/tag/queues
Slurm Script Generator
Using UVA’s High-Performance Computing Systems
Afton is the University of Virginia’s newest High-Performance Computing system. The Afton supercomputer is comprised of 300 compute node each with 96 compute cores based on the AMD EPYC 9454 architecture for a total of 28,800 cores. The increase in core count is augmented by a significant increase in memory per node compared to Rivanna. Each Afton node boasts a minimum of 750 Gigabytes of memory, with some supporting up to 1.5 Terabytes of RAM memory. The large amount of memory per node allows researchers to efficiently work with the ever-expanding datasets we are seeing across diverse research disciplines. The Afton and Rivanna systems provide access to 55 nodes with NVIDIA general purpose GPU accelerators (RTX2080, RTX3090, A6000, V100, A40, and A100), including an NVIDIA BasePOD.
ACCORD: Jupyter Lab
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Jupyter Lab allows for interactive, notebook-based analysis of data. A good choice for pulling quick results or refining your code in numerous languages including Python, R, Julia, bash, and others.
Learn more about Jupyter Lab
ACCORD: RStudio
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RStudio is the standard IDE for research using the R programming language.
Learn more about RStudio
ACCORD: Theia IDE
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Theia Python is a rich IDE that allows researchers to manage their files and data, write code with an intelligent editor, and execute code within a terminal session.
Learn more about the Theia Python IDE
FastX Web Portal
Overview FastX is a commercial solution that enables users to start an X11 desktop environment on a remote system. It is available on the UVA HPC frontends. Using it is equivalent to logging in at the console of the frontend.
Using FastX for the Web We recommend that most users access FastX through its Web interface. To connect, point a browser to:
https://fastx.hpc.virginia.edu
Off Campus? Connecting to Rivanna and Afton HPC systems from off Grounds via Secure Shell Access (SSH) or FastX requires a VPN connection. We recommend using the UVA More Secure Network if available. The UVA Anywhere VPN can be used if the UVA More Secure Network is not available.
Open OnDemand
Overview Open OnDemand is a graphical user interface that allows access to UVA HPC via a web browser. Within the Open OnDemand environment users have access to a file explorer; interactive applications like JupyterLab, RStudio Server & FastX Web; a command line interface; and a job composer and job monitor.
Logging in to UVA HPC The HPC system is accessible through the Open OnDemand web client at https://ood.hpc.virginia.edu. Your login is your UVA computing ID and your password is your Netbadge password. Some services, such as FastX Web, require the Eservices password. If you do not know your Eservices password you must change it through ITS by changing your Netbadge password (see instructions).
Open OnDemand: File Explorer
Open OnDemand provides an integrated file explorer to browse and manage small files. Rivanna and Afton have multiple locations to store your files with different limits and policies. Specifically, each user has a relatively small amount of permanent storage in his/her home directory and a large amount of temporary storage (/scratch) where large data sets can be staged for job processing. Researchers can also lease storage that is accessible on Rivanna. Contact Research Computing or visit the storage website for more information.
The file explorer provides these basic functions:
Renaming of files Viewing of text and small image files Editing text files Downloading & uploading small files To see the storage locations that you have access to from within Open OnDemand, click on the Files menu.
Open OnDemand: Job Composer
Open OnDemand allows you to submit Slurm jobs to the cluster without using shell commands.
The job composer simplifies the process of:
Creating a script Submitting a job Downloading results Submitting Jobs We will describe creating a job from a template provided by the system.
Open the Job Composer tab from the Open OnDemand Dashboard.
Go to the New Job tab and from the dropdown, select From Template. You can choose the default template or you can select from the list.
Click on Create New Job. You will need to edit the file that pops up, so click the light blue Open Editor button at the bottom.
Slurm Job Manager
SLURM Would you like to take an interactive SLURM quiz? y/N |
Overview UVA HPC is a multi-user, managed environment. It is divided into login nodes (also called frontends), which are directly accessible by users, and compute nodes, which must be accessed through the resource manager. Users prepare their computational workloads, called jobs, on the login nodes and submit them to the job controller, a component of the resource manager that runs on login nodes and is responsible for scheduling jobs and monitoring the status of the compute nodes.
We use Slurm, an open-source tool that manages jobs for Linux clusters.
