Content with tag epidemic .

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

Domain Champions are part of Campus Champions along with Regional and Student Champions

Domain 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 domain-info@xsede.org if you are interested in a discussion with a current domain champion, or in becoming a domain champion yourself.

DOMAIN CHAMPION INSTITUTION
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


Student Champions

Campus Champions programs include Regional, Student, and Domain Champions.

 

Student 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 info@campuschampions.org to recommend the student for the program and confirm their willingness to be the student's mentor. 

Questions? Email info@campuschampions.org.

 

 

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

Majid Memari

Chet Langin   Graduate 2021
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

John-Paul Robinson

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

Jaynal Pervez

Neuroscience Undergraduate 2024
University of Wyoming Rajiv Khadka Jared Baker   Graduate 2020
Yale University Sinclair Im Andy Sherman Applied Math Graduate 2022
           
GRADUATED          
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

 

Key Points
Student Champions
Regional Champions
Domain Champions
Contact Information

Champion Leadership Team

This page includes the Champions Leadership team and Regional Champions

Champion Staff
Name Institution Position
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

Regional Champions

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.

 

CHAMPION INSTITUTION DEPUTY CHAMPION INSTITUTION REGION
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


 

Key Points
Leadership table
Regional Champions table
Contact Information

XSEDE Impact Newsletter, April 2021

Center for AI Innovation Spring Seminar
Mondays, 12 pm EDT / 9 am PDT

XSEDE HPC Workshop: MPI
May 4-5, 11am-4:30pm EDT

ISC High Performance 2021 Digital
June 24 – July 2, 2021

PEARC21
July 19-22


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

Click here to see a big map with a legend.

See also the lists of Leadership Team and Regional LeadersDomain Champions and Student Champions.

Institution Campus Champions EPSCoR MSI
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    
SBGrid Consortium      
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    
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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  
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University of Louisiana at Lafayette Raju Gottumukkala  
University of Louisville Harrison Simrall  
University of Maine System Bruce Segee, Steve Cousins, Michael Brady Butler (student)  
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University of Massachusetts-Dartmouth Scott Field    
University of Memphis Qianyi Cheng    
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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  
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University of Missouri-Kansas City Paul Rulis    
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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
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University of North Carolina at Charlotte Christopher Maher    
University of North Dakota Aaron Bergstrom, David Apostal  
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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  
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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  
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Washington University in St Louis Xing Huang, Matt Weil, Matt Callaway    
Washington and Lee University Tom Marcais    
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Weill Cornell Medicine Joseph Hargitai    
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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  
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Williams College Adam Wang    
Winston-Salem State University Xiuping Tao  
Winthrop University Paul Wiegand  
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Woods Hole Oceanographic Institution Roberta Mazzoli, Richard Brey    
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Youngstown State University Feng George Yu    

LAST UPDATED: April 7, 2021

 

Key Points
Members
Institutions
Contact Info
Contact Information

 
April 2021 | Science Highlights, Announcements & Upcoming Events
 
XSEDE helps the nation's most creative minds discover breakthroughs and solutions for some of the world's greatest scientific challenges. Through free, customized access to the National Science Foundation's advanced digital resources, consulting, training, and mentorship opportunities, XSEDE enables you to Discover More. Get started here.
 
Science Highlights
 
Accelerating Alzheimer's Research
 
XSEDE-allocated supercomputers assist in study of nearly 50,000 brain scans
 
 
Access to XSEDE-allocated supercomputers has allowed for observation and quantification of thinning in the transentorhinal cortex of the brain during the early stages of Alzheimer's disease. Located in the temporal lobe of the brain, the transentorhinal cortex has been believed to be the first area impacted by Alzheimer's disease; however, until now, this was only able to be shown in autopsy results.
 
 
The transentorhinal cortex is shown as a pair of triangulated surfaces; the curved white lines represent cortical columns, which are used to accurately estimate thickness. Credit: Daniel Tward, UCLA.
 
MuST Program Simplifies Predictions of Material Properties
 
XSEDE ECSS scientist a leader in development of open-source tool for engineering new substances
 
 
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.
 
 
Yang Wang, computational scientist at PSC/ XSEDE ECSS consultant who helped develop MuST.
 
Getting to the Core of the HIV Replication
 
HIV-1 viral capsid simulations on XSEDE-allocated systems uncover nucleotide entry mechanism
 
 
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 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 HIV-1 virus has evolved a way to import into its core the nucleotides it needs to fuel DNA synthesis. Credit: Xu, et al.
 
