‘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.

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.

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.

Practicum AI Offered This Summer

The Practicum AI program will be offered this summer, from June 7–July 12. Practicum AI is led by Training and Biocomputing Specialist Dr. Matt Gitzendanner.

Practicum AI is a hands-on, applied AI curriculum developed for participants with a limited coding and math background. Using hands-on exercises and graphically-based, conceptual content, learners without extensive computational skills can begin exploring applied AI. While all sessions will be available via Zoom, registrants are encouraged to attend in person for the best opportunity to learn, interact with instructors and fellow students, and to ask questions. Practicum AI will be held in the UF Informatics Institute. Registration closes May 31. Visit this link to register.

Getting Started with AI │ June 7, 1-5pm
Introduction to artificial intelligence, how it can be applied in diverse disciplines, and some key ethical considerations.
Computing for AI │ June 14, 12:30-5pm
Getting started with the foundational tools used in AI research, including Jupyter Notebooks, Git and GitHub.com, and computer clusters, like HiPerGator.
Python for AI │ July 6 and July 7, 1-5pm
Introduction to the basics of Python programming, which is the predominant language used in AI. The course assumes no prior programming experience. Participants will learn the basics of Python to begin using AI frameworks for AI research.
Deep Learning Foundations (DLF) │ July 10, July 12, and July 13, 2-3:30pm
Introduction to neural networks–how they work and how to train them. Students must attend the July 6-7 Python course to participate in the three-day DLF course.

Women in HPC & AI Panel and Luncheon

UF Information Technology hosts semesterly Women in HPC & AI panel discussions to celebrate and promote women working in research computing and AI. These panels generate lively and collegial conversations and are thought-provoking as well as great networking opportunities. All students, faculty, and staff are welcome to attend the Spring 2023 event, which is free and includes lunch:

Date and Time: Wednesday, February 22 │ 12:00 – 1:30 p.m.
Location: Health Science Center Library, Communicore Building C1-121
Registration: Attend the Spring 2023 Panel and Lunch

The Spring 2023 panelists are:
Dr. Azra Bihorac, Senior Associate Dean for Research Affairs at College of Medicine; Professor of Medicine, Surgery and Anesthesiology
Dr. Yenisel Cruz-Almeida, Associate Professor, Department of Community Dentistry and Behavioral Sciences
Dr. Shreya Saxena, Assistant Professor, Department of Electrical & Computer Engineering
Dr. Borui Zhang, Natural Language Processing Specialist, Academic Research Consulting and Services, George A. Smathers Libraries

UF’s Women in HPC & AI chapter provides mentoring opportunities and resources for female students and research community members. Space for the event is limited, so please register early. Anyone with questions about the university’s WHPC & AI chapter is welcome to contact AI Support Team Lead Ying Zhang.

Supporting UF’s $1Billion Research Portfolio

UF’s research portfolio exceeded $1 billion for the first time in the fiscal year ending June 30, 2022. UFIT supports two applications– UFIRST and myinvestiGator–that enable researchers to manage their sponsored funding. Numerous financial analysts, developers, and data engineering staff are involved each week with the maintenance of these applications.

“A world-class research institution requires world-class administrative tools. Keeping our faculty and research support teams empowered through easily accessed, up-to-date information is key,” wrote Stephanie Gray, assistant vice president & director, Division of Sponsored Programs. “UFIT helps keep UF Research running with their excellent support of UFIRST and myinvestiGator.”

UFIRST Numbers
4,244 active users in FY22
14,677 new projects added to UFIRST in FY22

myinvestiGator Numbers
2,000 faculty and staff users in FY22
Approximately 17,000+ system logins in FY22

Assistance getting started on both applications is available through UF Research. Training materials and helpful companion docs for UFIRST and myinvestiGator are online:

Remote Computing Assistance Available

You don’t need to be on campus to receive research computing assistance. Remote support and virtual walk-in hours are available on your terms with UFIT Research Computing.

Using Zoom and Slack, researchers can get the consultation they need, when they need it. UFIT staff have years of experience with the university’s computing resources and are ready to support you and your project. Visit the Remote Support webpage to schedule an appointment.

UFIT’s proposal support service can help you stretch your research budget and save you time. Staff can provide personalized commitment letters and help write data management plans. UFIT also regularly offer virtual NVIDIA workshops and computing trainings to maximize your workflows within UF’s HiPerGator AI supercomputing environment. The
RC Training webpage lists upcoming events.

UFIT is committed to supporting the university’s researchers where they are, in Gainesville or around the globe. Please contact the Research Computing staff for assistance with our research computing portfolio of services.

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.

Proposal Support Available for Researchers

UFIT is committed to doing everything possible to enable the research community. In addition to providing high performance computing consulting, our staff can help make your sponsored funding proposals more competitive with letters and templates related to the computing and infrastructure needs of your project. There are four components that UFIT’s Research Computing staff can assist with:

1. The budget form showing the cost of computing services or hardware acquisition.
2. Some funding agencies require a commitment letter from Research Computing. We will be happy to write a letter for your specific project.
3. A description of the facilities in support of your project is available to include in the proposal’s facilities section.
4. An explicit data management plan (DMP) is required by most funding agencies, including the National Science Foundation and the National Institutes of Health. Research Computing staff are happy to assist you in developing a DMP and its associated budget.

The Research Computing website also has examples of justification text for Hardware Acquisition and Consulting Services. All of the templates and sample text mentioned above are available on https://www.rc.ufl.edu/research/proposal-support/. Please contact Research Computing Director Erik Deumens if you need assistance with your proposal’s computing infrastructure documentation.

Research Computing Support Available Remotely

Research computing consulting support is now available through remote channels. Based on the precautions taken by the university regarding the COVID-19 virus, facilitators who normally hold walk-in hours on campus are available via Zoom. The online support options for UF’s research community include:

  • Visiting the Research Computing website for information on services and the current status of HiPerGator.
  • Posting questions in the Slack #support channel. Research Computing staff monitor the channel and reply as quickly as possible. Use this link to join.
  • Attending a Zoom meeting during the listed walk-in hours. Please allow at least 5-10 minutes for your request to be acknowledged. If a facilitator is in another meeting, your Zoom call will be placed in a waiting room and answered as quickly as possible. Personal Zoom links are available here.

Researchers are welcome to contact Erik Deumens, director of Research Computing, about their consulting support needs.