‘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.

New NVIDIA DLI Workshop Offered in February

The University of Florida’s ambassadorship status with NVIDIA means that faculty, students, and staff have free training opportunities in accelerated computing and applied AI. Through the NVIDIA Deep Learning Institute (DLI) and in coordination with UFIT, a two-day Generative AI with Diffusion Models workshop is being offered for the first time at UF on February 22-23.

Day/Date/Time: Thursday and Friday, Feb. 22–23, from 12:00 – 4:00 p.m. each day

Location: Malachowsky Hall Auditorium – Room 1000

Register to Attend: Registration Link

The Generative AI with Diffusion Models workshop is taught by UF’s NVIDIA AI Technology Center Site Manager and Senior Data Scientist Kaleb Smith. Participants will gain a deeper understanding of denoising diffusion models to generate images from text prompts. Proficiency in PyTorch and deep learning models is required to attend, with participants who complete the 8-hour course earning a certificate of completion.

Learning highlights in this workshop include:

  • How to build a U-Net to generate images from pure noise
  • Improving the quality of generated images with the Denoising Diffusion process
  • Controlling the image output with context embeddings
  • Generating images from English text-prompts using CLIP

NVIDIA DLI workshops are in-person only and not recorded for later/repeat viewing. Anyone with questions about this workshop is welcome to contact Research Computing Training Team Lead Matt Gitzendanner.

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.

UF Strategic Investment Will Advance Research Software Engineering and Enable Leading-edge Data Modeling 

The University of Florida will soon have a software developer group to assist principal investigators and research teams, thanks to a $2-million award from UF President Ben Sasse’s strategic funding initiative

The Research Software Engineers to Enhance/Scale Computer Research project will enlist a group of individuals to use existing infrastructure like HiPerGator to work directly with researchers on their projects. These research software engineers (RSEs) will be skilled at technically advanced tasks, including creating scientific software, developing complex workflows involving data management and curation, and offering advice on research productivity and reproducibility.  

“The creation of a new research software engineering team will further advance UF as a research powerhouse,” Sasse said. “It’s great for UF and great for Florida. Bolstering HiPerGator’s capabilities helps us attract the best researchers, graduate students, and entrepreneurial minds to the state.” 

Forming the RSE team will enable a broader scale of computational research while enhancing UF’s profile and reputation. Having research software engineers positioned across campus and based in the central Research Computing department will be highly valuable to faculty throughout UF (considering not every department or lab has staff members that can develop the advanced programming needed for today’s supercomputing environment). 

UF Vice President and Chief Information Officer Elias Eldayrie is ecstatic to elevate support for UF’s research community. 

“This investment from the university will reap benefits for many years. The kind of research software engineers we will hire is a recruiting edge to attract and support the best minds in the academy,” Eldayrie said. “This level of research support is cutting-edge now but will become mandatory to attract and retain the best, in just a few years.”   

Eldayrie added that the work performed by the research software engineers will be done in the most effective way possible, freeing up students, faculty, and postdoctoral candidates to be more efficient with their time. 

UFIT’s Research Computing (RC) department empowers research and discovery at the university. UFIT-RC provides a rich services and resources ecosystem, including designing and running HiPerGator, the University of Florida supercomputer, complete with advanced AI capabilities. UFIT-RC offers training, support, and consulting, and enables HiPerGator access for faculty from other Florida universities and within the Southeastern Conference. More information about the services and resources provided are available on https://rc.ufl.edu/ or by contacting UFIT-RC Senior Director Erik Deumens

Powering and Cooling HiPerGator: The UF Data Center

HiPerGator, the University of Florida supercomputer, is housed in the UF Data Center (UFDC). While its power and ranking as the most powerful supercomputer in U.S. higher education is well known, not many people know about the components at the UFDC that help keep HiPerGator online and cooled.

