The new system, geared towards GPU computing, will be open for nationwide XSEDE allocations starting in June for projects beginning in August 2021.
Delta, a $10 million National Science Foundation-funded advanced computing system housed at the National Center for Supercomputing Applications at the University of Illinois, will soon be accessible to researchers across the country via XSEDE allocation.
Using a design that leverages graphics processing units (GPUs) in combination with CPU architectures well-suited for scientific computing, Delta will be particularly suited to evolving research needs that heavily rely on GPU-intensive activities. Once available, Delta will be the most performant GPU-based NSF resource, unlocking cutting-edge capabilities for researchers nationwide, regardless of location, via XSEDE.
"Everyone at NCSA is excited to get Delta up and operational for the NSF community," said Tim Boerner, Timothy Boerner, Deputy Project Director for both the XSEDE and Delta projects. "It is a very forward-looking system in a number of different ways, such as the focus on science gateways support, improved accessibility, the relaxed-POSIX file system we have planned, and of course the massive amount of GPU computing performance this system will add to the XSEDE allocations pool."
Delta's first allocations are expected to be made during the June XSEDE Resource Allocation Committee (XRAC) meeting, with jobs scheduled to go into production in August of this year. Delta was one of five NSF-funded systems awarded last summer, all of which will be partially allocated by XSEDE.
Read more about Delta below, and dive into the system's specifications here.
NCSA will integrate Delta into the national cyberinfrastructure ecosystem through the Extreme Science and Engineering Discovery Environment and partner with the Science Gateways Community Institute to provide platform access serving a broad range of needs. Boasting a non-POSIX file system with a POSIX-like interface, Delta allows applications to reap the benefits of modern file systems without rewriting code. And the Delta team will advance accessibility, providing greater usability of the interfaces by the widest possible audience, and in helping emerging research areas, such as computational archaeology and digital agriculture, take advantage of new computing methods.
Delta will provide ample professional development opportunities to adapt research applications to more optimally use its key features. Researchers who currently have GPU projects or are considering migrating to GPU architectures will find ready assistance in migrating the work to Delta.
Domain Champions are part of Campus Champions along with Regional and Student Champions
Domain Champions act as ambassadors by spreading the word about what XSEDE can do to boost the advancement of their field, based on their personal experience, and to connect interested colleagues to the right people/resources in the XSEDE community (XSEDE Extended Collaborative Support Services (ECSS) staff, Campus Champions, documentation/training, helpdesk, etc.). Domain Champions work within their discipline, rather than within a geographic or institutional territory.
The table below lists our current domain champions. We are very interested in adding new domains as well as additional champions for each domain. Please contact email@example.com if you are interested in a discussion with a current domain champion, or in becoming a domain champion yourself.
|Astrophysics, Aerospace, and Planetary Science||Matthew Route||Purdue University|
|Data Analysis||Rob Kooper||University of Illinois|
|Finance||Mao Ye||University of Illinois|
|Molecular Dynamics||Tom Cheatham||University of Utah|
|Genomics||Brian Couger||Oklahoma State University|
|Digital Humanities||Michael Simeone||Arizona State University|
|Genomics and Biological Field Stations||Thomas Doak, Sheri Sanders,||Indiana University, National Center for Genome Analysis Support|
|Chemistry and Material Science||Sudhakar Pamidighantam||Indiana University|
|Fluid Dynamics & Multi-phase Flows||Amit Amritkar||University of Houston|
|Chemistry||Christopher J. Fennell||Oklahoma State University|
|Geographic Information Systems||Eric Shook||University of Minnesota|
Last Updated: April 7, 2021
Campus Champions programs include Regional, Student, and Domain Champions.
Student Champion volunteer responsibilities may vary from one institution to another and depending on your Campus Champion Mentor. Student Champions may work with their Mentor to provide outreach on campus to help users access the best advanced computing resource that will help them accomplish their research goals, provide training to users on campus, or work on special projects assigned by your Mentor. Student Champions are also encouraged to attend the annual PEARC conference and participate in the PEARC student program as well as submit posters or papers to the conference.
To join the Student Champions program, the Campus Champion who will be their mentor should send a message to firstname.lastname@example.org to recommend the student for the program and confirm their willingness to be the student's mentor.
Questions? Email email@example.com.
|INSTITUTION||CHAMPION||MENTOR||FIELD OF STUDY||DESIGNATION||GRADUATION|
|Alabama Agricultural & Mechanical University||Georgianna Wright||Damian Clarke||Computer Science||Undergraduate||2022|
|Claremont Graduate University||Cindy Cheng||Jeho Park||Information Systems & Technology||Graduate||2022|
|Claremont Graduate University||Michael Espero||Asya Shklyar||Biostatistics, Neurocognitive Science||Graduate||2021|
|Claremont McKenna College||Zeyad Elkelani||Jeho Park||Political Science||Graduate||2021|
|Dillard University||Priscilla Saarah||Tomekia Simeon||Biology||Undergraduate||2022|
|Dillard University||Brian Desil||Tomekia Simeon||Physics||Undergraduate||2021|
|Drexel University||Cameron Fritz||David Chin||Computer Science||Undergraduate||2023|
|Florida A&M Univerisity||Rodolfo Tsuyoshi F. Kamikabeya||Hongmei Chi||Computer Information Science||Graduate||2021|
|Florida A&M Univeristy||Emon Nelson||Hongmei Chi||Computer Science||Graduate||2021|
|Georgia Institute of Technology||Sebastian Kayhan Hollister||Semir Sarajlic||Computer Science||Undergraduate||2021|
|Georgia Institute of Technology||Siddhartha Vemuri||Semir Sarajlic||Computer Science||Undergraduate||2021|
|Georgia State University||Kenneth Huang||Suranga Naranjan||Graduate||2021|
|Georgia State University||Melchizedek Mashiku||Suranga Naranjan||Computer Science||Undergraduate||2022|
|Howard University||Christina McBean||Marcus Alfred||Physics & Mathematics||Undergraduate||2021|
|Howard University||Tamanna Joshi||Marcus Alfred||Condensed Matter Theory||Graduate||2021|
|Indiana University||Ashley Brooks||Carrie Ganote||Physics||Graduate||2025|
|John Hopkins University||Jodie Hoh||Jaime Combariza, Anthony Kolasny, Kevin Manalo||Computer Science||Undergraduate||2022|
|Kansas State University||Mohammed Tanash||Dan Andresen||Computer Science||Gradudate||2022|
|Massachusetts Green HPC Center||Abigail Waters||Julie Ma||Clinical Psychology||Graduate||2022|
|North Carolina State University||Yuqing Du||Lisa Lowe||Statistics||Graduate||2021|
|Northwestern University||Sajid Ali||Alper Kinaci||Applied Physics||Graduate||2021|
|Oregon State University||McKenzie Hughes||CJ Keist||Biology||Undergraduate||2021|
|Pomona College||Nathaniel Getachew||Asya Shklyar||Computer Science & Mathematics||Undergraduate||2023|
|Pomona College||Omar Zintan Mwinila-Yuori||Asya Shklyar||Computer Science||Undergraduate||2022|
|Pomona College||Samuel Millette||Asya Shklyar||Computer Science||Undergraduate||2023|
|Prairie View A&M University||Chara Tatum||Suxia Cui||Computer Science||Undergraduate||2021|
|Prairie View A&M University||Kobi Tioro||Suxia Cui||Computer Engineering||Undergraduate||2021|
|Prairie View A&M University||Racine McLean||Suxia Cui||Computer Engineering||Undergraduate||2021|
|Prairie View A&M University||Virgie Leyva||Suxia Cui||Computer Engineering||Undergraduate||2021|
|Reed College||Jiarong Li||Trina Marmarelli||Math-Computer Science||Undergraduate||2021|
|Rensselaer Polytechnic Institute||James Flamino||Joel Geidt||Graduate||2022|
|Saint Louis University||Frank Gerhard Schroer IV||Eric Kaufmann||Physics||Undergraduate||2021|
|Southern Illinois University|| |
