diff --git a/.gitignore b/.gitignore
index 736d515de..1964e6457 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,5 @@
from_zendesk/cache/**
from_zendesk/import_worktree/**
public/*
+production/*
**.pyc
diff --git a/SPECIFICATION.md b/SPECIFICATION.md
index a67e52850..e91b65bb4 100644
--- a/SPECIFICATION.md
+++ b/SPECIFICATION.md
@@ -65,7 +65,6 @@ 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.
@@ -73,14 +72,27 @@ 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
diff --git "a/docs/General/Announcements/M\304\201ui_upgrade_is_complete.md" "b/docs/General/Announcements/M\304\201ui_upgrade_is_complete.md"
index ac532d0ca..ceea2acee 100644
--- "a/docs/General/Announcements/M\304\201ui_upgrade_is_complete.md"
+++ "b/docs/General/Announcements/M\304\201ui_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.
diff --git a/docs/General/FAQs/How_to_replace_my_2FA_token.md b/docs/General/FAQs/How_to_replace_my_2FA_token.md
index 227399c7f..3ef4abb5b 100644
--- a/docs/General/FAQs/How_to_replace_my_2FA_token.md
+++ b/docs/General/FAQs/How_to_replace_my_2FA_token.md
@@ -23,7 +23,7 @@ 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.
-
+
## Delete the Two-Factor token
@@ -31,15 +31,15 @@ Select the option 'Manage Two-Factor token' under 'Account'.
You should see the confirmation of the previous token.
-
+
After 'Delete Token' has been selected:
-
+
You will also receive an email confirmation:
-
+
## Related content
diff --git a/docs/General/FAQs/How_to_submit_feedback_or_a_new_idea_using_a_product_portal?.md b/docs/General/FAQs/How_to_submit_feedback_or_a_new_idea_using_a_product_portal?.md
index 0999a4336..5f0e2ae21 100644
--- a/docs/General/FAQs/How_to_submit_feedback_or_a_new_idea_using_a_product_portal?.md
+++ b/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.
-
+
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.
-
+
### What happens to the feedback?
diff --git a/docs/General/FAQs/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science?.md b/docs/General/FAQs/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science?.md
index 344e18049..6e006dd93 100644
--- a/docs/General/FAQs/What_software_environments_on_NeSI_are_optimised_for_Machine_Learning_and_data_science?.md
+++ b/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".
-
+
For more information on NeSI's model and approach to application
support, refer to our [policy for the management of scientific
diff --git a/docs/General/FAQs/When_does_CPU_efficiency_matter_more_than_speed?.md b/docs/General/FAQs/When_does_CPU_efficiency_matter_more_than_speed?.md
index a79955612..2e19bf9ff 100644
--- a/docs/General/FAQs/When_does_CPU_efficiency_matter_more_than_speed?.md
+++ b/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.
+parallel 4cpu tasks CPUs one after another. *](../../includes/images/4tasks.png)
diff --git a/docs/General/FAQs/Why_am_I_seeing_'Account_is_not_ready'?.md b/docs/General/FAQs/Why_am_I_seeing_'Account_is_not_ready'?.md
index 38b347f57..11e93a2e8 100644
--- a/docs/General/FAQs/Why_am_I_seeing_'Account_is_not_ready'?.md
+++ b/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.
-
+
diff --git a/docs/General/NeSI_Knowledge_Base/Formatting.md b/docs/General/NeSI_Knowledge_Base/Formatting.md
index 83c271d71..11bd57454 100644
--- a/docs/General/NeSI_Knowledge_Base/Formatting.md
+++ b/docs/General/NeSI_Knowledge_Base/Formatting.md
@@ -65,7 +65,7 @@ This is a [Link](https://www.w3schools.com/html/html_links.asp)
Image
-
+
------------------------------------------------------------------------
diff --git a/docs/General/NeSI_Policies/Account_Requests_for_non-Tuakiri_Members.md b/docs/General/NeSI_Policies/Account_Requests_for_non-Tuakiri_Members.md
index 558a2eb8b..3b93d9c18 100644
--- a/docs/General/NeSI_Policies/Account_Requests_for_non-Tuakiri_Members.md
+++ b/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).
-
+
> ### Warning
>
diff --git a/docs/General/NeSI_Policies/NeSI_Application_Support_Model.md b/docs/General/NeSI_Policies/NeSI_Application_Support_Model.md
index 84fe857dd..5ff1014a7 100644
--- a/docs/General/NeSI_Policies/NeSI_Application_Support_Model.md
+++ b/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:
diff --git a/docs/Getting_Started/Accessing_the_HPCs/Choosing_and_Configuring_Software_for_Connecting_to_the_Clusters.md b/docs/Getting_Started/Accessing_the_HPCs/Choosing_and_Configuring_Software_for_Connecting_to_the_Clusters.md
index ced6d5e38..ab948c227 100644
--- a/docs/Getting_Started/Accessing_the_HPCs/Choosing_and_Configuring_Software_for_Connecting_to_the_Clusters.md
+++ b/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.
diff --git a/docs/Getting_Started/Accessing_the_HPCs/Port_Forwarding.md b/docs/Getting_Started/Accessing_the_HPCs/Port_Forwarding.md
index 2e21916f2..3679adb43 100644
--- a/docs/Getting_Started/Accessing_the_HPCs/Port_Forwarding.md
+++ b/docs/Getting_Started/Accessing_the_HPCs/Port_Forwarding.md
@@ -128,12 +128,12 @@ 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.
-
+
You can also set up port forwarding using the MobaXterm tunnelling
interface.
-
+
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
@@ -141,7 +141,7 @@ first two examples allows us to avoid).
The two tunnels should look like this.
-
+
■ local port
■ remote port
diff --git a/docs/Getting_Started/Accessing_the_HPCs/Setting_Up_Two-Factor_Authentication.md b/docs/Getting_Started/Accessing_the_HPCs/Setting_Up_Two-Factor_Authentication.md
index 4074b7c9d..f5876077f 100644
--- a/docs/Getting_Started/Accessing_the_HPCs/Setting_Up_Two-Factor_Authentication.md
+++ b/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**
- 
+ 
3. Click the "**Setup Two-Factor Authentication device**" link.
- 
+ 
4. After clicking on "Continue" you will retrieve the QR code.
5. Open your Authy or Google Authenticator app and click on the add
diff --git a/docs/Getting_Started/Accessing_the_HPCs/Setting_Up_and_Resetting_Your_Password.md b/docs/Getting_Started/Accessing_the_HPCs/Setting_Up_and_Resetting_Your_Password.md
index a8bf3f5ff..e6c590446 100644
--- a/docs/Getting_Started/Accessing_the_HPCs/Setting_Up_and_Resetting_Your_Password.md
+++ b/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.
- 
+ 
**
3. Enter and verify your new password, making sure it follows the
[password
policy](https://support.nesi.org.nz/hc/en-gb/articles/360000336015).
- #### 
+ #### 
4. If the password set was successful, following confirmation label
will appear on the same page within few seconds
- 
+ 
5. Followed by an email confirmation similar to below
-
+
@@ -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. - 
+ 1. - 
5. Followed by an email confirmation similar to below
-
+
diff --git a/docs/Getting_Started/Accounts,_Projects_and_Allocations/Quarterly_allocation_periods.md b/docs/Getting_Started/Accounts,_Projects_and_Allocations/Quarterly_allocation_periods.md
index bc0e047eb..b2fb37a7b 100644
--- a/docs/Getting_Started/Accounts,_Projects_and_Allocations/Quarterly_allocation_periods.md
+++ b/docs/Getting_Started/Accounts,_Projects_and_Allocations/Quarterly_allocation_periods.md
@@ -26,7 +26,7 @@ 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:
-
+
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
@@ -34,7 +34,7 @@ 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).
-
+
## Existing allocations
diff --git a/docs/Getting_Started/Accounts,_Projects_and_Allocations/What_is_an_allocation?.md b/docs/Getting_Started/Accounts,_Projects_and_Allocations/What_is_an_allocation?.md
index 3310a1d81..89362311a 100644
--- a/docs/Getting_Started/Accounts,_Projects_and_Allocations/What_is_an_allocation?.md
+++ b/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.
diff --git a/docs/Getting_Started/Cheat_Sheets/Git:_Reference_Sheet.md b/docs/Getting_Started/Cheat_Sheets/Git:_Reference_Sheet.md
index 194e9c005..11111f864 100644
--- a/docs/Getting_Started/Cheat_Sheets/Git:_Reference_Sheet.md
+++ b/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`.
