Supercomputer simulations 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 simulation work was supported by XSEDE, the Extreme Science and Engineering Discovery Environment funded by the National Science Foundation. And it was carried out on the Stampede2 system here at the Texas Advanced Computing Center, as well as on the Bridges system at the Pittsburgh Supercomputing Center.

XSEDE awarded supercomputing access and expertise to biophysical chemist Juan R. Perilla and his lab at the University of Delaware. Chaoyi Xu, a graduate student in the Perilla Lab, was the lead author on the HIV viral capsid work, published with Perilla and other scientists December 2020 in PLOS Biology. Xu and Perilla join host Jorge Salazar on the Supersized Science podcast to talk about their research.

Computational modeling combined with experimental data can provide insights into these behaviors. But modeling over timescales long enough to mean anything has so far been limited to bits and pieces of the coronavirus, like its spike protein, which is a target for the current round of vaccines.

A new multiscale coarse-grained model of the complete SARS-CoV-2 virion, its core genetic material and capsid shell, has been developed using supercomputers. The new model offers scientists potential to gain new insights and vulnerabilities in the coronavirus’s large-scale behavior.

The Supersized Science podcast features interviews with Gregory Voth of the University of Chicago; and Rommie Amaro of the University of California, San Diego. They’re coauthors of a study that details the new computer model of the complete coronavirus, published in November 2020 in the Biophysical Journal.

It incapacitates its victims soon after infection with massive vomiting or diarrhea, leading to death from fluid loss in about 50 percent of the afflicted. The Ebola virus transmits only through bodily fluids, marking a key difference from the COVID-19 virus and one that has helped contain Ebola’s spread.

Ebola outbreaks continue to flare up in West Africa, although a vaccine developed in December 2019 and improvements in care and containment have helped keep Ebola in check.

Supercomputer simulations by a University of Delaware team that included an undergraduate supported by the XSEDE EMPOWER program are adding to the mix and helping to crack the defenses of Ebola’s coiled genetic material. This new research could help lead to breakthroughs in treatment and improved vaccines for Ebola and other deadly viral diseases such as COVID-19.

Podcast host Jorge Salazar talks with the research team about their findings on Ebola - Juan Perilla, Chaoyi Xu, Tanya Nesterova, and Nidhi Katyal.

Perilla is an Assistant Professor, Xu a PhD student, Nesterova an undergraduate researcher, and Katyal a postdoctoral researcher, all in the Perilla Lab, Department of Chemistry and Biochemistry, University of Delaware.

It builds a far-reaching ladder-like apparatus from core helical amino acids that latch on to its host cell, leading to infection. Scientists don’t yet fully understand the details of how the coronavirus binds and fuses.

Numan Oezguen is an instructor at the Microbiome Center of Texas Children’s Hospital and also at the Baylor College of Medicine. He’s developed a model simulating coronavirus binding and fusing on Longhorn, the graphics processing unit subsystem of the Frontera supercomputer at the Texas Advanced Computing Center (TACC). Dr. Oezguen joins host Jorge Salazar on the TACC podcast.

Story Link: https://www.tacc.utexas.edu/-/corona-s-ladder
Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Simulations on the National Science Foundation (NSF)-funded Frontera supercomputer at the Texas Advanced Computing Center (TACC) have revealed the atomic makeup of the coronavirus’s sugary shield. What’s more, simulation and modeling show that glycans also prime the coronavirus for infection. Scientists hope this basic research will add to the arsenal of knowledge needed to defeat the COVID-19 virus.

Podcast host Jorge Salazar interviews Rommie Amaro, a professor of chemistry and biochemistry at the University of California, San Diego to talk about her science team’s latest findings.

Story Link: www.tacc.utexas.edu/-/sugar-coating…s-for-infection
Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Podcast host Jorge Salazar interviews Rommie Amaro, a professor of chemistry and biochemistry at the University of California, San Diego. She’s leading efforts to build the first complete all-atom model of the SARS-COV-2 coronavirus envelope, its exterior component.

Story Link: www.tacc.utexas.edu/-/coronavirus-m…a-supercomputer
Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Scientists are using supercomputers to help understand the relatively rare event of salts in water passing through atomically-thin nanoporous membranes. This research could not only help make progress in desalination for fresh water; it has applications in decontaminating the environment, better pharmaceuticals, and more.

Advanced path sampling techniques and molecular dynamics simulations captured the kinetics of solute transport through nanoporous membranes, according to a study published online in the Cell journal Matter, January 2020.

Supercomputers supported the research through allocations on XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. Researchers ran simulations on the Stampede2 system at TACC .

Joining host Jorge Salazar on the podcast is study co-author Amir Haji-Akbari, an assistant professor of chemical and environmental engineering at Yale University.

Story Link: www.tacc.utexas.edu/-/supercomputer…nsport-research

Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

On Star Trek, the Romulans powered their spaceships with an artificial black hole. In reality, it turns out that black holes can drive the formation of stars and the evolution of whole galaxies.

An October 2019 study yielded results from RomulusC simulations, published in the Monthly Notices of the Royal Astronomical Society. Supercomputer simulations helped probe the ionized gas within and surrounding the intracluster medium, which fills the space between galaxies in a galaxy cluster.

The Stampede2 supercomputer at TACC and the Comet supercomputer at the San Diego Supercomputer Center played a role, through allocation awarded by XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. The scientists also used the NASA Pleiades supercomputer, eventually completing the simulation on 32,000 processors of the Blue Waters system at the National Center for Supercomputing Applications.

On the podcast are two study co-authors, Iryna Butsky and Tom Quinn, both in the Department of Astronomy at the University of Washington. Iryna Butsky is a PhD Student, and Tom Quinn is a Professor of Astronomy. Podcast host Jorge Salazar with the Texas Advanced Computing Center conducts the Q&A.