|Southern Illinois University||Manvith Mali||Chet Langin||Computer Science||Graduate||2021|
|Southwestern Oklahoma State University||Arianna Martin||Jeremy Evert||Computer Science & Music Performance||Undergraduate||2023|
|Southwestern Oklahoma State University||Kurtis D. Clark||Jeremy Evert||Computer Science||Undergraduate||2020|
|Texas Tech University||Misha Ahmadian||Tom Brown||Computer Science||Graduate||2022|
|The University of Tennessee at Chattanooga||Carson Woods||Tony Skjellum||Computer Science||Undergraduate||2021|
|University of Alabama at Birmingham||Shahram Talei||Physics||Graduate||2021|
|University of Arizona||Alexander Prescott||Blake Joyce||Geosciences||Graduate||2021|
|Univerity of Arkansas||Timothy "Ryan" Rogers||Jeff Pummill||Physical Chemistry||Graduate||2021|
|University of Central Oklahoma||Samuel Kelting||Evan Lemley||Mathematics/CS||Undergraduate||2021|
|University of Delaware||Parinaz Barakhshan||Anita Schwartz||Electrical and Computer Engineering||Graduate||2024|
|University of Maine||Michael Brady Butler||Bruce Segee||Physica/Computational Materials Science||Graduate||2022|
|University of Michigan||Daniel Kessler||Shelly Johnson||Statistics||Graduate||2022|
|University of Minnesota||Aneesh Venugopal||Ben Lynch||Electrical Engineering||Graduate||2021|
|University of Missouri||Ashkan Mirzaee||Predrag Lazic||Industrial Engineering||Graduate||2021|
|University of Nebraska||Natasha Pavlovikj||Adam Caprez||Computer Science||Graduate||2021|
|University of North Carolina Wilmington||Cory Nichols Shrum||Eddie Dunn|
|University of South Dakota||Adison Ann Kleinsasser||Computer Science||Graduate||2020|
|University of Texas at Dallas||Namira Pervez||Neuroscience||Undergraduate||2024|
|University of Wyoming||Rajiv Khadka||Jared Baker||Graduate||2020|
|Yale University||Sinclair Im||Andy Sherman||Applied Math||Graduate||2022|
|Boise State University||Mike Henry||Kyle Shannon||2020|
|Florida A&M Univerisity||George Kurian||Hongmei Chi||2019|
|Florida A&M Univerisity||Temilola Aderibigbe||Hongmei Chi||2019|
|Florida A&M Univerisity||Stacyann Nelson||Hongmei Chi||2019|
|Georgia State University||Mengyuan Zhu||Suranga Naranjan||2017|
|Georgia State University||Thakshila Herath||Suranga Naranjan||2018|
|Iowa State University||Justin Stanley||Levi Barber||2020|
|Jackson State Univeristy||Ebrahim Al-Areqi||Carmen Wright||2018|
|Jackson State University||Duber Gomez-Fonseca||Carmen Wright||2019|
|Midwestern State University||Broday Walker||Eduardo Colmenares||2020|
|Mississippi State University||Nitin Sukhija||Trey Breckenridge||2015|
|New Jersey Institute of Technology||Vatsal Shah||Roman Voronov||2020|
|North Carolina State University||Dheeraj Kalidini||Lisa Lowe||2020|
|North Carolina State University||Michael Dacanay||Lisa Lowe|
|Oklahoma State University||Phillip Doehle||Dana Brunson||2016|
|Oklahoma State University||Venkat Padmanapan Rao||Jesse Schafer||2019|
|Oklahoma State University||Raj Shukla||Dana Brunson||2018|
|Oklahoma State University||Nathalia Graf Grachet||Philip Doehle||2019|
|Rensselaer Polytechnic Institute||Jorge Alarcon||Joel Geidt||2016|
|Southern Illinois University||Aaron Walber||Chet Langin||2020|
|Southern Illinois University||Alex Sommers||Chet Langin||2018|
|Southern Illinois University||Sai Susheel Sunkara||Chet Langin||2018|
|Southern Illinois University||Monica Majiga||Chet Langin||2017|
|Southern Illinois University||Sai Sandeep Kadiyala||Chet Langin||2017|
|Southern Illinois University||Rezaul Nishat||Chet Langin||2018|
|Southern Illinois University||Alvin Gonzales||Chet Langin||2020|
|Texas A&M University - College Station||Logan Kunka||Jian Tao||2020|
|Tufts University||Georgios (George) Karamanis||Shawn G. Doughty||2018|
|University of Arkansas||Shawn Coleman||Jeff Pummill||2014|
|University of California - Merced||Luanzheng Guo||Sarvani Chadalapaka||2020|
|University of Central Florida||Amit Goel||Paul Weigand|
|University of Florida||David Ojika||Oleksandr Moskalenko||2018|
|University of Illinois at Chicago||Babak Kashir Taloori||Jon Komperda||2021|
|University of Iowa||Baylen Jacob Brus||Ben Rogers||2020|
|University of Houston Clear Lake||Tarun Kumar Sharma||Liwen Shih||2014|
|University of Houston-Downtown||Eashrak Zubair||Hong Lin||2020|
|University of Maryland Baltimore County||Genaro Hernadez||Paul Schou||2015|
|University of Michigan||Simon Adorf||Shelly Johnson||2019|
|University of Missouri||Alexander Barnes||Timothy Middelkoop||2018|
|University of North Carolina Wilmington||James Stinson Gray||Eddie Dunn||2018|
|University of Pittsburgh||Shervin Sammak||Kim Wong||2016|
|University of South Dakota||Adison Ann Kleinsasser||2020|
|University of South Dakota||Joseph Madison||Doug Jennewein||2018|
|University of Wyoming||Rajiv Khadka||Jared Baker||2020|
|Virginia Tech University||David Barto||Alana Romanella||2020|
|Virginia Tech University||Lu Chen||Alana Romanella||2017|
|West Chester University of Pennsylvania||Jon C. Kilgannon||Linh Ngo||2020|
|Winston-Salem State University||Daniel Caines||Xiuping Tao||2019|
Updated: March 25, 2020
Champion Leadership Team
This page includes the Champions Leadership team and Regional Champions
|Dana Brunson||Internet2||Campus Engagement Co-manager|
|Henry Neeman||University of Oklahoma||Campus Engagement Co-manager|
|Cathy Chaplin||Internet2||Champion Coordinator|
|Jay Alameda||University of Illinois Urbana-Champaign||Champion Fellows Coordinator & ECSS Liaison|
|Champion Elected Leadership Team|
|Thomas Cheatham||University of Utah||Champion Leadership Team (2020-2022)|
|Douglas Jennewein||Arizona State University||Champion Leadership Team (2018-2022)|
|Timothy Middelkoop||Internet2||Champion Leadership Team (2018-2022)|
|Julie Ma||MGHPCC||Champion Leadership Team (2018-2022)|
|Shelley Knuth||University of Colorado||Champion Leadership Team (2019-2021)|
|BJ Lougee||Federal Reserve Bank of Kansas (CADRE)||Champion Leadership Team (2019-2021)|
|Torey Battelle||Colorado School of Mines||Champion Leadership Team (2019-2021)|
|Champion Leadership Team Alumni|
|Hussein Al-Azzawi||University of New Mexico||Champion Leadership Team (2018-2020)|
|Aaron Culich||University of California-Berkeley||Champion Leadership Team (2017-2019)|
|Jack Smith||West Virginia Higher Education Policy Commission||Champion Leadership Team (2016-2018)|
|Dan Voss||University of Miami||Champion Leadership Team (2016-2018)|
|Erin Hodges||University of Houston||Champion Leadership Team (2017-2018)|
|Alla Kammerdiner||New Mexico State University||Champion Leadership Team (2017-2019)|
Updated: June 18, 2020
The Regional Champion Program is built upon the principles and goals of the XSEDE Champion Program. The Regional Champion network facilitates education and training opportunities for researchers, faculty, students and staff in their region that help them make effective use of local, regional and national digital resources and services. Additionally, the Regional Champion Program provides oversight and assistance in a predefined geographical region to ensure that all Champions in that region receive the information and assistance they require, as well as establish a bi-directional conduit between Champions in the region and the XSEDE champion staff, thus ensuring a more efficient dissemination of information, allowing finer grained support. Finally, the Regional Champions acts as a regional point of contact and coordination, to assist in scaling up the Champion program by working with the champion staff to coordinate and identify areas of opportunity for expanding outreach to the user community.
|Ben Nickell||Idaho National Labs||Nick Maggio||University of Oregon||1|
|Ruth Marinshaw||Stanford University||Aaron Culich||University of California, Berkeley||2|
|Kevin Brandt||South Dakota State University||3|
|Dan Andresen||Kansas State University||BJ Lougee||Federal Reserve Bank Of Kansas City CADRE||4|
|Mark Reed||University of North Carolina||5|
|Scott Hampton||University of Notre Dame||6|
|Scott Yockel||Harvard University||Scott Valcourt||Northeastern University||7|
|Anita Orendt||University of Utah||Shelley Knuth||University of Colorado||8|
Updated: November 12, 2020
Current Campus Champions
Current Campus Champions listed by institution. Participation as either an Established Program to Stimulate Competitive Research (EPSCoR) or as a minority-serving institution (MSI) is also indicated.