-
+
## Authentication
@@ -59,21 +59,21 @@ documentation](https://docs.github.com/en/authentication/connecting-to-github-wi
page, click your profile photo click **Settings**.
+ bar](../../includes/images/userbar-account-settings.png)
- In the "Access" section of the sidebar, click **SSH and GPG keys**.
- Click **New SSH key** or **Add SSH key**.
+ button](../../includes/images/ssh-add-ssh-key-with-auth.png)
- In the "Title" field, put "Mahuika" or "NeSI".
- Paste your key into the "Key" field.
+ field](../../includes/images/ssh-key-paste-with-type.png)
- Click **Add SSH key**.
diff --git a/docs/Getting_Started/Cheat_Sheets/Unix_Shell:_Reference_Sheet.md b/docs/Getting_Started/Cheat_Sheets/Unix_Shell:_Reference_Sheet.md
index b5533a08c..143e34ffd 100644
--- a/docs/Getting_Started/Cheat_Sheets/Unix_Shell:_Reference_Sheet.md
+++ b/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.
>
-> 
+> 
>
> If there are more than one possible completions, pressing tab again
> will show all those options.
>
-> 
+> 
>
> Use of the tab key can help navigate the filesystem, spellcheck your
> commands and save you time typing.
diff --git a/docs/Getting_Started/Getting_Help/System_status.md b/docs/Getting_Started/Getting_Help/System_status.md
index 6caa0d4a2..20724d357 100644
--- a/docs/Getting_Started/Getting_Help/System_status.md
+++ b/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)
-
+
## 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).
-
+
diff --git a/docs/Getting_Started/Next_Steps/Finding_Job_Efficiency.md b/docs/Getting_Started/Next_Steps/Finding_Job_Efficiency.md
index 46c2f603a..e2064dcb6 100644
--- a/docs/Getting_Started/Next_Steps/Finding_Job_Efficiency.md
+++ b/docs/Getting_Started/Next_Steps/Finding_Job_Efficiency.md
@@ -155,7 +155,7 @@ parent process).
Processes in green can be ignored
-
+
**RES** - Current memory being used (same thing as 'RSS' from sacct)
@@ -191,12 +191,12 @@ more details.
## Example
-
+
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 .
-
+
However, when looking at a plot of walltime it becomes apparent that
performance gains per CPU added drop significantly after 4 CPUs, and in
diff --git a/docs/Getting_Started/Next_Steps/MPI_Scaling_Example.md b/docs/Getting_Started/Next_Steps/MPI_Scaling_Example.md
index 1e6accba3..2237943dd 100644
--- a/docs/Getting_Started/Next_Steps/MPI_Scaling_Example.md
+++ b/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
-
+
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:
-
+
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
diff --git a/docs/Getting_Started/Next_Steps/MPI_Scaling_Example_-_Duplicate.md b/docs/Getting_Started/Next_Steps/MPI_Scaling_Example_-_Duplicate.md
index f911607c7..8d78e9bcd 100644
--- a/docs/Getting_Started/Next_Steps/MPI_Scaling_Example_-_Duplicate.md
+++ b/docs/Getting_Started/Next_Steps/MPI_Scaling_Example_-_Duplicate.md
@@ -204,7 +204,7 @@ 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
-
+
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
@@ -286,7 +286,7 @@ 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:
-
+
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
diff --git a/docs/Getting_Started/Next_Steps/Moving_files_to_and_from_the_cluster.md b/docs/Getting_Started/Next_Steps/Moving_files_to_and_from_the_cluster.md
index f9f35fda0..15113a4ba 100644
--- a/docs/Getting_Started/Next_Steps/Moving_files_to_and_from_the_cluster.md
+++ b/docs/Getting_Started/Next_Steps/Moving_files_to_and_from_the_cluster.md
@@ -76,7 +76,7 @@ This does not work for File Explorer (Windows default)
This does not work for Finder (Mac default)
-
+
If your default file manager does not support mounting over sftp, see
our documentation
@@ -89,7 +89,7 @@ window) opens up a graphical user interface that can be used for basic
file operations. You can drag and drop files in the file explorer or use
the up and down arrows on the toolbar to upload and download files.
-
+
You may also transfer files as described under 'Standard Terminal'
(provided
diff --git a/docs/Getting_Started/Next_Steps/Multithreading_Scaling_Example.md b/docs/Getting_Started/Next_Steps/Multithreading_Scaling_Example.md
index a11d1a71f..b5a99ef82 100644
--- a/docs/Getting_Started/Next_Steps/Multithreading_Scaling_Example.md
+++ b/docs/Getting_Started/Next_Steps/Multithreading_Scaling_Example.md
@@ -205,7 +205,7 @@ significant drop in marginal speed-up after eight CPU cores.
-
+
Looking at our jobs' memory use, we can see that as we increase the
number of CPUs taken by a job, the job's memory requirements increase
diff --git a/docs/Getting_Started/Next_Steps/Parallel_Execution.md b/docs/Getting_Started/Next_Steps/Parallel_Execution.md
index a117d8019..152aaeed7 100644
--- a/docs/Getting_Started/Next_Steps/Parallel_Execution.md
+++ b/docs/Getting_Started/Next_Steps/Parallel_Execution.md
@@ -42,13 +42,13 @@ single thread of a process forks into a number of parallel threads,
generally *via* a library such as OpenMP (Open MultiProcessing), TBB
(Threading Building Blocks), or pthread (POSIX threads).
-
+
*Fig. 1: In a serial operation, tasks complete
one after another.*
####
-
*
+
*
Fig. 2: Multi-threading involves dividing the process into multiple
'threads' which can be run across multiple cores.*
diff --git a/docs/Getting_Started/my.nesi.org.nz/Managing_NeSI_notifications.md b/docs/Getting_Started/my.nesi.org.nz/Managing_NeSI_notifications.md
index e72448592..bbb62bdc0 100644
--- a/docs/Getting_Started/my.nesi.org.nz/Managing_NeSI_notifications.md
+++ b/docs/Getting_Started/my.nesi.org.nz/Managing_NeSI_notifications.md
@@ -14,4 +14,4 @@ zendesk_section_id: 360001059296
-
+
diff --git a/docs/Getting_Started/my.nesi.org.nz/Managing_notification_preferences.md b/docs/Getting_Started/my.nesi.org.nz/Managing_notification_preferences.md
index 212347e39..5ef86bc5f 100644
--- a/docs/Getting_Started/my.nesi.org.nz/Managing_notification_preferences.md
+++ b/docs/Getting_Started/my.nesi.org.nz/Managing_notification_preferences.md
@@ -30,7 +30,7 @@ Use the 'Manage' button provided to open the externally hosted
preferences or the checkboxes for the NeSI Project-related
notifications.
-
+
diff --git a/docs/Getting_Started/my.nesi.org.nz/Navigating_the_my.nesi.org.nz_web_interface.md b/docs/Getting_Started/my.nesi.org.nz/Navigating_the_my.nesi.org.nz_web_interface.md
index d5dfc1fb6..14653def5 100644
--- a/docs/Getting_Started/my.nesi.org.nz/Navigating_the_my.nesi.org.nz_web_interface.md
+++ b/docs/Getting_Started/my.nesi.org.nz/Navigating_the_my.nesi.org.nz_web_interface.md
@@ -10,7 +10,7 @@ zendesk_article_id: 360003592875
zendesk_section_id: 360001059296
---
-
+
## Main navigation
diff --git a/docs/Getting_Started/my.nesi.org.nz/Requesting_to_renew_an_allocation_via_my.nesi.org.nz.md b/docs/Getting_Started/my.nesi.org.nz/Requesting_to_renew_an_allocation_via_my.nesi.org.nz.md
index dcd51ba06..c82617830 100644
--- a/docs/Getting_Started/my.nesi.org.nz/Requesting_to_renew_an_allocation_via_my.nesi.org.nz.md
+++ b/docs/Getting_Started/my.nesi.org.nz/Requesting_to_renew_an_allocation_via_my.nesi.org.nz.md
@@ -17,14 +17,14 @@ zendesk_section_id: 360001059296
from the list.
