docs/static/json/biodata.json

+{
+    "table_generated": "1970-01-01T00:00:00UTC",
+    "table_header": [
+      "Short",
+      "Section",
+      "Scientific",
+      "Source",
+      "Build",
+      "Type"
+    ],
+    "table_data": [
+      [
+        "sample",
+        "sample data",
+        "Scientific Sample Data",
+        "Sample Data Source",
+        "v1",
+        "Main Directory"
+      ]
+    ]
+}
\ No newline at end of file

docs/static/json/lmod.json

+{
+    "table_generated": "1970-01-01T00:00:00UTC",
+    "table_header": [
+      "Name",
+      "Version",
+      "Module Name",
+      "Prerequisites",
+      "Type",
+      "Domain",
+      "Description"
+    ],
+    "table_data": [
+      [
+        "hello-world",
+        "v1",
+        "hello-world/v1",
+        "None",
+        "application",
+        "Computer Science",
+        "Hello World"
+      ]
+    ]
+}
\ No newline at end of file

docs/static/json/swan_partitions.json

+{
+    "table_generated": "1970-01-01T00:00:00UTC",
+    "table_header": [
+      "Partition",
+      "Owner",
+      "Node total(NODExCPU/MEM/FEATURE)",
+      "Description",
+      "SLURM Specification",
+      "Max Job Run Time",
+      "Max CPUs Per User",
+      "Max Jobs PerUser"
+    ],
+    "table_data": [
+      [
+        "batch",
+        "shared",
+        "91 total (4x40/1510.0GB/opa; 85x56/250.0GB/cx6; 2x112/503.085GB/cx6)",
+        "(default, no specification)",
+        "#SBATCH --partition=batch",
+        "7-00:00:00",
+        "opa:160 cx6:4760",
+        "1000"
+      ]
+    ]
+}
\ No newline at end of file

docs/static/markdown/anvil-images.md

+|       Image Name                |  Username to Connect  |        Access instructions           |                                 Description                                       |
+| ------------------------------- | --------------------- | ------------------------------------ | --------------------------------------------------------------------------------- |
+| Alma Linux 8.10                 |  `almalinux`          | `ssh -l almalinux <ip address>`      | AlmaLinux is a free and open source Linux distribution that is binary-compatible with Red Hat Enterprise Linux (RHEL).|
+| Alma Linux 8.10 Xfce            |  `almalinux`          | [X2Go instructions](/anvil/connecting_to_linux_instances_using_x2go/)   | AlmaLinux 8.10 with the Xfce Desktop Environment pre-installed.|
+| Cloudera 5.12 GNOME             |  `cloudera`           | [X2Go instructions](/anvil/connecting_to_linux_instances_using_x2go/) | Cloudera 5.12 QuickStart VM. *Note*: Follow the X2Go instructions, but choose GNOME for the Session type instead of Xfce.|
+| Fedora 39 Cloud                 |  `fedora`             | `ssh -l fedora <ip address>`          | Fedora is a Linux distribution developed by the community-supported Fedora Project and sponsored by the Red Hat company.|
+| Fedora 40 Cloud                 |  `fedora`             | `ssh -l fedora <ip address>`          | Fedora is a Linux distribution developed by the community-supported Fedora Project and sponsored by the Red Hat company.|
+| Fedora 40 Xfce                  |  `fedora`             | [X2Go instructions](/anvil/connecting_to_linux_instances_using_x2go/) | Fedora 40 with the Xfce Desktop Environment pre-installed.|
+| Windows 10                      |  `.\cloud-user`       | [Windows instructions](/anvil/connecting_to_windows_instances)       | Windows 10 LTSC edition with remote desktop access.|
+| Windows 10 Matlab               |  `.\cloud-user`       | [Windows instructions](/anvil/connecting_to_windows_instances)       | Windows 10 LTSB with Matlab r2013b, r2014b, r2015b, r2016b, r2017a pre-installed. |
+| Windows 10 Matlab r2018b/r2019b |  `.\cloud-user`       | [Windows instructions](/anvil/connecting_to_windows_instances)       | Windows 10 LTSC with Matlab r2018b and r2019b pre-installed. |
+| Windows 10 SAS                  |  `.\cloud-user`       | [Windows instructions](/anvil/connecting_to_windows_instances)       | Windows 10 LTSC with SAS 9.4 pre-installed. |
+| Windows 10 Mathematica          |  `.\cloud-user`       | [Windows instructions](/anvil/connecting_to_windows_instances)       | Windows 10 LTSB with Mathematica 10.4 and 11.0 pre-installed.|
+| Windows 10 Mathematica 12.0     |  `.\cloud-user`       | [Windows instructions](/anvil/connecting_to_windows_instances)  | Windows 10 LTSC with Mathematica 12.0 pre-installed.|
+| Ubuntu Cloud 20.04 LTS          |   `ubuntu`            | `ssh -l ubuntu <ip address>`         | Ubuntu Cloud Image from the 20.04 Long Term Support release.|
+| Ubuntu Cloud 22.04 LTS          |   `ubuntu`            | `ssh -l ubuntu <ip address>`         | Ubuntu Cloud Image from the 22.04 Long Term Support release.|
+| Ubuntu 22.04 LTS Xfce           |   `ubuntu`            | [X2Go instructions](/anvil/connecting_to_linux_instances_using_x2go/) | Ubuntu 22.04 with the Xfce Desktop Environment pre-installed.|
+| MariaDB Server 10.5             |   `centos`/`root`     | `ssh -l centos <ip address>`/[MySQL instructions](/anvil/using_mysql)  | CentOS 7 based image with a pre-configured MariaDB server. |