|Campus Champion Institutions|
|Total Academic Institutions||300|
|Academic institutions in EPSCoR jurisdictions||79|
|Minority Serving Institutions||57|
|Minority Serving Institutions in EPSCoR jurisdictions||17|
|Non-academic, not-for-profit organizations||36|
|Total Campus Champion Institutions||336|
|Total Number of Champions||719|
LAST UPDATED: April 7, 2021
|Alabama A & M University||Damian Clarke, Raziq Yaqub, Georgiana Wright (student)||✔||✔|
|Albany State University||Olabisi Ojo||✔|
|Arizona State University||Michael Simeone (domain) , Sean Dudley, Johnathan Lee, Lee Reynolds, William Dizon, Ian Shaeffer, Dalena Hardy, Gil Speyer, Richard Gould, Chris Kurtz, Jason Yalim, Philip Tarrant, Douglas Jennewein, Marisa Brazil, Rebecca Belshe, Eric Tannehill, Zachary Jetson|
|Arkansas State University||Hai Jiang||✔|
|Austin Peay State University||Justin Oelgoetz|
|Bates College||Kai Evenson||✔|
|Baylor College of Medicine||Pavel Sumazin , Hua-Sheng Chiu, Hyunjae Ryan Kim|
|Baylor University||Mike Hutcheson, Carl Bell, Brian Sitton|
|Bentley University||Jason Wells|
|Bethune-Cookman University||Ahmed Badi||✔|
|Boise State University||Kyle Shannon, Jason Watt, Kelly Byrne, Mendi Edgar, Mike Ramshaw||✔|
|Boston Children's Hospital||Arash Nemati Hayati|
|Boston College||Simo Goshev|
|Boston University||Wayne Gilmore, Charlie Jahnke, Augustine Abaris, Brian Gregor, Katia Bulekova, Josh Bevan|
|Bowdoin College||Dj Merrill , Stephen Houser||✔|
|Bowie State University||Konda Karnati||✔|
|Brandeis University||John Edison|
|Brown University||Helen Kershaw, Maximilian King, Paul Hall, Khemraj Shukla, Mete Tunca, Paul Stey, Rohit Kakodkar||✔|
|California Baptist University||Linn Carothers||✔|
|California Institute of Technology||Tom Morrell|
|California State Polytechnic University-Pomona||Chantal Stieber|
|California State University - Fullerton||Justin Tran|
|California State University-Sacramento||Anna Klimaszewski-Patterson||✔|
|California State University-San Bernardino||Dung Vu, James MacDonell||✔|
|Carnegie Institution for Science||Floyd A. Fayton, Jr.|
|Carnegie Mellon University||Bryan Webb, Franz Franchetti, Carl Skipper|
|Case Western Reserve University||Roger Bielefeld, Hadrian Djohari, Emily Dragowsky, James Michael Warfe, Sanjaya Gajurel|
|Central State University||Mohammadreza Hadizadeh||✔|
|Centre College||David Toth||✔|
|Chapman University||James Kelly|
|Children's Mercy Kansas City||Shane Corder|
|Claremont Graduate University||Michael Espero (student), Cindy Cheng (student)|
|Claremont McKenna College||Jeho Park, Zeyad Elkelani (student)|
|Clark Atlanta University||Dina Tandabany||✔|
|Clarkson Univeristy||Jeeves Green, Joshua A. Fiske|
|Clemson University||Xizhou Feng, Corey Ferrier, Tue Vu, Asher Antao, Grigorio Yourganov||✔|
|Cleveland Clinic, The||Iris Nira Smith, Daniel Blankenberg|
|Clinton College||Terris S. Riley||✔||✔|
|Coastal Carolina University||Will Jones, Thomas Hoffman||✔|
|Colby College||Randall Downer||✔|
|Colgate University||Howard Powell, Dan Wheeler|
|College of Staten Island CUNY||Sharon Loverde||✔|
|College of William and Mary||Eric Walter|
|Colorado School of Mines||Torey Battelle, Nicholas Danes|
|Columbia University||Rob Lane, George Garrett|
|Columbia University Irving Medical Center||Vinod Gupta|
|Complex Biological Systems Alliance||Kris Holton|
|Cornell University||Susan Mehringer|
|Dakota State University||David Zeng||✔|
|Davidson College||Neil Reda (student), Michael Blackmon (student)|
|Dillard University||Tomekia Simeon, Brian Desil (student), Priscilla Saarah (student)||✔||✔|
|Doane University-Arts & Sciences||Mark Meysenburg, AJ Friesen||✔|
|Dominican University of California||Randall Hall|
|Drexel University||David Chin, Cameron Fritz (student)|
|Duke University||Tom Milledge|
|Earlham College||Charlie Peck|
|East Carolina University||Nic Herndon|
|East Tennessee State University||David Currie, Janet Keener, Vincent Thompson|
|Edge, Inc.||Forough Ghahramani|
|Emory University||Jingchao Zhang|
|Federal Reserve Bank Of Kansas City (CADRE)||BJ Lougee, Chris Stackpole, Michael Robinson|
|Federal Reserve Bank Of Kansas City (CADRE) - OKC Branch||Greg Woodward||✔|
|Federal Reserve Bank Of New York||Ernest Miller, Kevin Kelliher|
|Felidae Conservation Fund||Kevin Clark|
|Ferris State University||Luis Rivera, David Petillo|
|Florida A and M University||Hongmei Chi, Jesse Edwards, Yohn Jairo Parra Bautista, Rodolfo Tsuyoshi F. Kamikabeya (student), Emon Nelson (student)||✔|
|Florida Atlantic University||Rhian Resnick|
|Florida International University||David Driesbach, Cassian D'Cunha||✔|
|Florida Southern College||Christian Roberson|
|Florida State University||Paul van der Mark|
|Francis Marion University||K. Daniel Brauss, Jordan D. McDonnell||✔||✔|
|Franklin and Marshall College||Jason Brooks|
|GPN (Great Plains Network)||Kate Adams, James Deaton|
|George Mason University||Jayshree Sarma, Alastair Neil, Berhane Temelso, Swabir Silayi|
|George Washington University||Hanning Chen, Adam Wong, Glen Maclachlan, William Burke|
|Georgetown University||Alisa Kang|
|Georgia Institute of Technology||Mehmet Belgin, Semir Sarajlic, Nuyun (Nellie) Zhang, Sebastian Kayhan Hollister (student), Paul Manno, Kevin Manalo, Siddhartha Vemuri (student)|
|Georgia Southern University||Brandon Kimmons, Dain Overstreet|
|Georgia State University||Neranjan "Suranga" Edirisinghe Pathiran, Ken Huang, Thakshila Herath (student), Melchizedek Mashiku (student)||✔|
|Grinnell College||Michael Conner|
|Harrisburg University of Science and Technology||Donald Morton, Daqing Yun|
|Harvard Medical School||Jason Key|
|Harvard University||Scott Yockel, Plamen Krastev, Francesco Pontiggia|
|Harvey Mudd College||Aashita Kesarwani|
|Hood College||Xinlian Liu|
|Howard University||Marcus Alfred, Christina McBean (student), Tamanna Joshi (student)||✔|
|I-Light Network & Indiana Gigapop||Caroline Weilhamer (domain) , Marianne Chitwood (domain)|
|Idaho National Laboratory||Ben Nickell, Eric Whiting, Kit Menlove||✔|
|Idaho State University||Keith Weber, Dong Xu, Kindra Blair, Jack Bradley||✔|
|Illinois Institute of Technology||Jeff Wereszczynski|
|Indiana University||Abhinav Thota, Sudahakar Pamidighantam (domain) , Junjie Li, Thomas Doak (domain) , Carrie L. Ganote, Sheri Sanders (domain) , Bhavya Nalagampalli Papudeshi, Le Mai Weakley, Ashley Brooks (student)|
|Indiana University of Pennsylvania||John Chrispell|
|Internet2||Dana Brunson, Cathy Chaplin, John Hicks, Tim Middelkoop|
|Iowa State University||Andrew Severin, James Coyle, Levi Baber|
|Jackson State University||Carmen Wright, Duber Gomez-Fonseca (student)||✔||✔|
|James Madison University||Isaiah Sumner|
|Jarvis Christian College||Widodo Samyono||✔|
|John Brown University||Jill Ellenbarger||✔|
|Johns Hopkins University||Anthony Kolasny, Jaime Combariza, Jodie Hoh (student)|
|Juniata College||Burak Cem Konduk|
|KanREN (Kansas Research and Education Network)||Casey Russell||✔|
|Kansas State University||Dan Andresen, Mohammed Tanash (student), Kyle Hutson||✔|
|Kennesaw State University||Ramazan Aygun|
|Kentucky State University||Chi Shen||✔||✔|
|Lafayette College||Bill Thompson, Jason Simms, Peter Goode|
|Lamar University||Larry Osborne|
|Lane College||Elijah MacCarthy||✔|
|Langston University||Franklin Fondjo, Abebaw Tadesse, Joel Snow||✔||✔|
|Lawrence Berkeley National Laboratory||Andrew Wiedlea|
|Lawrence Livermore National Laboratory||Todd Gamblin|
|Lehigh University||Alexander Pacheco|
|Lipscomb University||Michael Watson|
|Lock Haven University||Kevin Range|
