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CSaW News

  • Scheduled Maintenance & Downtime
    • There is no scheduled maintenance at this time.
  • Updates
    • 08/26/2024 - HTCondor Cookbook & Apptainer Example
    • 07/29/2024 - Email Notifications
    • 04/03/2024 - JupyterHub
    • 01/04/2024 - HTCondor 23.0
    • 09/22/2023 - HTCondor 10.8
    • 01/12/2023 - CSCI Lab Scheduler Restored
    • 12/27/2022 - OS Updates, Account Changes
    • 05/10/2022 - GROMACS & Much More!
    • Older News

JupyterHub

  • JupyterHub
    • Overview
      • Accessing JupyterHub
      • Implementation
      • Limitations
      • Requesting resources
      • Basic JupyterLab usage
      • Stopping the JupyterLab server
    • Environments
      • Default
      • Remote Desktop
    • Using the Remote Desktop
      • Copy and Paste
        • Copy
          • The easy way…
          • If the easy way isn’t working…
        • Paste
      • Downloading Files with the browser
      • GPU Acceleration
    • Creating a Custom Python Environment (ipykernel)
    • Custom Containers (Apptainer)
      • Building Custom Containers
        • Extending Existing Containers
        • Building Containers From Scratch
      • Using Custom Containers

CSaW Docs

  • Getting Started
    • Logging in to the cluster
    • Navigating around the file system
      • The basics
      • Good places to know about on the file system
    • Copying files to and from the cluster
      • Copy files to the cluster
      • Copy files from the cluster
    • Using the job scheduler
      • Scheduling background information
      • Viewing the job queue and status of your jobs
      • Testing your software
      • Submitting a job
        • Determining the correct universe to run in
        • Writing a job submission script
        • Submitting to the vanilla universe
          • Super basic example
          • Basic example
          • Basic example with arguments
          • Queueing multiple jobs from the same file
          • Queueing multiple jobs from the same file with globbing
        • Submitting to the parallel universe
          • Basic OpenMPI example
      • Removing jobs
      • Cluster node status
    • Additional resources
      • Man pages
      • HTCondor Manual
      • Cluster F.A.Q.
      • Direct Support
  • HTCondor Submission File Examples
    • Apptainer
      • Overview
      • Using Existing Images
        • From Docker Hub
      • Running Containers
        • Run
        • Exec
        • Shell
        • Other Options
          • Mounting Other Directories
          • Using a GPU
      • Submitting to HTCondor
        • Using the Vanilla Universe
        • Using a GPU in the Vanilla Universe
        • Using the Container Universe
        • Leveraging a Container Registry
        • Transferring the Container Image
        • Using a GPU with the Container Universe
      • Building Your Own containers
        • Writing an Apptainer Definition File (.def)
        • Building the .sif File
        • Building With a Personal System
      • Unsupported Features
        • Fakeroot Containers
        • Notes on Docker Compatibility
      • Additional Notes / Tips
        • Apptainer Cache
        • Clearing Out Your Cache
    • GROMACS
      • Overview
      • Example Files
        • Download the Needed Files
      • Interacting with GROMACS via HTCondor
        • Getting an Interactive Prompt on a Compute Node
        • Submitting the mdrun job
      • Example Files Explained
        • gmx.sh
        • gmx-gpu.sh
        • mdrun-gpu.htsub
      • Currently Available Versions
      • Additional References
    • Notifications
      • Overview
      • Example Submission Files
      • Example Emails
      • Limits
    • Python
      • Basic Python
      • Virtual Environments
        • Using a Wrapper Script
        • Manually setting the PATH environment variable
      • Anaconda / Miniconda
        • Downloading and Installing Miniconda
  • HTCondor Cookbook
    • Overview
    • Submitting lots of Jobs
      • Setting the maximum number to run simultaneously
      • Setting the maximum number to keep around idle
      • Creating jobs from a list of files
      • Creating jobs from a list of directories
      • Digging deep into directories to find jobs
      • Creating jobs from a file of pre-determined arguments
      • Limiting the number of jobs for testing
    • Using GPUs from the CSE Cluster
    • Requesting an H100
    • Ensuring Access to InfiniBand
    • Submit your own recipes
  • Cluster F.A.Q.
    • How
      • How do I see my job status?
      • How do I see the status of all jobs, not just my own?
      • How do I remove my job?
      • How do I see the CPU resources in use and available?
      • How do I see the GPU resources in use and available?
      • How do I schedule a job to use multiple CPUs?
      • How do I schedule a job to use a GPU?
      • How do I get a shell on the node running my job so I can check on it?
      • How do I get an interactive shell on an execute node so I can test before submitting a job?
      • How do I build my software against CUDA?
      • How do I run my software against a particular version of CUDA / CUDNN?
      • How do I submit a job for running on the CSCI desktops?
        • From CSE or CSCI head node
        • From csci-lab-head as a CSCI student
        • From a CSCI lab system as a CSCI student
      • How do I manually specify my accounting group?
      • How do I connect to the VPN?
      • How much disk storage space do I have?
      • How do I use the scratch SSD space?
      • How do I run a job on a specific node?
      • How do I use the module system?
      • How do I use other versions of GCC?
    • Why
      • Why is my job in a “hold” state?
      • Why is my job still idle?
      • Why does condor_userprio show my user name with a group prefix?
      • Why is there a quota / limit on disk space?
      • Why does VS Code Remote - SSH plugin keep disconnecting me?
    • What
      • What is the maximum amount of resources I can request?
        • CSE cluster
        • CSCI cluster
        • CSCI desktops
      • What kind of jobs should I be running on CSCI desktops?
      • What happens if I use more resources than I request?
      • What does ‘Exec format error’ mean?
      • What is the cleanup policy for the scratch disk space?
      • What is Preemption and how do I opt into it?
  • System Details
    • College of Science and Engineering
      • Compute Nodes
        • Compute (8x)
        • Compute (8x)
        • Compute (4x)
      • Graphics Nodes
        • GPU (2x)
        • GPU (1x)
        • GPU (1x)
      • Support Systems & Miscellaneous
        • Head Node (x1)
        • Network
          • InfiniBand
          • Ethernet
    • Computer Science
      • Compute Nodes
        • Compute (8x)
      • Graphics Nodes
        • GPU (3x)
        • GPU (2x)
        • GPU (1x)
      • Support Systems & Miscellaneous
        • Head Node (1x)
        • Network
          • InfiniBand
          • Ethernet
    • Shared Storage
      • Main Storage (1x)
      • Backup Storage (1x)

