add docs for ondemand (#324)

docs/Scientific_Computing/.pages.yml

@@ -2,6 +2,7 @@ nav:
   - Supported_Applications
   - Training
   - Interactive_computing_using_Jupyter
+  - Interactive_computing_with_NeSI_OnDemand
   - The_NeSI_High_Performance_Computers
   - Running Jobs on Māui and Mahuika: Running_Jobs_on_Maui_and_Mahuika
   - Profiling_and_Debugging

docs/Scientific_Computing/Interactive_computing_with_NeSI_OnDemand/.pages.yml

@@ -0,0 +1,7 @@
+---
+nav:
+  - Interactive apps: interactive_apps
+  - How-to guide: how_to_guide.md
+  - ...
+  - changes_from_jupyter_on_nesi.md
+  - Release Notes: Release_Notes

docs/Scientific_Computing/Interactive_computing_with_NeSI_OnDemand/Release_Notes/index.md

@@ -0,0 +1,8 @@
+# NeSI OnDemand Release Notes
+
+!!! warning
+
+    NeSI OnDemand is in development and accessible to early access users only.
+    If you are interested in helping us test it please [contact us](mailto:[email protected]).
+
+- [v0.2.0 Release Notes](release_notes_0.2.0.md)

docs/Scientific_Computing/Interactive_computing_with_NeSI_OnDemand/Release_Notes/release_notes_0.2.0.md

@@ -0,0 +1,78 @@
+# v0.2.0 Release Notes
+
+!!! warning
+
+    NeSI OnDemand is in development and accessible to early access users only.
+    If you are interested in helping us test it please [contact us](mailto:[email protected]).
+
+## Release Summary
+
+NeSI OnDemand is NeSI’s new offering for providing researchers with access to JupyterLab and RStudio. We are adopting Open OnDemand technology, which enables us to build and extend the catalogue of web based applications.
+
+This is our first release to a group of early access users for feedback around NeSI OnDemand and the new login process.
+
+## Features
+
+- As a new step forward from Jupyter.NeSI, we have a new interactive environment NeSI OnDemand where you can launch NeSI apps for your research.
+
+    * Currently accessible via [https://163-7-144-39.sslip.io/](https://163-7-144-39.sslip.io/)
+
+- Apps currently supported
+
+    * JupyterLab with the following kernels: Python 3.8.2 (gimkl-2020a), Python 3.9.5 (gimkl-2020a), Python 3.10.5 (gimkl-2022a), and Python 3.11.3 (gimkl-2022a) 
+    * RStudio
+
+- Additional Apps (under development)
+
+    * In addition to the two core apps above, we have the following applications accessible, but are still under development, and are unsupported. We will update you with more information in the future releases as they stabilise.
+    * Virtual desktop
+    * Matlab
+    * VS Code-Server
+
+- New login process for the NeSI systems going forward
+
+    * NeSI is adopting a new Tuakiri based single sign on process for logging in to all NeSI services. This will mean that you won’t have to set up a separate NeSI account and password in order to be able to access NeSI services in the future.
+    * To ensure the security of our system, we have an additional OTP (one-time password) that is enforced on top of your institutional login. Over time, we will smooth out the user experience for setting this up and the frequency of having to enter the OTP.
+
+## Current known issues
+
+`Link to mahuika filesystem`
+
+:    This release is an ephemeral environment for gathering feedback around the system therefore we have not linked it with your research data on Mahuika/Maui. Any data stored on the system during this early test phase may disappear at any point.
+
+`"You are already logged in" message`
+
+:    If you have a browser session of NeSI OnDemand that is older than ~3 hours, and try to log back into the system, you may encounter a message saying “You are already logged in” without any actionable button. This is a known bug, and for now you would need to go back to the NeSI OnDemand URL ([https://163-7-144-39.sslip.io/](https://163-7-144-39.sslip.io/)) and you will arrive on the correct landing page.
+
+`User accounts with dots in the username`
+
+:    If you have an existing NeSI account with a dot as a part of your Linux username, there is a known bug with Open OnDemand and Kubernetes which prevents us from initiating some application. Currently RStudio has this issue and we are working on a fix.
+
+`Token expiry`
+
+:    This is another known bug where the back-end system token isn’t refreshed correctly after timeouts. If you run into error messages while trying to launch an app, you can resolve this by logging out of NeSI OnDemand, logging back in again and then clicking on Help button at the top right and selecting Restart Web Server.
+
+     [![restart_web_server](restart_web_server.png)](restart_web_server.png)
+
+`"Error -- can't find user for …" messages`
+
+:    If you see this message after logging in, please reach out to us at [[email protected]](mailto:[email protected]) and we will be able to fix this problem.
+
+`UX, wording, information display`
+
+:    Due to this environment being our test build, you may encounter many internal technical terms that will be addressed through future iterations.
+
+`User home folder default content`
+
+:    Pre-populated with [Desktop  Documents  Downloads  Music  Pictures  Public  Templates  Videos] folders, which is different to NeSI default.
+
+`User home folder permissions`
+
+:    Everybody seems to have read/execute access to all home folders.
+
+## Where to log tickets and give feedback
+
+We are in the early process of iterating and improving NeSI OnDemand. If you see any issues or suggestions, please let us know.
+
+- Please e-mail us on [[email protected]](mailto:[email protected]) with NeSI OnDemand as a part of the subject line and we will get back to you ASAP
+- Given that this is an early release, the SLA will not follow NeSI standard SLA (9am-5pm working days), and the environment may not be as stable as the production environment. We will support you with the best effort.