|Louisiana State University||Feng Chen, Blaise A Bourdin||✔|
|Louisiana State University - Alexandria||Gerard Dumancas||✔|
|Louisiana State University Health Sciences Center-New Orleans||Mohamad Qayoom||✔|
|Louisiana Tech University||Don Liu||✔|
|Marquette University||Craig Struble, Lars Olson, Xizhou Feng|
|Marshall University||Jack Smith||✔|
|Massachusetts Green High Performance Computing Center||Julie Ma, Abigail Waters (student)|
|Massachusetts Institute of Technology||Christopher Hill, Lauren Milechin|
|Medical University of South Carolina||Starr Hazard||✔|
|Miami University - Oxford||Jens Mueller|
|Michigan State University||Andrew Keen, Yongjun Choi, Dirk Colbry, Justin Booth, Dave Dai, Arthur "Chip" Shank II, Brad Fears|
|Michigan Technological University||Gowtham|
|Middle Tennessee State University||Dwayne John|
|Midwestern State University||Eduardo Colmenares-Diaz|
|Minnesota State University - Mankato||Maria Kalyvaki|
|Mississippi State University||Trey Breckenridge||✔|
|Missouri State University||Matt Siebert|
|Missouri University of Science and Technology||Buddy Scharfenberg, Don Howdeshell|
|Monmouth College||Christopher Fasano|
|Montana State University||Jonathan Hilmer||✔|
|Montana Tech||Bowen Deng||✔|
|Morgan State University||James Wachira||✔|
|NCAR/UCAR||Davide Del Vento|
|National University||Ali Farahani|
|Navajo Technical University||Jason Arviso||✔||✔|
|New Jersey Institute of Technology||Glenn "Gedaliah" Wolosh, Roman Voronov|
|New Mexico State University||Alla Kammerdiner, Diana Dugas, Strahinja Trecakov||✔||✔|
|New York University||Shenglong Wang|
|Noble Research Institute, LLC||Nick Krom, Perdeep Mehta||✔|
|North Carolina A & T State University||Ling Zu||✔|
|North Carolina Central University||Caesar Jackson, Alade Tokuta||✔|
|North Carolina State University at Raleigh||Lisa Lowe, Yuqing Du (student)|
|North Dakota State University||Dane Skow, Nick Dusek, Oluwasijibomi "Siji" Saula, Khang Hoang||✔|
|Northeastern University||Scott Valcourt|
|Northern Arizona University||Christopher Coffey, Jason Buechler, William Wilson|
|Northern Illinois University||Jifu Tan|
|Northwest Missouri State University||Jim Campbell|
|Northwestern State University (Louisiana Scholars' College)||Brad Burkman||✔|
|Northwestern University||Pascal Paschos, Alper Kinaci, Sajid Ali (student)|
|OWASP Foundation Learning Gateway Project||Bev Corwin, Laureano Batista, Zoe Braiterman, Noreen Whysel|
|Ohio Supercomputer Center||Karen Tomko, Keith Stewart, Sandy Shew|
|Ohio Supercomputer Center||Karen Tomko, Keith Stewart, Sandy Shew|
|Oklahoma Baptist University||Yuan-Liang Albert Chen||✔|
|Oklahoma Innovation Institute||John Mosher||✔|
|Oklahoma State University||Brian Couger (domain) , Jesse Schafer, Christopher J. Fennell (domain) , Phillip Doehle, Evan Linde, Venkat Padmanapan Rao (student), Bethelehem Ali Beker (student)||✔|
|Old Dominion University||Wirawan Purwanto|
|Oral Roberts University||Stephen R. Wheat||✔|
|Oregon State University||David Barber, CJ Keist, Mark Keever, Dylan Keon, Mckenzie Hughes (student)|
|Penn State University||Chuck Pavloski, Wayne Figurelle, Guido Cervone, Diego Menendez, Jeff Nucciarone|
|Pittsburgh Supercomputing Center||Stephen Deems, John Urbanic|
|Pomona College||Asya Shklyar, Andrew Crawford, Omar Zintan Mwinila-Yuori (student), Samuel Millette (student), Sanghyun Jeon, Nathaniel Getachew (student)|
|Portland State University||William Garrick|
|Prairie View A&M University||Suxia Cui, Racine McLean (student), Kobi Tioro (student), Chara Tatum (student), Virgie Leyva (student)||✔|
|Princeton University||Ian Cosden|
|Purdue University||Xiao Zhu, Tsai-wei Wu, Matthew Route (domain) , Eric Adams|
|RAND Corporation||Justin Chapman|
|RENCI||Laura Christopherson, Chris Erdmann, Chris Lenhardt|
|Reed College||Trina Marmarelli, Johnny Powell , Ben Poliakoff, Jiarong Li (student)|
|Rensselaer Polytechnic Institute||Joel Giedt, James Flamino (student)|
|Rhodes College||Brian Larkins|
|Rice University||Qiyou Jiang, Erik Engquist, Xiaoqin Huang, Clinton Heider, John Mulligan|
|Rochester Institute of Technology||Andrew W. Elble , Emilio Del Plato, Charles Gruener, Paul Mezzanini, Sidney Pendelberry|
|Rowan University||Ghulam Rasool|
|Rutgers University||Shantenu Jha, Bill Abbott, Paul Framhein, Galen Collier, Eric Marshall, Vlad Kholodovych, Bala Desinghu, Sue Oldenburg|
|SUNY Downstate Health Sciences University||Zaid McKie-Krisberg|
|SUNY at Albany||Kevin Tyle, Nicholas Schiraldi|
|Saint Louis University||Eric Kaufmann, Frank Gerhard Schroer IV (student)|
|Saint Martin University||Shawn Duan|
|San Diego State University||Mary Thomas||✔|
|San Jose State University||Sen Chiao, Werner Goveya|
|Slippery Rock University of Pennsylvania||Nitin Sukhija|
|Sonoma State University||Mark Perri||✔|
|South Carolina State University||Biswajit Biswal, Jagruti Sahoo||✔||✔|
|South Dakota School of Mines and Technology||Rafal M. Oszwaldowski||✔|
|South Dakota State University||Kevin Brandt, Roberto Villegas-Diaz (student), Rachael Auch, Chad Julius||✔|
|Southeast Missouri State University||Marcus Bond|
|Southern Connecticut State University||Yigui Wang|
|Southern Illinois University||Shaikh Ahmed, Majid Memari (student), Manvith Mali (student)|
|Southern Illinois University-Edwardsville||Kade Cole, Andrew Speer|
|Southern Methodist University||Amit Kumar, Merlin Wilkerson, Robert Kalescky|
|Southern University and A & M College||Shizhong Yang, Rachel Vincent-Finley||✔||✔|
|Southwestern Oklahoma State University||Jeremy Evert, Kurtis D. Clark (student), Hamza Jamil (student), Arianna Martin (student)||✔|
|Spelman College||Yonas Tekle||✔|
|Stanford University||Ruth Marinshaw, Zhiyong Zhang|
|Swarthmore College||Andrew Ruether|
|Temple University||Richard Berger, Edwin Posada|
|Tennessee Technological University||Mike Renfro|
|Texas A & M University-College Station||Rick McMullen, Dhruva Chakravorty, Jian Tao, Brad Thornton|
|Texas A & M University-Corpus Christi||Ed Evans, Joshua Gonzalez||✔|
|Texas A&M University-San Antonio||Smriti Bhatt||✔|
|Texas Southern University||Farrukh Khan||✔|
|Texas State University||Shane Flaherty||✔|
|Texas Tech University||Tom Brown, Misha Ahmadian (student)|
|Texas Wesleyan University||Terrence Neumann|
|The College of New Jersey||Shawn Sivy|
|The Jackson Laboratory||Shane Sanders, Bill Flynn||✔|
|The University of Tennessee - Health Science Center||Billy Barnett|
|The University of Tennessee-Chattanooga||Carson Woods (student), Tony Skjellum|
|The University of Texas at Austin||Kevin Chen|
|The University of Texas at Dallas||Frank Feagans, Gi Vania, Jaynal Pervez, Christopher Simmons, Namira Pervez (student)|
|The University of Texas at El Paso||Rodrigo Romero, Vinod Kumar||✔|
|The University of Texas at San Antionio||Brent League, Jeremy Mann, Zhiwei Wang, Armando Rodriguez, Thomas Freeman, Ritu Arora||✔|
|Tinker Air Force Base||Zachary Fuchs, David Monismith||✔|
|Trinity College||Peter Yoon|
|Tufts University||Shawn Doughty|
|Tulane University||Hideki Fujioka, Hoang Tran, Carl Baribault||✔|
|United States Department of Agriculture - Agriculture Research Service||Nathan Weeks|
|United States Geological Survey||Janice Gordon, Jeff Falgout, Natalya Rapstine|
|University at Buffalo||Dori Sajdak, Andrew Bruno|
|University of Alabama at Birmingham||John-Paul Robinson, Shahram Talei (student)||✔|
|University of Alaska||Liam Forbes, Kevin Galloway||✔||✔|
|University of Arizona||Jimmy Ferng, Mark Borgstrom, Moe Torabi, Adam Michel, Chris Reidy, Chris Deer, Cynthia Hart, Ric Anderson, Todd Merritt, Dima Shyshlov, Blake Joyce, Alexander Prescott (student)|
