Fifth Annual Texas A&M Research Computing Symposium
Last Update: May 31, 2022
Symposium Details
Dates: May 23-26, 2022
Location:
Talks and Workshops - Innovative Learning Classroom Building (ILCB) (map)
Banquet and Poster Session - Interdisciplinary Life Science Building (ILSB) (map)
Questions? Call us at (979) 458-8414 or email help@hprc.tamu.edu
Texas A&M's High Performance Research Computing is hosting a series of talks and workshops May 23-26, 2022 to showcase the A&M community’s work in computing and data-intensive research. There will be an opportunity for students to present their work at the poster session.
Keynote Talks
Monday May 23, 2022
Accelerating Computing for Transforming Convergence and Geospatial Sciences
Shaowen Wang, Ph.D., Professor and Head of the Department of Geography and Geographic Information Science, University of Illinois Urbana-Champaign (UIUC)
Abstract: Geospatial discovery and innovation have been undergoing an extreme digital transformation enabled by artificial intelligence and cyberGIS during the past decade. This transformational trend seems likely to persist into the foreseeable future. Meanwhile cyberGIS has emerged as a new generation of geographic information science and systems (GIS) based on holistic integration of high-performance and distributed computing, data-driven knowledge discovery, visualization and visual analytics, and collaborative problem-solving capabilities. This presentation discusses challenges and opportunities for advancing convergence and geospatial sciences to tackle an array of pressing sustainability and resilience challenges through cyberGIS-enabled holistic computing approaches.
Bio: Shaowen Wang is Professor and Head of the Department of Geography and Geographic Information Science; and Affiliate Professor of the Department of Computer Science, Department of Urban and Regional Planning, and School of Information Sciences at the University of Illinois Urbana-Champaign (UIUC). He has served as Founding Director of the CyberGIS Center for Advanced Digital and Spatial Studies at UIUC since 2013. He served as Associate Director of the National Center for Supercomputing Applications for CyberGIS from 2010 to 2017. His research interests include geographic information science and systems (GIS), advanced cyberinfrastructure and cyberGIS, complex social and environmental problems, computational and data sciences, geospatial science and technology, high-performance and distributed computing, and spatial analysis and modeling. He has received research funding from several U.S. federal and state agencies (e.g., CDC, DOE, Illinois EPA, NASA, NIH, NSF, USDA, and USGS) and industry, and served as the Principal Investigator (PI) of more than $30 million competitive research grants. He currently serves as the PI and Director of the NSF Institute for Geospatial Understanding through an Integrative Discovery Environment (I-GUIDE). He has published over 160 peer-reviewed papers and edited or co-edited several books and proceedings. He has served as an action editor of GeoInformatica, associate editor of SoftwareX, and guest editor or editorial board member for multiple other journals, book series, and proceedings. He received the NSF CAREER Award in 2009. He was named a Helen Corley Petit Scholar for 2011-2012, Centennial Scholar for 2013-2016, and Richard and Margaret Romano Professorial Scholar for 2018-2021 by UIUC’s College of Liberal Arts and Sciences. He is a Fellow of the American Association for the Advancement of Science (AAAS) and Fellow of the American Association of Geographers (AAG). He received the 2022 AAG Distinguished Scholarship Honors. He served as President of the University Consortium for Geographic Information Science from 2016 to 2017, and as a member of the Board on Earth Sciences and Resources of the National Academies of Sciences, Engineering, and Medicine from 2015 to 2020. He has supervised more than 30 PhD students and postdoctoral fellows, and many of his advisees are holding positions at major research universities, premier research and development laboratories, and leading geospatial companies.
Tuesday May 24, 2022
Democratizing Science through Advanced Cyberinfrastructure
Manish Parashar, Ph.D., Office Director, Office of Advanced Cyberinfrastructure (OAC), National Science Foundation
Abstract: Science and engineering (S&E) research is being transformed by the increasing availability and scales of computation and data and the national cyberinfrastructure (CI) ecosystem has become a key catalyst for discovery and innovation. It is thus imperative, now more than ever that all researchers can equally benefit from the opportunities for scientific exploration enabled by computation and data. In this talk I will discuss NSF’s vision for a national CI ecosystem that ensures broad, fair, and equitable access to advanced resources, services, and expertise. Such a CI ecosystem can drive new thinking and enable transformative discoveries for all, democratizing science in the 21st century
Bio: Manish Parashar is Office Director of the Office of Advanced Cyberinfrastructure at the National Science Foundation (NSF) where he oversees investments in national cyberinfrastructure. He also serves as Co-Chair of the National Science and Technology Council’s Subcommittee on the Future Advanced Computing Ecosystem and the National Artificial Intelligence Research Resource Task Force. Manish is on assignment to NSF from the University of Utah where he is the Director of the Scientific Computing and Imaging Institute, Chair in Computational Science and Engineering, and Professor in the School of Computing. Manish is Fellow of AAAS, ACM, and IEEE. For more information, please visit http://manishparashar.org.
