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  • richardmitnick 12:20 pm on July 13, 2017 Permalink | Reply
    Tags: Chinese Sunway ThaihuLight supercomputer currently #1 on the TOP500 list of supercomputers, How supercomputers are uniting the US and China, Science Node,   

    From Science Node: “How supercomputers are uniting the US and China” 

    Science Node bloc
    Science Node

    12 July 2017
    Tristan Fitzpatrick

    38 years ago, US President Jimmy Carter and China Vice Premier Deng Xiaoping signed the US – China Agreement on Cooperation in Science and Technology, outlining broad opportunities to promote science and technology research.

    Since then the two nations have worked together on a variety of projects, including energy and climate research. Now, however, there is another goal that each country is working towards: The pursuit of exascale computing.

    At the PEARC17 conference in New Orleans, Louisiana, representatives from the high-performance computing communities in the US and China participated in the first international workshop on American and Chinese collaborations in experience and best practice in supercomputing.

    Both countries face the same challenges implementing and managing HPC resources across a large nation-state. The hardware and software technologies are rapidly evolving, the user base is ever-expanding, and the technical requirements for maintaining these large and fast machines is accelerating.

    It would be a major coup for either country’s scientific prowess if exascale computing could be reached, as it’s believed to be the order of processing for the human brain at the neural level. Initiatives like the Human Brain Project consider it to be a hallmark to advance computational power.

    “It’s less like an arms race between the two countries to see who gets there first and more like the Olympics,” says Dan Stanzione, executive director at the Texas Advanced Computing Center (TACC).

    TACC Maverick HP NVIDIA supercomputer

    TACC Lonestar Cray XC40 supercomputer

    Dell Poweredge U Texas Austin Stampede Supercomputer. Texas Advanced Computer Center 9.6 PF

    TACC HPE Apollo 8000 Hikari supercomputer

    TACC Maverick HP NVIDIA supercomputer

    “We’d like to win and get the gold medal but hearing what China is doing with exascale research is going to help us get closer to this goal.”

    ___________________________________________________________________

    Exascale refers to computing systems that can perform a billion billion calculations per second — at least 50 times faster than the fastest supercomputers in the US.

    ___________________________________________________________________

    Despite the bona fides that would be awarded to whomever achieves the milestone first, TACC data mining and statistics group manager Weijia Xu stresses that collaboration is a greater motivator for both the US and China than just a race to see who gets there first.

    “I don’t think it’s really a competition,” Xu says. “It’s more of a common goal we all want to reach eventually. How you reach the goal is not exactly clear to everyone yet. Furthermore, there are many challenges ahead, such as how systems can be optimized for various applications.”

    The computational resources at China’s disposal could make it a great ally in the pursuit of exascale power. As of June 2017, China has the two fastest supercomputers in the top 500 supercomputers list, followed by five entries from the United States in the top ten.

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    Chinese Sunway ThaihuLight supercomputer, currently #1 on the TOP500 list of supercomputers.

    “While China has the top supercomputer in the world, China and the US probably have about fifty percent each of those top 500 machines besides the European countries,” says Si Liu, HPC software tools researcher at TACC. “We really believe if we have some collaboration between the US and China, we could do some great projects together and benefit the whole HPC community.”

    Besides pursuing the elusive exascale goal, Stanzione says the workshop opened up other ideas for how to improve the overall performance of HPC efforts in both nations. Co-located participants spoke on topics ranging from in situ simulations, artificial intelligence, and deep learning, among others.

    “We also ask questions like how do we run HPC systems, what do we run on them, and how it’s going to change in the next few years,” Stanzione says.“It’s a great time to get together and talk about details of processors, speeds, and feeds.”

    See the full article here .

    Please help promote STEM in your local schools.
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    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 1:21 pm on July 8, 2017 Permalink | Reply
    Tags: , , , , , , , Science Node, , UCSD Comet supercomputer   

    From Science Node: “Cracking the CRISPR clock” 

    Science Node bloc
    Science Node

    05 Jul, 2017
    Jan Zverina

    SDSC Dell Comet supercomputer

    Capturing the motion of gyrating proteins at time intervals up to one thousand times greater than previous efforts, a team led by University of California, San Diego (UCSD) researchers has identified the myriad structural changes that activate and drive CRISPR-Cas9, the innovative gene-splicing technology that’s transforming the field of genetic engineering.