|University of Arkansas||David Chaffin, Jeff Pummill, Pawel Wolinski, Timothy "Ryan" Rogers (student)||✔|
|University of Arkansas at Little Rock||Albert Everett||✔|
|University of California Merced||Sarvani Chadalapaka, Robert Romero|
|University of California-Berkeley||Aaron Culich, Chris Paciorek|
|University of California-Davis||Bill Broadley, Timothy Thatcher|
|University of California-Irvine||Harry Mangalam||✔|
|University of California-Los Angeles||TV Singh|
|University of California-Riverside||Bill Strossman, Charles Forsyth||✔|
|University of California-San Diego||Cyd Burrows-Schilling, Claire Mizumoto|
|University of California-San Francisco||Jason Crane|
|University of California-Santa Barbara||Sharon Solis, Sharon Tettegah||✔|
|University of California-Santa Cruz||Jeffrey D. Weekley||✔|
|University of Central Florida||Glenn Martin, Jamie Schnaitter, Fahad Khan, Shafaq Chaudhry|
|University of Central Oklahoma||Evan Lemley, Samuel Kelting (student)||✔|
|University of Chicago||Igor Yakushin, Ryan Harden|
|University of Cincinnati||Kurt Roberts, Larry Schartman, Jane E Combs|
|University of Colorado||Shelley Knuth, Andy Monaghan, Daniel Trahan|
|University of Colorado, Denver/Anschutz Medical Campus||Amy Roberts, Farnoush Banaei-Kashani|
|University of Delaware||Anita Schwartz, Parinaz Barakhshan (student), Michael Kyle||✔|
|University of Florida||Alex Moskalenko, David Ojika|
|University of Georgia||Guy Cormier|
|University of Guam||Rommel Hidalgo, Eugene Adanzo, Randy Dahilig, Jose Santiago, Steven Mamaril||✔||✔|
|University of Hawaii||Gwen Jacobs, Sean Cleveland||✔||✔|
|University of Houston||Jerry Ebalunode||✔|
|University of Houston-Clear Lake||David Garrison, Liwen Shih|
|University of Houston-Downtown||Hong Lin, Dexter Cahoy||✔|
|University of Idaho||Lucas Sheneman||✔|
|University of Illinois||Mao Ye (domain) , Rob Kooper (domain) , Dean Karres, Tracy Smith|
|University of Illinois at Chicago||Himanshu Sharma, Jon Komperda, Leonard Apanasevich||✔|
|University of Indianapolis||Steve Spicklemire|
|University of Iowa||Ben Rogers, Sai Ramadugu, Adam Harding, Joe Hetrick, Cody Johnson, Genevieve Johnson, Glenn Johnson, Brendel Krueger, Kang Lee, Gabby Perez, Brian Ring, John Saxton, Elizabeth Leake, Giang Rudderham|
|University of Kansas||Riley Epperson||✔|
|University of Kentucky||Vikram Gazula, James Griffioen||✔|
|University of Louisiana at Lafayette||Raju Gottumukkala||✔|
|University of Louisville||Harrison Simrall||✔|
|University of Maine System||Bruce Segee, Steve Cousins, Michael Brady Butler (student)||✔|
|University of Maryland Eastern Shore||Urban Wiggins||✔|
|University of Maryland-Baltimore County||Roy Prouty, Randy Philipp||✔|
|University of Maryland-College Park||Kevin M. Hildebrand||✔|
|University of Massachusetts Amherst||Johnathan Griffin|
|University of Massachusetts-Boston||Jeff Dusenberry, Runcong Chen||✔|
|University of Massachusetts-Dartmouth||Scott Field|
|University of Memphis||Qianyi Cheng|
|University of Miami||Dan Voss, Warner Baringer|
|University of Michigan||Gregory Teichert , Shelly Johnson, Todd Raeker, Daniel Kessler (student)|
|University of Minnesota||Eric Shook (domain) , Ben Lynch, Joel Turbes, Doug Finley, Aneesh Venugopal (student), Charles Nyguyen|
|University of Mississippi Medical Center||Kurt Showmaker||✔|
|University of Missouri-Columbia||Derek Howard, Asif Ahamed Magdoom Ali, Brian Marxkors, Ashkan Mirzaee (student), Christina Roberts, Predrag Lazic, Phil Redmon|
|University of Missouri-Kansas City||Paul Rulis|
|University of Montana||Tiago Antao||✔|
|University of Nebraska||Adam Caprez, Natasha Pavlovikj (student), Tom Harvill||✔|
|University of Nebraska Medical Center||Ashok Mudgapalli||✔|
|University of Nevada-Reno||Fred Harris, Scotty Strachan, Engin Arslan||✔|
|University of New Mexico||Hussein Al-Azzawi, Matthew Fricke||✔||✔|
|University of North Carolina||Mark Reed, Mike Barker|
|University of North Carolina - Greensboro||Jacob Tande|
|University of North Carolina - Wilmington||Eddie Dunn, Ellen Gurganious, Cory Nichols Shrum (student)|
|University of North Carolina at Charlotte||Christopher Maher|
|University of North Dakota||Aaron Bergstrom, David Apostal||✔|
|University of North Georgia||Luis A. Cueva Parra , Yong Wei|
|University of North Texas||Charles Peterson, Damiri Young|
|University of Notre Dame||Dodi Heryadi, Scott Hampton|
|University of Oklahoma||Henry Neeman, Kali McLennan, Horst Severini, James Ferguson, David Akin, S. Patrick Calhoun, Jason Speckman||✔|
|University of Oregon||Nick Maggio, Robert Yelle, Michael Coleman, Jake Searcy, Mark Allen|
|University of Pennsylvania||Gavin Burris|
|University of Pittsburgh||Kim Wong, Matt Burton, Fangping Mu, Shervin Sammak, Donya Ramezanian|
|University of Puerto Rico Mayaguez||Ana Gonzalez||✔||✔|
|University of Rhode Island||Kevin Bryan, Gaurav Khanna||✔|
|University of Richmond||Fred Hagemeister|
|University of South Carolina||Paul Sagona, Ben Torkian, Nathan Elger||✔|
|University of South Dakota||Ryan Johnson, Bill Conn||✔|
|University of South Florida-St Petersburg||Tylar Murray|
|University of Southern California||Virginia Kuhn (domain) , Cesar Sul, Derek Strong (domain) , Andrea Renney (domain) , Tomasz Osinski (domain) , Marco Olguin (domain)|
|University of Southern Mississippi||Brian Olson , Gopinath Subramanian||✔|
|University of St Thomas||William Bear, Keith Ketchmark, Eric Tornoe|
|University of Tennessee - Knoxville||Deborah Penchoff|
|University of Tulsa||Peter Hawrylak||✔|
|University of Utah||Anita Orendt, Tom Cheatham (domain) , Brian Haymore (domain)|
|University of Vermont||Andi Elledge, Yves Dubief||✔|
|University of Virginia||Ed Hall, Katherine Holcomb|
|University of Washington||Nam Pho|
|University of Wisconsin-La Crosse||David Mathias, Samantha Foley|
|University of Wisconsin-Madison||Todd Shechter|
|University of Wisconsin-Milwaukee||Dan Siercks, Darin Peetz|
|University of Wyoming||Bryan Shader, Dylan Perkins||✔|
|University of the Virgin Islands||Marc Boumedine||✔||✔|
|Utah Valley University||George Rudolph|
|Valparaiso University||Paul Lapsansky, Paul M. Nord, Nicholas S. Rosasco|
|Vassar College||Christopher Gahn|
|Virginia Tech University||James McClure, Alana Romanella, Srijith Rajamohan|
|Washburn University||Karen Camarda, Steve Black||✔|
|Washington State University||Rohit Dhariwal, Peter Mills|
|Washington University in St Louis||Xing Huang, Matt Weil, Matt Callaway|
|Washington and Lee University||Tom Marcais|
|Wayne State University||Patrick Gossman, Michael Thompson, Aragorn Steiger, Sara Abdallah (student)|
|Weill Cornell Medicine||Joseph Hargitai|
|Wesleyan University||Henk Meij|
|West Chester University of Pennsylvania||Linh Ngo|
|West Texas A & M University||Anirban Pal|
|West Virginia Higher Education Policy Commission||Jack Smith||✔|
|West Virginia University||Guillermo Avendano-Franco , Blake Mertz, Nathaniel Garver-Daniels||✔|
|West Virginia University Institute of Technology||Sanish Rai||✔|
|Wichita State University||Terrance Figy||✔|
|Williams College||Adam Wang|
|Winston-Salem State University||Xiuping Tao||✔|
|Winthrop University||Paul Wiegand||✔|
|Wofford College||Beau Christ||✔|
|Woods Hole Oceanographic Institution||Roberta Mazzoli, Richard Brey|
|Yale University||Andrew Sherman, Kaylea Nelson, Benjamin Evans, Sinclair Im (student)|
|Youngstown State University||Feng George Yu|
LAST UPDATED: April 7, 2021
Advanced Computing for Social Change Institute
Providing transformative student experiences through the application of XSEDE resources and services.
