Accessibility Change + Updating Intro to Rio tutorial

content/notes/rio-intro/01-hpcuva.md

@@ -17,7 +17,7 @@ These systems are used to process and store public data, internal use data, or s
 
 **Rio (High Security)**
 
-Rio is designed for processing and storing HSD such as HIPAA, FERPA, dbGAP, etc. 
+Rio is designed for processing and storing HSD such as HIPAA, FERPA, Controlled Access Data (CAD), etc. 
 
 Rio is not CUI certified yet; use the Ivy VM instead. 
 

content/notes/rio-intro/03-ivy-rio.md

@@ -22,5 +22,5 @@ Ivy Linux VMs can serve as a frontend for accessing the Rio HPC system (availabl
 
 **Rio**
 
-Rio is used for large-scale analysis of HIPAA, FERPA, and dbGaP  data.
+Rio is used for large-scale analysis of HIPAA, FERPA, and CAD.
 

content/notes/rio-intro/05-access.md

@@ -7,7 +7,7 @@ menu:
     rio-intro:
 ---
 
-Principal Investigators (PIs) can request access by submitting an Ivy Linux VM request through the   [services app](https://services.rc.virginia.edu/).
+Principal Investigators (PIs) can request access by submitting an Ivy Linux VM request through the [services app](https://services.rc.virginia.edu/).
 
 Research staff may apply for an exception.
 

content/notes/rio-intro/07-userprovisioning.md

@@ -15,6 +15,4 @@ Once a project is approved, a PI and her/his researchers must sign a RUDA (one f
 Each researcher must also complete the  _[High Security Awareness Training (HSAT)](http://in.virginia.edu/hsat-training)_. This must be completed to permit each researcher access to the HSVPN filter.
 
 
-> <small>More information on security training and HSVPN access can be found [here](https://www.rc.virginia.edu/userinfo/ivy/) on the RC website.</small>
-
 

content/notes/rio-intro/08-connecting.md

@@ -7,11 +7,11 @@ menu:
     rio-intro:
 ---
 
-Before connecting to your VM, you must install the following on your personal machine/device.
-  * Install the Cisco AnyConnect Secure Mobility Client.
-  * Install Opswat.
-  * Install Duo MFA on personal smartphone.
-  * See  [here on the RC website](https://www.rc.virginia.edu/userinfo/ivy/) for details.
+Before connecting to your VM, you must install the following on your workstation.
+  * Cisco AnyConnect Secure Mobility Client.
+  * Opswat.
+  * Duo MFA on personal smartphone.
+  * See [here on the RC website](https://www.rc.virginia.edu/userinfo/ivy/) for details.
 
 There are two ways to connect to your Linux VM:
 

content/notes/rio-intro/09-access-ssh.md

@@ -16,7 +16,7 @@ Steps:
 ```bash
 ssh [mst3k@10.xxx.xxx.xxx](mailto:mst3k@10.xxx.xxx.xxx)
 ```
-, where `mst3k` is replaced with your user ID and the `x`'s are replaced with your VM's IP address (given in the Services app).
+`mst3k` is replaced with your user ID and the `x`'s are replaced with your VM's IP address (given in the Services app).
 
 {{< figure src=/notes/rio-intro/img/rio-intro_5.png alt="Screenshot showing a terminal window in MobaXterm with the command ssh mst3k@10.xxx.xxx.xxx entered, demonstrating how a user connects to their Rio VM over SSH using their user ID and VM IP address. The command line interface displays a green and yellow bar with the date, time, and file path /home/mobaxterm." width=90% height=90% >}}
 

content/notes/rio-intro/11-access-browser.md

@@ -12,11 +12,10 @@ Steps:
 
 1. Start the HSVPN
 2. Open a web browser and enter the IP address for your VM (e.g., `https://10.xxx.xxx.xxx`). If you get a warning message, you may need to click on Advanced Settings and/or a Connect Anyway option, depending on your web browser.
-3. Upon login, you will see a selection of different graphical applications that you can use.
 
