Open OnDemand User Guide

HPC Cluster @ Vogelwarte

Version 1.0 | Last Updated: December 2025 | Thx to Claude Code

Introduction

What is Open OnDemand?

Open OnDemand (OOD) is a web-based portal that provides easy access to the VoWa HPC cluster. Through your web browser, you can:

Accessing Open OnDemand

Portal URL: https://hpc.vogelwarte.ch

Authentication: Single Sign-On (SSO) via your Vogelwarte Microsoft/Azure AD account

Requirements:

Getting Started

First Login

  1. Navigate to https://hpc.vogelwarte.ch
  2. Click the login button
  3. Authenticate using your Vogelwarte credentials (same as email/Office 365)
  4. You'll be redirected to the Open OnDemand dashboard

Dashboard Overview

After logging in, you'll see the OOD dashboard with:

Storage Access

Your home directory and shared storage are automatically accessible:

Location Path on hpc Path on Windows (Mac) Purpose
Home Directory ~/ or /home/vogelwarte.ch/[username] \\pallidus.vogelwarte.ch\[username] Personal files and settings
SciData ~/SciData Z:\SciData Shared scientific data storage (CephFS)
Scratch ~/scratch Z:\SciData\ORG_Vogelwarte\scratch High-performance temporary storage
Data /mnt/ceph Direct access to CephFS shared storage

Note: The SciData and scratch directories are symbolic links created automatically in your home directory for convenient access.

Interactive Applications

Open OnDemand provides several interactive applications that run on compute nodes with dedicated resources.

JupyterLab

Description: Modern web-based interface for Jupyter notebooks, code editing, and data visualization.

Pre-installed Packages:

How to Launch:

  1. Click Interactive Apps → JupyterLab
  2. Configure your session:
    • Account: Select your Slurm account (usually sci_it or root)
    • Partition: Choose compute for general work
    • Number of cores: 1-16 (start with 2)
    • Memory (GB): 1-64 (start with 4)
    • Hours: Maximum session time (1-72 hours)
  3. Click Launch
  4. Wait for the job to start (status: Queued → Running)
  5. Click Connect to JupyterLab when ready

Tips:

RStudio Server

Description: Full RStudio IDE in your browser for R programming and statistical analysis.

Pre-installed Packages:

How to Launch:

  1. Click Interactive Apps → RStudio Server
  2. Configure your session:
    • Account: Select your Slurm account
    • Partition: Choose compute
    • Number of cores: 1-16 (start with 2)
    • Memory (GB): 4-64 (R can be memory-intensive, start with 8GB)
    • Hours: Session duration
  3. Click Launch
  4. Wait for job allocation
  5. Copy passwordbecause for security reason there is a temprary login
  6. Click Connect to RStudio Server
  7. Enter login [username] and copied temporary password

Tips:

VS Code Server (Code Server)

Description: Full-featured Visual Studio Code development environment in your browser.

Pre-installed Tools:

Python:

JavaScript/TypeScript:

System Tools:

How to Launch:

  1. Click Interactive Apps → Code Server
  2. Configure your session:
    • Account: Select your Slurm account
    • Partition: Choose compute
    • Number of cores: 1-8 (start with 2)
    • Memory (GB): 2-32 (start with 4)
    • Hours: Session duration
  3. Click Launch
  4. Copy temporary password
  5. Connect when ready
  6. Enter temporary password

Tips:

Remote Desktop (MATE)

Description: Full Linux desktop environment with graphical applications.

Use Cases:

How to Launch:

  1. Click Interactive Apps → Desktop
  2. Configure resources (similar to other apps)
  3. Choose MATE desktop environment
  4. Launch and connect
  5. Use the desktop like a regular Linux workstation

Tips:

Resource Selection Guidelines

Choosing the right resources helps you get work done efficiently without wasting cluster capacity:

Application Typical Use Cores Memory Duration
JupyterLab Data exploration 2 4 GB 2-4 hours
JupyterLab Data processing 4-8 8-16 GB 4-8 hours
RStudio Interactive analysis 2-4 8 GB 2-4 hours
RStudio Large datasets 8-16 32-64 GB 4-8 hours
Code Server Development 2 4 GB 4-8 hours
Desktop GUI applications 4 8 GB 2-4 hours

Remember: You can always launch a new session with more resources if needed. Start small and scale up.

