/tag/hpc
Virginia Women in HPC - Student Lightning Talks: November 12, 2024
On November 12, 2024 from 1-2 p.m. EST, Virginia Women in High Performance Computing (VA-WHPC) will be hosting 8 students as they present research lightning talks to members of the HPC community from across Virginia. See here for details.
Interested in giving a lightning talk? You’ll get 3 minutes and 1-2 slides to tell us all about your research. Don’t miss this chance to practice your presentation skills and share your research with a diverse audience! Sign up here by the end of today, October 24th! A helpful guide on how to give a successful lightning talk is available here
Miniforge and UVA HPC
Overview Miniforge provides the Conda and Mamba package managers, with the default channel being conda-forge.
(Mamba is a reimplementation of the Conda package manager in C++ that uses a state-of-the-art library “libsolv” for much faster dependency solving.)
We have transitioned from Anaconda to Miniforge on Oct 15, 2024. See here for details.
Available Versions The current installation of Miniforge
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider miniforge The output of the command shows the available Miniforge
module versions.
For detailed information about a particular Miniforge
module, including how to load the module, run the module spider command with the module’s full version label.
Afton Cluster Dedicated to Prof. John Hawley
On September 16, 2024, RC dedicated the new Afton computing cluster to the memory of John F. Hawley (1958-2021), late Professor of Astronomy who was a leading researcher in computational astrophysics. He also served in the Office of the Dean of the College and Graduate School of Arts and Sciences for nine years, first as Associate Dean for the Sciences and later as Senior Associate Dean for Academic Affairs. The ceremony featured some remarks by Josh Baller, Associate Vice President for Research Computing, and Scott Ruffner, Director of Infrastructure for Research Computing, along with a recorded message from Provost Ian Baucom.
Thermal properties of materials from first-principles
Prof. Esfarjani’s group is using the HPC cluster to develop the Anharmonic LAttice DYNamics (ALADYN) software suite to calculate thermal transport properties and phase transitions from first-principles. The codes can extract force constants, solve the Boltzmann transport equation, predict thermal equilibrium based on the self-consistent phonon theory, and run molecular dynamics simulations within an anharmonic force field. The figure shows the phonon density of states and dispersion curve of Ge obtained from ALADYN.
PI: Keivan Esfarjani, PhD (Department of Materials Science & Engineering)
Virginia Women in HPC - Building and Maintaining Supportive Communities
When: Sep 03, 2023, 01:00 PM EST (US and Canada).
What: Join us for a first of its kind Women in High Performance Computing (WHPC) event, co-hosted by the Northeast, Purdue, and Virginia WHPC chapters to engage in discussions about current challenges and opportunities for fostering a more diverse and inclusive WHPC community. Our panelists will provide an overview of their chapters’ community activities and offer insights into navigating hurdles and fostering professional growth within HPC.
The format for this event will be a brief presentation by the hosts followed by theme-focused breakout rooms where participants will be invited to share their experience and personal perspective.
Research Computing Open House 2024
UPDATE: The Research Computing Open House was held on a blustery, rainy day, but the spirits of the staff and attendees were not dampened. Turnout was above expectations despite the wet weather. Attendees enjoyed the buffet and their interactions with RC staff.
The winners of the random-drawing prizes were
Maria Luana Morais, SOM Matt Panzer, SEAS Artun Duransoy, SEAS
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.
RC's Data Analytics Center (DAC): Now Serving UVA's Research Community
The Data Analytics Center is UVA’s new hub for the management and analysis of your large research data. Need help with your computational research? DAC staff specialize in key domain areas such as image processing, text analysis, bioinformatics, computational chemistry and physics, neural networks, and more. And because the DAC team is located within Research Computing, they can assist in getting your workflows running on the University’s high-performance cluster or secure data system. They can answer your basic computational questions or, through funded engagements, be embedded in your projects.
Big data doesn’t have to be a big deal. Learn how DAC can assist with your computational research – schedule an initial consultation with one of their data analysts by submitting a consultation request.
