to use the Māui
+Each allocation on Māui ../../../ an entitlement to use the Māui
 ancillary nodes equally with other NeSI projects having Māui allocations
 at that time.
 

docs/Getting_Started/Cheat_Sheets/Git:_Reference_Sheet.md

@@ -21,7 +21,7 @@ developing, managing and distributing code.
 Full Git documentation can be
 found [here](https://git-scm.com/docs/git), or using `man git`.
 
-![Git\_Diagram.svg](../includes/Git_Diagram.svg)
+![Git\_Diagram.svg](../../includes/images/Git_Diagram.svg)
 
 ## Authentication
 
@@ -59,21 +59,21 @@ documentation](https://docs.github.com/en/authentication/connecting-to-github-wi
     page, click your profile photo click **Settings**.
 
     <span class="procedural-image-wrapper">![Settings icon in the user
-    bar](../includes/userbar-account-settings.png)</span>
+    bar](../../includes/images/userbar-account-settings.png)</span>
 
 -   In the "Access" section of the sidebar, click **SSH and GPG keys**.
 
 -   Click **New SSH key** or **Add SSH key**.
 
     <span class="procedural-image-wrapper">![SSH Key
-    button](../includes/ssh-add-ssh-key-with-auth.png)</span>
+    button](../../includes/images/ssh-add-ssh-key-with-auth.png)</span>
 
 -   In the "Title" field, put "Mahuika" or "NeSI".
 
 -   Paste your key into the "Key" field.
 
     <span class="procedural-image-wrapper">![The key
-    field](../includes/ssh-key-paste-with-type.png)</span>
+    field](../../includes/images/ssh-key-paste-with-type.png)</span>
 
 -   Click **Add SSH key**.
 

docs/Getting_Started/Cheat_Sheets/Unix_Shell:_Reference_Sheet.md

@@ -374,12 +374,12 @@ Bring up the manual of a command (in this case ls).
 > Pressing the 'tab' key once will automatically complete the line if it
 > is the only option. e.g. 
 >
-> ![complete1.gif](../includes/complete1.gif)
+> ![complete1.gif](../../includes/images/complete1.gif)
 >
 > If there are more than one possible completions, pressing tab again
 > will show all those options.
 >
-> ![complete2.gif](../includes/complete2.gif)
+> ![complete2.gif](../../includes/images/complete2.gif)
 >
 > Use of the tab key can help navigate the filesystem, spellcheck your
 > commands and save you time typing.

docs/Getting_Started/Getting_Help/System_status.md

@@ -33,7 +33,7 @@ use the link included at the bottom of the notification email message
 See also our support article [Managing NeSI notification
 preferences](https://support.nesi.org.nz/hc/en-gb/articles/4563294188687)
 
-![mceclip0.png](../includes/mceclip0_0.png)
+![mceclip0.png](../../includes/images/mceclip0_0.png)
 
 ## status.nesi.org.nz
 
@@ -42,4 +42,4 @@ NeSI does publish service incidents and scheduled maintenance via
 Interested parties are invited to subscribe to updates (via SMS or
 email).
 
-<img src="../includes/mceclip0_1.png" width="880" height="772" />
+<img src="../../includes/images/mceclip0_1.png" width="880" height="772" />

docs/Getting_Started/Next_Steps/Finding_Job_Efficiency.md

@@ -155,7 +155,7 @@ parent process).
 
 Processes in green can be ignored
 
-<img src="../includes/how_to_read_htop.png" alt="how_to_read_htop.png" width="929" height="252" />
+<img src="../../includes/images/how_to_read_htop.png" alt="how_to_read_htop.png" width="929" height="252" />
 
 **RES** - Current memory being used (same thing as 'RSS' from sacct)
 
@@ -191,12 +191,12 @@ more details.
 
 ## Example
 
-![qdyn\_eff.png](../includes/qdyn_eff.png)
+![qdyn\_eff.png](../../includes/images/qdyn_eff.png)
 
 From the above plot of CPU efficiency, you might decide a 5% reduction
 of CPU efficiency is acceptable and scale your job up to 18 CPU cores . 
 
-![qdyn\_walltime.png](../includes/qdyn_walltime.png)
+![qdyn\_walltime.png](../../includes/images/qdyn_walltime.png)
 
 However, when looking at a plot of walltime it becomes apparent that
 performance gains per CPU added drop significantly after 4 CPUs, and in

docs/Getting_Started/Next_Steps/MPI_Scaling_Example.md

@@ -202,7 +202,7 @@ our script with 2, 3, 4, 5 and 6 physical CPUs and plot the results:
     6054939.ext+   extern          00:06:57    00:00.006    12      44K  COMPLETED 
     6054939.0      python          00:06:51     01:18:37     6  174028K  COMPLETED 
 
-![MPIscalingMem.png](../includes/MPIscalingMem_0.png)
+![MPIscalingMem.png](../../includes/images/MPIscalingMem_0.png)
 
 First, looking at the plot of memory usage per task vs CPUs it would at
 appears that memory usage per task remains constant, regardless of how
@@ -284,7 +284,7 @@ increasing as we add more seeds, but the maximum memory per CPU doesn't
 seem to change much. Let's try plotting this data to help us better
 understand what is happening:
 
-![MPIseedsvtime.png](../includes/MPIseedsvtime_0.png)
+![MPIseedsvtime.png](../../includes/images/MPIseedsvtime_0.png)
 
 This confirms our assumption of wall-time scaling linearly with number
 of iterations. Since our 5,000 seed job to 7 minutes and 41 seconds we