-{{< figure src=/notes/rio-intro/img/rio-intro_6.jpg caption="Graphical application options available when accessing a Rio VM through a web browser: JupyterHub, RStudio, and FastX Desktop." alt="Screenshot showing the login interface for accessing a Rio virtual machine through a web browser. Three application icons are displayed — JupyterHub, RStudio Server, and FastX Desktop — representing the graphical tools users can launch on their VM after connecting via HTTPS." width=90% height=90% >}}
+Logging in will take you to a web application called Open OnDemand (OOD). 
+
 
-These applications run on the VM itself and do not use HPC resources.
 
 
 

content/notes/rio-intro/12-VM-storage.md

@@ -0,0 +1,26 @@
+---
+title: VM Storage
+date: 2025-11-12-03:53:56Z
+type: docs 
+weight: 653
+menu: 
+    rio-intro:
+---
+
+Storage is split across two sets of directories. 
+
+1. Personal directory 
+
+The personal directory for individual data storage is mounted under `/home/$USER`. Little space is allotted for `/home` directories per VM. Individual home folders are personal, and not shareable. 
+
+2. Shared storage space 
+
+Shared storage space is mounted under `/standard/ivy-hip-name` where `ivy-hip-name` is replaced by the name of your Ivy project's Grouper group name. 
+
+The default of Research Standard Storage is 1TB. PIs can get more when first requesting the Ivy project. Storage can be resized using our [Storage Request Form](https://www.rc.virginia.edu/form/storage/).
+
+### Rio Caveat 
+
+One caveat to consider when working in the Rio environment is that `/home` is not mounted on Rio compute nodes. This means that if your compute jobs reference any files in your `/home` storage, they will not be found. Ivy VMs not using Rio can ignore this condition. 
+
+We recommend working exclusively out of the VM's Research Standard storage directly for Rio. Individual user subdirectories are automatically created under `/standard` to organize the space. 

content/notes/rio-intro/17-transferring-data.md → content/notes/rio-intro/13-transferring-data.md

@@ -11,7 +11,7 @@ menu:
 
 **UVA IVY-DTN** is the the official collection for moving files into High-Security Research Standard Storage.
 
-To transfer data to High-Security Research Standard Storage, please see the special instructions [here on the RC website](https://www.rc.virginia.edu/userinfo/ivy/).
+To transfer data to High-Security Research Standard Storage, please see the special Globus instructions [here on the RC website](https://www.rc.virginia.edu/userinfo/ivy/).
 
 > Ensure that you are  __NOT__ connected to the HSVPN. Data transfer will not work if you are connected to the HSVPN.
 

content/notes/rio-intro/14-OOD.md

@@ -0,0 +1,13 @@
+---
+title: Open OnDemand
+date: 2025-11-12-03:53:56Z
+type: docs 
+weight: 855
+menu: 
+    rio-intro:
+---
+
+Open OnDemand is a web application that allows for HPC access through a graphical browser window. 
+
+
+{{< figure src=/notes/rio-intro/img/OOD.png alt="Screenshot of the Open OnDemand web interface. The top navigation bar shows menu options: 'Jobs,' 'Clusters,' 'Interactive Apps,' and 'My Interactive Sessions.' The center of the page displays the Open OnDemand logo with the text: 'OnDemand provides an integrated, single access point for all of your HPC resources.'" caption="Features of the application are accessible using the top gray bar: Jobs, Clusters, and Interactive Apps." width=90% height=90% >}}

content/notes/rio-intro/15-active-jobs.md

@@ -0,0 +1,13 @@
+---
+title: Active Jobs
+date: 2025-11-12-03:53:56Z
+type: docs 
+weight: 855
+menu: 
+    rio-intro:
+        parent: Open OnDemand
+---
+
+The Jobs tab on the OOD menu bar contains the active jobs tab. This shows all jobs currently running or queued on all partitions for all users. You can filter the search for **All Jobs** or **Your Jobs**. 
+
+The Filter search bar allows you to narrow jobs by either user, queue, job name, job ID, or job status (running, queued, completed). More job details can be viewed using the dropdown to the left of a given job. Completed jobs will be visible only for a short while as they are exiting. 

