‘Hero’ Calculation Capability Yields Significant Achievement

Basic biology textbooks will tell you that all life on Earth is built from four types of molecules: proteins, carbohydrates, lipids, and nucleic acids.  But what if we could actually show that these “molecules of life,” such as amino acids and DNA bases, can be formed naturally in the right environment? Researchers at the University of Florida are using HiPerGator – the fastest supercomputer in U.S. higher education – to test this experiment. 

“Our previous success enabled us to use Machine Learning and AI to calculate energies and forces on molecular systems, with results that are identical to those of high-level quantum chemistry but around 1 million times faster,” said Adrian Roitberg, Ph.D., a professor in UF’s Department of Chemistry who has been using Machine Learning to study chemical reactions for six years. “These questions have been asked before but, due to computational limitations, previous calculations used small numbers of atoms and could not explore the range of time needed to obtain results. But with HiPerGator, we can do it.” 

HiPerGator – with its AI models and vast capacity for Graphics Processing Units, or GPUs (specialized processors designed to accelerate graphics renderings) – is transforming the molecular research game. Until a decade ago, conducting research on the evolution and interactions of large collections of atoms and molecules could only be done using simple computer simulation experiments; the computing power needed to handle the datasets just wasn’t available.  Read the full press release here.

UFIT Senior Director Erik Deumens explained how this full takeover of HiPerGator was possible: 

“HiPerGator has the unique capability to run very large ‘hero’ calculations that use the entire machine, with the potential to lead to breakthroughs in science and scholarship,” Deumens said. “When we found out about the work Dr. Roitberg’s group was doing, we approached him to try a ‘hero’ run with the code he developed.” 

Researchers interested in discussing using HiPerGator for hero calculations are welcome to contact Dr. Deumens.

UFIT Announces Spring Research Computing Training Schedule

This semester’s Research Computing training schedule is packed with a variety of HiPerGator, Practicum AI workshops free for faculty, lab staff , postdoctoral candidates, and students.

Traditional, single-session Research Computing training options will be held on Thursdays in person and online from 10:40 a.m. – 12:00 p.m. Sessions include Introduction to Research Computing & HiPerGator, SLURM Submission Scripts, and Jupyter Notebook and Managing Conda Environments. A three-day Git and GitHub workshop in March, developed by Drs. Catia Silva and Matt Gitzendanner, will feature hands-on activities with no coding background or prerequisites required.

Practicum AI is returning this Spring with two beginner course series: Deep Learning Foundations and Python for AI. Both training series are intended for participants with limited experience who want to explore using applied AI. All Practicum AI sessions will be available via Zoom or in person at Malachowsky Hall’s NVIDIA Auditorium (room 1000).

Visit https://rc.ufl.edu/calendar/ to view the full training schedule and register for any of the workshops. Anyone with questions about Research Computing training, or who is interested is setting up a custom training for their lab team or a class, is welcome to contact Training Team Lead Dr. Matt Gitzendanner.

Getting Started with HiPerGator

To assist researchers and instructors in getting started with HiPerGator, UFIT produced a series of videos that explain the processes for setting up a HiPerGator account, training and support for UF’s high-performance computing environment, and using HiPerGator in undergraduate courses:

Getting Started with HiPerGator

Teaching with HiPerGator

UFIT also has a video explaining what ResVault is. That system can be used for computing on highly regulated data like export controlled data. HiPerGator is also certified to allow working with PHI if the proper procedure is followed.

Our Research Computing staff look forward to meeting you and enabling your line of inquiry. You’ll find many additional resources on the https://rc.ufl.edu/ website to help you begin your journey in UF’s high-performance computing environment, and staff are available for in-person and online consultations as needed to fit your schedule. Please contact Senior Director Erik Deumens if you have any questions about getting started with HiPerGator and our campus’s research computing ecosystem.

Multiple Storage Options for Research

Storage provided by UFIT’s Research Computing department is for research and educational data, code, and documents used on HiPerGator and its ecosystem. Registered HiPerGator users are allotted 40GB of storage in their home directory, but depending on the research project, more storage may be needed. To support research and discovery, UFIT manages three DDN EXAScaler filesystems and offers three tiers of additional storage–blue, orange, and red.

Blue for job input/output
Orange for “warm” storage
Red for Nvidia DGX A100 SuperPod workflows

Faculty with long-term projects should become familiar with the service levels included with each tier level. The storage offerings are described on the storage use policy page.
Access to additional storage resources is obtained either as a hardware investment or service investment. Learn more about HiPerGator hardware and service investments here:
https://rc.ufl.edu/get-started/purchase-allocation/. Typically, the turnaround time for provisioning additional storage resources is two to three business days.

Researchers from UF, SUS institutions, or SEC universities who would like a consult about their project’s storage needs are welcome to contact the Research Computing staff.

Collaborate with NVIDIA Center at UF

University of Florida researchers have the opportunity to collaborate with NVIDIA experts to accelerate their workflow, improve performance on algorithms, and have regular consults during their project. The NVIDIA AI Technology Center at UF (NVAITC) is a joint research center of UF and NVIDIA, with a mission to advance artificial intelligence education and research. The NVAITC is the first in the U.S. and enables UF’s researchers access to NVIDIA experts and be early adopters of NVIDIA’s advanced technologies.

Both research groups and individual researchers are eligible to apply. The NVAITC is university-wide so faculty from any college or department are welcome to become an NVAITC collaborator.