docs/static/markdown/class-guidelines.md

+The following guidelines apply to any accounts and groups created for the purposes of courses and coursework: 
+
+1) User accounts added to a class group will be removed from the class group one (1) calendar week after the end of the semester. 
+User accounts solely used in class groups will be locked at this time as well. All files/data in user account directories
+($HOME, $WORK, and $COMMON) contained within the class group will be removed at that time. It will be the students’ responsibility 
+to copy any files they would like to keep to a more permanent location before that time. Each student who applies to join 
+the class group must read and agree to these guidelines in advance. The class group owner’s account will be unaffected. 
+Additionally, HCC should be notified in advance of any other accounts, such as teaching assistants, that should not be removed. 
+If a student account is also a member of another, non-coursework, HCC group (e.g., a research group of a faculty member), 
+the user account and the associated files/data under the research group will not be affected. Students will be notified 
+throughout the semester (up to (3) three emails) that they will need to backup their data elsewhere, and it is encouraged 
+that instructors provide reminders in-class.
+
+
+2) All Anvil instances created for the class, excluding the group owner’s instances, will be removed one (1) calendar week after the semester ends. 
+All files/data/software associated with the instances will be removed at that time.
+
+
+3) The class group will be disabled one (1) calendar week after the end of the semester. To re-use a class group for a 
+future semester, the group owner will need to request that the class group be “renewed” using the Class Group Renewal 
+form at least one (1) calendar week before the group will be used. If the group owner plans to teach a new class 
+using HCC resources, they should apply for a new group specific for the class using the course catalog code as 
+the preferred group name, such as “csce123”. As part of the renewal form, HCC encourages optionally uploading a 
+class roster to help expedite the account approval process to avoid the need to manually approve each account.

docs/static/markdown/common-power-off.md

+!!! failure "$COMMON Retirement - **{{ hcc.common.retirement_date }}**"
+    The Common filesystem will be retired from service on **{{ hcc.common.retirement_date }}**!!! 
+    
+    Any jobs on Swan trying to start with the `{{ hcc.common.variable }}` filesystem or `--licenses=common` will not be able to be submitted. 
+
+    **Any data under **`{{ hcc.common.path }}`** or **`{{ hcc.common.variable }}`** will be lost if it is not moved to another location before the retirement  date of {{ hcc.common.retirement_date }}.**
+    
+    It is strongly recommended to begin moving data and updating workflows immediately to avoid lossing data.
+    
+    More information on the retirement is available on the [Common Retirement FAQ Page](/FAQ/common_retirement). If you have any questions about the retirement, please email <a href="mailto:hcc-support@unl.edu" class="external-link">{{ hcc.support_email }}</a>.