content/notes/rio-intro/16-clusters.md

@@ -0,0 +1,11 @@
+---
+title: Clusters
+date: 2025-11-12-03:53:56Z
+type: docs 
+weight: 860
+menu: 
+    rio-intro:
+        parent: Open OnDemand
+---
+
+The Clusters tab on the OOD menu bar opens a new browser tab with a Linux command line interface for shell access. This gives you terminal access to the frontend Ivy VM, similar to logging in via SSH. Here, you can manipulate files, install software packages for Python & R, and submit command line jobs. Running processes here does not utilize Rio compute node resources.

content/notes/rio-intro/17-interactive-apps.md

@@ -0,0 +1,17 @@
+---
+title: Interactive Apps
+date: 2025-11-12-03:53:56Z
+type: docs 
+weight: 865
+menu: 
+    rio-intro:
+        parent: Open OnDemand
+---
+
+Open OnDemand offers GUI applications to interactively run jobs on Rio compute nodes. Job submissions are managed by a resource manager called Slurm. 
+
+The following applications are available: 
+- JupyterLab
+- RStudio Server
+- FastX Desktop
+

content/notes/rio-intro/18-requesting-session.md

@@ -0,0 +1,39 @@
+---
+title: Requesting a Session
+date: 2025-11-12-03:53:56Z
+type: docs 
+weight: 900
+menu: 
+    rio-intro:
+        parent: Open OnDemand 
+---
+
+To request an interactive session, select one of the applications from the dropdown. This will prompt you to fill in the desired resources for your interactive job. 
+
+{{< figure src=/notes/rio-intro/img/jupyterlab.png alt="Open OnDemand JupyterLab launch form showing fields: Partition set to Standard, 1 hour, 1 core, 6 GB memory, allocation hpc_build, and a Launch button." width=45% height=45% >}}
+
+The above example is for starting a JupyterLab session.
+
+### Choosing Resource Requests
+
+**Partition:** Standard or GPU (only select GPU if you are using GPU-enabled code). 
+
+**Time:** Time limit for your session. Once reached, your session will terminate along with any running code. This cannot be adjusted once set. 
+
+**Cores:** Used in parallel processing. Your code must be modified to take advantage of using multiple cores. 
+
+**Memory:** A good rule of thumb is to request 2 to 3 times the size of the data that you are reading in or generating. 
+
+**Optional Slurm Option:** This field is used to input one of the many other Slurm options. 
+
+### Queueing the Session
+
+Once you've filled out the resource request form, click the Launch button at the bottom to queue your job. While queued, the job will wait for the resources you've asked for to become available. Requests with higher resource requests (more cores, more memory, more time) may wait longer. 
+
+{{< figure src=/notes/rio-intro/img/queue.png alt="Open OnDemand interface showing a queued JupyterLab session with creation time, one-hour request, session ID link, and a Delete button." caption="Example of a JupyterLab session waiting in the queue on Open OnDemand." width=90% height=90% >}}
+
+### Launching the Session
+
+When the job has started, the status will change from Queued to Running. A button will appear to open a browser, launching the interactive session.
+
+{{< figure src=/notes/rio-intro/img/runningjob.png alt="Open OnDemand interface showing a running JupyterLab session. The display includes the host node name, creation time, remaining time, session ID link, a Delete button, and a blue 'Connect to Jupyter' button." caption="Example of a JupyterLab session that has started running and is ready to connect in Open OnDemand." width=90% height=90% >}}

content/notes/rio-intro/19-interactive-desktop.md

@@ -0,0 +1,23 @@
+---
+title: Interactive Desktop
+date: 2025-11-12-03:53:56Z
+type: docs 
+weight: 950
+menu: 
+    rio-intro:
+        parent: Open OnDemand 
+---
+
+The Interactive Desktop application launches a virtual desktop session.
+
+The Desktop app is a great tool for managing files and launching applications with a graphical user interface.
+
+A Firefox browser is available and can be used to browse the web. The browser must be launched from a terminal with the
+network proxy set. Use the following commands in a terminal:
+```bash
+export HTTPS_PROXY=http://figgis-s.hpc.virginia.edu:8080
+
+export HTTP_PROXY=http://figgis-s.hpc.virginia.edu:8080
+
+firefox
+```