    By shedding light on the biophysical details governing the mechanics of CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats) activity, the study provides a fundamental framework for designing a more efficient and accurate genome-splicing technology that doesn’t yield ‘off-target’ DNA breaks currently frustrating the potential of the CRISPR-Cas9- system, particularly for clinical uses.


    Shake and bake. Gaussian accelerated molecular dynamics simulations and state-of-the-art supercomputing resources reveal the conformational change of the HNH domain (green) from its inactive to active state. Courtesy Giulia Palermo, McCammon Lab, UC San Diego.

    “Although the CRISPR-Cas9 system is rapidly revolutionizing life sciences toward a facile genome editing technology, structural and mechanistic details underlying its function have remained unknown,” says Giulia Palermo, a postdoctoral scholar with the UC San Diego Department of Pharmacology and lead author of the study [PNAS].

    See the full article here
    .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 12:05 pm on July 1, 2017 Permalink | Reply
    Tags: NRENs - national research and education networks, Science Node, Solar energy benefits education and research in Africa, Solar-powered batteries   

    From Science Node: “Solar energy benefits education and research in Africa” 

    Science Node bloc
    Science Node

    28 June, 2017
    Megan Ray Nichols

    1
    No image caption or credit.

    Research and education networks are under threat in Africa due to frequent power outages. Solar-powered batteries may hold the key to network resilience and scientific autonomy.

    It’s hard to imagine that in our technologically advanced society that there are people without electricity, but this is exactly what happens in many parts of Africa.

    With many remote regions and an unstable electrical grid, the science and education made possible by national research and education networks (NRENs) are often in jeopardy. Solar-powered batteries might just be the solution.

    Electricity, education, and research in Africa

    It is estimated that millions of families in Africa are without power, and the policies the government must enact to make electricity more available are slow in coming. Finding a viable and economical way to connect everyone to the grid has been a challenge.


    Wow!! Power to the people. Microgrids, like the one featured in this Tesla video, combine solar panels and rechargeable batteries to liberate remote regions from the tyranny of power outages. Courtesy Tesla.

    Electrical service disruption directly affects network operating centers (NOCs), network point-of presences (PoPs), research institutions, and students throughout the continent.

    “Information and communication technology (ICT) services define our daily lives,” notes Stein Mkandawire, chief technical officer for the Zambia Research and Education Network.

    “Funding standby generators for daily running of NOCs, PoPs and institutions is required, and that results in high service provision costs.”

    Even in less remote locales with an electrical infrastructure in place, blackouts occur frequently. The net result is an extreme hindrance for the scientific and educational projects underway in Africa.

    “Power outages often worsen the challenges faced when establishing NRENs in Africa because periods where power mains fail in excess of two days are still common,” says Isaac Kasana, CEO of the Research and Education Network for Uganda (RENU).

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    Here comes the sun. Electrical infrastructure is often taxed by the rugged expanses of Africa, handicapping scientific communications. Solar power is lighting the way to a solution. Courtesy McKinsey and Co.

    “Failure is so repetitive that the mains-charged battery systems are unable to sustain sufficient levels of operating autonomy to prevent site power shutdowns from occurring.”

    Power outages not only affect a specific site or campus but also the connectivity of other linked campuses. For instance, RENU’s network follows a sub-ring topology with typically eight or nine daisy-chained campus networks.

    Multiply that by the number of researchers, teachers, students, and communities depending on ICT services, and the fragility of the enterprise becomes apparent.

    In the face of these challenges, NREN engineers are looking to solar power as a way to sustain electricity during frequent blackouts.

    Harnessing solar power

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    Solar power. No image credit

    Being able to tap into solar energy for electrical power works best when there is a way to store that energy. In the past, batteries haven’t always worked as well as they should.

    But with advances in technology, solar-powered rechargeable batteries now make renewable energy systems reliable and viable.

    “Many African countries have plenty of sunshine which can be used as alternative source of energy, so solar energy is a means to sustain the NRENs in times of blackouts,” says Mkandawire.

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    The doctor is in. Remote researchers (and their data) cut off by intermmitent power supplies may find respite with implementation of solar-powered rechargeable batteries. Courtesy Johns Hopkins School of Public Health.

