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How a Single Chemical Bond Balances Cells Between Life and Death

With SLAC's X-ray laser and synchrotron, scientists measured exactly how much energy goes into keeping a crucial chemical bond from triggering a cell's death spiral.

New Efficient, Low-Temperature Catalyst for Converting Water and CO to Hydrogen Gas and CO2

Scientists have developed a new low-temperature catalyst for producing high-purity hydrogen gas while simultaneously using up carbon monoxide (CO). The discovery could improve the performance of fuel cells that run on hydrogen fuel but can be poisoned by CO.

Study Sheds Light on How Bacterial Organelles Assemble

Scientists at Berkeley Lab and Michigan State University are providing the clearest view yet of an intact bacterial microcompartment, revealing at atomic-level resolution the structure and assembly of the organelle's protein shell. This work can help provide important information for research in bioenergy, pathogenesis, and biotechnology.

A Single Electron's Tiny Leap Sets Off 'Molecular Sunscreen' Response

In experiments at the Department of Energy's SLAC National Accelerator Laboratory, scientists were able to see the first step of a process that protects a DNA building block called thymine from sun damage: When it's hit with ultraviolet light, a single electron jumps into a slightly higher orbit around the nucleus of a single oxygen atom.

Researchers Find New Mechanism for Genome Regulation

The same mechanisms that separate mixtures of oil and water may also help the organization of an unusual part of our DNA called heterochromatin, according to a new study by Berkeley Lab researchers. They found that liquid-liquid phase separation helps heterochromatin organize large parts of the genome into specific regions of the nucleus. The work addresses a long-standing question about how DNA functions are organized in space and time, including how genes are silenced or expressed.

The Rise of Giant Viruses

Research reveals that giant viruses acquire genes piecemeal from others, with implications for bioenergy production and environmental cleanup.

Grasses: The Secrets Behind Their Success

Researchers find a grass gene affecting how plants manage water and carbon dioxide that could be useful to growing biofuel crops on marginal land.

SLAC Experiment is First to Decipher Atomic Structure of an Intact Virus with an X-ray Laser

An international team of scientists has for the first time used an X-ray free-electron laser to unravel the structure of an intact virus particle on the atomic level. The method dramatically reduces the amount of virus material required, while also allowing the investigations to be carried out several times faster than before. This opens up entirely new research opportunities.

New Perspectives Into Arctic Cloud Phases

Teamwork provides insight into complicated cloud processes that are important to potential environmental changes in the Arctic.

Illuminating a Better Way to Calculate Excitation Energy

In a new study appearing this week in The Journal of Chemical Physics, researchers demonstrate a new method to calculate excitation energies. They used a new approach based on density functional methods, which use an atom-by-atom approach to calculate electronic interactions. By analyzing a benchmark set of small molecules and oligomers, their functional produced more accurate estimates of excitation energy compared to other commonly used density functionals, while requiring less computing power.


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Chicago Quantum Exchange to Create Technologically Transformative Ecosystem

The University of Chicago is collaborating with the U.S. Department of Energy's Argonne National Laboratory and Fermi National Accelerator Laboratory to launch an intellectual hub for advancing academic, industrial and governmental efforts in the science and engineering of quantum information.

Department of Energy Awards Six Research Contracts Totaling $258 Million to Accelerate U.S. Supercomputing Technology

Today U.S. Secretary of Energy Rick Perry announced that six leading U.S. technology companies will receive funding from the Department of Energy's Exascale Computing Project (ECP) as part of its new PathForward program, accelerating the research necessary to deploy the nation's first exascale supercomputers.

Cynthia Jenks Named Director of Argonne's Chemical Sciences and Engineering Division

Argonne has named Cynthia Jenks the next director of the laboratory's Chemical Sciences and Engineering Division. Jenks currently serves as the assistant director for scientific planning and the director of the Chemical and Biological Sciences Division at Ames Laboratory.

Argonne-Developed Technology for Producing Graphene Wins TechConnect National Innovation Award

A method that significantly cuts the time and cost needed to grow graphene has won a 2017 TechConnect National Innovation Award. This is the second year in a row that a team at Argonne's Center for Nanoscale Materials has received this award.