Workshops
Introduction to AlphaFold for 3D Protein Structure Prediction on Grace
Wednesday, May 25 9:30AM - 12:00PM (ILCB 224)
HPRC is offering a 2 1/2-hour workshop on Alphafold for 3D protein structure prediction on Grace. In this workshop, participants will learn about how to run AlphaFold on Grace, HPRC's flagship system and the fundamentals of Alphafold as applied to real world applications.
Presentation Slides: (pdf)
Prerequisites: HPRC account on Grace Topics will include:- Introduction to AlphaFold
- Running AlphaFold on Grace
- AlphaFold Workflows
- Visualizing AlphaFold results
Implementing AI/ML Workloads on Graphcore's IPU based system
Wednesday, May 25 9:00AM - 1:00PM (ILCB 237)
Graphcore is hosting a 4-hour workshop on implementing AI/ML workloads on Graphcore's IPU based systems which will be a component of HPRC's NSF funded FASTER and upcoming ACES systems. Participants will be guided through hands-on exercises by Graphcore specialist.
Presentation Slides: (pdf)
Prerequisites: High level understanding of AI/ML concepts and frameworks Topics will include:-
Introduction to Graphcore, IPU, and Poplar
- TensorFlow1 - TF1 porting examples, using on-device loops and infeeds, half- and mixed-precision, model-parallel
- TensorFlow2 & Keras - porting examples and optimization, mixed-precision, replication, model-parallel, and custom training loops
- PyTorch - PopTorch example, DataLoader, options to optimize performance, efficient data loading, observing tensors, and fine-tuning BERT
Frameworks on IPU
Intel OneAPI AI Analytic Toolkit (ILCB 233)
Wednesday, May 25 1:00PM - 5:00PM
Intel is hosting a 4-hour workshop on Intel's OneAPI AI Analytic Toolkit and the performance benefits achieved on intel XPUs (CPUs, GPUs) from using the Intel optimizations. This workshop will be presented by Intel engineers. Participants will receive a certificate of completion from Intel. HPRC's upcoming NSF funded ACES system will include Intel CPUs and GPUs.
The workshop will cover Intel optimizations implemented on top of stock versions of data science libraries like NumPy, SciPy, Scikit Learn, and DL frameworks like Tensorflow and Pytorch. Hands on exercises will be followed to showcase how to get started using Intel OneAPI AI Analytic Toolkit software and the performance benefits achieved from using Intel optimizations.
Prerequisites: High level understanding of AI/ML concepts and frameworks. Please see specific Skill Level requirements as listed in the agenda.
-
Lecture - What is OneAPI - AI Analytics Toolkit
- Skill Level – High level understanding of some data science Python libraries, Python beginner level
- Overview of optimizations inside Python
- Exercise https://github.com/mtolubaeva/numpy-tests
- Expected Outcome be able to see the performance benefit of using IDP libraries over stock Python libraries like NumPy, SciPy etc.
- Skill Level – High level understanding of Scikit Learn library, Python beginner level
- Overview of optimizations inside SciKit Learn
- Exercise https://github.com/oneapi-src/oneAPI-samples/tree/master/AI-and-Analytics/Features-and-Functionality/Intel_Extension_For_SKLearn_Performance_SVC_Adult
- Individual time to complete exercise, Q&A
- Expected Outcome – be able to run an SVC algorithm with Intel Extension for Scikit-learn and compare its performance against the original stock version of scikit-learn. Students will see that patching scikit-learn results in a significant increase in performance over the original scikit-learn while also maintaining the same precision.
- Skill Level – High level understanding of Deep Learning concepts, Pytorch beginner level
- Overview types of optimizations, PyTorch
- Exercise https://github.com/jingxu10/retinanet_ipex
- Expected Outcome be able to see the performance benefit of using Intel Optimizations for Pytorch over stock Pytorch framework.
- Skill Level – High level understanding of Deep Learning concepts, Tensorflow beginner level
- Overview types of optimizations, TensorFlow
- Exercise https://github.com/oneapi-src/oneAPI-samples/tree/master/AI-and-Analytics/Features-and-Functionality/IntelTensorFlow_PerformanceAnalysis
- Expected Outcome be able to see the performance benefit from using Intel Optimizations for Tensorflow over stock Tensorflow framework.