Allocations
Time on Rivanna/Afton is allocated as Service Units (SUs). One SU corresponds to one core-hour. Multiple SUs make up what is called an allocation (e.g., a new allocation = 1M SUs). Allocations are managed through Grouper (requires VPN connection) groups that should be created by Principal Investigators (PIs) before they submit an allocation request. Eligibility and Account Creation All UVA faculty are eligible to serve as PI and request access to RC services (e.g. storage & HPC allocations, virtual machines, microservices) for their research group. Postdocs and staff are encouraged to use an allocation provided by a faculty sponsor, although they may request their own allocation pending departmental or RC approval.
Virginia Women in HPC Events in September & October
VA-WHPC September Event - Leadership Journeys Time: Sep 19, 2023, 01:00 PM EST (US and Canada).
Join us for our next community event featuring Dr. Neena Imam as she shares her personal view of challenges and successes experienced throughout her inspiring leadership journey in research, HPC and AI computing. Come learn about career strategies, ask questions, and contribute to our discussion of how the playing field may be leveled to offer equitable IT & HPC leadership opportunities for women and minorities.
Dr. Imam earned a PhD in Electrical Engineering and has been engaged in research and computing in a variety of roles.
NVIDIA DGX BasePOD™
Introducing the NVIDIA DGX BasePOD™ As artificial intelligence (AI) and machine learning (ML) continue to change how academic research is conducted, the NVIDIA DGX BasePOD, or BasePOD, brings new AI and ML functionality UVA’s High-Performance Computing (HPC) system. The BasePOD is a cluster of high-performance GPUs that allows large deep-learning models to be created and utilized at UVA.
The NVIDIA DGX BasePOD™ on Rivanna and Afton, hereafter referred to as the POD, is comprised of:
10 DGX A100 nodes with 2TB of RAM memory per node 80 GB GPU memory per GPU device Compared to the regular GPU nodes, the POD contains advanced features such as:
GPU-enabled Software and UVA HPC
Please note that certain modules can only run on specific GPU types. This will be displayed in a message upon loading the module.
Certain software applications may also able to take advantage of the advanced capabilities provided by the NVIDIA DGX BasePOD™.
Learn More Module Category Description alphafold bio gpu Open source code for AlphaFold amber chem gpu Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. cellpose bio gpu a generalist algorithm for cellular segmentation clara-parabricks bio gpu NVIDIA Parabricks is the only GPU-accelerated computational genomics toolkit that delivers fast and accurate analysis for sequencing centers, clinical teams, genomics researchers, and next-generation sequencing instrument developers.
Virginia Women in HPC - Student Lightning Talks
What: Join us in welcoming 11 undergraduate and graduate students from across Virginia to talk about their research. The talks will be lightning style format allowing 3 minutes for students to present and 1-2 questions and 1-2 questions from the audience. Don’t miss out on this fantastic opportunity to hear about a variety of research topics within HPC!
Event Time: April 4, 2023, 01:00 PM EST (US and Canada).
Featured Speakers: Lakshmi Miller - Graduate Student
Aerospace and Ocean Engineering, Virginia Tech
“CFD Informed Maneuvering of AUVs”
Rashmi Chawla - Graduate Student
Aerospace Engineering, Virginia Tech
“Multiphysics Modeling of UHTCs using Material Point Method”
Workshops
UVA Research Computing provides training opportunities covering a variety of data analysis, basic programming and computational topics. All of the classes listed below are taught by experts and are freely available to UVa faculty, staff and students.
New to High-Performance Computing? We offer orientation sessions to introduce you to the Afton & Rivanna HPC systems on Wednesdays (appointment required).
Wednesdays 3:00-4:00pm Sign up for an “Intro to HPC” session Upcoming Workshops DATE WORKSHOP INSTRUCTOR There are currently no training events scheduled. Please check back soon! Research Computing is partnering with the Research Library and the Health Sciences Library to deliver workshops covering a variety of research computing topics.
education,
workshops
bioinformatics,
containers,
HPC,
image processing,
Ivy,
Matlab,
programming,
Python,
R,
Rivanna,
Shiny
Virginia Women in HPC - Women in HPC & IT Leadership Roles
Topic: Women in HPC & IT Leadership Roles.