Story Link: www.tacc.utexas.edu/-/simulations-r…lusters-details

Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

On the podcast are Yasushi Kondo and Deepti Karandur, both postdoctoral researchers in the John Kuriyan Lab at UC Berkeley. Karandur is also a postdoctoral fellow at the Howard Hughes Medical Institute. Kondo and Karandur are co-authors of a study published October of 2019 in the journal Science that determined the structure of a complex of proteins called B-Raf kinase, short for Rapidly Accelerated Fibrosarcoma. B-Raf kinase is a protein that’s part of the signal chain that starts outside the cell and goes inside to direct cell growth. This larger signal pathway is important for cancer research, which seeks to understand out-of-control cell growth. About 50 percent of melanomas have a specific single mutation on B-Raf, and it’s became an important drug target. Strangely though, drugs that inhibit the mutant had a down side. They activated other undesired proteins, called wild-type B-Raf kinases, which again triggered melanoma.

The science team modeled the B-Raf protein and other proteins in the chemical pathway using supercomputer allocations on XSEDE, the Extreme Science and Engineering Discovery Environment funded by the National Science Foundation. They used the Stampede2 system at TACC as well as the Bridges system at the Pittsburgh Supercomputer Center.

This new research by Kondo and Karandur’s science team has found how the paradoxical B-Raf activation happens. Drs. Kondo and Karandur are interviewed by podcast host Jorge Salazar, with the Texas Advanced Computing Center.

Fleming Crim, the Chief Operating Officer of the National Science Foundation, gave opening remarks at the dedication event for the launch of Frontera. TACC Podcast host Jorge Salazar interviewed Crim about the NSF-funded Frontera system and the value of supercomputers for fundamental research.

TACC podcast host Jorge Salazar interviewed President Fenves shortly afterwards, where he spoke on the impact the NSF-funded Frontera supercomputer will have on the university and the world at large.

Joining host Jorge Salazar on the podcast are Dan Stanzione, Executive Director of the Texas Advanced Computing Center and Associate Vice-President for Research at the University of Texas at Austin; and Doug James, former Deputy Director for High Performance Computing at the Texas Advanced Computing Center. Most of the computational resources mentioned on the podcast such as the Stampede2 supercomputer are funded by the National Science Foundation.

Full Q&A at this link:www.tacc.utexas.edu/texascale/2018/…e-workforce-gap

Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Supercomputer simulations show that at the atomic level, material stress doesn’t behave symmetrically. That’s according to a study published September of 2018 in the Proceedings of the Royal Society A. The findings could help scientists come up with new materials such as glass or metal that doesn’t ice up.

On the podcast to talk more about the stress study is Liming Xiong, Assistant Professor, Department of Aerospace Engineering, Iowa State University. Dr. Xiong used supercomputer allocations on XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. That gave Xiong access to the Comet system at the San Diego Supercomputer Center; and Jetstream, a cloud environment supported by Indiana University, the University of Arizona, and the Texas Advanced Computing Center. Podcast host Jorge Salazar interviewed Liming Xiong.

Story: https://www.tacc.utexas.edu/-/a-new-way-to-see-stress-using-supercomputers

Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

The unexpected effect comes from the action of an electric field on water in very narrow pores and in very thin materials. That’s according to research by Aleksei Aksimentiev and James Wilson of the Department of Physics at the University of Illinois at Urbana–Champaign. They published their findings in Physical Review Letters, June of 2018.

Aksimentiev and Wilson used supercomputer time awarded through XSEDE, the Extreme Science and Engineering Discover Environment, funded by the National Science. Foundation. XSEDE allocations allowed the researchers use of the Stampede1 and Stampede2 systems at the Texas Advanced Computing Center; and Blue Waters at the National Center for Supercomputer Applications.

Aleksei Aksimentiev joins podcast host Jorge Salazar to talk more about the study.

Story: www.tacc.utexas.edu/-/simulations-s…-dna-sequencing

Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

On this TACC podcast, host Jorge Salazar interviewed Manish Parashar, Office Director for the the Office of Advanced Cyberinfrastructure at the National Science Foundation. Dr. Parashar took time out during the announcement event at TACC to talk more about the Frontera supercomputer.

Story Link: www.tacc.utexas.edu/-/a-new-fronter…nce-discoveries

Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

The scientists modeled mantle plumes on the Stampede supercomputer of the Texas Advanced Computing Center through an allocation on XSEDE, the eXtreme Science and Engineering Discovery Environment funded by the National Science Foundation. And through XSEDE they also took advantage of Science Gateways and of the Campus Champions program at the University of Michigan.

With that support they showed, for the first time, details of how mantle plumes form and how they rise from Earth's mantle. What's more, the researchers say their work could guide future experiments with seismic imaging and help get to the bottom of mysteries like the origin of Hawaii's volcanos.

The international science team published their results on mantle plumes in January of 2018 in the American Geophysical Union's Journal of Geophysical Research, Solid Earth.

Podcast host Jorge Salazar interviews study authors Ross Maguire and Jeroen Ritsema of the University of Michigan.

Researchers assembled and annotated for the first time the genome of Seriola dorsalis, also known as California Yellowtail, a fish of high value to the sashimi, or raw seafood industry.

The science team members were from the U.S. National Marine Fisheries Service, Iowa State University, and the Instituto Politécnico Nacional in Mexico. They published their results January of 2018 in the journal BMC Genomics.

Assembling and annotating a genome is like building a three dimensional jigsaw puzzle, and the Seriola dorsalis genome had 685 million pieces - its base pairs of DNA - to put together.