Intel Distribution for Python (IDP)
Full Schedule (All times are CDT)
Last Update: May 31, 2022
| Monday, May 23 | Keynote and Research Talks (ILCB Rm. 224 map) |
|---|---|
| 8:20AM - 8:50AM | Check-in (ILCB 237) |
| 8:50AM - 9:00AM | Welcoming Remarks |
| 9:00AM - 9:45AM | Flames, Fire Tornadoes, and the Blue Whirl … What More Can There Be? — Multi-scale numerical simulations now show the way. Prof. Elaine Oran, Aerospace Engineering Member of the National Academy of Engineering |
| 9:45AM - 10:15AM | Theory/computation role in tuning surface/electrolyte interfaces for enhancing catalytic performance Prof. Perla Balbuena, Chemical Engineering |
| 10:15AM - 10:30AM | Break Sponsored by Dell Technologies (ILCB 237) |
| 10:30AM - 10:40AM | Opening Remarks: Prof. Jack Baldauf Interim Vice President for Research, Texas A&M University Division of Research |
| 10:40AM - 11:40AM | Keynote: Accelerating Computing for Transforming Convergence and Geospatial Sciences Prof. Shaowen Wang Professor and Head of the Department of Geography and Geographic Information Science, University of Illinois Urbana-Champaign (UIUC) |
| 11:40AM - 1:00PM | Lunch Sponsored by Dell Technologies (ILCB Mezzanine) |
| 1:00PM - 1:30PM | Machine Learning for Atmospheric Modeling (pdf) Prof. Istvan Szunyogh, Atmospheric Sciences |
| 1:30PM - 2:00PM | A Geospatial Cyberinfrastructure for Convergence Science Prof. Zhe Zhang, Geography |
| 2:00PM - 2:30PM | Data-Driven Methods for Accelerating Vibrational Spectroscopy Modeling at the Medium to Large Scale Prof. Daniel Tabor, Chemistry |
| 2:30PM - 2:50PM | Break Sponsored by Hewlett Packard Enterprise (ILCB 237) |
| 2:50PM - 3:20PM | Beyond Graphite for Li-ion Batteries: Searching for Lithium Metal Alternatives Using Quantum Mechanical Prof. Jorge Seminario, Chemical Engineering |
| 3:20PM - 3:50PM | Making Scientific Discoveries with Scientific Machine Learning Dr. Ming Zhong, Texas A&M Institute of Data Science |
| Open Session/Poster Setup (ILSB Lobby) | |
| 5:00PM - 7:00PM | Banquet and Poster Session Sponsored by Liqid (ILSB Lobby) |
| Tuesday, May 24 | Keynote and Research Talks (ILCB Rm. 224 map) |
| 8:20AM - 8:45AM | Check-in (ILCB 237) |
| 8:45AM - 9:00AM | Opening Remarks: Prof. Costas Georghiades Senior Associate Vice President for Research, Texas A&M University Division of Research |
| 9:00AM - 10:00AM | Keynote: Democratizing Science through Advanced Cyberinfrastructure Dr. Manish Parashar Office Director, Office of Advanced Cyberinfrastructure (OAC), National Science Foundation |
| 10:00AM - 10:30AM | Next Generation Composability, FASTER and ACES Dr. Lisa Perez, High Performance Research Computing |
| 10:30AM - 10:45AM | Break Sponsored by Intel Corporation (ILCB 237) |
| 10:45AM - 11:15AM |
Adaptive Bayesian Sum of Trees Model for Covariate Dependent Spectral Analysis (pdf) Prof. Scott Bruce, Statistics |
| 11:15AM - 11:45AM |
Modes of Motions of a Coronavirus Prof. Goong Chen, Math |
| 11:45AM-1:00PM | Lunch Sponspored by NVIDIA (ILCB Mezzanine) |
| 1:00PM - 1:50PM | Accelerating the secondary analysis of next generation sequencing data with NVIDIA Parabricks (pdf) Dr. Greg Zynda, NVIDIA Senior Solutions Architect |
| 1:50PM - 2:30PM | End-to-End Optimization of AlphaFold2 on Intel Architecture (pdf) Dr. Luke Ge, Intel AI Technical Solution Specialist |
| 2:30PM - 2:50PM | Break Sponsored by Intel Corporation (ILCB 237) |
| 2:50PM - 3:30PM | How learning physical laws can help the energy industry Dr. Nefeli Moridis, NVIDIA Developer Relationship Manager for Subsurface, Global Energy Team |
| 3:30PM - 4:00PM | Recombination-aware phylogenomics in mammals Dr. Nicole Foley, Veterinary Integrative Biosciences |
| 4:00PM - 5:00PM | Open Session |