When: October 12, 2022 01:00 PM, Eastern Time (US and Canada).
Join us for our Fall community meeting to hear from female leaders in the HPC & IT field sharing challenges and successes experienced throughout their careers. Don’t miss this fantastic opportunity to learn about career strategies, share your experience, and contribute to our discussion of how the playing field may be leveled to offer equitable HPC & IT leadership opportunities for women and minorities. Attendees are invited to share their own experiences and engage with panelists during this interactive Q&A session.
`ssh` on UVA HPC
The secure shell ssh is the primary application used to access the HPC system from the command line.
Connecting to a Remote Host For Windows, MobaXterm is our recommended ssh client; this package also provides an SFTP client and an X11 server in one bundle.
Mac OSX and Linux users access the cluster from a terminal through OpenSSH, which are preinstalled on these operating systems. Open a terminal (on OSX, the Terminal application) and type
ssh -Y mst3k@login.hpc.virginia.edu where mst3k should be replaced by your user ID. You will generally need to use this format unless you set up your user account on your Mac or Linux system with your UVA ID.
Mission
Research Computing empowers UVA researchers to achieve more with cutting-edge computational resources. Our support team strives to create innovative solutions for researchers who need help solving complex optimization, parallelization, workflow, and data analysis issues. We build and maintain the University’s best computing platforms while educating the next generation of researchers on the power of advanced computing.
Research Computing Student Workers
The Research Computing Student Worker Program is dedicated to supporting RC staff and advancing computational research at UVA. Through this program, student workers will undertake short-term projects, relieving RC staff of certain responsibilities and allowing them to devote more time to scaling support for complex, research-domain endeavors. This initiative not only benefits RC staff but also provides students with valuable exposure to high-performance computing (HPC) and scientific computing early in their academic journey. Student Manager: Gladys K. Andino, PhD, Strategic Services and Education Manager For any questions, please email rc-studentjobs@virginia.edu. Check out our Student Workers!
Adam Eubanks Matthew Galitz Hariprasad Periyasamy Mohan Shankar Steven Siadaty Jennifer Vo Recent Projects Student: Adam Eubanks Project Description: Adam contributed to the XALT containerization project by developing a Docker container for running XALT on UVA RC clusters.
Rivanna Storage
There are a variety of options for storing large-scale research data at UVa. Public and Internal Use data storage systems can be accessed from the Rivanna and Afton high performance computing systems.
Storage Directories Name Quota Price Data Protection Accessible from Best Practices /home 200GB Free 1-week snapshots Rivanna/Afton /home is best used as a working directory when using Rivanna/Afton interactively. Slurm jobs run against /home will be slower than those run against /scratch. The /home directory is a personal storage space that is not shareable with other users. /scratch 10TB Free No backups, Data removed 90 days after last file access time Rivanna/Afton /scratch is a high performance parallel filesystem that is suitable for large scale computational work.
The Make Tool
Overview Make is a program used primarily on Unix systems to manage compiling and linking (building) programs written in C, C++, Fortran, or other compiled languages. Make operates on targets using rules to create those targets. It has a set of built-in rules but users may write their own or override the default rules. Make scans the dependencies of each target looking for files newer than the target. If it finds them, it recreates the target. Targets may and usually do depend on other targets; make will work its way through the chain to rebuild the final target, which is typically an executable.
BART Web
BART (Binding Analysis for Regulation of Transcription) Web Working with researchers in the Zang Lab in the Center for Public Health Genomics
(CPHG), RC helped launch BARTweb,
an interactive web-based tool for users to analyze their Genelist or ChIP-seq datasets. BARTweb is a containerized
Flask front-end (written in Python) that ingests files and submits them to a more robust Python-based genomics pipeline
running on Rivanna, UVA’s high performance computing cluster (HPC). This architecture – of a public web application that
uses a supercomputer to process data – is a new model for UVA, and one that eases the learning curve for researchers who
Computing Systems
UVA Research Computing can help you find the right system for your computational workloads. From supercomputers to HIPAA secure systems to cloud-based deployments with advanced infrastructure, various systems are available to researchers.