docs/Scientific_Computing/Interactive_computing_with_NeSI_OnDemand/changes_from_jupyter_on_nesi.md

@@ -0,0 +1,9 @@
+# Changes from Jupyter on NeSI
+
+!!! warning
+
+    NeSI OnDemand is in development and accessible to early access users only.
+    If you are interested in helping us test it please [contact us](mailto:[email protected]).
+
+- JupyterLab is no longer the main user interface but is just another application to be launched via the OnDemand interface
+- RStudio, MATLAB and Virtual Desktop applications are accessed directly from OnDemand instead of via JupyterLab

docs/Scientific_Computing/Interactive_computing_with_NeSI_OnDemand/how_to_guide.md

@@ -0,0 +1,58 @@
+# NeSI OnDemand how-to guide
+
+!!! warning
+
+    NeSI OnDemand is in development and accessible to early access users only.
+    If you are interested in helping us test it please [contact us](mailto:[email protected]).
+
+## How to log in
+
+Go to NeSI OnDemand (Early test instance URL: https://163-7-144-39.sslip.io/). It will automatically take you to the Tuakiri login screen.
+
+![image-20240903-110950](https://github.com/user-attachments/assets/2eccbaad-cd70-489b-9938-663f3fd30082)
+
+Select your affiliated institution, and log in using your institutional account. Example below shows the University of Auckland login screen.
+
+![image-20240903-111115 (1)](https://github.com/user-attachments/assets/d1006331-8128-421a-b678-16b29fe74a0e)
+
+After logging in, you will be asked to set up your OTP (one-time password) for NeSI. This is an OTP in addition to your institutional 2FA. We are currently enforcing an additional layer of OTP to make sure our system is secure, as the institutions federated by Tuakiri all have different security policies. We aim to improve this step as we iterate, so that you won’t be asked for the two different OTPs every time you try to log in.
+
+![image-20240903-111555](https://github.com/user-attachments/assets/4ba7b6bd-a5de-4fc9-a11a-f52154f5587b)
+
+Scan the barcode with your preferred authenticator app (e.g. Google Authenticator), and enter the one-time code (6 digit number) along with a device name (e.g. my mobile) and Submit and you are good to go.
+
+Once you have already set up NeSI OTP, you will be shown the following screen instead of the one above, where you can enter the 6 digit number from your authenticator app.
+
+![image-20240903-111247](https://github.com/user-attachments/assets/8d84be5d-347f-4a86-8b35-576cb55ffdee)
+
+After successfully logging in, you will be presented with the following NeSI OnDemand screen.
+
+![image-20240903-112029](https://github.com/user-attachments/assets/f4aed975-0f47-4e08-b783-d96271a56374)
+
+
+
+## How to launch JupyterLab / RStudio
+
+From the home screen, you can click on the app you would like to launch, e.g. JupyterLab, and you will be taken to the following screen.
+
+![image-20240903-112130](https://github.com/user-attachments/assets/62e37323-4a8f-48ba-b7a5-613c218b43a6)