The researchers were awarded computational allocations from XSEDE, the eXtreme Science and Engineering Discovery Environment funded by the National Science Foundation. That gave them access to the Blacklight system at the Pittsburg Supercomputing Center to assemble the Seriola dorsalis genome. XSEDE also allocated use of the Stampede1 supercomputer at the Texas Advanced Computing Center to analyze and annotate the fish genome. What's more, the science team got direct help from workflow experts through the XSEDE Campus Champions program at PSC.

Podcast host Jorge Salazar interviews two scientists and co-authors of the first-ever genomics work - Andrew Severin, Facility Manager; and Arun Seetharam, Associate Scientist. They're both at the Genome Informatics Facility of Iowa State University.

South by Southwest 2018 hosts a panel on March 10th called Quantum Computing: Science Fiction to Science Fact. Experts on quantum computing make up the panel, including Jerry Chow of IBM; Bo Ewald of D-Wave Systems; Andrew Fursman of 1QBit; and Antia Lamas-Linares of the Texas Advanced Computing Center at UT Austin.

Dr. Lamas-Linares is a Research Associate in the High Performance Computing group at TACC. Her background is as an experimentalist with quantum computing systems, including work done with them at the Centre for Quantum Technologies in Singapore. She joins podcast host Jorge Salazar to talk about her South by Southwest panel and about some of her latest research on quantum information.

A science panel on AI and water management meets in Austin, Texas on February 17th at the 2018 meeting of the American Association for the Advancement of Science. Suzanne Pierce moderates and co-organized the panel. Pierce is a Research Scientist in Dynamic Decision Support Systems and part of the Data Management & Collections Group of the Texas Advanced Computing Center.

Podcast host Jorge Salazar interviews Suzanne Pierce of TACC about the Intelligent Systems for Geosciences community, of which she is on the steering committee; her panel on AI and water management at the AAAS, and the work TACC is doing to support efforts to bridge advanced computing with Earth science.

Solar cells have a problem with heat. Photovoltaics on solar panels lose some energy as heat in when they convert sunlight to electricity. The reverse holds true for LED lights, which convert electricity into light.

Scientists call the heat loss in LEDs and solar cells non-radiative recombination. And they’ve struggled to understand the basic physics of this heat loss, especially for materials with molecules of over 20 atoms.

Podcast host Jorge Salazar interviews Benjamin Levine, an associate professor in the Department of Chemistry at Michigan State University. Dr. Levine models the behavior caused by defects in materials, such as doping bulk silicon to transform it into semiconductors in transistors, LEDs, and solar cells. Levine and has used over 975,000 compute hours on the Maverick supercomputer, a dedicated visualization and data analysis resource architected with 132 NVIDIA Tesla K40 "Atlas" GPUs for remote visualization and GPU computing to the national community.

XSEDE, the eXtreme Science and Engineering Discovery Environment funded by the National Science Foundation, provided the allocation.

Scientists don’t yet understand the details of osteogenesis, or how bones form. A study found that silica combined with engineered silk derived from the dragline of golden orb weaver spider webs could be fine-tuned to activate genes in human stem cells that initiated biomineralization, a key step in bone formation.

The study appeared September 2017 in the journal Advanced Functional Materials. The authors used supercomputers through and allocation from XSEDE, the Xtreme Science and Engineering Discovery Environment, funded by the National Science Foundation. Stampede at the Texas Advanced Computing Center (TACC) and Comet at the San Diego Supercomputing Center helped scientists model the protein folding of integrin, an essential step in the intracellular pathways that lead to osteogenesis. This research will help larger efforts to cure bone disorders such as osteoporosis or calcific aortic valve disease.

Joining host Jorge Salazar of TACC on the podcast to talk about the bone formation study are Zaira Martín-Moldes of the Kaplan Lab at Tufts University and Davoud Ebrahimi at the Laboratory for Atomistic and Molecular Mechanics of the Massachusetts Institute of Technology.

A great mystery for scientists is the evidence of powerful jets of electrons and protons that shoot out of the top and bottom of some black holes. Yet no one knows how these jets form. Computer code called Cosmos now fuels supercomputer simulations of black hole jets and is starting to reveal the mysteries of black holes and other space oddities.

Cosmos code developer Chris Fragile joins host Jorge Salazar on the TACC podcast. Fragile is a professor in the Physics and Astronomy Department of the College of Charleston.

Also featured on the podcast is Damon McDougall, a Research Associate in the HPC Applications at the Texas Advanced Computing Center, also appointed jointly at the Institute for Computational Engineering and Sciences of the University of Texas at Austin. McDougall spoke more about XSEDE Extended Collaborative Support Services.

A summer camp at TACC smoothed the way for high school students to learn about the science behind building design for earthquakes. It's called Code @ TACC DesignSafe. The summer camp was funded by DesignSafe, a national program supported by the National Science Foundation.

DesignSafe is a web-based research platform of the Natural Hazards Engineering Research Infrastructure Network that helps engineers build safer structures that can better withstand natural hazards such as earthquakes and windstorms.

The Code @ TACC DesignSafe Camp students were given a project under budget to design their own custom building models outfitted with sensors that recorded their movement as they were shaken under laboratory conditions based on historical earthquake data.

TACC Podcast host Jorge Salazar interviews Joon-Yee Chuah, Outreach Coordinator at the Texas Advanced Computing Center; Chunxiao Ge, a physics and biology teacher at the Colorado River Collegiate Academy of Bastrop ISD; and Patty Hill, an algebra teacher at Kealing Middle School at Austin ISD.

TACC Podcast host Jorge Salazar interviewed Greg Fenves, President of UT Austin, to discuss Stampede2 and the importance of supercomputers to the university.