2. From the green (middle) panel click the links menu and select "More
Resource Details"
- 
+ 
3. Click the Plus button icon 'action' next to the compute allocation
line item
- 
+ 
4. Verify the preset values and add a comment in case you update
some.
Finally, click 'Submit'
- 
+ 
### Can I request any allocation size?
diff --git a/docs/Getting_Started/my.nesi.org.nz/The_NeSI_Project_Request_Form.md b/docs/Getting_Started/my.nesi.org.nz/The_NeSI_Project_Request_Form.md
index 3618aeefa..3c56245ce 100644
--- a/docs/Getting_Started/my.nesi.org.nz/The_NeSI_Project_Request_Form.md
+++ b/docs/Getting_Started/my.nesi.org.nz/The_NeSI_Project_Request_Form.md
@@ -24,7 +24,7 @@ below.
[https://my.nesi.org.nz](https://my.nesi.org.nz/projects/apply) and
login. Select "Apply for Access" from the sidebar navigation on the
left.
- 
+ 
2. Choose from the following items:
- **If you are returning to continue work on a draft request** you
started earlier, choose the link based on the date/time or title
diff --git a/docs/NeSI_Service_Subscriptions/Overview/What_is_a_Subscription?.md b/docs/NeSI_Service_Subscriptions/Overview/What_is_a_Subscription?.md
index bd33ea323..f83adaa8c 100644
--- a/docs/NeSI_Service_Subscriptions/Overview/What_is_a_Subscription?.md
+++ b/docs/NeSI_Service_Subscriptions/Overview/What_is_a_Subscription?.md
@@ -17,7 +17,7 @@ Subscribing to NeSI's services provides you with:
- Managed entitlements on NeSI's HPC platform for your research
- projects and programmes. This includes access to:
+ projects and programmes. This ../../../ access to:
- high-capacity CPUs, GPUs and high memory nodes
diff --git a/docs/NeSI_Service_Subscriptions/Service_Governance/Service_Governance_contact.md b/docs/NeSI_Service_Subscriptions/Service_Governance/Service_Governance_contact.md
index 71a8095d8..d3df83ee8 100644
--- a/docs/NeSI_Service_Subscriptions/Service_Governance/Service_Governance_contact.md
+++ b/docs/NeSI_Service_Subscriptions/Service_Governance/Service_Governance_contact.md
@@ -12,7 +12,7 @@ zendesk_section_id: 7348925662223
As part of our service agreements, we request you name a Service
Governance Contact on behalf of your institution. The role of this
-person includes:
+person ../../../:
- acting as a primary liaison / contact person on behalf of your
institution for anything related to the service Subscription
diff --git a/docs/Scientific_Computing/HPC_Software_Environment/Compiling_software_on_Mahuika.md b/docs/Scientific_Computing/HPC_Software_Environment/Compiling_software_on_Mahuika.md
index 7fc6dbfbd..35d2aa64c 100644
--- a/docs/Scientific_Computing/HPC_Software_Environment/Compiling_software_on_Mahuika.md
+++ b/docs/Scientific_Computing/HPC_Software_Environment/Compiling_software_on_Mahuika.md
@@ -317,7 +317,7 @@ error (with the exception of character case in Fortran source code).
# Cray Programming Environment
-The Cray Programming Environment includes the Cray compiler, various
+The Cray Programming Environment ../../../ the Cray compiler, various
libraries and tools. These work nicely together and provide certain
user-friendly features by using compiler wrappers. This works very
similar as the Cray XC environment, provided on Māui, and is described
diff --git a/docs/Scientific_Computing/HPC_Software_Environment/Connecting_to_a_Virtual_Desktop_(SSH).md b/docs/Scientific_Computing/HPC_Software_Environment/Connecting_to_a_Virtual_Desktop_(SSH).md
index 4d073c999..44845b840 100644
--- a/docs/Scientific_Computing/HPC_Software_Environment/Connecting_to_a_Virtual_Desktop_(SSH).md
+++ b/docs/Scientific_Computing/HPC_Software_Environment/Connecting_to_a_Virtual_Desktop_(SSH).md
@@ -89,7 +89,7 @@ that command.
Recommend setting scaling to 'remote'
-
+
# Examples
@@ -121,7 +121,7 @@ forwarded port (`--help` for more options).
Then in a web browser navigate to your forwarded address. e.g.
-
+
## On a compute node
diff --git a/docs/Scientific_Computing/HPC_Software_Environment/NICE_DCV_Setup.md b/docs/Scientific_Computing/HPC_Software_Environment/NICE_DCV_Setup.md
index f48c4cd40..5efbd4356 100644
--- a/docs/Scientific_Computing/HPC_Software_Environment/NICE_DCV_Setup.md
+++ b/docs/Scientific_Computing/HPC_Software_Environment/NICE_DCV_Setup.md
@@ -151,7 +151,7 @@ connections to look like this:
### To connect to Māui
-
+
When setting up and using the connections, note the following:
### To connect to Mahuika
@@ -213,7 +213,7 @@ successful login with the client or browser. You can then use the
application launcher to start an application. You can also launch the
terminal application by right-clicking on the desktop and selecting
"Konsole". This will give you access to the NeSI software stack that
-includes various [visualisation software
+../../../ various [visualisation software
solutions](https://support.nesi.org.nz/knowledge/articles/360000700295/en-gb?brand_id=30406&return_to=%2Fhc%2Fen-gb%2Farticles%2F360000700295).
# Disconnecting and Stopping a Session
diff --git a/docs/Scientific_Computing/HPC_Software_Environment/Scikit-learn_(linear_regression).md b/docs/Scientific_Computing/HPC_Software_Environment/Scikit-learn_(linear_regression).md
index 4f0f5a082..7609b5208 100644
--- a/docs/Scientific_Computing/HPC_Software_Environment/Scikit-learn_(linear_regression).md
+++ b/docs/Scientific_Computing/HPC_Software_Environment/Scikit-learn_(linear_regression).md
@@ -32,7 +32,7 @@ test/, respectively. An example of image is test/img49.jpg.
display test/img49.jpg
+class="s1">
which shows five, partially overlapping dots. Note that
along with the images, a comma separated values (csv) file (e.g.
@@ -88,7 +88,7 @@ same directory as classify.py. This file contains the predictions for
the first 50 test images, which will vary for each training but the
result will look like:
-(The
+(The
purple images have no dots.) With each image the number of dots is
displayed as well as the value inferred by the model in parentheses. The
inferred values are to be rounded to the nearest integer. Plot titles in
diff --git a/docs/Scientific_Computing/HPC_Software_Environment/Thread_Placement_and_Thread_Affinity.md b/docs/Scientific_Computing/HPC_Software_Environment/Thread_Placement_and_Thread_Affinity.md
index 6992d1eb8..29256645c 100644
--- a/docs/Scientific_Computing/HPC_Software_Environment/Thread_Placement_and_Thread_Affinity.md
+++ b/docs/Scientific_Computing/HPC_Software_Environment/Thread_Placement_and_Thread_Affinity.md
@@ -42,7 +42,7 @@ cores, and each physical core is split into two logical cores using a
technology called
[Hyperthreading](https://support.nesi.org.nz/hc/en-gb/articles/360000568236)).
-A processor also includes caches - a
+A processor also ../../../ caches - a
[cache](https://en.wikipedia.org/wiki/CPU_cache) is very fast memory
that stores data that will be needed for the next computations, which
avoids that the processor has to wait for data coming from the much
@@ -54,7 +54,7 @@ cores (our current HPCs have 18 to 20 cores). Each core can also be
further divided into two logical cores (or hyperthreads, as mentioned
before).