    Since most days have sufficient periods of intense sunshine, this would ensure near-continuous solar charging. When tied into a hybrid-charged power system, batteries can greatly enhance NREN resilience.

    “For up-country campuses and rural-located research stations (such as the NIH station at Rakai), solar-charged batteries may provide the most cost-efficient means of powering connectivity and other ICT equipment, says Kasana. “This will increase an NREN’s national coverage by enabling the connection of remote research stations and enhancing access for researchers who have to be based at such remote sites.”

    By supplying countries with a reliable source of power from solar, African NRENs can send a steady stream of services to institutions, research bases, and communities. This in turn, gives better access to learning materials.

    The benefits of solar power

    There are many affordable options for families in Africa to bring electricity through solar power into their homes. Using apps on their phones and equipment they can buy at the store, they can power their homes for less than $60 per year. Several places have already started using solar power — it provides electricity to areas that desperately need it, creates jobs, and furthers research and education.

    An education is one of life’s most precious acquisitions. But without the resources needed to teach and learn, knowledge-creation stalls.

    Solar power is brightening the future of science and research in Africa.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 3:27 pm on June 25, 2017 Permalink | Reply
    Tags: , , , Science Node, , TACC Lonestar supercomputer, TACC Stampede supercomputer   

    From Science Node: “Computer simulations and big data advance cancer immunotherapy” 

    Science Node bloc
    Science Node

    09 Jun, 2017 [Where has this been?]
    Aaron Dubrow

    1
    Courtesy National Institute of Allergy and Infectious Diseases.

    Supercomputers help classify immune response, design clinical trials, and analyze immune repertoire data.
    Scanning electron micrograph of a human T lymphocyte (also called a T cell) from the immune system of a healthy donor. Immunotherapy fights cancer by supercharging the immune system’s natural defenses (include T-cells) or contributing additional immune elements that can help the body kill cancer cells. [Credit: NIAID]

    The body has a natural way of fighting cancer – it’s called the immune system, and it is tuned to defend our cells against outside infections and internal disorder. But occasionally, it needs a helping hand.

    In recent decades, immunotherapy has become an important tool in treating a wide range of cancers, including breast cancer, melanoma and leukemia.

    But alongside its successes, scientists have discovered that immunotherapy sometimes has powerful — even fatal — side-effects.

    Identifying patient-specific immune treatments

    Not every immune therapy works the same on every patient. Differences in an individual’s immune system may mean one treatment is more appropriate than another. Furthermore, tweaking one’s system might heighten the efficacy of certain treatments.

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    Scanning electron micrograph of a human T lymphocyte (also called a T cell) from the immune system of a healthy donor. Immunotherapy fights cancer by supercharging the immune system’s natural defenses (include T-cells) or contributing additional immune elements that can help the body kill cancer cells. [Credit: NIAID]

    Researchers from Wake Forest School of Medicine and Zhejiang University in China developed a novel mathematical model to explore the interactions between prostate tumors and common immunotherapy approaches, individually and in combination.

    In a study published in Nature Scientific Reports, they used their model to predict how prostate cancer would react to four common immunotherapies.

    The researchers incorporated data from animal studies into their complex mathematical models and simulated tumor responses to the treatments using the Stampede supercomputer at the Texas Advanced Computing Center (TACC).

    Dell Poweredge U Texas Austin Stampede Supercomputer. Texas Advanced Computer Center 9.6 PF

    “We do a lot of modeling which relies on millions of simulations,” says Jing Su, a researcher at the Center for Bioinformatics and Systems Biology at Wake Forest School of Medicine and assistant professor in the Department of Diagnostic Radiology.

    “To get a reliable result, we have to repeat each computation at least 100 times. We want to explore the combinations and effects and different conditions and their results.”

    TACC’s high performance computing resources allowed the researchers to highlight a potential therapeutic strategy that may manage prostate tumor growth more effectively.

    Designing more efficient clinical trials

    Biological agents used in immunotherapy — including those that target a specific tumor pathway, aim for DNA repair, or stimulate the immune system to attack a tumor — function differently from radiation and chemotherapy.

    Because traditional dose-finding designs are not suitable for trials of biological agents, novel designs that consider both the toxicity and efficacy of these agents are imperative.