Greg Fenves: Stampede2 is a fabulous technology. But technology ultimately comes from people's ideas. And what we've been able to do at the University of Texas and with the Texas Advanced Computing Center is bring some of the smartest people to work with our partners, Dell and Intel, to create fabulous new technology that can then be deployed and is now being deployed to take an unprecedented look at these tough challenges that we face as a society.

The Code @ TACC Wearables Camp guided 27 high school students from the Austin area in how to fashion wearable circuits that responded to things like light and temperature and were connected to the Internet of Things. Podcast host Jorge Salazar interviews Joonyee Chuah, Outreach Coordinator at the Texas Advanced Computing Center.

Podcast host Jorge Salazar interviews Peter Couvares, staff scientist at LIGO; University of California Santa Barbara physicist Robert Sugar; and Ming Xue, Professor in the School of Meteorology at the University of Oklahoma and Director of the Center for Analysis and Prediction of Storms.

Stampede helped researchers make discoveries across the full spectrum of science, including insight into diseases like cancer and Alzheimer's; the insides of stars and the signals of gravitational waves; natural disaster prediction of hurricanes, earthquakes, and tornados; and more efficient engineering in projects such as designing better rockets and quieter airplanes.

Through nearly all of its service, Stampede was ranked in the Top 10 most powerful computers in the world, and it was the flagship system of the National Science Foundation's Office of Advanced Cyberinfrastructure, which provides academic researchers access to technologies and expertise that drive U.S. innovation and open new frontiers for discovery.

Podcast host Jorge Salazar interviews Dan Stanzione, Executive Director of the Texas Advanced Computing Center; Bill Barth, Director of High Performance Computing and a Research Scientist at the Texas Advanced Computing Center; and Tommy Minyard, Director of Advanced Computing Systems at the Texas Advanced Computing Center.

The students divided themselves into teams each with specific roles of principal investigator, validation engineer, software developer, and roboticist. They assembled a robotic car from a kit and learned how to program its firmware. The robotic cars had sensors that measured the distance to objects in front, and they could be programmed to respond to that information by stopping or turning or even relaying that information to another car near it. Teams were assigned a final project based on a real-world problem, such as what action to take when cars arrive together at a four-way stop.

Podcast host Jorge Salazar interviews Joonyee Chuah, outreach coordinator at the Texas Advanced Computing Center; and Katrina Van Houten, teacher, Del Valle High School.

What if scientists could realize their dreams with big data? On the one hand you have parallel file systems for number crunching. On the other, you have Hadoop file systems, made for cloud computing with data analytics. The problem is that one doesn't know what the other is doing. You have to copy files from parallel to Hadoop. Doing that is so slow it can turn a supercomputer into a super slow computer.

Computer scientists developed in 2015 a way for parallel and Hadoop to talk to each other. It's a cross-platform Hadoop reader called PortHadoop, short for portable Hadoop. The scientist have since improved it, and it's now called PortHadoop-R. It's good enough to start work with real data in the NASA Cloud library project. The data are used for real-time forecasts of hurricanes and other natural disasters; and also for long-term climate prediction.

A supercomputer at TACC helped the researchers develop PortHadoop-R. The system is called Chameleon, a cloud testbed funded by the National Science Foundation. Chameleon is a large-scale, reconfigurable environment for cloud computing research co-located at the Texas Advanced Computing Center and also at the University of Chicago.

Chameleon allows researchers 'bare-metal access,' the ability to change and adapt the supercomputer's hardware and customize it to improve reliability, security, and performance.

Sun's PortHadoop research was funded by the National Science Foundation and the NASA Advanced Information Systems Technology Program (AIST).

Feature Story: www.tacc.utexas.edu/-/reaching-for-…-with-chameleon

Music Credits: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Wrangler uses 600 terabytes of flash storage that speedily reads and write files. This lets it fly past bottlenecks with big data that can slow down even the fastest computers.

Podcast host Jorge Salazar interviews graduate student Karanjeet Singh; and Chris Mattmann, Chief Architect in the Instrument and Science Data, Systems Section of NASA's Jet Propulsion Laboratory at the California Institute of Technology. Mattmann is also an adjunct Associate Professor of Computer Science at the University of Southern California and a member of the Board of Directors for the Apache Software Foundation.

Scientists have taken the closest look yet at molecule-sized machinery called the human preinitiation complex. It basically opens up DNA so that genes can be copied and turned into proteins. The science team formed from Northwestern University, Berkeley National Laboratory, Georgia State University, and UC Berkeley. They used a cutting-edge technique called cryo-electron microscopy and combined it with supercomputer analysis. They published their results May of 2016 in the journal Nature.

Over 1.4 million 'freeze frames' of the human preinitiation complex, or PIC, were obtained with cryo-electron microscopy. They were initially processed using supercomputers at the National Energy Research Scientific Computing Center. This sifted out background noise and reconstructed three-dimensional density maps that showed details in the shape of the molecule that had never been seen before.

Study scientists next built an accurate model that made physical sense of the density maps of PIC. For that they XSEDE, the eXtream Science and Engineering Discovery Environment, funded by the National Science Foundation. Through XSEDE, the Stampede supercomputer at the Texas Advanced Computing Center modeled the human pre initiation complex for this study. Their computational work on molecular machines also includes XSEDE allocations on the Comet supercomputer at the San Diego Supercomputing Center.

Podcast host Jorge Salazar interviews Lori Diachin of Lawrence Livermore National Laboratory. She's the Director for the Center for Applied Scientific Computing and Research Program Manager and Point of Contact for the Office of Science Advanced Scientific Computing Research organization. She also leads the Frameworks Algorithms and Scalable Technologies for Mathematics (FASTMath) SciDAC center.

This year Dr. Diachin was the Chair of the Technical Program at SC16. Right before the conference she spoke by phone to talk about the highlights and some changes happening at SC16.