-
+
It is very important to note the following:
diff --git a/docs/Scientific_Computing/Interactive_computing_using_Jupyter/Jupyter_on_NeSI.md b/docs/Scientific_Computing/Interactive_computing_using_Jupyter/Jupyter_on_NeSI.md
index f85aa1047..15dad0613 100644
--- a/docs/Scientific_Computing/Interactive_computing_using_Jupyter/Jupyter_on_NeSI.md
+++ b/docs/Scientific_Computing/Interactive_computing_using_Jupyter/Jupyter_on_NeSI.md
@@ -128,8 +128,8 @@ client. Some things to note are:
To end a JupyterLab session, please select "Hub Control Panel" under the
File menu then "Stop My Server". Finally, click on "Log Out".
-
-
+
+
If you click "Log Out" without stopping your server, the server will
continue to run until the Slurm job reaches its maximum wall time.
diff --git a/docs/Scientific_Computing/Interactive_computing_using_Jupyter/MATLAB_via_Jupyter_on_NeSI.md b/docs/Scientific_Computing/Interactive_computing_using_Jupyter/MATLAB_via_Jupyter_on_NeSI.md
index 9b9b561a7..29df00604 100644
--- a/docs/Scientific_Computing/Interactive_computing_using_Jupyter/MATLAB_via_Jupyter_on_NeSI.md
+++ b/docs/Scientific_Computing/Interactive_computing_using_Jupyter/MATLAB_via_Jupyter_on_NeSI.md
@@ -28,18 +28,18 @@ NeSI](https://support.nesi.org.nz/hc/en-gb/articles/360001555615).
In the JupyterLab interface, MATLAB can be started using the
corresponding entry in the launcher.
-# 
+# 
Clicking on this entry will open a separate tab in your web browser,
where you will see the following status information page.
-# 
+# 
MATLAB may take a few minutes to load, once it does you will be put
straight into the MATLAB environment.
You can open the status page at any time by clicking the
-[
](https://github.com/mathworks/jupyter-matlab-proxy/raw/main/img/tools_icon.png)
+[
](https://github.com/mathworks/jupyter-matlab-proxy/raw/main/img/tools_icon.png)
button.
> ### Note
@@ -55,13 +55,13 @@ the info panel.
If you do not wish to use a network license you can click the 'Unset
License Server Address' button.
-# 
+# 
If you have no licence address set you can instead authenticate using a
MathWorks email address, provided you have a valid license associated to
your account.
-# 
+# 
# Troubleshooting
diff --git a/docs/Scientific_Computing/Interactive_computing_using_Jupyter/RStudio_via_Jupyter_on_NeSI.md b/docs/Scientific_Computing/Interactive_computing_using_Jupyter/RStudio_via_Jupyter_on_NeSI.md
index ca6865a88..787f890a1 100644
--- a/docs/Scientific_Computing/Interactive_computing_using_Jupyter/RStudio_via_Jupyter_on_NeSI.md
+++ b/docs/Scientific_Computing/Interactive_computing_using_Jupyter/RStudio_via_Jupyter_on_NeSI.md
@@ -26,7 +26,7 @@ NeSI](https://support.nesi.org.nz/hc/en-gb/articles/360001555615).
In the JupyterLab interface, RStudio can be started using the
corresponding entry in the launcher.
-
+
Clicking on this entry will open a separate tab in your web browser,
where RStudio will be accessible.
@@ -122,7 +122,7 @@ a failure by JupyterLab. Please try to start RStudio again from the
launcher. If the problem persists, contact our support team at
.
-
+
If you have disabled javascript in your web browser, you will need to
enter your password manually in the RStudio login screen. To retrieve
diff --git a/docs/Scientific_Computing/Manuals_and_User_Guides_/Manuals.md b/docs/Scientific_Computing/Manuals_and_User_Guides_/Manuals.md
index d7dba7870..1ef18c5bb 100644
--- a/docs/Scientific_Computing/Manuals_and_User_Guides_/Manuals.md
+++ b/docs/Scientific_Computing/Manuals_and_User_Guides_/Manuals.md
@@ -31,7 +31,7 @@ guides.
Guides](https://software.intel.com/en-us/documentation/view-all?search_api_views_fulltext=¤t_page=0&value=78151,83039;20813,80605,79893,20812,20902;20816;20802;20804)
- [Allinea
Forge](http://content.allinea.com/downloads/userguide-forge.pdf)
- (includes DDT and MAP, now called Arm Forge)
+ (../../../ DDT and MAP, now called Arm Forge)
- [Nvidia Documentation](https://docs.nvidia.com/cuda/)
- [cuda-gdb](https://docs.nvidia.com/cuda/cuda-gdb/) debugger
- [cuda-memcheck](https://docs.nvidia.com/cuda/cuda-memcheck/) memory
diff --git a/docs/Scientific_Computing/Manuals_and_User_Guides_/XC50_Aries_Network_Architecture.md b/docs/Scientific_Computing/Manuals_and_User_Guides_/XC50_Aries_Network_Architecture.md
index 10a644480..e57564a91 100644
--- a/docs/Scientific_Computing/Manuals_and_User_Guides_/XC50_Aries_Network_Architecture.md
+++ b/docs/Scientific_Computing/Manuals_and_User_Guides_/XC50_Aries_Network_Architecture.md
@@ -16,7 +16,7 @@ the backplane. On Māui, this implies each chassis contains 64 nodes, or
2,560 Skylake cores. There are 3 chassis in an XC50 cabinet, and two
XC50 cabinets are an Electrical "group". Māui has 1.5 groups.
-
+
The performance characteristics are:
diff --git a/docs/Scientific_Computing/Profiling_and_Debugging/Debugging.md b/docs/Scientific_Computing/Profiling_and_Debugging/Debugging.md
index 335173d24..ef2cbaf66 100644
--- a/docs/Scientific_Computing/Profiling_and_Debugging/Debugging.md
+++ b/docs/Scientific_Computing/Profiling_and_Debugging/Debugging.md
@@ -85,7 +85,7 @@ information are provided into the application stdout and a HTML file is
created. Thus this could also be a handy alternative for print
statements without touching the code.
-[](https://mand35.github.io/NeSI_docu_ext/ddt_sample.html)
+[](https://mand35.github.io/NeSI_docu_ext/ddt_sample.html)
[See full example page
here.](https://mand35.github.io/NeSI_docu_ext/ddt_sample.html)
@@ -110,7 +110,7 @@ launching an application with DDT (RUN).
In the RUN menu the different settings for the executable need to be
specified.
-
+
Beside Application location and name, we need to specify arguments,
working directory, MPI and OpenMP settings. If we have no interactive
@@ -124,7 +124,7 @@ Variables section you can load necessary modules.
After submitting the task, DDT launches the application (wait for the
workload manager if necessary) and opens the following window.
-
+
In the top part the processes and threads can be selected. The
application is paused at the initialization phase, giving the user the
diff --git a/docs/Scientific_Computing/Profiling_and_Debugging/Profiler:_ARM_MAP.md b/docs/Scientific_Computing/Profiling_and_Debugging/Profiler:_ARM_MAP.md
index 8d7800364..3f00f6601 100644
--- a/docs/Scientific_Computing/Profiling_and_Debugging/Profiler:_ARM_MAP.md
+++ b/docs/Scientific_Computing/Profiling_and_Debugging/Profiler:_ARM_MAP.md
@@ -96,11 +96,11 @@ The GUI can be started after loading `module load forge` and launching
map
[](https://nesi.github.io/perf-training/python-scatter/images/ARM_MAP_main.png)
+main](../../includes/images/ARM_MAP_main.png)](https://nesi.github.io/perf-training/python-scatter/images/ARM_MAP_main.png)
Click on “PROFILE”.
-
+
In the profile menu we need to specify the *executable/application* (in
this case `python`), the arguments (here `scatter.py` and any additional
@@ -121,7 +121,7 @@ profile information.
By default the profile window is divided into the following three main
sections (click on picture to enlarge).
-[](https://nesi.github.io/perf-training/python-scatter/images/ARM_MAP_scatter_mpi.png)
+[](https://nesi.github.io/perf-training/python-scatter/images/ARM_MAP_scatter_mpi.png)
On top, various metrics can be selected in the “Metrics” menu. In the
middle part, a source code navigator connects line by line source code
@@ -145,7 +145,7 @@ using the *Metrics* Menu*.*
As an example, “CPU instructions” presents the usage of different
instruction sets during the program run time.