Cluster Account & Project Requests

  • Cluster Account Creation
    • Requirements
    • Request your account creation
    • Get confirmation
    • Testing your account
  • Cluster Senior Project Creation
    • Overview
    • Requirements
    • Request your group and storage space
    • Get confirmation
    • Testing your account

Contact

  • Support
    • Email
    • Microsoft Teams
    • In Person

Appendix

  • Glossary
  • Index
CSaW
  • JupyterHub

JupyterHub

Accessing JupyterHub

CSaW’s JupyterHub instances are reachable from on campus or via the VPN when at home.

The CSE JupyterHub instance can be reached by visiting:

  • https://cse-head.cluster.cs.wwu.edu

The CSCI JupyterHub instance can be reached by visiting:

  • https://csci-head.cluster.cs.wwu.edu

JupyterHub on CSaW

  • Overview
    • Accessing JupyterHub
    • Implementation
    • Limitations
    • Requesting resources
    • Basic JupyterLab usage
    • Stopping the JupyterLab server
  • Environments
    • Default
    • Remote Desktop
  • Using the Remote Desktop
    • Copy and Paste
    • Downloading Files with the browser
    • GPU Acceleration
  • Creating a Custom Python Environment (ipykernel)
  • Custom Containers (Apptainer)
    • Building Custom Containers
    • Using Custom Containers
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