The Advanced Computing for Social Change Institute offers unique opportunities, co-located with professional conferences, for undergraduate students who want to enhance their skillset and create positive change in their community.
The programs recruit students from diverse disciplines and backgrounds who want to work collaboratively to:
- Learn to apply data analysis and computational thinking to a social challenge
- Experience the latest tools and techniques for exploring data through visualization
- Expand skills in team-based problem solving
- Learn how to communicate ideas more effectively to the general public
- Be currently enrolled as a full time undergraduate student at an accredited college/university
- Be a U.S. citizen or permanent resident of the United States (for ACSC only)
- Not plan to graduate the semester before or two months after the program
- Have a minimum overall GPA of at least 2.5/4.0 (or equivalent)
- Be able to attend a full challenge or competition during program dates
- Complete the online application form before the deadline
Students from any undergraduate background are eligible, although some preference will be given to women, minorities, students from majors outside computer science, and students at the sophomore or junior level.
Students will be assigned to teams to ensure a balance of backgrounds, and an advisor will be assigned to each team. The costs of airfare, lodging, meals, and conference registration will be provided.
APPLICATION DEADLINE: August 2, 2021. Notification of acceptance to be sent in August 2021.
The next Advanced Computing for Social Change (ACSC) event will take place in 2022.
APPLICATION DEADLINE: The application will open in the winter.
Visit the ACSC FAQ for details.
HIV-1 viral capsid simulations on XSEDE-allocated Stampede2, Bridges, Darwin systems uncover nucleotide entry mechanism
By Jorge Salazar, Texas Advanced Computing Center (TACC)
The HIV-1 virus has evolved a way to import into its core the nucleotides it needs to fuel DNA synthesis, according to research led by Juan R. Perilla at the University of Delaware. Using the TACC Stampede2 and PSC Bridges supercomputers, Perilla's team has shown for the first time that a virus performs an activity such as recruiting small molecules from a cellular environment into its core to conduct a process beneficial for its life cycle. Credit: Xu, et al.
Viruses lurk in the grey area between the living and the nonliving, according to scientists. Like living things, they replicate but they don't do it on their own. The HIV-1 virus, like all viruses, needs to hijack a host cell through infection in order to make copies of itself.
Supercomputer simulations supported by the National Science Foundation-funded Extreme Science and Engineering Discovery Environment (XSEDE) have helped uncover the mechanism for how the HIV-1 virus imports into its core the nucleotides it needs to fuel DNA synthesis, a key step in its replication. It's the first example found where a virus performs an activity such as recruiting small molecules from a cellular environment into its core to conduct a process beneficial for its life cycle.
The computational biophysics research, published December 2020 in PLOS Biology, challenges the prevailing view of the viral capsid, long considered to be just a static envelope housing the genetic material of the HIV-1 virus.
"To my knowledge, it's the first piece of work that comprehensively shows an active role of the capsids in regulating a very specific lifecycle of the virus, not only computationally, but also in vitro assays and ultimately in the cells," said study co-author Juan R. Perilla, a biophysical chemist at the University of Delaware.
The research team collaborated with several research groups, including experimental groups at the University of Pittsburgh School of Medicine and the Harvard Medical School. These groups validated the predictions from molecular dynamics (MD) simulations by using atomic force microscopy and transmission electron microscopy.
"For our part, we used MD simulations," said lead author Chaoyi Xu, a graduate student in the Perilla Lab. "We studied how the HIV capsid allows permeability to small molecules, including nucleotides, IP6, and others." IP6 is a metabolite that helps stabilize the HIV-1 capsid.
It's rare for a computational paper to be in a biology journal, explained Perilla. "The reason this is possible is that we are discovering new biology," he said. The biology relates to the stability of the virus to import small molecules that it needs for certain metabolic pathways. "In the context of HIV, it's the fuel for the reverse transcription that occurs inside of the capsid."
Cooperative binding of small molecules to the central hexamer cavity. Two-dimensional free energy landscapes of deoxyadenosine triphosphate translocation through the cavity, in the presence of an additional IP6. Pathways connecting interior and exterior shown as a dashed line, with representative structures corresponding translocation events. Credit: Xu, et al.
The enzyme reverse transcriptase generates complimentary DNA, one-half of DNA that pairs up in the cell to complete the full invading viral DNA. The viral DNA enters the host cell nucleus, integrates into the host cell DNA, and uses the cell's machinery to crank out new viral DNA.
"In these series of experiments and computational predictions, what we have shown is that the capsid itself plays an active role in the infective cycle," Perilla said. "It regulates the reverse transcription — how the viral DNA synthesizes inside of the capsid." He explained that these processes are the result of millions of years of co-evolution between the virus and the target cell.
"Without supercomputers, the computational part of the study would have been impossible," added Xu. The challenge was that the biological problem of nucleotide translocation would require a longer timescale than would be possible to sample using atomistic molecular dynamics simulations.
Instead, the researchers used a technique called umbrella sampling coupled with Hamiltonian replica exchange. "The advantage of using this technique is that we can separate the whole translocation process into small windows," Xu said. In each small window, they ran individual small MD simulations in parallel on supercomputers.
"By using the resources provided from XSEDE, we were able to run and not only test the translocation processes, but also the effects of small molecules binding on the translocation process by comparing the free energy differences calculated from our results."
Chaoyi Xu (upper left) and Juan R. Perilla (bottom), Department of Chemistry & Biochemistry, University of Delaware. Jorge Salazar of TACC (upper right).
XSEDE awarded Perilla and his lab access to two supercomputing systems used in the HIV capsid research: Stampede2 at the Texas Advanced Computing Center (TACC); and Bridges at the Pittsburgh Supercomputing Center (PSC).
"TACC and PSC have been extremely generous to us and very supportive," Perilla said.
"When I transferred from Stampede1 to Stampede2, the hardware was a big improvement. At the time, we were fascinated with the Intel Xeon Skylake nodes. They were fantastic," Perilla said.
"On Bridges, we took advantage of the high memory nodes. They have these massive memory machines with 3 and 12 terabytes of inline memory. They're really good for analysis. Bridges provides a very unique service to the community," he continued.