    Chunyan Cai, assistant professor of biostatistics at UT Health Science Center (UTHSC)’s McGovern Medical School, uses TACC systems to design new kinds of dose-finding trials for combinations of immunotherapies.

    4

    Writing in the Journal of the Royal Statistics Society Series C (Applied Statistics), Cai and her collaborators, Ying Yuan, and Yuan Ji, described efforts to identify biologically optimal dose combinations for agents that target the PI3K/AKT/mTOR signaling pathway, which has been associated with several genetic aberrations related to the promotion of cancer.

    After 2,000 simulations on the Lonestar supercomputer for each of six proposed dose-finding designs, they discovered the optimal combination gives higher priority to trying new doses in the early stage of the trial.

    TACC Lonestar Cray XC40 supercomputer

    The best case also assigns patients to the most effective dose that is safe toward the end of the trial.

    “Extensive simulation studies show that the design proposed has desirable operating characteristics in identifying the biologically optimal dose combination under various patterns of dose–toxicity and dose–efficacy relationships,” Cai concludes.

    Whether in support of population-level immune response studies, clinical dosing trials, or community-wide efforts, TACC’s advanced computing resources are helping scientists put the immune system to work to better fight cancer.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 12:35 pm on June 10, 2017 Permalink | Reply
    Tags: , , Irish Centre for High-End Computing, , , PRACE, , Science Node, Sinéad Ryan, ,   

    From Science Node= Women in STEM-“A day in the life of an Irish particle physicist” Sinéad Ryan 

    Science Node bloc

    Science Node

    02 Jun, 2017
    Tristan Fitzpatrick

    2
    Sinéad Ryan is a quantum chromodynamics expert in Dublin. She relies on PRACE HPC resources to calculate the mass of quarks, gluons, and hadrons — and uncover the secrets of the universe.

    Uncovering the mysteries of the cosmos is just another day in the office for Sinéad Ryan.

    2

    Ryan, professor of theoretical high energy physics at Trinity College Dublin, specializes in quantum chromodynamics (QCD). The field examines how quarks and gluons form hadrons, the fundamental starting point of our universe.

    “Quarks and gluons are the building blocks for everything in the world around us and for our universe,” says Ryan. “The question is, how do these form the matter that we see around us?”

    To answer this, Ryan performs numerical simulations on high-performance computing (HPC) resources managed by the Partnership for Advanced Computing in Europe’s (PRACE).

    “I think PRACE is crucial for our field,” says Ryan, “and I’m sure other people would tell you the same thing.”

    When quarks are pulled apart, energy grows between them, similar to the tension in a rubber band when it is stretched. Eventually, enough energy is produced to create more quarks which then form hadrons in accordance with Einstein’s equation E=MC2.

    The problem, according to Ryan, comes in solving the equations of QCD. PRACE’s HPC resources make Ryan’s work possible because they enable her to run simulations on a larger scale than simple pen and paper would allow.

    “It’s a huge dimensional integral to solve, and we’re talking about solving a million times a million matrices that we must invert,” says Ryan.

    “This is where HPC comes in. If you want to make predictions in the theory, you need to be able to do the simulations numerically.”

    In Ireland, the Irish Centre for High-End Computing is one resource Ryan has tapped in her research, but PRACE enables her and her collaborators to access resources not just locally but across the world.

    IITAC IBM supercomputer

    “This sort of work tends to be very collaborative and international,” says Ryan. “We can apply through PRACE for time on HPC machines throughout Europe. In my field, any machine anywhere is fair game.”

    Besides providing resources, PRACE also determines whether HPC resources are suitable for the kinds of research questions scientists are interested in answering.

    “PRACE’s access to these facilities means that good science gets done on these machines,” says Ryan. “These are computations that are based around fundamental questions posed by people who have a track record for doing good science and asking the right questions. I think that’s crucial.”

    Without PRACE’s support, Ryan’s work examining how quarks and gluons form matter and the beginnings of our universe would be greatly diminished, leaving us one step further behind uncovering the building blocks of the universe.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 7:56 pm on June 9, 2017 Permalink | Reply
    Tags: , , Science Node, SDSC- San Diego Supercomputer Center,   

    From Science Node: “XSEDE cuts through the noise” 

    Science Node bloc
    Science Node

    06 June, 2017
    Alisa Alering

    3
    Courtesy LIGO; Caltech; MIT; Sonoma State; Aurore Simonnet.

    Over two billion years ago, when multicellular life had only just begun to evolve on Earth, two black holes collided and merged to form a new black hole.