Honeywell UOP and Argonne Seek Research Collaborations in Catalysis Under Technologist in Residence Program

Researchers at Argonne are collaborating with Honeywell UOP scientists to explore innovative energy and chemicals production.

Follow the Fantastic Voyage of the ICARUS Neutrino Detector

The ICARUS neutrino detector, born at Gran Sasso National Lab in Italy and refurbished at CERN, will make its way across the sea to Fermilab this summer. Follow along using an interactive map online.

JSA Awards Graduate Fellowships for Research at Jefferson Lab

Jefferson Sciences Associates announced today the award of eight JSA/Jefferson Lab graduate fellowships. The doctoral students will use the fellowships to support their advanced studies at their universities and conduct research at the Thomas Jefferson National Accelerator Facility (Jefferson Lab) - a U.S. Department of Energy nuclear physics laboratory managed and operated by JSA, a joint venture between SURA and PAE Applied Technologies.

Muon Magnet's Moment Has Arrived

On May 31, the 50-foot-wide superconducting electromagnet at the center of the Muon g-2 experiment saw its first beam of muon particles from Fermilab's accelerators, kicking off a three-year effort to measure just what happens to those particles when placed in a stunningly precise magnetic field. The answer could rewrite scientists' picture of the universe and how it works.

Seven Small Businesses to Collaborate with Argonne to Solve Technical Challenges

Seven small businesses have been selected to collaborate with researchers at Argonne to address technical challenges as part of DOE's Small Business Vouchers Program.

JSA Names Charles Perdrisat and Charles Sinclair as Co-Recipients of its 2017 Outstanding Nuclear Physicist Prize

Jefferson Science Associates, LLC, announced today that Charles Perdrisat and Charles Sinclair are the recipients of the 2017 Outstanding Nuclear Physicist Prize. The 2017 JSA Outstanding Nuclear Physicist Award is jointly awarded to Charles Perdrisat for his pioneering implementation of the polarization transfer technique to determine proton elastic form factors, and to Charles Sinclair for his crucial development of polarized electron beam technology, which made such measurements, and many others, possible.


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Oxygen: The Jekyll and Hyde of Biofuels

Scientists are devising ways to protect plants, biofuels and, ultimately, the atmosphere itself from damage caused by an element that sustains life on earth.

The Rise of Giant Viruses

Research reveals that giant viruses acquire genes piecemeal from others, with implications for bioenergy production and environmental cleanup.

Grasses: The Secrets Behind Their Success

Researchers find a grass gene affecting how plants manage water and carbon dioxide that could be useful to growing biofuel crops on marginal land.

New Perspectives Into Arctic Cloud Phases

Teamwork provides insight into complicated cloud processes that are important to potential environmental changes in the Arctic.

Mountaintop Plants and Soils to Become Out of Sync

Plants and soil microbes may be altered by climate warming at different rates and in different ways, meaning vital nutrient patterns could be misaligned.

If a Tree Falls in the Amazon

For the first time, scientists pinpointed how often storms topple trees, helping to predict how changes in Amazonia affect the world.

Turning Waste into Fuels, Microbial Style

A newly discovered metabolic process linking different bacteria in a community could enhance bioenergy production.

Department of Energy Awards Six Research Contracts Totaling $258 Million to Accelerate U.S. Supercomputing Technology

Today U.S. Secretary of Energy Rick Perry announced that six leading U.S. technology companies will receive funding from the Department of Energy's Exascale Computing Project (ECP) as part of its new PathForward program, accelerating the research necessary to deploy the nation's first exascale supercomputers.

Electrifying Magnetism

Researchers create materials with controllable electrical and magnetic properties, even at room temperature.

One Step Closer to Practical Fast Charging Batteries

Novel electrode materials have designed pathways for electrons and ions during the charge/discharge cycle.


Berkeley Lab's Open-Source Spinoff Serves Science

Article ID: 676049

Released: 2017-06-07 12:05:38

Source Newsroom: Lawrence Berkeley National Laboratory

  • Credit: Marillyn Chung/Berkeley Lab

    Greg Kurtzer invented software called Singularity to enable the use of containers in high-performance computing

Scientists used to come to Gregory Kurtzer of Lawrence Berkeley National Laboratory’s (Berkeley Lab’s) IT department a lot, asking for a better way to use software containers in a high-performance computing (HPC) environment. After a while he got tired of saying, “Sorry, not possible.” So he invented a solution and named it Singularity.