Lori Diachin: I think the most important thing I'd like people to know about SC16 is that it is a great venue for bringing the entire community together, having these conversations about what we're doing now, what the environment looks like now and what it'll look like in five, ten fifteen years.

The fact that so many people come to this conference allows you to really see a lot of diversity in the technologies being pursued, in the kinds of applications that are being pursued - from both the U.S. environment and also the international environment. I think that's the most exciting thing that I think about when I think about supercomputing.

The podcast interview features John McCalpin, a Research Scientist in the High Performance Computing Group at the Texas Advanced Computing Center and Co-Director of the Advanced Computing Evaluation Laboratory at TACC.

Twenty-five years ago as an oceanographer at the University of Delaware, Dr. McCalpin developed the STREAM benchmark. It continues to be widely used as a simple synthetic benchmark program that measures sustainable memory bandwidth and the corresponding computation rate for simple vector kernels. Dr. McCalpin was invited to speak at SC16. His talk is titled, "Memory Bandwidth and System Balance in HPC Systems."

John McCalpin: The most important thing for an application-oriented scientist or developer to understand is whether or not their workloads are memory-bandwidth intensive. It turns out that this is not as obvious as one might think… Due to the complexity of the systems and difficulties in understanding hardware performance counters, these can be tricky issues to understand.

If you are in an area that tends to use high bandwidth, you can get some advantage from system configurations. It's fairly easy to show, for example if you're running medium-to-high bandwidth codes you don't want to buy the maximum number of cores, the maximum frequency in the processors because those carry quite a premium and don't deliver any more bandwidth than less expensive processors.

You can sometimes get additional improvements through algorithmic changes, which in some sense don't look optimal because they involve more arithmetic. But if they don't involve more memory traffic the arithmetic may be very close to free and you may be able to get an improved quality of solution. In the long run, if you need orders of magnitude more bandwidth than is currently available there's a set of technologies that are sometimes referred to as processor in memory - I call it processor at memory - technologies that involves cheaper processors distributed out to adjacent to the memory chips. Processors are cheaper, simpler, lower power. That could allow a significant reduction in cost to build the systems, which allows you to build them a lot bigger and therefore deliver significantly higher memory bandwidth. That's a very revolutionary change.

Computers hardware speeds have grown exponentially for the past 50 years. We call this Moore's Law. But we haven't seen a Moore's Law for software. That's according to Sadasivan Shankar of Harvard University. He said that the reason for that is a lack of communication and close collaboration between hardware developers and the users trying to solve problems in fields like social networking, cancer modeling, personalized medicine, or designing the next generation battery for electrical storage.

Dr. Shankar proposes a new paradigm in which the software applications should be part of the design of new computer architectures. He calls this paradigm Co-Design 3.0. Shankar was invited to speak about it at the SC16 conference.

Sadasivan Shankar: We want to see what will make high performance computing personalizable. How can we train the upcoming workforce on different aspects of all the components, the architecture, hardware, algorithms, and software? This is why I think universities play an important role in this, as much as the national labs have been playing on high performance computing. We want to be able to solve the real problems – cancer cures, personalized medicine, new battery materials, new catalysts, eliminate toxic materials. Both research and development are needed to enable this paradigm. Can we essentially do them faster and economically? The computing has brought us very far. But can we take it even farther? That's the question that we should ask ourselves. 

XSEDE identified 20 graduate and undergrad students to participate in a week-long event called Advanced Computing for Social Change. The event is hosted by XSEDE, TACC and SC16.

The SC16 Social Action Network student cohort will tackle a computing challenge. They will learn how to mine through a variety of data sets such as social media data encompassing a number of years and across large geographic regions. To complete their analysis in a timely fashion they will learn how to organize the large data sets to allow fast queries.

The students of the SC16 Social Action Network will also use a computational modeling tool called risk terrain modeling that has been used to predict crime using crime statistics. This technique was first introduced to TACC in work done with the Cook County Hospital in Chicago, Illinois. The work used statistical data to predict child maltreatment in an effort to put programs in place to prevent it.

Kelly Gaither: Advanced Computing for social change is an initiative that we started to really use our collective capabilities, here at TACC and more broadly at supercomputing centers across the nation, to work on problems that we know have need for advanced computing. You can think of it as data analysis, data collection, all the way to visualization and everything in between to really work on problems of societal benefit. We want to make a positive change using the skill sets we already have.

The SC16 supercomputing conference takes place in Salt Lake City, Utah November 13-18, 2016. The event showcases the latest in supercomputing to advance scientific discovery, research, education and commerce. 

West explained that long-term efforts are underway at SC16 to promote diversity in the supercomputing community. These include a new double-blind review of technical papers; a new standing subcommittee focused on diversity and inclusion added to the conference organizing committee; adoption of demographics measurements of the SC16 conference committee and attendees; active recruitment of student volunteers at organizations and universities that serve underrepresented groups; on-site child care; an added official code of conduct; fellowships that promote inclusivity; and continued support of the Women and IT Networking program.

John West: For me, (diversity) is a numbers problem. If you look at HPC (high performance computing), more and more communities are adopting advanced computing as a baseline tool for their research. I think a big part of this shift is HPC has been around for a long time. More and more communities are starting to become aware of it. But it's also driven by the success of efforts at TACC and other HPC centers that are pushing this idea of science environments that are front-ended by user-friendly technologies that help flatten the learning curve that we've traditionally had that is a real barrier to new communities of users coming into HPC. That success is driving more people to use HPC. And as we have more users, we're going to have to provide more resources to these folks. We need more highly qualified staff in the provider community, both in the centers themselves and in the organizations that create scientific software that people use… If we're going to try and broaden that talent pipeline to grow the workforce to meet the growing demand, the best opportunity to do that is to try and grab a larger share of that untapped pool of talent.