-[](https://nesi.github.io/perf-training/python-scatter/images/ARM_MAP_scatter_mpi_CPU.png)
+[](https://nesi.github.io/perf-training/python-scatter/images/ARM_MAP_scatter_mpi_CPU.png)
The lower part can also be used to check the *application output* or
show statistics on basis of *files* or *functions*.
diff --git a/docs/Scientific_Computing/Release_Notes_jupyter.nesi.org.nz/jupyter.nesi.org.nz_release_notes_16-09-2021.md b/docs/Scientific_Computing/Release_Notes_jupyter.nesi.org.nz/jupyter.nesi.org.nz_release_notes_16-09-2021.md
index fa113e22d..8837ca6d4 100644
--- a/docs/Scientific_Computing/Release_Notes_jupyter.nesi.org.nz/jupyter.nesi.org.nz_release_notes_16-09-2021.md
+++ b/docs/Scientific_Computing/Release_Notes_jupyter.nesi.org.nz/jupyter.nesi.org.nz_release_notes_16-09-2021.md
@@ -20,7 +20,7 @@ zendesk_section_id: 360001150156
fixes](https://jupyterlab.readthedocs.io/en/stable/getting_started/changelog.html#id12)
- Updated to JupyterHub 1.4.2
- Rendering time remaining, CPU and Memory usage in the top menu bar
- 
+ 
- Confirmed JupyterLab extension for version control using Git
working
See
diff --git "a/docs/Scientific_Computing/Running_Jobs_on_M\304\201ui_and_Mahuika/Mahuika_Extension.md" "b/docs/Scientific_Computing/Running_Jobs_on_M\304\201ui_and_Mahuika/Mahuika_Extension.md"
index 3bdcbf916..ef66cdf96 100644
--- "a/docs/Scientific_Computing/Running_Jobs_on_M\304\201ui_and_Mahuika/Mahuika_Extension.md"
+++ "b/docs/Scientific_Computing/Running_Jobs_on_M\304\201ui_and_Mahuika/Mahuika_Extension.md"
@@ -27,7 +27,7 @@ requested by a job.
AMD Milan CPU overview, each node has two of these:
-
+
**AMD-EPYC-Milan-architecture**
from
diff --git a/docs/Scientific_Computing/Supported_Applications.md b/docs/Scientific_Computing/Supported_Applications.md
new file mode 100644
index 000000000..8b1378917
--- /dev/null
+++ b/docs/Scientific_Computing/Supported_Applications.md
@@ -0,0 +1 @@
+
diff --git a/docs/Scientific_Computing/Supported_Applications/ABAQUS.md b/docs/Scientific_Computing/Supported_Applications/ABAQUS.md
index 46ca98baf..2593d3049 100644
--- a/docs/Scientific_Computing/Supported_Applications/ABAQUS.md
+++ b/docs/Scientific_Computing/Supported_Applications/ABAQUS.md
@@ -132,7 +132,7 @@ to a job.
-
+
diff --git a/docs/Scientific_Computing/Supported_Applications/BRAKER.md b/docs/Scientific_Computing/Supported_Applications/BRAKER.md
index c6f2e73e6..8ab712c72 100644
--- a/docs/Scientific_Computing/Supported_Applications/BRAKER.md
+++ b/docs/Scientific_Computing/Supported_Applications/BRAKER.md
@@ -72,7 +72,7 @@ Artistic License
>
>
>
-> - 
+> - 
> - Downloaded filename will be in the format of **gm\_key\_64.gz. **
> - Decompress this file with `gunzip gm_key_64.gz` and move it to
> home directory as a **hidden** file under the filename `.gm_key`
diff --git a/docs/Scientific_Computing/Supported_Applications/Cylc.md b/docs/Scientific_Computing/Supported_Applications/Cylc.md
index c66899d24..61f666f70 100644
--- a/docs/Scientific_Computing/Supported_Applications/Cylc.md
+++ b/docs/Scientific_Computing/Supported_Applications/Cylc.md
@@ -160,7 +160,7 @@ of the png file. To visualise the file you can type
Here, we see that our workflow "simple" has a "taskC", which waits for
"taskA" and "taskB" to complete,
-
+
The "1" indicates that this workflow graph is executed only once.
diff --git a/docs/Scientific_Computing/Supported_Applications/Downloading_CMIP6_data_using_globus.md b/docs/Scientific_Computing/Supported_Applications/Downloading_CMIP6_data_using_globus.md
index fc068c871..2375d24d9 100644
--- a/docs/Scientific_Computing/Supported_Applications/Downloading_CMIP6_data_using_globus.md
+++ b/docs/Scientific_Computing/Supported_Applications/Downloading_CMIP6_data_using_globus.md
@@ -98,17 +98,17 @@ class="s1">https://auth.globus.org/v2/oauth2/authorize?prompt=login&access\_type
Point your web browser to the above URL (which will be
different for you).
-
+
Select Globus Id and say "Allow".
-
+
You will then get a code,
-
+
which you can paste into your terminal, eg
diff --git a/docs/Scientific_Computing/Supported_Applications/FDS.md b/docs/Scientific_Computing/Supported_Applications/FDS.md
index 76516170b..2ae362c47 100644
--- a/docs/Scientific_Computing/Supported_Applications/FDS.md
+++ b/docs/Scientific_Computing/Supported_Applications/FDS.md
@@ -57,11 +57,11 @@ and
## Scaling with MPI
-
+
## Scaling with oMP
-
+
diff --git a/docs/Scientific_Computing/Supported_Applications/Find_execution_hot_spots_with_VTune.md b/docs/Scientific_Computing/Supported_Applications/Find_execution_hot_spots_with_VTune.md
index 5d473ecd8..89b8c1e0f 100644
--- a/docs/Scientific_Computing/Supported_Applications/Find_execution_hot_spots_with_VTune.md
+++ b/docs/Scientific_Computing/Supported_Applications/Find_execution_hot_spots_with_VTune.md
@@ -100,6 +100,6 @@ threads.
-
+
diff --git a/docs/Scientific_Computing/Supported_Applications/JupyterLab.md b/docs/Scientific_Computing/Supported_Applications/JupyterLab.md
index 39caf3751..01c1a9b3a 100644
--- a/docs/Scientific_Computing/Supported_Applications/JupyterLab.md
+++ b/docs/Scientific_Computing/Supported_Applications/JupyterLab.md
@@ -132,7 +132,7 @@ click 'Tools > MobaSSH Thunnel (port forwarding)':
the remote server (right upper box, second line)
- Save
-
+
## Launch the JupyterLab server
@@ -218,7 +218,7 @@ Finally, you need to open your local web browser and copy and paste the
URL specified by the JupyterLab server into the address bar. After
initializing Jupyter Lab you should see a page similar to:
-
+
# Kernels
diff --git a/docs/Scientific_Computing/Supported_Applications/Keras.md b/docs/Scientific_Computing/Supported_Applications/Keras.md
index 857b6d3e1..6a5aa628b 100644
--- a/docs/Scientific_Computing/Supported_Applications/Keras.md
+++ b/docs/Scientific_Computing/Supported_Applications/Keras.md
@@ -49,7 +49,7 @@ test/, respectively. An example of image is test/img49.jpg.
display test/img49.jpg
+class="s1">
which shows five, partially overlapping dots. Note that
along with the images, a comma separated values (csv) file (e.g.
@@ -117,7 +117,7 @@ same directory as classify.py. This file contains the predictions for
the first 50 test images, which will vary for each training but the
result will look like:
-
+
(The purple images have no dots.) With each image the
number of dots is displayed as well as the value inferred by the model
diff --git a/docs/Scientific_Computing/Terminal_Setup/Jumping_Lander_node..md b/docs/Scientific_Computing/Terminal_Setup/Jumping_Lander_node..md
index 9e4d9af34..93c39fc87 100644
--- a/docs/Scientific_Computing/Terminal_Setup/Jumping_Lander_node..md
+++ b/docs/Scientific_Computing/Terminal_Setup/Jumping_Lander_node..md
@@ -60,7 +60,7 @@ click 'Tools > MobaSSH Tunnel (port forwarding)':
- Specify the local port number on the local side (left)
- Save
-
+
# PuTTY
diff --git a/docs/Scientific_Computing/Terminal_Setup/MobaXterm_Setup_(Windows).md b/docs/Scientific_Computing/Terminal_Setup/MobaXterm_Setup_(Windows).md
index 523e70370..8095160dc 100644
--- a/docs/Scientific_Computing/Terminal_Setup/MobaXterm_Setup_(Windows).md
+++ b/docs/Scientific_Computing/Terminal_Setup/MobaXterm_Setup_(Windows).md
@@ -48,9 +48,9 @@ transfer GUI.
field, as well as your NeSI username in the Username field for
the gateway SSH server then select OK to close the window.