Within a few months of its release last year, Singularity took off. Computing-heavy scientific institutions worldwide—from Stanford University to the Massachusetts Institute of Technology to various sites on the European Grid e-Infrastructure—flocked to the software. Singularity was also recently recognized by HPCwire editors as one of five new technologies to watch.

“Singularity has been making huge strides in the computing community,” Kurtzer said, with some surprise, adding that Open Science Grid, a consortium that provides distributed computing resources for scientific research, has served over 20 million containers with Singularity.

It’s now on its seventh release (version 2.2.1) and has caught on so quickly that Kurtzer has launched SingularityWare LLC to further develop and support the open-source software. The company is being funded by RStor Inc., a startup based in Saratoga, California. Kurtzer, the long-time technical lead and architect for the HPC Services group at Berkeley Lab with a joint appointment at UC Berkeley, will shift to an advisory role at the Lab in order to focus on Singularity.

“Berkeley Lab makes some Lab-developed software available at no cost to maximize its impact and to participate in the open-source software community,” said Elsie Quaite-Randall, Berkeley Lab’s Chief Technology Transfer Officer. “Singularity fosters innovation as open-source software, and now SingularityWare LLC—like other Berkeley Lab startups—will set out to expand the reach and adoption of an important technology.”

Who needs containers, anyway?

A typical case where users might need Singularity is if they want to run an application such as Google’s TensorFlow. “They may need a very specific version of Tensor Flow installed,” Kurtzer said. “They can create a container to do that in about five minutes. Then they can take that container, bring it to our environment and run it, even if we don’t have that version of Tensor Flow installed.”

Software containers make it possible to take your entire computing environment, including your files and all the applications you want to run, and encapsulate it so it can be easily replicated on another machine without worrying whether the new machine has a compatible operating system, libraries, applications, and so forth.

“Containers share some of the use cases of virtual machines but without the code redundancy and performance hit associated with virtualization,” Kurtzer said. “Singularity containers allow a user to encapsulate an entire OS (operating system) environment and use it on a shared HPC system like any other program, without an admin doing anything.”

Another example where Singularity would be useful would be allowing other scientists to reproduce experiments. “Say you just published an article. Wouldn’t it be nice to have a location you can cite where someone can download the Singularity container and replicate all the experiments?” Kurtzer asked. “Someone can enter the container, and now they’re sitting in the exact same environment as you were.”

Containerization was developed for enterprise environments, where it has become very popular, especially with the rise of Docker’s container technology. “Docker’s container solution is for the enterprise. But the scientific use case is quite different,” Kurtzer said. “Our goal isn’t to run as many containers as we can on a single host, with each having the illusion of sole occupancy and isolation, but to run maybe one, and enable it to utilize all the resources on that host. It’s kind of the opposite of isolation!”

So Kurtzer started working on his own solution, and four months later, the first version was released last spring. “When I started working on it, I asked, what do scientists really need from containers? They need reproducibility, mobility, and also freedom¾the ability to install their own applications and run in their own environment, and store it just like any other data file,” Kurtzer said. “That’s what Singularity solves for scientific computing.”

Long tail of science

Kurtzer chose the name Singularity for its meaning in astronomy. “As I understand it, it’s the culmination of a whole bunch of matter in the universe forming a single infinitely dense point,” he said. “That’s what I was thinking when I was creating Singularity—taking everything necessary to create a reproducible scientific environment and putting it in one file.”

Singularity also enables users to run legacy workflows easily. Kurtzer cites one example of how his group saved an 18-year-old workflow from failing hardware and was able to convert it to a Singularity container that is still being used in production today.

Kurtzer believes Singularity will benefit scientists who may not even know they need it. “We’re trying to reach out to more scientists and engage with additional groups, especially those who are not traditional HPC users, also known as the computational ‘long tail of science,’” Kurtzer said. “We have a lot of users that are running computationally intensive jobs on their laptops and workstations and not making use of the dedicated computational cycles that are designed specifically for computing and available to them. With Singularity we can easily make these large computing resources tangible.”

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Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel Prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit www.lbl.gov.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.