The SC16 supercomputing conference takes place in Salt Lake City, Utah November 13-18, 2016. The event showcases the latest in supercomputing to advance scientific discovery, research, education and commerce. 

What's new is that Hikari is the first supercomputer in the US to use solar panels and High Voltage Direct Current, or HVDC for its power. Hikari hopes to demonstrate that HVDC works not only for supercomputers, but also for data centers and commercial buildings.

The Hikari project is a collaboration headed by NTT Facilities, based out of Japan and with the support of the New Energy and Industrial Technology Development Organization, or NEDO.

NTT Facilities partnered with the University of Texas at Austin to begin demonstration tests of the HVDC power feeding system for the Hikari project in late August 2016. What it aims to show is that the high-capacity HVDC power equipment and lithium-ion batteries of Hikari can save 15 percent in energy compared to conventional systems.

Podcast host Jorge Salazar discusses the Hikari HVDC project with Toshihiro Hayashi, Assistant Manager in the Engineering Divisions of NTT Facilities, Japan; and Jim Stark, Director of Engineering and Construction for the Electronic Environments Corporation, a Division of NTT Facilities.

The simulations done on the Stampede and Lonestar systems at TACC will guide a real experiment later this summer in 2016 with the recently upgraded Texas Petawatt Laser, one of the most powerful in the world.

The scientists say the quest for producing gamma rays from non-radioactive materials will advance basic understanding of things like the inside of stars. What's more, gamma rays are used by hospitals to eradicate cancer, image the brain, and they're used to scan cargo containers for terrorist materials. Unfortunately no one has yet been able to produce gamma ray beams from non-radioactive sources. These scientists hope to change that.

On the podcast are the three researchers who published their work May of 2016 in the journal Physical Review Letters. Alex Arefiev is a research scientist at the Institute for Fusion Studies and at the Center for High Energy Density Science at UT Austin. Toma Toncian is the assistant director of the Center of High Energy Density Science. And the lead author is David Stark, a scientist at the Los Alamos National Laboratory. Jorge Salazar hosted the podcast.

Chancellor McRaven spoke of his path to lead the UT System of 14 Institutions, the importance of supercomputers to Texans and to the nation, the new Dell Medical School, and more.

William McRaven: "Behind all of this magnificent technology are the fantastic faculty, researchers, interns, our corporate partners that are part of this, the National Science Foundation, there are people behind all of the success of the TACC. I think that's the point we can never forget."

Mosquitos carry and spread the Zika virus, which can cause birth defects and other symptoms like fever. The U.S. Centers for Disease Control is now ramping up collection of data that tracks Zika spread. But big gaps exist in linking different kinds of data, and that makes it tough for experts to predict where it will go next and what to do to prevent it.

The Texas Advanced Computing Center provided time on the Wrangler data intensive supercomputer as a virtual workspace for the Zika hackers.

Featured on the podcast are Ari Kahn, Texas Advanced Computing Center; and Eddie Garcia, Cloudera. Podcast hosted by Jorge Salazar of TACC.

As more scientists share not only their results but their data and code, Docker is helping them reproduce the computational analysis behind the results.

What's more, Docker is one of the main tools used in the Agave API platform, a platform-as-a-service solution for hybrid cloud computing developed at TACC and funded in part by the National Science Foundation.

Podcast host Jorge Salazar talks with software developer and researcher Joe Stubbs about using Docker for science. Stubbs is a Research Engineering and Scientist Associate in the Web & Cloud Services group at the Texas Advanced Computing Center.

New discoveries might lie buried deep in the data of human fossils. That's according to Denné Reed, an associate professor in the Department of Anthropology at The University of Texas at Austin (UT Austin). Reed is the principal investigator of PaleoCore, an informatics initiative funded by the National Science Foundation (NSF).

The PaleoCore project aims to get researchers of human origins worldwide all on the same page with their fossil data. Reed said PaleoCore is doing this by implementing data standards; making a place to store all data of human fossils; and developing new tools to collect the data. What he hopes to come out of this are deeper insights into our origins from better integration and sharing between different research projects in paleoanthropology and paleontology.

"We've tried to take advantage of some of the geo-processing and database capabilities that are available through Wrangler to create large archives," Reed said. The big data Reed wants to archive on Wrangler are the entirety of the fossil record on human origins. PaleoCore will also include geospatial data such as satellite imagery. "For many of the countries that we're working in, this is their cultural heritage. We need to be able to ensure that not only are the data rapidly available, accessible, searchable, and everything else, but that they're safely archived," Reed said.

Music Credits: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Saving energy saves money. Scientists at Oak Ridge National Laboratory (ORNL) are using supercomputers to do just that by making virtual versions of millions of buildings in the U.S. The Wrangler data-intensive supercomputer is working jointly with ORNL's Titan in a project called Autotune that trims the energy bills of buildings.

Computer scientist Joshua New of the ORNL Building Technology Research and Integration Center is the principal investigator of the Autotune project, funded by the U.S. Department of Energy. Autotune takes a simple software model of a building's energy use and optimizes it to match reality.

"What we're trying to do is create a crude model from publicly available data," New said. "Then the Autotune project takes utility bill data, whether it's monthly electrical utility bills, or hourly bills from advanced metering infrastructure, and calibrates that software model to match measured data." New said that once Autotune calibrates the model well enough, it can be legally used in multiple ways including for optimal building retrofit packages.

Music Credits: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Scientists at the Hofmann Lab of UT Austin are using the Wrangler data-intensive supercomputer to find orthologs — genes common to different species. They'll search for them in each of the major lineages of vertebrates — mammals, birds, reptiles, amphibians and fishes.