+
+You can select the number of cores and memory needed and click on Launch to start the application. Currently our system is reserved with limited number of virtual CPUs and RAM, so selecting a value too high on the number will result in a failure message. On successful launch, you will see a screen similar to below:
+
+![image-20240903-112408](https://github.com/user-attachments/assets/b428b472-4612-4116-b815-6a8c17637a6a)
+
+Once the session is ready, you will see a button labeled Connect to Jupyter (or other app of your choice), which upon clicking will take you to the JupyterLab in this example as seen below:
+
+![image-20240903-112553](https://github.com/user-attachments/assets/c106b182-7f4a-494c-a48d-d67e97ef2dbf)
+
+
+
+## How to access your project directory
+
+For this test release, you will be presented only with our ephemeral storage, and access to the research files you have in Mahuika/Maui will be linked in a future release.
+
+
+
+## OTP token reset process (lost OTP device)
+
+Please contact [email protected] with NeSI OnDemand as a part of the subject line and we will get back to you ASAP.

docs/Scientific_Computing/Interactive_computing_with_NeSI_OnDemand/index.md

@@ -0,0 +1,31 @@
+# Interactive computing with NeSI OnDemand
+
+!!! warning
+
+    NeSI OnDemand is in development and accessible to early access users only.
+    If you are interested in helping us test it please [contact us](mailto:[email protected]).
+
+## Overview
+
+NeSI OnDemand is powered by [Open OnDemand](https://openondemand.org/) and provides web-based, interactive access to NeSI's cluster.
+
+## Connecting to NeSI OnDemand
+
+Connect to NeSI OnDemand: [https://ondemand.nesi.org.nz](https://ondemand.nesi.org.nz/).
+
+For more information see the [How-to guide](how_to_guide.md).
+
+## Interactive applications
+
+A number of interactive applications can be accessed through NeSI OnDemand, including:
+
+- [JupyterLab](interactive_apps/JupyterLab/index.md)
+- [RStudio](interactive_apps/RStudio.md)
+- [MATLAB](interactive_apps/MATLAB.md)
+- [Code server](interactive_apps/code_server.md)
+- [Virtual desktop](interactive_apps/virtual_desktop.md)
+
+## Release notes
+
+Release notes can be found [here](Release_Notes/index.md) and the main differences
+compared to our Jupyter on NeSI service are described [here](changes_from_jupyter_on_nesi.md).

docs/Scientific_Computing/Interactive_computing_with_NeSI_OnDemand/interactive_apps/.pages.yml

@@ -0,0 +1,8 @@
+---
+nav:
+  - JupyterLab: JupyterLab
+  - RStudio: RStudio.md
+  - MATLAB: MATLAB.md
+  - Code server: code_server.md
+  - Virtual desktop: virtual_desktop.md
+  - ...

docs/Scientific_Computing/Interactive_computing_with_NeSI_OnDemand/interactive_apps/JupyterLab/.pages.yml

@@ -0,0 +1,5 @@
+---
+nav:
+  - Jupyter_kernels_Tool_assisted_management.md
+  - Jupyter_kernels_Manual_management.md
+  - ...