docs/static/markdown/events/hybrid_expectations_05-2025.md

+### Workshop Recommendations
+
+To make the most of this workshop, we strongly encourage active participation throughout the entire session, including participating in the hands-on exercises and asking questions throughout the workshop. 
+
+If you are stuck or not sure on something at any point of the workshop, please let us know and we would be happy to help. 
+
+Participation can be accomplished by using the sticky notes, raising hands, or if you are remote, using the Zoom Reactions or use the Zoom chat box.
+

docs/static/markdown/events/hybrid_reactions_05-2025.md

+### Sticky Notes and Reactions
+
+Throughout the workshop, we will use sticky notes and Zoom reactions to indicate status. These help instructors and helpers in the workshop assist with various issues and provide formative feedback during the workshops.
+
+!!! tip "Please make sure the sticky note is visibly on both the front and back of your laptop"
+
+- **Yellow Sticky Note / Green Check Reaction**: All good to go
+- **Red Sticky Note / Red "X" Reaction**: I need help or I am not ready to continue
+
+{% include "./zoom_reactions_05-2025.md" %}

docs/static/markdown/events/in-person_expectations_05-2025.md

+### Workshop Recommendations
+
+To make the most of this workshop, we strongly encourage active participation throughout the entire session, including participating in the hands-on exercises and asking questions throughout the workshop. 
+
+If you are stuck or not sure on something at any point of the workshop, please let us know and we would be happy to help. 
+
+Participation can be accomplished by using the sticky notes or raising hands.
+

docs/static/markdown/events/in-person_reactions_05-2025.md

+### Sticky Notes and Reactions
+
+Throughout the workshop, we will use sticky notes to indicate status. These help instructors and helpers in the workshop assist with various issues and provide formative feedback during the workshops.
+
+!!! tip "Please make sure the sticky note is visibly on both the front and back of your laptop"
+
+- **Yellow Sticky Note**: All good to go
+- **Red Sticky Note**: I need help or I am not ready to continue
+

docs/static/markdown/events/ood_setup_hybrid_05-2025.md

+!!! warning "Please make sure to complete the setup steps below each week."
+
+    1. Ensure your HCC Account is active.
+
+    2. Sign into Swan's Open OnDemand Portal: {{ hcc.swan.ood.url }}
+
+    3. When you have signed into the Swan Open OnDemand Portal, please put up your Yellow Sticky Note or Green Checkmark.
+
+    **If you have any issues logging in or accesing Swan, please visit our [event troubleshooting guide here](/Events/general_materials/#troubleshooting-logging-into-swan)**

docs/static/markdown/events/zoom_expectations_05-2025.md

+### Workshop Recommendations
+
+To make the most of this workshop, we strongly encourage active participation throughout the entire session, including participating in the hands-on exercises and asking questions throughout the workshop. 
+
+If you are stuck or not sure on something at any point of the workshop, please let us know and we would be happy to help. 
+
+Participation can be accomplished by using the Zoom Reactions or use the Zoom chat box.

docs/static/markdown/events/zoom_reactions_05-2025.md

+??? note "How to use Zoom Reactions"
+    1. In the menu bar at the bottom of the Zoom window, click on `React`.
+    
+        ![](/images/events/guides/zoom_menu_bar_05-2025.png)
+    
+    2. In the pop up panel, select the appropriate reaction. 
+
+        ![](/images/events/guides/zoom_react_panel_05-2025.png)
+    
+    Full Details: https://support.zoom.com/hc/en/article?id=zm_kb&sysparm_article=KB0063323

docs/stylesheets/extra.css

+:root  > * {
+  --md-primary-fg-color:        #D00000;
+  --md-primary-fg-color--light: #FEFDFA;
+  --md-primary-fg-color--dark:  #14151a;
+}
+
+/* Add padding to bottom of content to prevent overlap */
+.md-main {
+  padding-bottom: 80px; /* adjust based on footer height */
+}