"What we want to know is, even though they've evolved independently, whether it's possible that some of the same genes are important in regulating this behavior, in particular expression of these genes in the brain while monogamous males are reproductively active," said Rebecca Young. Young is a research associate in the Department of Integrative Biology and at the Center for Computational Biology and Bioinformatics, UT Austin.

Music Credits: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

They share the award with their study co-authors, who utilized the Stampede supercomputer of the Texas Advanced Computing Center and the IBM Sequoia supercomputer at Lawrence Livermore National Laboratory.

The award-winning study modeled the flow thousands of kilometers deep in the mantle, which moves Earth's plates and triggers unpredictable events like volcanic eruptions and massive earthquakes.

The SC15 supercomputing conference took place in Austin, November 15-20, 2015. SC showcases the latest in high performance computing, networking, storage and analysis to advance scientific discovery, research, education and commerce.

The study, "An Extreme-Scale Implicit Solver for Complex PDEs: Highly Heterogeneous Flow in Earth's Mantle," was funded in part by the National Science Foundation and the Department of Energy.

Co-authors include Johann Rudi and Omar Ghattas of ICES; A. Cristiano Malossi, Peter Staar, Yves Ineichen, Costas Bekas, and Alessandro Curioni at the Foundations of Cognitive Solutions, IBM Research – Zurich, Switzerland; Tobin Isaac of ICES; Georg Stadler of the Courant Institute of Mathematical Sciences, New York; and Michael Gurnis of the Seismological Laboratory at CalTech.

Omar Ghattas: The absolute large number of cores and the big scaling result was done on the IBM system at Livermore. We couldn't have done it without the IBM guys.

But the actual science runs, a lot of the day-to-day stuff, testing of the solvers - Johann was using TACC's Stampede system.

Johann Rudi: Mainly, my research was done on the Stampede supercomputer at TACC. One part of the work is developing algorithms. That was wholly supported by TACC machines.

And also, the help that I got from TACC a couple of times was very valuable to me. There were certain small issues that I couldn't even see from where I was working with the machine. But people from the internal status, running the systems, they could see when something was going wrong. They actually helped a lot.

I was happy to work with TACC. Especially Bill Barth. I remember him helping me a lot. I was glad.

The development of the solvers was done on TACC. Also, everything in the paper that shows the scientific results, the visualizations - these were also done on TACC machines. The science part was also supported by TACC.

Manuela Campanelli is a professor at the Rochester Institute of Technology and the Director of the Center for Computational Relativity and Gravitation. Dr. Campanelli was invited to give a presentation at SC15 titled "Revealing the Hidden Universe with Supercomputer Simulations of Black Hole Mergers."

Dr. Campanelli uses the computational resources of XSEDE, the Extreme Science and Engineering Discovery Environment, to probe the mysteries of black holes. She spoke by Skype to talk about that and about the 100th anniversary of Einstein's field equations and about her work that takes on the complexity of accurately describing black hole mergers.

The SC15 supercomputing conference takes place in Austin, November 15-20, 2015. SC15 showcases the latest in high performance computing, networking, storage and analysis to advance scientific discovery, research, education and commerce.

Manuela Campanelli: General Relativity is celebrating this year a hundred years since its first publication in 1915, when Einstein introduced his theory of General Relativity, which has revolutionized in many ways the way we view our universe. For instance, the idea of a static Euclidean space, which had been assumed for centuries and the concept that gravity was viewed as a force changed. They were replaced with a very dynamical concept of now having a curved space-time in which space and time are related together in an intertwined way described by these very complex, but very beautiful equations.

Dr. Jordan uses the computational resources of XSEDE, the Extreme Science and Engineering Discovery Environment, to model earthquakes and help reduce their risk to life and property. Dr. Jordan was invited to speak at SC15 on the Societal Impact of Earthquake Simulations at Extreme Scale.

The SC15 supercomputing conference takes place in Austin, November 15-20, 2015. SC15 showcases the latest in high performance computing, networking, storage and analysis to advance scientific discovery, research, education and commerce.

Thomas Jordan: One thing people need to understand is we need a lot of supercomputer time in order to be able to do these calculations. Some of our simulation models that are based on the simulation of earthquake physics can take hundreds of millions of hours of computer time to generate.

These are very complex system-level calculations. They're of the similar complexity of trying to calculate what Earth's climate is going to be like in 50 years because of human activities and CO2 charging of the atmosphere. It's a similar scale of problem.

These problems that deal with natural hazards and the complexity of the Earth system really require very large computers to be able to simulate that activity. We're frankly looking forward to the day when computers are ten times or a hundred times or more faster than they are today.

A recipient of the National Science Board's Public Service Award, Alda is a visiting professor at and founding member of Stony Brook University's Alan Alda Center for Communicating Science, where he helps develop innovative programs on how scientists communicate with the public. He is also on the Board of Directors of the World Science Festival.

SC15 is the 27th annual International Conference for High Performance Computing, Networking, Storage and Analysis. The event showcases the latest in supercomputing to advance scientific discovery, research, education and commerce. 

Alan Alda: I think the kind of transformation that's already been brought about by high performance computing is extraordinary. And for it to go further and fully realize its potential requires another kind of transformation…

Powerful computing affects all our lives and can hopefully save our lives. It can eventually help us survive some of our unfortunate efforts that have affected climate, for instance. To model climate change is one of the great benefits we're going to get from supercomputing. The trouble is, to really help the public understand all the benefits that they can get from supercomputing, it has to be communicated with clarity so that they get it and they get excited by it…

I think we have to transform the scientists who are explaining this to the public before the public will allow them and participate with them in transforming their own lives with this amazing ability to model things on supercomputers.