On related work, the Perilla Lab has also employed through XSEDE the PSC Bridges-AI system, and they have been part of the early user science program for PSC's Bridges-2 platform.
Molecular mechanism for nucleotide translocation through the HIV-1 CA hexamer. a) Nucleotide diffuses between the capsid exterior and central cavity. (b) Nucleotide binds to Arg18 and Lys25. (c) Second nucleotide enters. (d) Phosphate group of second nucleotide interacts with Arg18. (e) Second nucleotide enhances interactions between Lys25 and the first nucleotide. (f) Thermal fluctuations facilitate dissociation of dNTP. (g) Second nucleotide occupies canonical binding position (b) for a single nucleotide in the cavity. Credit: Xu, et al.
"We've enjoyed this early science period on Bridges-2," Perilla said. "The experts at PSC want us to hammer the machine as much as we can, and we're happy to do that. We have a lot of work that needs to be done."
Perilla related that the XSEDE Campus Champion program has also helped in his mission for training the next generation of computational scientists. The program enlists 600+ faculty and staff at more than 300 universities to help students, faculty, and postdocs take full advantage of XSEDE's cyberinfrastructure resources.
"We received an immense amount of help from our XSEDE Campus Champion, Anita Schwartz." Perilla said. "She helped us with everything that is related to XSEDE. We also took advantage of the training programs. The younger members of our lab took advantage of the training opportunities offered by XSEDE."
Xu recalled finding them helpful for learning how to get started using XSEDE supercomputers, and also for learning the Simple Linux Utility for Resource Management (SLURM), which is the project job management used for supercomputers.
"By taking these courses, I familiarized myself with using these supercomputers, and also to use them to solve our research questions," Xu said.
What's more, the University of Delaware launched in December 2020 the Darwin supercomputer, a new XSEDE-allocated resource.
Stampede2 at TACC (left) and Bridges at PSC (right) are allocated through the NSF-funded Extreme Science and Engineering Discovery Environment (XSEDE).
"The students in the group have had the opportunity to train on these fantastic machines provided by XSEDE, they're now at the point that they're expanding that knowledge to other researchers on campus and explaining the details of how to make the best use of the resource," Perilla said. "And now that we have an XSEDE resource here on campus, it's helping us create a local community that is as passionate about high performance computing as we are,"
Perilla sees this latest work on the HIV-1 capsid as providing a new target for therapeutic development. Because there is no cure for HIV and the virus keeps getting drug resistance, there's a constant need to optimize anti-retroviral drugs.
Said Perilla: "We're very enthusiastic about supercomputers and what they can do, the scientific questions they allow us to pose. We want to reproduce biology. That's the ultimate goal of what we do and what supercomputers enable us to do."
The study, "Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis," was published December 17, 2020 in the journal PLOS Biology. The authors are Chaoyi Xu, Brent Runge, Roman Zadorozhnyi, Tatyana Polenova, and Juan R. Perilla of the University of Delaware; Douglas K. Fischer, Jinwoo Ahn, and Zandrea Ambrose of the University of Pittsburgh School of Medicine; Wen Li and Alan N. Engelman of Harvard Medical School; Sanela Rankovic and Itay Rousso of the Ben-Gurion University of Negev; Robert A. Dick of Cornell University; Christopher Aiken of the Vanderbilt University Medical Center. This work was supported by the US National Institutes of Health grants P50AI1504817, P20GM104316, R01AI147890, R01AI070042, and R01AI107013.
At a Glance
- Mechanism found for how HIV-1 virus imports nucleotides into its core that fuel DNA synthesis, a key step in its replication.
- First example found where a virus recruits small molecules from a host cell into its core to conduct a process beneficial for its life cycle.
- Supercomputer molecular dynamics simulations helped test translocation and free energy calculations
- Research supported by the NSF-funded XSEDE through TACC Stampede2 and PSC Bridges
- HIV-1 capsid research provides potential for new drug targets for therapeutic development such as improved anti-retroviral drugs.
The XSEDE ecosystem includes many types of software installed and supported by XSEDE staff, by service providers, community software providers, science gateways and other software integrators, and the users, researchers, and educators that use XSEDE.
To find software installed on XSEDE allocated resources and available from the command line and the batch job execution environment visit the:
To discover packaged software, cloud images, software from science gateways, community provided software, and all other forms of software and advanced digital services that are part of the XSEDE ecosystem visit the:
Software in network accessible services
Software available thru network accessible XSEDE enterprise services is described in the Services page.
Software available thru network accessible Science Gateways is described in the Science Gateways page.
Community Software Areas
XSEDE's Community Software Areas (CSAs) allow science gateways and other research software providers and integrators to install, advertise, share, and support their own software on XSEDE resources. A CSA is a disk directory that is outside the software provider's home directory where they can install their software executables, scripts, libraries, and small data files. XSEDE Service Providers (SPs) create and provide access to the disk directory, and may also backup the disk directory, help advertise the software modules in that directory used to access the software, and may provide software usage statistics.
If the software provider and SP advertise CSA modules, XSEDE provides a comprehensive XSEDE Software Discovery interface where users can discover both community and XSEDE provided software.
To request a new CSA the software provider must first request a startup allocation (if they don't already have a regular allocation) to gain access to the resource(s) where the CSA will be created. Once the provider has an allocation giving them access to a resource they should next request the CSA directory on the desired resources by contacting the XSEDE Help Desk.
Consult the Resources page for a brief description of XSEDE systems.
Consult the CSA availability page for details on which XSEDE systems support CSAs.
Once the software provider has an allocation and the CSA directory they can install their software in the directory and publish software modules to enable discovery.
Software providers may view their software and point users at the XSEDE Software Discovery interface.
XSEDE ECSS scientist a leader in development of open-source tool for engineering new substances
By Ken Chiacchia, Pittsburgh Supercomputing Center
|Using the KKR-CPA method, the MuST software converts the complex surroundings of an atom in a random alloy (brass, an alloy of copper and zinc, in this case) to an "effective medium" that averages the properties of the surrounding atoms.|
Materials science gives us substances with novel properties that enable new technologies. But engineering these materials can take tremendous computing power. An international collaboration in which a scientist in XSEDE's Extended Collaborative Support Service (ECSS) played a leading role has developed MuST, a new, open-source supercomputing code that radically reduces the complexity of the calculations. MuST—named for the "multiple scattering theory" on which it's based—makes it possible to simulate samples of material large enough for real-world relevance in much less time.
Why It's Important
Materials science is important for making our world run better, and at less expense. Doping a silicon wafer with a small quantity of impurity atoms can change it from being an electrical conductor to an insulator to a semiconductor—one of those miracle substances we take for granted but which make our computer-aided modern lives possible. Altering the ratio of atoms in a glass mixture can produce a nearly unbreakable smartphone screen. Changing the composition of a metal can make it stronger, lighter, or easier to manufacture and form to shape.
"It's a many-body problem, so it is impossible to solve…[Instead] we need to solve the distributed-equation-effective potential—it's called ‘the swamp.' By solving this equation, [we] solve the electron density, which answers the question of the energy of the original many-body problem."—Yang Wang, Pittsburgh Supercomputing Center (PSC)
The problem is, materials science is complicated. Particularly when a material has many different elements in it, understanding its properties—and how it can be engineered to do what we want—involves taking into consideration the interactions between each atom, its neighbors, their neighbors, and so on. This many-body problem, which is impossible to solve exactly, can be approximated to a high level of confidence with computers. But with the complicated rules of quantum chemistry that govern materials at the atomic scale, the complexity ramps up when you try to simulate more than a few atoms of a material. This is a problem, as small numbers of atoms may have different properties than the same material in real-world bulk. Particularly for disordered materials—some of the most promising and interesting materials for development—this complexity quickly pushes the problem beyond the point at which even the world's largest supercomputers can crunch it.
How XSEDE Helped
|Yang Wang, computational scientist at PSC and an XSEDE ECSS consultant.|
Enter Yang Wang, senior computational scientist at PSC and ECSS consultant, and an international collaboration with the Oak Ridge National Laboratory, Universität Augsburg, University of the Chinese Academy of Sciences, Louisiana State University, and Middle Tennessee State University. They developed MuST, a software package that uses density functional theory (DFT) for ab initio investigation of disordered materials—that is, predicting materials' properties from first principles.
Ab initio quantum chemistry methods is a time-tested way to accurately predict the properties of a substance. It also helps lab scientists focus expensive real-world experiments on the most promising candidates, speeding development. But the computational cost of DFT calculations typically scales with the third power of the number of electrons—in other words, if computing the behavior of a given number of electrons in a material takes a certain amount of time and power to calculate, twice as many will take eight times as much, three will take 27 times as much and four times as many 64 times as much. This puts a tight limit on how many atoms can be simulated, since more atoms means more electrons.