-
+
-
+
1. Click 'OK' on the open window, usually this will start a new session
immediately. *See usage below.*
@@ -71,7 +71,7 @@ transfer GUI.
You will see your saved session in the left hand panel under 'Sessions'.
Double click to start.
-
+
You will be prompted by dialogue box.
diff --git a/docs/Scientific_Computing/Terminal_Setup/Putty_(noSCP).md b/docs/Scientific_Computing/Terminal_Setup/Putty_(noSCP).md
index 6042fa5ca..dd1fb1a40 100644
--- a/docs/Scientific_Computing/Terminal_Setup/Putty_(noSCP).md
+++ b/docs/Scientific_Computing/Terminal_Setup/Putty_(noSCP).md
@@ -22,25 +22,25 @@ zendesk_section_id: 360000189696
- 
+ 
2\. Open Connection > Data and enter in your username under
'Auto-Login username.
-
+
3\. Open Connection > SSH and 'Share SSH connections if possible'.
-
+
4\. Do this
SCRAP THAT, THOUGHT IT WORKED BUT IT
DIDN'T
-
+
@@ -48,4 +48,4 @@ DIDN'T
Save session
-
+
diff --git a/docs/Scientific_Computing/Terminal_Setup/Ubuntu_LTS_terminal_(Windows_10).md b/docs/Scientific_Computing/Terminal_Setup/Ubuntu_LTS_terminal_(Windows_10).md
index 8a8d7b92c..40c931008 100644
--- a/docs/Scientific_Computing/Terminal_Setup/Ubuntu_LTS_terminal_(Windows_10).md
+++ b/docs/Scientific_Computing/Terminal_Setup/Ubuntu_LTS_terminal_(Windows_10).md
@@ -24,7 +24,7 @@ Ubuntu LTS Terminal.
1. Open the Microsoft store, search for 'Ubuntu', find and install
'Ubuntu 18.04 LTS' or 'Ubuntu 20.04 LTS'
- 
+ 
@@ -33,8 +33,8 @@ Ubuntu LTS Terminal.
for a second time (If the above dialogue box reappears, close as
before and download/install will begin.
- 
- 
+ 
+ 
3. Launch “Ubuntu 18.04 LTS” from start menu and wait for the first
@@ -45,14 +45,14 @@ Ubuntu LTS Terminal.
will be prompted to “Enter new UNIX username” and press
<Enter>. This username can be anything you want.
- 
+ 
5. Now, type in a new password for the username you picked and press
<Enter>. (Again this password is anything you want). Then
retype the password to confirm and press <Enter>
- 
+ 
6. To create a symbolic link to your Windows filesystems in your home
directory run the following command replacing c with the name of
your Windows filesystems found in /mnt/.
diff --git a/docs/Scientific_Computing/Terminal_Setup/WinSCP-PuTTY_Setup_(Windows).md b/docs/Scientific_Computing/Terminal_Setup/WinSCP-PuTTY_Setup_(Windows).md
index 037400bcc..567e290e8 100644
--- a/docs/Scientific_Computing/Terminal_Setup/WinSCP-PuTTY_Setup_(Windows).md
+++ b/docs/Scientific_Computing/Terminal_Setup/WinSCP-PuTTY_Setup_(Windows).md
@@ -29,7 +29,7 @@ WinSCP can be downloaded [here](https://winscp.net/eng/download.php).
Upon startup:
-
+
1. Add a *New Site* and set:
@@ -48,11 +48,11 @@ Upon startup:
> you.
-
+
5\. Open Advanced Settings.
-
+
6\. Navigate to *Connection > Tunnel *and set:
@@ -72,12 +72,12 @@ recommend you use the PuTTY terminal instead.
2.In WinSCP open 'Tools > Preferences'
-
+
3\. Under *Integration > Applications* enable *Remember session
password and pass it to PuTTY*
-
+
@@ -93,7 +93,7 @@ SSH Client' is selected).
2\. Under *Integration > Applications* and add -X after
PuTTY/Terminal client path.
-**
+**
3\. Restart your session.
@@ -107,23 +107,23 @@ PuTTY/Terminal client path.
Files can be dragged, dropped and modified in the WinSCP GUI just like
in any windows file system.
-
+
- Will open a **PuTTY terminal**.
+ Will open a **PuTTY terminal**.
Assuming you followed the steps setting up PuTTY, this should
automatically enter in your details.
- Will open the default **WinSCP
+ Will open the default **WinSCP
terminal**. While the functionality is identical to any other terminal
the interface is slightly abstracted, with a separate window for input
and command history drop-down.
- Type here to **change
+ Type here to **change
directory**.** **The GUI doesn't follow your current terminal directory
like MobaXterm so must be changed manually. (Recommend making this
larger as the default is very hard to type in).
- **Bookmark** current directory.
+ **Bookmark** current directory.
> ### Important
>
diff --git a/docs/Scientific_Computing/Terminal_Setup/Windows_Subsystem_for_Linux_(WSL).md b/docs/Scientific_Computing/Terminal_Setup/Windows_Subsystem_for_Linux_(WSL).md
index fa4eaaa4e..df8fa3c77 100644
--- a/docs/Scientific_Computing/Terminal_Setup/Windows_Subsystem_for_Linux_(WSL).md
+++ b/docs/Scientific_Computing/Terminal_Setup/Windows_Subsystem_for_Linux_(WSL).md
@@ -27,9 +27,9 @@ WSL is enabled by default on later versions of Windows 10.
## Enabling WSL
1. Open 'Turn Windows features on or off'
- 
+ 
2. Scroll down and tick the 'Windows Subsystem for Linux' option.
- 
+ 
Click OK
3. Wait for the installation to finish then restart your computer.
diff --git a/docs/Scientific_Computing/Terminal_Setup/X11_on_NeSI.md b/docs/Scientific_Computing/Terminal_Setup/X11_on_NeSI.md
index 96300e688..cf1a8b83a 100644
--- a/docs/Scientific_Computing/Terminal_Setup/X11_on_NeSI.md
+++ b/docs/Scientific_Computing/Terminal_Setup/X11_on_NeSI.md
@@ -40,14 +40,14 @@ Download links for X-servers can be found below.
Make sure you have launched the server and it is running in the
background, look for
-this  symbol in your taskbar
+this  symbol in your taskbar
> ### Note
>
> MobaXterm has a build in X server, no setup required. By default the
> server is started alongside MobaXterm. You can check it's status in
> the top left hand corner
-> (=on, =off).
+> (=on, =off).
# X-Forwarding
@@ -67,9 +67,9 @@ Make sure the `-Y` or `-X` flag is included
Under 'session settings' for your connection make sure the X-11
forwarding box is checked.
-
+
-If the  button in the top
+If the  button in the top
right corner of your window is coloured, the X-server should be running.
# X-Forwarding with *tmux*
diff --git a/docs/Storage/Data_Transfer_Services/Data_Transfer_using_Globus_V5.md b/docs/Storage/Data_Transfer_Services/Data_Transfer_using_Globus_V5.md
index 74298208a..a53dc1047 100644
--- a/docs/Storage/Data_Transfer_Services/Data_Transfer_using_Globus_V5.md
+++ b/docs/Storage/Data_Transfer_Services/Data_Transfer_using_Globus_V5.md
@@ -105,7 +105,7 @@ endpoint "NeSI Wellington DTN V5" from the list, and you will be asked
to authenticate your access to the endpoint. Click Continue to the next
step.