Program Announcements
 
NCSA's Delta System to be Allocable by XSEDE this Summer
 
 
Delta, NCSA's newest supercomputer, is expected to be available for allocation via XSEDE starting in June 2021 for projects beginning in August 2021. The new system, which will be the most performant GPU computing resource in NSF's portfolio, seeks to combine cutting-edge GPUs with advanced research computing CPU architectures to meet large memory demands and enable innovation.
 
Researchers and Gateways looking to expand their use of GPU supercomputing are encouraged to begin preparing proposals now. Read more about Delta, including specifications, at the link below.
 
 
XSEDE Cyberinfrastructure Integration (XCI) Updates
 
 
The XSEDE Cyberinfrastructure Integration (XCI) team plans to transition the XSEDE web single sign-on (SSO) login service in April, which will require users using XSEDE credentials to login with multi-factor authentication (MFA). The Pegasus team and XSEDE are looking for interested volunteer XSEDE SPs and XSEDE-allocated researchers or Science Gateway developers to participate in a pilot over the next few months to make scientific workflow capabilities more accessible on XSEDE.
 
 
Community Announcements
 
Register by June 9 for Gateway Focus Week
 
 
Gateway Focus Week, offered by the Science Gateways Community Institute (SGCI), is an intensive workshop designed for innovative research teams to work together on producing a strong sustainability plan. The full Focus Week curriculum is now offered in a new format: online, over the course of two weeks. Register by June 9 to join the next session, taking place June 14-24, 2021. Attendees may choose to either attend the full workshop or attend sessions "a la carte."
 
 
PEARC21 Call for Participation
 
 
ACM PEARC21 Conference — Evolution Across All Dimensions will take place virtually from July 18-22, 2021 and will explore the current practice and experience in advanced research computing including workforce development, training, diversity, applications and software, and systems and software. 
 
Submission Deadlines:
 
Tutorials and Workshops: February 9, 2021
Full Papers: March 9, 2021
Short Papers: April 13, 2021
Invited resubmissions: April 20, 2021
Panels: May 9, 2021
Birds of a Feather: May 9, 2021
Posters: May 16, 2021
Visualizations: May 23, 2021
 
 
Register Today for GlobusWorld, May 12-14, 2021
 
 
GlobusWorld brings together researchers, systems administrators, developers, and IT leaders from top computing centers, labs, and universities. The event is designed to provide new insights into managing research data and storage at scale, as well as building and using cutting-edge applications, portals, and gateways. This year's event will be virtual in light of the COVID-19 pandemic. Attendance is free but registration is required.
 
 
Upcoming Dates and Deadlines
 

 


 
March 2021 | Science Highlights, Announcements & Upcoming Events
 
XSEDE helps the nation's most creative minds discover breakthroughs and solutions for some of the world's greatest scientific challenges. Through free, customized access to the National Science Foundation's advanced digital resources, consulting, training, and mentorship opportunities, XSEDE enables you to Discover More. Get started here.
 
Science Highlights
 
Supercomputing the Secrets of the Inner Ear
 
XSEDE-allocated supercomputers aid in study of key proteins involved in hearing and balance
 
 
The ears don't just help you hear. They also help a person walk, stand, and stay balanced. In fact, they work together with other systems in the body to help one understand our place in space. Many people who have sensations of vertigo find that the problem lies in their inner ears.
 
Researchers are studying cadherin-23 (CDH23) and protocadherin-15 (PCDH15), two large proteins involved in hearing loss and balance disorders, thanks to supercomputing resources allocated by XSEDE.
 
 
Credit: Marcos Sotomayor, The Ohio State University
 
MIT Researchers Use Machine Learning to Advance Computational Chemistry
 
XSEDE-allocated resources simulate complex models
 
 
Even though computational chemistry represents a challenging arena for machine learning, a team of researchers from the Massachusetts Institute of Technology (MIT) may have made it easier.
 
Thanks to allocations from XSEDE, they succeeded in developing an artificial intelligence (AI) approach to detect electron correlation — the interaction between a system's electrons — which is vital but expensive to calculate in quantum chemistry.
 
 
Multi-reference character of 3,165 structures as evaluated by two of the 15 diagnostics used by experts in the field, nHOMO[MP2] (top left) and C02 (top right). Bottom panels show all 15 diagnostics displayed using the uniform manifold approximation and projection (UMAP), with the bottom/top 10% for the two metrics shown as solid blue/red circles. Credit: Kulik et al, MIT.
 
