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CSaW News
Scheduled Maintenance & Downtime
01/02/2025 - OS Upgrade & HTCondor Upgrade
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 account confirmation
Testing your account
Cluster Senior Project Creation
Overview
Requirements
Request your group and storage space
Get project confirmation
Testing your accounts
Contact
Support
Email
Microsoft Teams
In Person
Appendix
Glossary
Index
CSaW
Computational Science at Western (CSaW)
Computational Science at Western (CSaW)
CSaW News
Scheduled Maintenance & Downtime
01/02/2025 - OS Upgrade & HTCondor Upgrade
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
Environments
Using the Remote Desktop
Creating a Custom Python Environment (ipykernel)
Custom Containers (Apptainer)
CSaW Docs
Getting Started
Logging in to the cluster
Navigating around the file system
Copying files to and from the cluster
Using the job scheduler
Additional resources
HTCondor Submission File Examples
Apptainer
GROMACS
Notifications
Python
HTCondor Cookbook
Overview
Submitting lots of Jobs
Using GPUs from the CSE Cluster
Requesting an H100
Ensuring Access to InfiniBand
Submit your own recipes
Cluster F.A.Q.
How
Why
What
System Details
College of Science and Engineering
Computer Science
Shared Storage
Cluster Account & Project Requests
Cluster Account Creation
Requirements
Request your account creation
Get account confirmation
Testing your account
Cluster Senior Project Creation
Overview
Requirements
Request your group and storage space
Get project confirmation
Testing your accounts
Contact
Support
Email
Microsoft Teams
In Person
Appendix
Glossary
Index