-
+
@@ -117,7 +117,7 @@ that.
-
+
The NeSI Wellington DTN V5 endpoint is protected by a second factor
authentication (2FA-same as accessing NeSI clusters). In the
@@ -129,7 +129,7 @@ not*** use any additional characters or spaces between your password and
the token number.)
-
+
After the login, you will navigate to the default root(display as "/")
path, then you could change the path to
@@ -148,25 +148,25 @@ Navigate to your selected directory. e.g. the *nobackup* filesystem
*/nesi/nobackup/<project\_code>* and select the two-endpoint panel
for transfer.
-
+
Select the target endpoint and authenticate.
When you have activated endpoints in both transfer windows, you can
start transferring files between them.
-
+
Select files you wish to transfer and select the corresponding "Start"
button:
-
+
To find other NeSI endpoints, type in "nesi\#":
-
+
## In brief:
@@ -176,7 +176,7 @@ To find other NeSI endpoints, type in "nesi\#":
- If this is your first time, you will need to create a Globus
account.
- Open the two-endpoint panel
- 
located
+ 
located
on the top-right of the *File Manager* page.
- Select the Endpoints you wish to move files between (start typing
"nesi\#" to see the list of NeSI DTNs to select from).
@@ -191,7 +191,7 @@ To find other NeSI endpoints, type in "nesi\#":
Storage
Allocation](https://support.nesi.org.nz/hc/en-gb/articles/4405623499791-Globus-V5-Paths-Permissions-Storage-Allocation)).
- Transfer the files by clicking the appropriate
- button depending on the
+ button depending on the
direction of the transfer.
- Check your email for confirmation about the job completion report.
diff --git a/docs/Storage/Data_Transfer_Services/Data_transfer_between_NeSI_and_a_PC_without_NeSI_two-factor_authentication.md b/docs/Storage/Data_Transfer_Services/Data_transfer_between_NeSI_and_a_PC_without_NeSI_two-factor_authentication.md
index cf0c99079..de730c708 100644
--- a/docs/Storage/Data_Transfer_Services/Data_transfer_between_NeSI_and_a_PC_without_NeSI_two-factor_authentication.md
+++ b/docs/Storage/Data_Transfer_Services/Data_transfer_between_NeSI_and_a_PC_without_NeSI_two-factor_authentication.md
@@ -46,7 +46,7 @@ have registered and created an account on Globus.
- You should now see your new guest collection at
-
+
## Step 2: Download and install Globus Connect Personal
@@ -68,7 +68,7 @@ Note: By default your entire home directory will be exposed. It is good
practice to only share specific directories. You can remove your home
directory by highlighting it and clicking on the "-" sign.
-
+
## Step 4: Test a file transfer
@@ -80,4 +80,4 @@ directory by highlighting it and clicking on the "-" sign.
be seen in the picture below.
- Click on the files you want to transfer and press "Start"
-
+
diff --git a/docs/Storage/Data_Transfer_Services/Globus_V5_Paths,_Permissions,_Storage_Allocation.md b/docs/Storage/Data_Transfer_Services/Globus_V5_Paths,_Permissions,_Storage_Allocation.md
index ca325a6ac..d117d8a8f 100644
--- a/docs/Storage/Data_Transfer_Services/Globus_V5_Paths,_Permissions,_Storage_Allocation.md
+++ b/docs/Storage/Data_Transfer_Services/Globus_V5_Paths,_Permissions,_Storage_Allocation.md
@@ -16,7 +16,7 @@ If you point Globus File Manager to an endpoint collection where you
have an account/access, it will open a single panel pointing to the root
path directory, displayed as '`/home/`'.
-
+
### On NeSI's Māui/Mahuika clusters this means:
diff --git a/docs/Storage/Data_Transfer_Services/Globus_V5_endpoint_activation_.md b/docs/Storage/Data_Transfer_Services/Globus_V5_endpoint_activation_.md
index 54456fe25..bc695a0f2 100644
--- a/docs/Storage/Data_Transfer_Services/Globus_V5_endpoint_activation_.md
+++ b/docs/Storage/Data_Transfer_Services/Globus_V5_endpoint_activation_.md
@@ -17,7 +17,7 @@ zendesk_section_id: 360000040596
When you select an endpoint to transfer data to/from, you may be asked
to authenticate with that endpoint:
-
+
Transfers are only possible once you have supplied credentials that
authenticate your access to the endpoint. This process is known as
"activating the endpoint". The endpoint remains active for 24 hours.
@@ -31,7 +31,7 @@ authentication (2FA-same as accessing NeSI clusters). In the
not*** use any additional characters or spaces between your password and
the token number.)
- 
+ 
Check the status of your endpoints at
[ ](https://www.globus.org/app/console/endpoints)
diff --git a/docs/Storage/Data_Transfer_Services/Initial_Globus_Sign-Up,_and_your_Globus_Identities.md b/docs/Storage/Data_Transfer_Services/Initial_Globus_Sign-Up,_and_your_Globus_Identities.md
index 320fb7c1b..a0f7741d5 100644
--- a/docs/Storage/Data_Transfer_Services/Initial_Globus_Sign-Up,_and_your_Globus_Identities.md
+++ b/docs/Storage/Data_Transfer_Services/Initial_Globus_Sign-Up,_and_your_Globus_Identities.md
@@ -21,7 +21,7 @@ route to setting up your Globus account is:
#### Log in to https://globus.org using your google identity:
-
+
2\) Link other Globus identities to your primary identity
@@ -38,7 +38,7 @@ If you have other identities in Globus (for example, a globusID), link
them to your Google ID account following the instructions at
:
- 
+ 
diff --git a/docs/Storage/Data_Transfer_Services/Personal_Globus_Endpoint_Configuration.md b/docs/Storage/Data_Transfer_Services/Personal_Globus_Endpoint_Configuration.md
index b1c4079a2..34ad8cbb2 100644
--- a/docs/Storage/Data_Transfer_Services/Personal_Globus_Endpoint_Configuration.md
+++ b/docs/Storage/Data_Transfer_Services/Personal_Globus_Endpoint_Configuration.md
@@ -23,7 +23,7 @@ Globus's [Endpoints administered by
you](https://app.globus.org/endpoints?scope=administered-by-me) to see
whether your endpoint shows up as active.
-
+
## Personal Endpoint file-transfer and sharing
@@ -38,7 +38,7 @@ eScience Infrastructure*.
Check if your account already has this membership by viewing the [Globus
Plus](https://app.globus.org/account/plus) tab under your Account:
-
+
If you do not see an entry for *New Zealand eScience Infrastructure* on
this page, then:
diff --git a/docs/Storage/Data_Transfer_Services/Re-creating_Shared_Collections_and_Bookmarks_in_Globus_V5.md b/docs/Storage/Data_Transfer_Services/Re-creating_Shared_Collections_and_Bookmarks_in_Globus_V5.md
index bcf710267..2ec600e34 100644
--- a/docs/Storage/Data_Transfer_Services/Re-creating_Shared_Collections_and_Bookmarks_in_Globus_V5.md
+++ b/docs/Storage/Data_Transfer_Services/Re-creating_Shared_Collections_and_Bookmarks_in_Globus_V5.md
@@ -26,25 +26,25 @@ In summary:
1. To re-create existing Collections, select *Share* and *Create Guest
Collection
- 
+ 
*
2. Enter the [file
path](https://support.nesi.org.nz/hc/en-gb/articles/4405623499791)
of the directory to be shared.
- 
+ 
This can also be copied from your existing Shared Collection on
*NeSI Wellington DTN
- 
+ 
*
3. Add Permissions for an individual or a Group (existing, or create a
new group)
- 
+ 
4. Users you share with will receive an email notification containing a
link to the new *Guest Collection*.
@@ -54,12 +54,12 @@ In summary:
1. Create bookmarks to **NeSI Wellington DTN V5** and new Guest
Collections
- 
+ 
2. Bookmarks to *NeSI Wellington DTN* and Shared Collections on *NeSI
Wellington DTN* should be deleted.