    With a mass 49 times that of our sun, the massive collision set off ripples in space-time that radiated from the event like waves from a stone thrown into a pond. Predicted by Albert Einstein in 1916 and known as gravitational waves, those ripples are still traveling.


    Surf’s up! The Extreme Science and Engineering Discovery Environment (XSEDE) provides the HPC resources required to pluck gravitational waves from the noise found on LIGO detectors. Courtesy XSEDE.

    Able to pass through dust, matter, or anything else without being distorted, gravitational waves carry unique information about cosmic events that can’t be obtained in any other way. When the waves reach Earth, they give astrophysicists a completely new way to explore the universe.

    The first such waves were detected on September 14, 2015 by the Laser Interferometer Gravitational-Wave Observatory (LIGO) Scientific Collaboration. In the months since, two more gravitational wave events have been confirmed, one in December 2015 and the most recent on January 4, 2017.


    Caltech/MIT Advanced aLigo Hanford, WA, USA installation


    Caltech/MIT Advanced aLigo detector installation Livingston, LA, USA

    Cornell SXS, the Simulating eXtreme Spacetimes (SXS) project


    Gravitational waves. Credit: MPI for Gravitational Physics/W.Benger-Zib

    ESA/eLISA the future of gravitational wave research

    Signal from noise

    When gravitational waves pass by, they change the distance between objects. The change is so infinitesimal that it can’t be felt, or seen with a microscope. But incredibly sensitive scientific instruments—interferometers—can detect a change that is a thousand times smaller than a proton.

    The LIGO Scientific Collaboration, a body of more than 1,000 international scientists who collectively perform LIGO research, operates two interferometers located over 2000 miles apart in Washington and Louisiana, USA.

    Despite the sensitivity of the instruments, it’s not easy to detect a gravitational wave. When a signal is received, scientists must determine what it means and how likely it is to be noise or a real gravitational wave. Making that determination requires high-performance computing.

    Since 2013, LIGO has collaborated with the Extreme Science and Engineering Discovery Environment (XSEDE), a National Science Foundation (NSF)-funded cyberinfrastructure network that includes not just high-performance computing systems but also experts who help researchers move projects forward.

    Better, faster, cheaper

    In order to validate the discovery of a gravitational wave, researchers measure the significance of the signal by calculating a false alarm rate for the event.


    Making waves, taking names. The top part of the animation shows two black holes orbiting each other until they merge, and the lower part shows the two distinct gravitational waves emitted. Thanks to supercomputers at TACC and SDSC, researchers can pick out these waves from other detector noise. Courtesy Simulating eXtreme Spacetimes collaboration.

    TACC Maverick HP NVIDIA supercomputer

    TACC Lonestar Cray XC40 supercomputer

    Dell Poweredge U Texas Austin Stampede Supercomputer. Texas Advanced Computer Center 9.6 PF

    TACC HPE Apollo 8000 Hikari supercomputer

    TACC Maverick HP NVIDIA supercomputer

    SDSC Triton HP supercomputer

    SDSC Gordon-Simons supercomputer

    SDSC Dell Comet supercomputer

    Once confirmed, further supercomputer analysis is used to extract precise estimates of the physical properties of the event, including the masses of the colliding objects, position, orientation, and distance from the Earth, carefully checking millions of combinations of these characteristics and testing how well the predicted waveform matches the signal detected by LIGO.

    To draw larger conclusions about the nature of black holes requires careful modeling based on the received data. Each simulation can take from a week to one month to complete, depending upon the complexity.

    Such intensive data analysis requires large scale high-throughput computing with parallel workflows at the scale of tens of thousands of cores for long periods of time. LIGO has been allocated millions of hours on XSEDE’s high-performance computers, including Stampede at the Texas Advanced Computing Center (TACC) and Comet at the San Diego Supercomputer Center (SDSC).

    Over the first year of XSEDE’s collaboration with LIGO, XSEDE worked to increase the speed of the applications, making them 8-10x faster on average.