Facilities Statement - Are you submitting a grant proposal and need standard information about UVA research computing environments? Get it here. High Performance Computing - Rivanna and Afton A traditional high performance cluster with a resource manager, a large file system, modules, and MPI processing. Get Started with UVA HPC Secure Computing for Highly Sensitive Data - Ivy A multi-platform, HIPAA-compliant system for secure data that includes dedicated virtual machines (Linux and Windows), JupyterLab Notebooks, and Apache Spark.
Political Sentiment Analysis
The nature of political communication has been fundamentally altered by the emergence of social media. In earlier eras, social scientists, journalists, and citizens could focus on static statements by politicians and candidates in order to understand the nature of political discourse. Social scientists studying political communication would design surveys and focus groups to understand which messages were received by citizens, and with what effect. Today, as news moves to digital platforms and as political figures increasingly rely on social media, political communication is fundamentally dynamic. Studying patterns of communication among politicians, their supporters, and their critics requires scholarly focus on the content, sentiment, and framing of posts on various social media platforms.
Pricing
Below is a schedule of prices for Research Computing resources.
High Performance Computing Allocations Type SU Limits Cost SU Expiration Standard None Free 12 months Purchased None $0.01 Never Instructional 100,000 Free 2 weeks after last training session A service unit (SU) resembles usage of a trackable hardware resource for a specified amount of time. In its simplest form 1 SU = 1 core hour, but the SU charge rate can vary based on the specific hardware used. Resources like GPUs and memory may incur additional SU charges. About Allocations
Storage Name Security Cost Research Project Standard $70/TB per year Research Standard Standard $45/TB per year (Each PI with an RC account will be granted up to 10 TB of Research Standard Storage at no charge1) High-Security Research Standard High $45/TB/year Storage Details Request Storage
ACCORD: Jupyter Lab
Back to Overview
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
Back to Overview
RStudio is the standard IDE for research using the R programming language.
Learn more about RStudio
ACCORD: Theia IDE
Back to Overview
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
High Performance Computing
Research Computing supports all UVA researchers who are interested in writing code to address their scientific inquiries. Whether these programming tasks are implemented interactively, in a series of scripts or as an open-source software package, services are available to provide guidance and enable collaborative development. RC has specific expertise in object-oriented programming in Matlab, R, and Python.
Examples of service areas include:
Collaborating on package development Reviewing and debugging code Preparing scripts to automate or expedite tasks Developing web interfaces for interactive data exploration Advising on integration of existing software tools UVA has three local computational facilities available to researchers: Rivanna, Afton, and Ivy.
UVA HPC Software
Overview Research Computing at UVA offers a variety of standard software packages for all UVA HPC users. We also install requested software based on the needs of the high-performance computing (HPC) community as a whole. Software used by a single group should be installed by that group’s members, ideally on leased storage controlled by the group. Departments with a set of widely-used software packages may install them to the lsp_apps space. The Research Computing group also provides limited assistance for individual installations.
For help installing research software on your PC, please contact Research Software Support at res-consult@virginia.edu.
Software Modules and Containers Software on the HPC system is accessed via environment modules or containers.
ACCESS: Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support
The NSF’s ACCESS (Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support) program builds upon the successes of the 11-year XSEDE project, while also expanding the ecosystem with capabilities for new modes of research and further democratizing participation. ACCESS Home: access-ci.org access-ci.org/about Allocations Allocations: allocations.access-ci.org Documentation Support: support.access-ci.org Community Engagement ACCESS: support.access-ci.org/affinity-groups Campus Champions: https://campuschampions.cyberinfrastructure.org UVa Research Computing has two Champions, Ed Hall and Katherine Holcomb For more help, please feel free to contact RC staff to set up a consultation or visit us during office hours.