-
+
diff --git a/docs/Storage/Data_Transfer_Services/Register_for_a_Globus_ID.md b/docs/Storage/Data_Transfer_Services/Register_for_a_Globus_ID.md
index 48b8c4fa5..6845d6fbd 100644
--- a/docs/Storage/Data_Transfer_Services/Register_for_a_Globus_ID.md
+++ b/docs/Storage/Data_Transfer_Services/Register_for_a_Globus_ID.md
@@ -19,7 +19,7 @@ Go to
https://www.globusid.org
to create or set preferences associated with your Globus ID.
-
+
From [ https://www.globusid.org](%C2%A0https://www.globusid.org) ,
select "Create A Globus ID".
@@ -27,7 +27,7 @@ select "Create A Globus ID".
Enter a username/password of your choice, and the value "NeSI" in the
Organization field.
-
+
Your email address will be verified - check your email and copy/paste
the verification code you receive into the next page and submit. Upon
@@ -35,13 +35,13 @@ verification, your account will be enabled. Unless you have an
pre-existing Globus account, * press "
Continue"*
-
+
Your Globus registration is complete. Grant Globus permission to access
your identity and act on your behalf by checking "Allow" on the next
box.
-
+
You can now log into the
diff --git a/docs/Storage/File_Systems_and_Quotas/I-O_Performance_Considerations.md b/docs/Storage/File_Systems_and_Quotas/I-O_Performance_Considerations.md
index 459ceb690..ec9f3591f 100644
--- a/docs/Storage/File_Systems_and_Quotas/I-O_Performance_Considerations.md
+++ b/docs/Storage/File_Systems_and_Quotas/I-O_Performance_Considerations.md
@@ -43,7 +43,7 @@ as DVS (Data Virtualisation Service), to expose the Spectrum Scale file
systems to XC compute nodes. DVS adds an additional layer of hardware
and software between the XC compute nodes and storage (see Figure).
- 
+ 
Figure 1: Cray XC50 DVS architecture.
diff --git a/docs/Storage/File_Systems_and_Quotas/NeSI_File_Systems_and_Quotas.md b/docs/Storage/File_Systems_and_Quotas/NeSI_File_Systems_and_Quotas.md
index 29ddacea2..e412ae0cb 100644
--- a/docs/Storage/File_Systems_and_Quotas/NeSI_File_Systems_and_Quotas.md
+++ b/docs/Storage/File_Systems_and_Quotas/NeSI_File_Systems_and_Quotas.md
@@ -40,7 +40,7 @@ command:
The values for 'nn\_storage\_quota' are updated approximately every hour
and cached between updates.
-## 
+## 
# File System Specifications
diff --git a/docs/Storage/Nearline_long-term_storage/Nearline_Long-Term_Storage_Service.md b/docs/Storage/Nearline_long-term_storage/Nearline_Long-Term_Storage_Service.md
index d042f92db..6560ca522 100644
--- a/docs/Storage/Nearline_long-term_storage/Nearline_Long-Term_Storage_Service.md
+++ b/docs/Storage/Nearline_long-term_storage/Nearline_Long-Term_Storage_Service.md
@@ -11,6 +11,9 @@ vote_count: 2
vote_sum: 2
zendesk_article_id: 360001169956
zendesk_section_id: 360000042255
+prereq: |
+ - Thing 1
+ - Thing 2
---
@@ -475,7 +478,7 @@ will be merged in the Nearline file system. Further, when retrieving
data from Nearline, keep in mind that the directory structure up to your
projectID will be retrieved:
-
+
# Underlying mechanism
diff --git a/docs/Storage/Release_Notes_Nearline/Long-Term_Storage_-_Nearline_release_notes__v1.1.0.14.md b/docs/Storage/Release_Notes_Nearline/Long-Term_Storage_-_Nearline_release_notes__v1.1.0.14.md
index 4612459cf..1507f3b96 100644
--- a/docs/Storage/Release_Notes_Nearline/Long-Term_Storage_-_Nearline_release_notes__v1.1.0.14.md
+++ b/docs/Storage/Release_Notes_Nearline/Long-Term_Storage_-_Nearline_release_notes__v1.1.0.14.md
@@ -15,14 +15,14 @@ zendesk_section_id: 360000502675
*Released 5 November 2020.*
-This release includes the following changes:
+This release ../../../ the following changes:
- `nlls`, `nlget`, `nlpurge`, `nlput` and `nljobstatus` now come with
a debug mode, accessible via the `--debug` command line switch.
- Help documentation, as well as the usage message when a nearline
command is run with incorrect arguments, has been improved.
-- `nljobstatus` now includes more comprehensive job status
- information. In particular, the job status message now includes a
+- `nljobstatus` now ../../../ more comprehensive job status
+ information. In particular, the job status message now ../../../ a
brief description of the stage the job is up to, and whether the job
is at that moment pending (waiting in a queue to start the next
operation), running, or complete.
diff --git a/docs/Storage/Release_Notes_Nearline/Long-term_Storage_-_Nearline_release_notes_v1.1.0.19.md b/docs/Storage/Release_Notes_Nearline/Long-term_Storage_-_Nearline_release_notes_v1.1.0.19.md
index 95843bdd2..bcfbb44ee 100644
--- a/docs/Storage/Release_Notes_Nearline/Long-term_Storage_-_Nearline_release_notes_v1.1.0.19.md
+++ b/docs/Storage/Release_Notes_Nearline/Long-term_Storage_-_Nearline_release_notes_v1.1.0.19.md
@@ -13,7 +13,7 @@ zendesk_section_id: 360000502675
*Released Thursday 4 March 2021.*
-This release includes a number of significant changes and new features:
+This release ../../../ a number of significant changes and new features:
- The `nltraverse` command is now supported by an `nlcompare` command.
With `nlcompare`, you can compare a directory within `/nesi/project`
diff --git a/docs/format.md b/docs/format.md
new file mode 100644
index 000000000..17c21d6d3
--- /dev/null
+++ b/docs/format.md
@@ -0,0 +1,85 @@
+`# Header 1`
+
+# Header 1
+
+`## Header 2`
+
+## Header 2
+
+`### Header 3`
+
+### Header 3
+
+`#### Header 4`
+
+#### Header 4
+
+`**bold**`
+**bold**
+
+`_italic`
+_italic_
+
+```md
+!!! info
+ This is a test admonation.
+```
+
+!!! info
+ This is a test admonation.
+
+```md
+=== "Tab One"
+ someting in the tab
+=== "Tab two"
+ something else
+```
+
+=== "Tab One"
+ someting in the tab
+=== "Tab two"
+ something else
+
+```md
+\```py
+import somepackage
+
+formatting = True
+if formatting:
+ Print(formatting) # A comment
+\```
+```
+
+```python
+import somepackage
+
+formatting = True
+if formatting:
+ Print(formatting) # A comment
+```
+
+```md
+![This is an image]("includes/images/3rgk_assembly-1.jpeg")
+```
+
+![This is an image]("includes/images/3rgk_assembly-1.jpeg")
+
+```md
+[External Link]("https://example.com")
+
+```
+
+[External Link]("https://example.com")
+
+```md
+[Internal Link]("General/Announcements")
+
+```
+
+[Internal Link]("General/Announcements")
+
+```md
+[Hover over me](https://example.com "I'm a link with a custom tooltip.")
+```
+
+[Hover over me](https://example.com "I'm a link with a custom tooltip.")
diff --git a/docs/index.md b/docs/index.md
index 0fea3bef5..7505f2103 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -10,6 +10,7 @@ search from the top menu.
person_add
+
## How to request an account
For information on getting an account and allocation with us, please
diff --git a/docs/info.md b/docs/info.md
new file mode 100644
index 000000000..6dbb6cf8d
--- /dev/null
+++ b/docs/info.md
@@ -0,0 +1 @@
+{{ macros_info() }}
\ No newline at end of file
diff --git a/overrides/main.html b/overrides/main.html
index 5cc0475ba..8db3daa20 100644
--- a/overrides/main.html
+++ b/overrides/main.html
@@ -11,6 +11,12 @@
offical support documentation.
-
{% include "partials/header.html" %}
+{% if page.meta and page.meta.prereq %}
+
+ {% for pre in page.meta.prereq %}
+ - {{pre}}
+ {% endfor %}
+
>
+{% endif %}
{% endblock %}