MuST takes advantage of locally self-consistent multiple scattering theory (LSMS) to simplify the problem. Instead of, say, calculating the interactions of an aluminum atom in an Al-Cr-Fe-Co-Ni alloy with each aluminum, chromium, iron, cobalt, and nickel atom nearby, it calculates those other atoms as a kind of average "soup" in which the aluminum atom sits.
"The soup reproduces the total behavior of these other atoms in their proportions in that alloy instead of accounting for each atom individually … Each domain has its own potential, which you then add together to get an effective potential for the whole space. You can treat it as single-site scattering potential."—Yang Wang, PSC
MuST's simplification, using a combination of the Korringa-Kohn-Rostoker and coherent potential approximation methods (KKR-CPA), reduces the complexity of the computation enormously. Instead of scaling to the third power, it scales with the number of electrons. Instead of 64 times the computing power enabling you to calculate four times as many electrons, it enables you to simulate 64 times as many.
Initial work with MuST, which has been available to the general scientific community since December 2019, has produced results as good as or better than those of gold-standard methods such as the coupled cluster single-double and triple or quantum monte carlo techniques, which require much more computing power. It also goes beyond the reach of those methods when large numbers of atoms (thousands or more) are involved.
Goals for the future include incorporating the LSMS method with typical medium embedding, a different type of "soup" than used in the CPA method and which is designed to include physics that are not addressed by CPA. This would allow scientists to capture the metal-insulator transition phenomena driven by disorder in quantum materials, and integrate the Kubo-Greenwood formula into the package. This will, in turn, enable the investigation of electronic transport in disordered structures. The movement of electrons through a material underlies the phenomenon of electrical flow in pure metals but isn't nearly as well understood in materials with disorder caused by impurities or by alloying different metals.
Scientists can download the program—and join the team to develop MuST—here.
At a Glance:
Materials science gives us substances with novel properties that enable new technologies.
Engineering these materials can take tremendous computing power.
An international collaboration in which a scientist in XSEDE's Extended Collaborative Support Service (ECSS) played a leading role has developed MuST, a new, open-source supercomputing code that radically reduces the complexity of the calculations.
The new software makes it possible to simulate samples of material large enough for real-world relevance in much less time.
Previous years' ECSS seminars may accessed through these links:
March 16, 2021
HPC for epidemic modeling with limited data: COVID-19 case studies
Presenter(s): Kelly Pierce (TACC)
The novel coronavirus (SARS-CoV-2) emerged in late 2019 and spread globally in early 2020. Initial reports suggested the associated disease, COVID-19, produced rapid epidemic growth and caused high mortality. As the virus sparked local epidemics in new communities, health systems and policy makers were forced to make decisions with limited information about the spread of the disease. The UT COVID-19 Modeling Consortium formed in response to the urgent need for increased situational awareness and developed a library of COVID-19 models to project infections and healthcare burdens. These models were used to inform policy decisions in the city of Austin, Texas and as part of the CDC COVID-19 mortality and infection model ensembles. Now one year into the pandemic, the Consortium has expanded the scope of its work to include estimates of infection introductions in schools, statistically informed guidelines for genomic surveillance to detect novel variants, and equitable vaccine distribution. As an early partner in the Consortium, the Texas Advanced Computing Center (TACC) has provided support in software development, data management, and long-term modeling infrastructure development. This talk will overview the joint work of the Consortium and TACC, with an emphasis on the impact of limited data availability in epidemiological modeling and the role of high-performance computing in supporting fast turn-around of time-sensitive results.
February 16, 2021
MuST – A high performance computing software package for the ab initio study of materials
Presenter(s): Yang Wang (Pittsburgh Supercomputing Center)
Ab initio calculation is one of the most popular computational practices in the HPC user community. It aims to study molecules or materials using quantum mechanics as its fundamental principle, rather than being based upon empirical or semi-empirical models. In the past decade, several computational tools developed for ab initio calculation have become available to the research community. In this presentation, I will introduce MuST, an open source software project supported by NSF CSSI program. MuST package is designed for enabling ab initio investigation of disordered materials. It is developed based on multiple scattering theory with Green function approach in the framework of density functional theory, and is built upon decades of development of research codes that include 1) KKR method, which is an all-electron, full-potential, ab initio electronic structure calculation method; 2) KKR-CPA method, which is a highly efficient ab initio method for the study of random alloys, and 3) Locally Self-consistent Multiple Scattering (LSMS) method, which is a linear scaling ab initio code capable of treating extremely large disordered systems from the first principles using the largest parallel supercomputers available. Strong disorder and localization effects can also be studied in real system within the LSMS formalism with cluster embedding in an effective medium, e.g., DMFT, DCA, or TMDCA, enabling a scalable approach for the ab initio studies of quantum materials. I will show the latest development of the MuST project, and discuss its potential applications.
January 19, 2021
Introduction to Jetstream2 - Accelerating Science and Engineering on Demand
Presenter(s): Jeremy Fischer (Indiana University)
This talk will give an overview of Jetstream and the award of Jetstream2. We'll discuss successes, failures, and some things we learned along the way. We'll discuss use cases and try to provide plenty of time for questions about the system at the end of the session.
Exosphere, User-Friendly Interface for Research Clouds
Presenter(s): Chris Martin (University of Arizona) Julian Pistorius (University of Arizona)
Exosphere is a client interface for managing computing workloads on OpenStack cloud infrastructure. It is a user-friendly alternative to Horizon, the default OpenStack graphical interface. Exosphere can be used with most research cloud infrastructure, requiring near-zero custom integration work. The Exosphere team aims to bring advanced features of research clouds within reach of non-advanced users, such as elastic workload scaling, GPU-accelerated streaming desktops, and secure, reproducible sharing of data science workbench environments. Link to Slides
October 20, 2020
Presenter(s): Sergiu Sanielevici (PSC)
Neocortex will be a highly innovative resource at PSC that will accelerate AI-powered scientific discovery by vastly shortening the time required for deep learning training, foster greater integration of artificial deep learning with scientific workflows, and provide revolutionary new hardware for the development of more efficient algorithms for artificial intelligence and graph analytics.
Presenter(s): Shawn Brown (PSC)
Bridges-2, PSC's newest supercomputer, will provide transformative capability for rapidly evolving, computation-intensive and data-intensive research, creating opportunities for collaboration and convergent research. It will support both traditional and non-traditional research communities and applications. Bridges-2 will integrate new technologies for converged, scalable HPC, machine learning and data; prioritize researcher productivity and ease of use; and provide an extensible architecture for interoperation with complementary data-intensive projects, campus resources, and clouds.
September 15, 2020
High Resolution Spatial Temporal Analysis of Whole-Head 306-Channel Magnetoencephalography & 66-Channel Electroencephalography Brain Imaging in Humans During Sleep
Presenter(s): David Shannahoff-Khalsa (UCSD) Mona Wong (SDSC) Jeff Sale (SDSC)
In chronobiology, the circadian rhythm is known as the 24-hr sleep-wake cycle. The ultradian rhythm has a shorter cycle with approximately a 1-3 hour periodicity, with considerable variability. This project's goal is to follow up on our earlier EEG work during sleep, and that of others, that has identified a rhythm of how the two cerebral hemispheres alternate in dominance with coupling to the ultradian rhythm of the rapid eye movement (REM) and non-rapid eye movement (NREM) sleep cycle. Here we are also comparing whole head and regional variations in cerebral dominance to gain better insight to this novel rhythm during sleep. This rhythm of alternating cerebral hemispheric dominance also manifests during the waking state, and it is apparently coupled to every major bodily system and now presents as a novel rhythm regulated by the central and autonomic nervous systems via the hypothalamus. With the support of XSEDE ECSS, this project has processed 306-channel magnetoencephalography that includes 3 signal types (1 magnetometer, 2 opposing gradiometers) and 66-channel EEG recordings from 4 normal healthy sleep subjects. We are analyzing the data to compare the 4 signal types filtered into 6 frequency bands, over the whole head and 6 discrete regions of the head to see how they vary with the REM and NREM sleep stages. Our analysis includes a relatively new algorithm called Fast Orthogonal Search that is well suited for analyzing the periodicity in nonlinear dynamical systems. Our analysis also includes unique methods in visualization for observing how these patterns of left minus right hemisphere power exhibit during sleep stages.