Backup Batteries

HiPerGator and the other computers housed in the UFDC, along with the chilled water pumps and air handlers, are run by high-power batteries. These batteries ensure that the computers get clear power without spikes or brown-outs. There is enough power available in the UFDC to keep all systems operating for about 10 minutes after an external utilities power failure. During those 10 minutes, UFDC diesel generators begin providing continuing power. The diesel generator and the chillers cool their water to 55F to send to the air handlers, which then cool the air that is used to cool the computers.

Air Exchange

To get fresh air throughout the UFDC and avoid sick-building syndrome, 10% of the air inside the data hall is constantly replaced with outside air, which is cleaned by removing particles and living mold and spores.

UF Data Center Generators

The UFDC has two generators. One has a horse-power capacity of 2.25 MW and produces 1 MW of electricity if the utilities’ power becomes unavailable. A second, similar 4 MW diesel produces the remaining 2.2 MW of electricity to provide the full 3.2 MW that the UFDC is rated for.

Transparent Floor Tiles

The HiPerGator room has a raised floor of about three feet. This is because the mostly empty space is needed to allow cold air to be delivered to the front of the computers. The fans inside the computers blow the cold air past the hot CPUs, with the hot air being returned through the ceiling to the air handlers in hallways outside the 5000 sq. ft. HiPerGator room.

Air Handlers

Speaking of the air handlers, they blow hot air past the radiators that have 55F water flowing through them. All 125,000 cubic feet of air in the HiPerGator data hall must be replaced twice every minute to avoid HiPerGator overheating! The ideal temperature for the HiPerGator room? It is 60F.

Even with the cooling requirements for a supercomputer, HiPerGator is ranked high up on the worldwide green-500 computing list, and the UF Data Center is a certified LEED® building. Learn more about HiPerGator here.

Second Annual AI Days at UF

AI Days is back at the University of Florida from Oct. 16-20. All faculty, students, and staff are welcome to join UF’s AI2 Center for five days of competitions, faculty panels, and AI events.

Oct. 16 — Student Competitions

Students are invited to compete in three competitions that feature up to $60,000 in prizes. Registration deadlines and requirements vary. Visit ai.ufl.edu/ai-days/ for information about each competition.

Oct. 17-18 — AI Teaching & Research Symposium, Poster Presentations

This year’s AI Days includes a two-day symposium on various topics of AI teaching and research.  View the schedule here. Faculty, students, and staff are also invited to present posters featuring AI in their discipline. (Registration is required to present.)

Oct. 19 — AI Workforce Readiness

Thursday’s panel features experts on navigating an AI-integrated workforce and the new realities of conducting a job search with an AI perspective.

Oct. 20 — College-Specific AI Events

Departments across campus are hosting events to conclude the 2023 AI Days, including UFIT which is facilitating an NIVIDIA Deep Learning Institute (DLI) workshop on using the new Omniverse tool. The DLI workshop is titled, “Synthetic Data Generation for Training Computer Vision Models.”

First Event in Malachowsky Hall’s NVIDIA Auditorium

The Malachowsky Hall for Data Science and Information Technology (DSIT) is a 263,000 sq. ft. academic and research collaboration building for AI and machine learning innovation. Named for UF alumnus and NVIDIA co-founder Chris Malachowsky, it seems very appropriate that the first event in DSIT’s NVIDIA Auditorium is an NVIDIA workshop:

Title: Synthetic Data Generation for Training Computer Vision Models
Date: Friday, Oct. 20 │ 9:00 – 12:30 p.m.
Location: NVIDIA Auditorium, Malachowsky Hall Rm. 1000

To register email UFIT Communications with your name, UFID number, and home department or lab affiliation. The workshop is part of NVIDIA’s Deep Learning Institute and will be taught by an NVIDIA instructor. The full synopsis, including links to review prior to the workshop, is available here.

NOTE: Registrants must complete additional NVIDIA steps to be fully registered for the Oct. 20 workshop. Be sure to read the synopsis and take the appropriate steps provided to ensure your NVIDIA Developer Program account is activated and your DLI cloud space is ready for you to fully engage in the workshop. Anyone with questions about this workshop is welcome to contact UFIT’s AI Support Manager Ying Zhang.

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.