docs/submitting_jobs/.nav.yml

+title: Submitting Jobs

docs/submitting_jobs/app_specific/index.md

+---
+title: "Application Specific Guides"
+weight: 100
+---
+
+!!! note
+    All of the examples below are available in a single repository at https://github.com/unlhcc/job-examples.
+
+## In-depth guides for running applications on HCC resources
+
+This repository contains scripts, data, and submit files for running many popular applications on the Holland Computing Center clusters.
+
+#### Applications included:
+- **BLAST** – includes advanced examples
+- **MATLAB**
+- **Python**
+- **R** – includes advanced examples
+- **Mathematica**
+- **Gaussian**
+- **Jupyter Notebook** – including Python and R scripts
+- **GAMESS**
+- **And More...**
+<br>
+<br>
+- [Application Examples](https://github.com/unlhcc/job-examples)
+- [Submitting ANSYS Jobs](./submitting_ansys_jobs/)
+- [Submitting MATLAB Jobs](./submitting_matlab_jobs/)
+- [Submitting R Jobs](./submitting_r_jobs/)
+
+
+For assistance or support regarding these examples or any HCC resources, please contact us at **[hcc-support@unl.edu](mailto:hcc-support@unl.edu)**.
+

content/submitting_jobs/app_specific/submitting_ansys_jobs.md → docs/submitting_jobs/app_specific/submitting_ansys_jobs.md

-+++
-title = "Submitting ANSYS Jobs"
-description =  "How to submit ANSYS jobs on HCC resources."
-+++
+---
+title: Submitting ANSYS Jobs
+summary: "How to submit ANSYS jobs on HCC resources."
+---
+
+!!! note
+    The ANSYS software licenses are managed by College of Engineering. To arrange access to ANSYS on HCC resources, contact Paul Pokorny ([paul.pokorny@unl.edu](mailto:paul.pokorny@unl.edu)).
 
-ANSYS license is purchased by College of Engineering. Only users from CoE can access ANSYS on HCC resources. To be added to the 'ansys' group, send an email to hcc-support@unl.edu.
 
 The number of ANSYS tasks is restricted by its license. 
 For research computations, users need to add the line below to their job submission file.
-{{< highlight batch >}}
+```code
 #SBATCH --licenses=ansys_research
-{{< /highlight >}}
+```
 For teaching purposes, users need to add
-{{< highlight batch >}}
+```bat
 #SBATCH --licenses=ansys_teaching
-{{< /highlight >}}
+```
 
 ### Running ANSYS scripts in batch
 
-{{% panel theme="info" header="ANSYS.submit" %}}
-{{< highlight batch >}}
-#!/bin/sh
+!!! note "ANSYS.submit"
+    ```bat
+    #!/bin/bash
     #SBATCH --ntasks=1
     #SBATCH --time=00:30:00
     #SBATCH --mem-per-cpu=1024
@@ -30,12 +32,12 @@ For teaching purposes, users need to add
     
     module load ansys/19.2
     YOUR_ANSYS_COMMAND
-{{< /highlight >}}
-{{% /panel %}}
-Details of SLURM job submission can be found at [SUBMITTING JOBS]({{< relref "submitting_jobs" >}}).
+    ```
+
+Details of SLURM job submission can be found at [SUBMITTING JOBS](/submitting_jobs/).
 
 ### Running ANSYS interactively
 
-1. To use graphical user interface, users need to first setup X11 forwarding. [HOW TO SETUP X11 FORWARDING]({{< relref "how_to_setup_x11_forwarding" >}})
-1. Start an interactie job using srun. NOTE: users need to add \--licenses=ansys_research or \--licenses=ansys_teaching to the srun command. [SUBMITTING AN INTERACTIVE JOB]({{< relref "creating_an_interactive_job" >}})
+1. To use graphical user interface, users need to first setup X11 forwarding. [HOW TO SETUP X11 FORWARDING](/connecting/how_to_setup_x11_forwarding/)
+1. Start an interactie job using srun. NOTE: users need to add \--licenses=ansys_research or \--licenses=ansys_teaching to the srun command. [SUBMITTING AN INTERACTIVE JOB](../../creating_an_interactive_job/)
 1. After the interactive job starts, execute "module load ansys/19.2", then run the ANSYS command, e.g. fluent, from command line. The GUI will show up if steps 1-2 are configured correctly.