XSEDE: Extreme Science and Engineering Development Environment
XSEDE’s Mission was to substantially enhance the productivity of a growing community of scholars, researchers, and engineers through access to advanced digital services that support open research; and coordinate and add significant value to the leading cyberinfrastructure resources funded by the NSF and other agencies. — The XSEDE project ended on August 31, 2022 and was succeeded by the ACCESS project.
XSEDE Home: www.xsede.org
Frequently Asked Questions
General Do you have a general computing question?
Read our FAQ› Rivanna and Afton High Performance Computing Platforms
Read our FAQ › Ivy Secure Data Computing Platform
Read our FAQ › Storage Research Data Storage & Transfer
Read our FAQ ›
Rivanna and Afton FAQs
General Usage Allocations Research Software Job Management Storage Management Data Transfer Downloading Files Other Questions General Usage How do I gain access to Rivanna/Afton? A faculty member must first request an allocation on the HPC system. Full details can be found here.
How do I log on to Rivanna/Afton? Use an SSH client from a campus-connected machine and connect to login.hpc.virginia.edu. Instructions for using ssh and other login tools, as well as recommended clients for different operating systems, are here. You can also access the HPC system through our Web-based interface Open OnDemand or FastX.
Off Campus? Connecting to Rivanna and Afton HPC systems from off Grounds via Secure Shell Access (SSH) or FastX requires a VPN connection.
Graphical SFTP/SCP Transfer Tools
Several options are available to transfer data files between a local computer and the HPC system through user-friendly, graphical methods.
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. Only Windows and Mac OSX operating systems are supported by the Cisco client provided by ITS. Linux users should refer to these unsupported instructions to install and configure a VPN. The More Secure Network requires authentication through Duo; users should follow the instructions on the dialog box to enter "
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.
Pulse Laser Irradiation and Surface Morphology
Dr. Zhigilei and his team are using Rivanna to perform large-scale atomistic simulations aimed at revealing fundamental processes responsible for the modification of surface morphology and microstructure of metal targets treated by short pulse laser irradiation. The simulations are performed with a highly-optimized parallel computer code capable of reproducing collective dynamics in systems consisting of up to billions of atoms. As a result, the simulations naturally account for the complexity of the material response to the rapid laser energy deposition and provide clear visual representations, or “atomic movies,” of laser-induced dynamic processes. The mechanistic insights revealed in the simulations have an immediate impact on the development of the theoretical understanding of laser-induced processes and assist in optimization of laser processing parameters in current applications based on laser surface modification and nanoparticle generation in laser ablation.
Fluid Dynamics and Reef Health
Professor Reidenbach and his team are using Rivanna to run computational fluid dynamics simulations of wave and tide driven flows over coral reefs in order to determine how storms, nutrient inputs, and sediments impact reef health. This is an image of dye fluxing from the surface of the Hawaiian coral Porites compressa utilizing a technique known as planar laser induced fluorescence (PLIF). Reefs such as this one have been severely impacted by human alteration, both locally through additional inputs of sediments and nutrients, and globally through increased sea surface temperatures caused by climate change. Reidenbach is hopeful that his computational models will allow scientists to better predict the future health of reefs based on human activity and improve global reef restoration efforts.
Economic Market Behavior
While conducting research for a highly-technical study of market behavior, Dr. Ciliberto realized that he needed to parallelize an integration over a sample distribution. RC staff member Ed Hall successfully parallelized Ciliberto’s Matlab code and taught him how to do production runs on the University’s high-performance clusters. “The second stage estimator was computationally intensive,” Ciliberto recalls. “We needed to compute the distribution of the residuals and unobservables for multiple parameter values and at many different points of the distribution, which requires parallelizing the computation. Ed Hall’s expertise in this area was crucial. In fact, without Ed’s contribution, this project could not have been completed.
