ClinWulf's Open OnDemand portal gives approved clinical research teams 8 apps in the browser: Jupyter, RStudio, VS Code, a Linux desktop, and tools for genomics, visualization, and machine learning. Everything runs inside ClinWulf, the cluster for work with protected health information (PHI).
On this page: All apps at a glance · Launching an app · App notes · Working with PHI · Troubleshooting
All apps at a glance
| App | What it's for | Menu group |
|---|---|---|
| Jupyter Notebook | Python notebooks, on CPU or GPU | Servers |
| JupyterLab | The newer Jupyter interface, with files, notebooks, and terminals side by side | Sandbox |
| RStudio Server | R and RStudio in the browser | Servers |
| Code Server | VS Code in the browser | Editors & IDEs |
| ClinWulf Desktop | A full Linux desktop for any graphical program | Desktops |
| IGV | Integrative Genomics Viewer for sequencing data | Visualization |
| ParaView | Scientific and medical 3D visualization | Visualization |
| TensorBoard | Browse machine learning training logs | Visualization |
The portal also has the everyday tools: Clinwulf Cluster Shell Access (a terminal), Files (your home folder), Active Jobs, Job Composer for batch jobs, and System Status. See the OnDemand overview.
Launching an app
ClinWulf has CPU and GPU queues, each in three lengths: short for quick sessions, long for up to 8 hours, and extra for up to 10 days. GPU short sessions last up to 2 hours. Pick a CPU queue unless your work uses a GPU.
| Setting | What to choose |
|---|---|
| Queue | CPU Short, Long, or Extra; or GPU Short, Long, or Extra. The form shows the time limit for each. |
| Hours | How long the session runs, within the queue's limit. It ends at this limit, so save your work before then. |
| GPUs | Only used on GPU queues. Most forms have a Number of GPUs list (0, 1, 2, or 4). On Jupyter Notebook, RStudio Server, and the Desktop, you type the GPU type and count instead, for example a100:1. |
| Memory | Start small (4 to 16 GB) and increase if the app runs out. Big requests wait longer. |
| Project directory | Where the app starts. It defaults to your home folder, /vast/home/<netid>. Point it at your study's data folder. |
| Additional modules | Optional. Software modules to load before the app starts. |
- Fill in the form and click Launch. The session card moves from Queued to Starting to Running.
- Click the connect button on the card to open the app in a new tab.
- When you're done, click Delete on the card so the resources go back to others. Closing the browser tab doesn't stop the job.
App notes
| App | Good to know |
|---|---|
| Jupyter Notebook | The classic notebook interface. Choose a GPU queue and a GPU for deep learning, or a CPU queue for everything else. More in Jupyter notebooks. |
| JupyterLab | The newer Jupyter interface. It's listed under Sandbox while it's being tested. The Modules to load box starts with jupyterlab/2025. |
| RStudio Server | RStudio in the browser, with cores and memory you choose. More in RStudio. |
| Code Server | VS Code 4.105 in the browser, opened in the project folder you choose. More in Code Server. |
| ClinWulf Desktop | A full Linux desktop on a compute node, for graphical programs that don't have their own app. It offers the CPU short and long queues and the GPU short queue. More in WolfieHPCDesktop. |
| IGV | IGV 2.19 for viewing alignments, variants, and other genomic tracks. Set the project directory to where your BAM or VCF files are. |
| ParaView | ParaView 6.0.1 for 3D visualization of imaging and simulation data, so large files stay on ClinWulf. |
| TensorBoard | TensorBoard 2.20 for TensorFlow or PyTorch training logs. Choose the GPU version only on a GPU queue. Set log directory to the folder with your events files. |
Working with PHI
ClinWulf is where RCI's clusters handle PHI, and the OnDemand apps keep your analysis inside it: notebooks, R sessions, and viewers all run on ClinWulf's compute nodes and read data from ClinWulf storage.
- Use only the data your IRB protocol approves, and keep it in your study's folders on ClinWulf.
- Think before downloading anything through the Files app. Moving PHI to a laptop or another system must follow your IRB protocol and any data use agreement.
- Don't take PHI to SeaWulf or NVwulf; those clusters aren't for PHI.
Questions about what's allowed for your study? Ask your IRB, or open a ticket and mention ClinWulf.
Troubleshooting
My session stays Queued
The queue is busy. Try a CPU queue if you don't need a GPU, ask for less memory or fewer GPUs, or shorten the hours. You can check how busy ClinWulf is under Clusters then System Status.
The app says it ran out of memory
Delete the session and launch again with more memory.
I can't find my files
Check the project directory on the launch form. Apps start in your home folder unless you point them somewhere else.
My session ended in the middle of my work
Sessions stop at the hours you asked for. Save often, and use a long or extra queue for longer work.
Related: OnDemand overview · OnDemand apps on SeaWulf · OnDemand apps on NVwulf · About ClinWulf