| Wednesday, May 25 | Workshops (ILCB Rm. 224, 233, 237 map) |
| 9:30 AM - 12:00 PM |
AlphaFold2 Workshop Introduction (pdf) Introduction to AlphaFold for 3D Protein Structure Prediction on Grace (pdf) Dr. Michael Dickens and Devon Boland ILCB 224 |
12:00PM - 1:00 PM | Lunch Sponsored by DataDirect Networks (DDN) |
| 9:00AM - 1:00 PM | Graphcore: Implementing AI/ML workloads on Graphcore's IPU based system (pdf) Dr. Alexander Tsyplikhin and Dr. Mario Krell, Graphcore ILCB 237 |
| 1:00PM - 5:00PM | Intel OneAPI AI Analytic Toolkit Louie Tsai, Intel Artificial Intelligence Consultant ILCB 233 |
| Thursday, May 26 | SWEETER Annual Meeting(ILCB Rm. 233) |
| 10:00AM - 10:15AM | Meet and Greet |
| 10:15AM - 10:25AM | Remarks on UTRGV Prof. Soumya Mohanty, Astronomy & Astrophysics, UTRGV |
| 10:25AM - 10:35AM | Remarks on Rice University Erik Engquist, Director, Center for Research Computing, Rice University |
| 10:35AM - 10:45AM | Remarks on UTSA Prof. Jeff Prevost, Electrical and Computer Engineering, Rice University Co-Founder and Assistant Director of The Open Cloud Institute |
| 10:45AM - 10:55AM | Remarks on TACC Charlie Dey, Director, Training and Professional Development |
| 10:55AM - 11:00AM | Break |
| 11:00AM - 11:10AM | Opening Remarks Dr. Honggao Liu, Executive Director, High Performance Research Computing, TAMU |
| 11:10AM - 12:00PM | Discussion on Regional Computing |
| 12:00PM - 1:30PM | Lunch |
| 1:30PM - 2:15PM | West Campus Data Center Tour of Grace and Faster |
Posters
HPC for Biofluids
Author(s): Vishal Kandala
Department: Mechanical Engineering
Uncertainty-aware Deep Learning for Explainable Post-disaster Damage Assessment
Author(s): Chih-Shen Cheng, Amir H. Behzadan, Arash Noshadravan
Department: Civil Engineering
Disordered Polymer Folding Behavior Directly from Sequence
Author(s): Tzu-Hsuan Chao
Department: Chemistry
Reclassification of Botryococcus braunii Chemical Races into Three Species Based on a Comparative Genomics Analysis
Author(s): Devon J. Boland, Ivette Cornejo-Corona, Daniel R. Browne, Rebecca L. Murphy, Daryl T. Morishige, John Mullet, Shigeru Okada, and Timothy P. Devarenne
Department: Biochemistry & Biophysics
Stereoactive Electron Lone Pairs as a Design Principle for Anion Batteries
Author(s): Wasif Zaheer, Justin L. Andrews, Jinghua Guo, and Sarbajit Banerjee
Department: Chemistry
Reinforcement Learning on Large Network Routing Optimization
Author(s): Diya Li
Department: Geography
Machine Learning Based Monte Carlo Simulation of Protein Folding
Author(s): Curran Watson
Department: Chemistry
Embedding Petroleum Reservoir Physics into Machine Learning
Author(s): Emilio Coutinho and Eduardo Gildin
Department: Petroleum Engineering
Dispersion mechanism of cellulose nanocrystals enabled carbonaceous nanomaterials in aqueous media
Author(s): Ozge Kaynan, Lisa Perez, and Amir Asadi
Department: Materials Science & Engineering
The Microenvironment of the Bone Marrow Niche in Canine Osteosarcoma
Author(s): McKaela Hodge, Shay Bracha, and Brian W. Davis
Department: Veterinary Integrative Biosciences
Influence of environmental species on the surface oxidation energetics of MoS2
Author(s): Quentarius Moore, Dr. Fanglue Wu, Dr. Scott Bobbitt, and Dr. James Batteas
Department: Chemistry
Using ISRES+, an evolutionary optimization algorithm to fit experimental data in systems biology models
Authors(s): Razeen Shaikh, Prasad Bandodkar, and Dr. Gregory Reeves
Department: Chemical Engineering
Thanks to our Sponsors!
Texas A&M Research Computing Symposium is supported in part by NSF award #1925764, CC* Team: SWEETER -- SouthWest Expertise in Expanding, Training, Education and Research and NSF award #2112356, ACSS: ACES - Accelerating Computing for Emerging Sciences.