Supercomputer Illustrates Mechanical Process of Cancer Growth
 
XSEDE-allocated resource enables researchers to show cellular "pushing" of collagen
 
 
According to the World Health Organization, one in six worldwide deaths has been attributed to cancer. However, these fatalities were not due to initial malignant tumors — the deaths were caused by the spread of cancer cells to surrounding tissues and subsequent tumor growth.
 
These tissues, which consist largely of collagen, have been the focus of a recent collaborative study by a team from Stanford University and Purdue University. To accomplish their work, the researchers utilized XSEDE allocations to study cancer cell division as what drives the growth of primary and metastatic tumors. Their research singled out the pushing mechanism as the key factor in allowing mitosis to occur.
 
 
Schematic of model system (left) and results of simulations showing deformation of collagen matrix (center and right) as cell undergoes division. Fcyto is constant inward force applied to the cell membrane near the cell equator to simulate cytokinetic ring contraction and Fls is force generated by cell during mitosis. Credit: T. Kim (Purdue), O. Chaudhuri (Stanford), and S. Nam (Harvard).
 
Program Announcements
 
PSC's Bridges-2 and SDSC's Expanse Now Allocable by XSEDE
 
 
Two relatively new NSF-funded supercomputers, the Bridges-2 platform at the Pittsburgh Supercomputing Center (PSC), and Expanse at the San Diego Supercomputer Center (SDSC), are available for allocation requests via XSEDE. Users who wish to access either resource can request allocations through normal XSEDE allocation channels, including the upcoming March 15-April 15 allocation cycle. More information about each individual resource may be found at the link below.
 
 
New Cornell Virtual Workshop Training Opportunities Available with XSEDE
 
 
Four new Cornell Virtual Workshop training topics are available at the XSEDE User Portal:
  • Getting Started on Frontera
  • Introduction to Advanced Cluster Architectures
  • Using the Jetstream APIs
  • Python for Data Science: Part 2 - Data Modeling and Machine Learning
 
Cornell Virtual Workshop topics are freely available at all times to the entire scientific community — researchers, HPC practitioners, students, and educators — at XSEDE Online Training.
 
 
Community Announcements
 
Frontera Expansio
 
 
Watch out, disasters and pandemics! The fastest university supercomputer in the world just got faster — thanks to an expansion from the National Science Foundation (NSF)Dell, and Intel — and will help scientists solve societal problems by providing urgent access to massive computing power.
 
 
Apply for a One-on-One Engagement with Trusted CI
 
 
One of Trusted CI's core activities is conducting one-on-one engagements with NSF projects and facilities. Topics for engagements include anything broadly in the scope of information security and can include the development of new cybersecurity programs, assessing existing cybersecurity programs, software assurance, identity management, or recommendations on new software features. The application deadline for engagements to be executed July-December 2021 is April 2, 2021.
 
 
PEARC21 Call for Participation
 
 
ACM PEARC21 Conference — Evolution Across All Dimensions will take place virtually from July 18-22, 2021 and will explore the current practice and experience in advanced research computing including workforce development, training, diversity, applications and software, and systems and software. 
 
Submission Deadlines:
 
Tutorials and Workshops: February 9, 2021
Full Papers: March 9, 2021
Short Papers: April 13, 2021
Invited resubmissions: April 20, 2021
Panels: May 9, 2021
Birds of a Feather: May 9, 2021
Posters: May 16, 2021
Visualizations: May 23, 2021
 
 
News from Globus
 
 
Upcoming Dates and Deadlines
 

 


Advanced Computing for Social Change Institute

Providing transformative student experiences through the application of XSEDE resources and services.


Making change through ACSCI

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

Eligibility:

  • 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 Details

The upcoming Computing4Change (C4C) event will be co-located with the SC21 conference Nov 14-19, 2021.

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.

Key Points
Developing a Diverse Workforce
Infusing Computational Science
Expanding Instructional Resources
Contact Information

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.

Software

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.

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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:

Content with tag epidemic .

March 16, 2021

HPC for epidemic modeling with limited data: COVID-19 case studies

Presenter(s): Kelly Pierce (TACC)

Presentation Slides

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)

Presentation Slides

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)

Presentation Slides

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

Introducing Neocortex

Presenter(s): Sergiu Sanielevici (PSC)

Presentation Slides

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.

Introducing Bridges-2

Presenter(s): Shawn Brown (PSC)

Presentation Slides

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)

Presentation Slides

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.


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