File Management

Files App

The built-in file manager lets you:

Accessing the File Manager:

  1. Click Files in the top menu
  2. Choose a location:
    • Home Directory: Your personal files
    • SciData: Shared scientific data
    • Any custom path

Common Operations:

Data Transfer

Small Files (<100 MB): Use the web file manager upload/download feature.

Large Files (>100 MB): Use command-line tools via shell access:

# From your local machine to cluster
scp large_file.tar.gz username@hpc.vogelwarte.ch:/home/username@vogelwarte.ch/

# Using rsync for efficient transfer
rsync -avzP local_directory/ username@hpc.vogelwarte.ch:~/remote_directory/

# From cluster to local machine
scp username@hpc.vogelwarte.ch:~/results.zip ./

Shared Data Storage:

Shell Access

Cluster Shell Access

Open OnDemand provides web-based terminal access to the cluster.

How to Access:

  1. Click Clusters in the top menu
  2. Select Shell Access or your cluster name
  3. A terminal window opens in your browser

What You Can Do:

Session Timeouts:

Tips:

Basic Slurm Commands

If you need to submit batch jobs from the shell:

# View partition information
sinfo

# Submit a batch job
sbatch job_script.sh

# Check your job queue
squeue -u $USER

# Cancel a job
scancel <job_id>

# View job details
scontrol show job <job_id>

# View cluster usage
squeue

Note: Most users will use interactive apps and won't need to submit batch jobs directly.

Best Practices

Resource Management

  1. Request Appropriate Resources

    • Don't over-request cores/memory you won't use
    • Start small and scale up if needed
    • Consider other users sharing the cluster

  2. Session Duration

    • Choose realistic time limits
    • Terminate sessions when done (don't leave them running)
    • Save your work frequently

  3. Data Storage

    • Home directory: Personal files, code, small datasets
    • SciData: Shared datasets, collaborative projects
    • Scratch: Temporary high-I/O work (files may be deleted)

Security

  1. Authentication

    • Never share your credentials
    • Log out when finished
    • Use VPN when accessing remotely

  2. Data Handling

    • Don't store sensitive data without proper permissions
    • Check file permissions for shared data
    • Follow institutional data policies

Performance

  1. Efficient Computing

    • Close unused applications to free resources
    • Use appropriate partitions for your work
    • Optimize code before requesting large resources

  2. File Operations

    • Use rsync for large transfers
    • Avoid many small file operations
    • Clean up old files and data regularly

Troubleshooting

Common Issues

Issue: Cannot log in

Issue: Interactive app won't start (stays in "Queued" state)

Issue: Session disconnected unexpectedly

Issue: Application runs out of memory

Issue: Can't access shared data

Issue: Files don't appear in file manager

Getting Help

Before Contacting Support:

  1. Note the exact error message
  2. Record what you were trying to do
  3. Check this guide and FAQs
  4. Try basic troubleshooting steps

Session Information: When reporting issues with interactive apps, provide:

Support

Documentation

Contact

VoWa HPC Support Team

What to Include in Support Requests:

System Status

Check Cluster Status:

Appendix

Slurm Accounts

Your jobs run under Slurm accounts for resource tracking:

Account Description Typical Use
sci_it IT Science Account General scientific computing
root Root Account Administrative or special projects

Check your accounts:

sacctmgr show user $USER

Partitions

Compute resources are divided into partitions:

Partition Description Typical Resources
normal General computing Standard CPU nodes

Software Environment

Containerized Applications: All interactive apps run in Apptainer (formerly Singularity) containers, providing:

Custom Software: Contact support if you need:

Keyboard Shortcuts

In Web Shell:

In File Manager:

In Interactive Apps: Depends on the application (JupyterLab, RStudio, VS Code each have their own shortcuts)

Changelog

Version 1.0 (December 2025)

Quick Reference Card

URLs

Getting Help

Resource Recommendations

Storage Paths

End of User Guide

This guide is maintained by the SciIT-Team. Suggestions and corrections welcome!

Revision #3
Created 2025-12-03 06:04:21 UTC by Stefan Hofstetter
Updated 2025-12-03 12:41:40 UTC by Stefan Hofstetter