XALT tracks user codes and environments on a computer cluster. Robert McLay and Mark Fahey of the Argonne National Laboratory will be co-leading a session called "Understanding User-Level Activity on Today's Supercomputers with XALT" at SC15.

The SC15 supercomputing conference takes place in Austin, November 15-20, 2015. SC15 showcases the latest in high performance computing, networking, storage and analysis to advance scientific discovery, research, education and commerce.

Robert McLay: XALT is a tool that me and my colleague, Dr. Mark Fahey, put together to help people try and use our systems. We run the system. We manage the system. We develop software for the system and install software for our users. We want to know what's used and what's not. XALT gives us a way to find out in a very inexpensive way.

Matz was part of a study funded by the National Science Foundation and the Australian Institute of Marine Science. In June of 2015 they published results in the journal Science that found the first evidence that corals can genetically adapt to warmer waters from climate change.

Podast host Jorge Salazar interviewed Matz about his computationally-based findings and about open source tools other scientists can freely use to analyze genomes of plants and animals.

New supercomputer simulations have come closer than ever to capturing real behavior of human heart valves.

The studies focused on how heart valve tissue realistically responds to blood flow. And to be clear this is ongoing research, meaning they don't have all the answers yet, but they do say they've made progress on a really tough problem that potentially affects hundreds of thousands of people each year with hearth disease. The scientists say their new supercomputer models can potentially help doctors make more durable repair and replacement of heart valves.

Supercomputers have helped scientists find a surprising link between cross-shaped pieces of DNA and human cancer, according to a study at The University of Texas at Austin.

DNA naturally folds itself into cross-shaped structures called cruciforms that jut out along the sprawling length of its double helix. The DNA cruciforms typically aren't anything to worry about. In fact, previous evidence show that DNA cruciforms are essential to life. They enable DNA replication, part of how cells make copies of themselves. And they help initiate gene expression, which makes proteins. What's more small DNA cruciforms are commonly found inside our bodies. Scientists estimate as many as 500,000 cruciform-forming sequences of DNA can exist on average in a normal human genome.

What the UT scientists are doing is investigating the origins of human cancer. And what they've found is that these tiny cruciforms - just a small shape of normal DNA - are linked to mutations that can elevate cancer risk.

An international science team reported a discovery of gigantic rock structures hidden deep under East Asia, centered on the Tibetan Plateau. Scientists used supercomputers to process earthquake data and make images in 3-D down to depths of about 900 kilometers, or about 560 miles below ground. Scientists from China, Canada, and the U.S. worked together to publish their results March of 2015 in the American Geophysical Union Journal of Geophysical Research, Solid Earth.

The study area is a hotspot for earthquakes. And it's surrounded by networks of seismographic stations, 1869 stations in all. That's where scientists got their data to take cat scans of the Earth using the supercomputer model they developed.

The science team says their research could potentially help discover hidden pockets of hydrocarbon resources like oil and gas. More broadly they say their work will help explore the Earth hidden miles under East Asia and elsewhere.

For the first time ever, scientists designed completely from scratch a protein molecule that behaves like a slice of life. It mimics a natural protein found in living cells that transports ions across a cell membrane. The cell membrane surrounds living   cells like an envelope. And ion transport through the membrane helps keep us alive. It lets nutrients in and waste out of cells, and it also transmits signals between nerve cells of the brain and spinal cord.

Scientists used the Stampede supercomputer at TACC to model the stability and dynamics of the designed protein. They did this with an allocation through XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. The researchers published their results in the journal Science in December 2014.

 This research has wide potential application, such as targeting medicines more specifically into cancer cells and driving charge separation potentially for harvesting energy for batteries.

In the podcast Dahan talks about some interesting intersections where science meets software development, and she predicts the next big thing at SXSW -- science!

Maytal Dahan: It'd be really great if we could get developers of all kinds – user interface, web, application developers – who are interested to learn how science impacts the world we live in today, and how to engage and possibly contribute their skills to science projects…A developer at a start-up doesn't always get to meet a scientist creating an API for their application.

Things changed when a multi-university collaboration produced a set of new supercomputer models of galaxies called FIRE, The Feedback in Realistic Environments. FIRE simulations ran on the Stampede supercomputer at TACC, an XSEDE resource funded by the National Science Foundation.

Theoretical astrophysicist Philip Hopkins of CalTech led a 2014 study of initial results that found that star activity - like supernova explosions or even just starlight - plays a big part in the formation of other stars and the growth of galaxies. Philip Hopkins spoke more about galaxies on FIRE.

Dr. Matsuoka is a professor and leader of the Tsubame project, one of the world's fastest and most efficient supercomputing grid clusters. Tsubame is at the Global Scientific Information and Computing Center, hosted by the Tokyo Institute of Technology. We spoke with Sathoshi Matsuoka on the opening night of a busy convention floor at SC14.

Dr. Sterling is the executive associate director and chief scientist at the Center for Research in Extreme Scale Technologies at Indiana University, Bloomington. He's won the Gordon Bell Prize for innovations in high performance computing, and he laid the foundation for the current paradigm of supercomputers by co-developing the Beowulf cluster of commodity Linux cluster computing.

Sterling's latest project is the ParalleX execution model being tested in part on XSEDE resources here at TACC with the Stampede supercomputer.

Dr. Smarr is the director of the California Institute for Telecommunications and Information Technology, and he holds the Harry E. Gruber professorship in Computer Science and Engineering at the Jacobs School of Engineering of the University of California in San Diego.

Larry Smarr's spent his early career as an astrophysicist computing the dynamics of black holes. In the mid-1980s he led the proposal to the National Science Foundation that created the first national supercomputing center specifically for university researchers, the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign. His work there led to the creation of Mosaic, the world's first widely used graphical Web browser.

This clip is from an interview released mid-November as part of coverage of the SC14 conference.