Tracking Bug Movements
Ed Hall worked with the Brodie Lab in the Biology department, to set up a workflow to analyze videos of bug tracking experiments on the Rivanna Linux cluster. They wanted to use the community Matlab software (idTracker) for beetle movement tracking. Their two goals were to shorten the software runtime and to automate the process. There was a large backlog of videos to go through. Ed installed the idTracker software on Rivanna and modified the code to parallelize the bug tracking process. He wrote and documented shell scripts to automate their workflow on the cluster.
PI: Edmund Brodie, PhD (Department of Biology)
Logging in to the UVA HPC systems
The UVA HPC systems (Rivanna and Afton) are accessible through a web portal, secure shell terminals, or a remote desktop environment. For of all of these access points, your login is your UVA computing ID and your password is your Eservices password. If you do not know your Eservices password you must change it through ITS.
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.
MobaXterm
MobaXterm is the recommended login tool for Windows users. It bundles a tabbed ssh client, a graphical drag-and-drop sftp client, and an X11 window server for Windows, all in one easy-to-use package. Some other tools included are a simple text editor with syntax coloring and several useful Unix utilities such as cd, ls, grep, and others, so that you can run a lightweight Linux environment on your local machine as well as use it to log in to a remote system.
Download To download MobaXterm, click the link below. Select the “Home” version, “Installer” edition,
Download MobaXterm
Run the installer as directed.
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.
Quantifying Cerebral Cortex Regions
A powerful new technique for quantifying regions of the cerebral cortex was developed by Nick Tustison and James Stone at the University of Virginia along with collaborators from the University of Pennsylvania. It was evaluated using large data sets comprised of magnetic resonance imaging (MRI) of the human brain processed on a high-performance computing cluster at the University of Virginia. By making this technique available as open-source software, other neuroscientists are now able to investigate various hypotheses concerning the relationship between brain structure and development. Tustison’s and Stone’s software has been widely disseminated and is being actively incorporated into a variety of clinical research studies, including a collaborative effort between the Department of Defense and Department of Veterans Affairs, exploring the long term effects of traumatic brain injury (TBI) among military service members.
Software Modules
The lmod modules system on the HPC system enables users to easily set their environments for selected software and to choose versions if appropriate.
The lmod system is hierarchical; not every module is available in every environment. We provide a core environment which contains most of the software installed by Research Computing staff, but software that requires a compiler or MPI is not in that environment and a compiler must first be loaded.
View All Modules Basic Commands List all available software
module avail Use key to list all modules in a particular category. The current choices are
base, bio, cae, chem, compiler, data, debugger, devel, geo, ide, lang, lib, math, mpi, numlib, perf, phys, system, toolchain, tools, vis, licensed Example:
UVA HPC Software List
Module Category Description R lang R is a free software environment for statistical computing and graphics. abinit chem ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. abseil lib Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.
What is Research Computing?
UVA Research Computing (RC) is a new program that aims to support computational biomedical research by providing advanced cyberinfrastructure and expertise in data analysis at scale. Our mission is to foster a culture of computational thinking and promote interdisciplinary collaboration in various data-driven research domains. We offer services related to high performance computing, cloud architecture, scientific programming and big data solutions. We also aim to promote computationally intensive research at UVA through collaborative efforts such as UVA’s own CADRE (Computation And Data Resource Exchange) and XSEDE (Extreme Science and Engineering Discovery Environment).
One of our driving philosophies is that researchers already have medical and scientific expertise, and should not have to become computing experts on top of that.
User Guides
High Performance Computing Standard and high security HPC to run your code, generally written in R, Python or shell scripts.
Computing Environments at UVA
Research Computing (UVA-RC) serves as the principal center for computational resources and associated expertise at the University of Virginia (UVA). Each year UVA-RC provides services to over 433 active PIs that sponsor more than 2463 unique users from 14 different schools/organizations at the University, maintaining a breadth of systems to support the computational and data intensive research of UVA’s researchers.
High Performance Computing UVA-RC’s High Performance Computing (HPC) systems are designed with high-speed networks, high performance storage, GPUs, and large amounts of memory in order to support modern compute and memory intensive programs. UVA-RC operates two HPC systems, Rivanna and Afton.