Interested in working with the NVAITC? Begin the process by contacting UF Site Manager Kaleb Smith. Dr. Smith is a senior data scientist with NVIDIA and evaluates prospective collaborations. For additional information or to request a consultation about the process, please email UFIT Research Computing’s AI Team Lead Ying Zhang.

UF-NVIDIA Hackathon: May 17-25

“Attending the 2023 Hackathon will help our team optimize our models to run on HiPerGator and increase their efficiency and performance,” wrote Warrington College of Business Assistant Professor Ivy Munoko. “We use a large dataset with tens of millions of data points.”

Partnering with NVIDIA and OpenACC, the second annual UF-NVIDIA GPU Hackathon began this week. Ten teams of computational researchers and developers are participating, including three external teams representing the National Oceanic and Atmospheric Administration, the University of Alabama, and Arizona State University. Each team is receiving mentorship in GPU programming, high-performance computing, and data applications from NVIDIA and UFIT staff. Professor Munoko’s team includes Karla Saldaña Ochoa, assistant professor, College of Design, Construction, and Planning, and Maxim Terekhov, Ph.D. candidate, Department of Information Systems and Operations Management.

The hackathon is an opportunity to port, accelerate, and optimize scientific applications with programming models and tools hosted through HiPerGator. Participants are also developing a deeper understanding of HiPerGator’s computational capabilities while utilizing applications on the latest supercomputing hardware. Researchers with questions about the hackathon or who would like to schedule a consult about UF-AI computing support may contact Applications Specialist and AI Support Team Lead Ms. Ying Zhang.

2023 UF+NVIDIA Hackathon

Together with NVIDIA and OpenACC, UFIT is hosting the second annual University of Florida Open Hackathon from May 17 – May 25, 2023.

Advanced parallel computing or GPU skills are NOT required. However, it is helpful for teams to know the basics of GPU programming and profiling. The application deadline is March 1, 2023, with selected teams being notified shortly thereafter.

Scientist and computing experts from NVIDIA, along with UFIT’s Research Computing AI team, will serve as mentors to help the hackathon teams optimize their code for GPU acceleration. UFIT will provide HiPerGator as the work platform for the hackathon. Priority acceptance will be given to UF-affiliated research groups and their collaborators, but faculty, students, and research staff from all Florida universities and SEC member institutions are encouraged to apply. Anyone with questions about the application process or the hackathon contest format are welcome to contact AI Support Team Lead Ms. Ying Zhang.

UFIT Awarded Contract with USDA

UFIT was recently awarded a multi-year contract to collaborate with the USDA’s Agricultural Research Service (ARS) to deliver AI training. UFIT Research Computing staff will offer sessions using established AI Practicum training modules as as develop new modules in consult with ARS staff. This contract will enhance existing Practicum AI content and allow UFIT to more rapidly build online content for the UF community and beyond. The new modules developed with the USDA will also be available to UF faculty, staff and students, with particular benefit to the IFAS community.

Part of the contract’s funding will be used to hire a new AI training staff member, who will develop the new training modules, deliver in-person sessions, and produce online content for UF’s Professional Workforce Development site.

Eight new, four-hour, beginner and intermediate courses are planned. As well, and in consult with ARS and IFAS, some advanced AI topics are under consideration including areal image analysis, agriculture-specific computer vision, genomics, and agriculture-specific reinforcement learning for robotics.

Production of online content is underway. The in-person content already available to the UF community will be offered to ARS staff starting in Spring 2023. Anyone with questions about UFIT’s contract with the USDA is welcome to email Training and Biocomputing Specialist Dr. Matt Gitzendanner.

Optimizing Performance on the NVIDIA Platform

UFIT is offering a 90-minute tutorial, “Performance Analysis and Optimization on the NVIDIA Platform,” on April 14. The tutorial is free and open to faculty, students, and staff.

Tutorial: Performance Analysis and Optimization on the NVIDIA Platform
Date: Thursday, April 14, 2022
Time: 12:00 PM – 1:30 PM
Pre-registration is required

The tutorial will be lead by an NVIDIA scientist who will present an introduction to performance analysis on accelerated CPU-GPU servers. Attendees will learn how to use NVIDIA Nsight Visual Studio profiling tools to understand the behavior of AI and high-performance applications to determine what optimization steps are appropriate for improving the overall time-to-solution.

Registrants will be sent the secure Zoom link the day before the tutorial. Anyone with questions about this event may contact UFIT’s AI Team Lead and Senior Application Developer Ying Zhang.

UF and Nvidia Co-Hosting Hackathon

UF and Nvidia, in collaboration with OpenACC, are jointly hosting the UF Hackathon from March 29–April 6, 2022. The deadline for teams to apply is
Feb. 21, with selected teams being notified shortly thereafter.

UFIT’s AI team, along with Nvidia AI staff, will serve as mentors to help teams parallelize and optimize code for GPU acceleration. UFIT is also providing HiPerGator AI as the work platform for the UF Hackathon. Teams from the University of Florida have priority during the application process, but teams from other Florida universities and all SEC universities are also able to apply.

The UF Hackathon is a multi-day, intensive hands-on event designed to help computational scientists and researchers port and optimize their applications using GPUs. It pairs participants with dedicated mentors experienced in GPU programming and development in AI, high performance computing, and data science applications. The event will utilize computing resources from HiPerGator AI, currently ranked as the 2nd most powerful supercomputer in U.S. higher education.

Participating teams will leave the event either with applications running on GPUs or a clear roadmap of next steps to leverage GPUs. Anyone with questions about the UF-Nvidia Hackathon may contact Ms. Ying Zhang, applications specialist and AI team lead for UFIT.