    “The strategic collaboration between the two NSF-funded projects allows for accelerated scientific discovery which also translates into cost-savings for LIGO on the order of tens of millions of dollars so far,” says Pedro Marronetti, Gravitational Physics program director at the NSF.

    Waves of the future

    LIGO plans to upgrade its observatories and improve the sensitivity of its detectors before the next observational period begins in late 2018. LIGO predicts that once its observatories reach their most sensitive state, they may able to detect as many as 40 gravitational waves per year.

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    More instruments like LIGO will soon be listening for waves around the world in Italy, Japan, and India. Scientists also hope to place interferometers in orbit in order to avoid interference from Earth noise.

    And that means much more computing power will be required to verify the signals and extract information about the nature and origins of our universe.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 1:12 pm on May 27, 2017 Permalink | Reply
    Tags: 1 millionº and breezy: Your solar forecast, , , , Science Node, ,   

    From Science Node: “1 millionº and breezy: Your solar forecast” 

    Science Node bloc
    Science Node

    24 May, 2017
    Alisa Alering

    Space is a big place, so modeling activities out there calls for supercomputers that match. PRACE provided scientists the resources to run the Vlasiator code and simulate the solar wind around the earth.

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    Courtesy Minna Palmroth; Finnish Meteorological Institute.

    Outer space is a tough place to be a lonely blue planet.

    With only a thin atmosphere standing between a punishing solar wind and the 1.5 million species living on its surface, any indication of the solar mood is appreciated.

    The sun emits a continuous flow of plasma traveling at speeds up to 900 km/s and temperatures as high as 1 millionº Celsius. The earth’s magnetosphere blocks this wind and allows it to flow harmlessly around the planet like water around a stone in the middle of a stream.

    Magnetosphere of Earth, original bitmap from NASA. SVG rendering by Aaron Kaase

    But under the force of the solar bombardment, the earth’s magnetic field responds dramatically, changing size and shape. The highly dynamic conditions this creates in near-Earth space is known as space weather.

    Vlasiator, a new simulation developed by Minna Palmroth, professor in computational space physics at the University of Helsinki, models the entire magnetosphere. It helps scientists to better understand interesting and hard-to-predict phenomena that occur in near-Earth space weather.

    Unlike previous models that could only simulate a small segment of the magnetosphere, Vlasiator allows scientists to study causal relationships between plasma phenomena for the first time and to consider smaller scale phenomena in a larger context.

    “With Vlasiator, we are simulating near-Earth space with better accuracy than has even been possible before,” says Palmroth.

    Navigating near-Earth

    Over 1,000 satellites and other near-Earth spacecraft are currently in operation around the earth, including the International Space Station and the Hubble Telescope.

    Nearly all communications on Earth — including television and radio, telephone, internet, and military — rely on links to these spacecraft.

    Still other satellites support navigation and global positioning and meteorological observation.

    New spacecraft are launched every day, and the future promises even greater dependence on their signals. But we are launching these craft into a sea of plasma that we barely understand.

    “Consider a shipping company that would send its vessel into an ocean without knowing what the environment was,” says Palmroth. “That wouldn’t be very smart.”

    Space weather has an enormous impact on spacecraft, capable of deteriorating signals to the navigation map on your phone and disrupting aviation. Solar storms even have the potential to overwhelm transformers and black out the power grid.

    Through better comprehension and prediction of space weather, Vlasiator’s comprehensive model will help scientists protect vital communications and other satellite functions.

    Three-level parallelization

    The Vlasiator’s simulations are so detailed that it can model the most important physical phenomena in the near-Earth space at the ion-kinetic scale. This amounts to a volume of 1 million km3 — a massive computational challenge that has not previously been possible.

    After being awarded several highly competitive grants from the European Research Council, Palmroth secured computation time on HPC resources managed by the Partnership for Advanced Computing in Europe (PRACE).

    4
    Hazel Hen

    She began with the Hornet supercomputer and then its successor Hazel Hen, both at the High-Performance Computing Center Stuttgart. Most recently she has been using the Marconi supercomputer at CINECA in Italy.

    7
    Marconi supercomputer at CINECA in Italy

    Palmroth’s success is due to three-level parallelization of the simulation code. Her team uses domain decomposition to split the near-Earth space into grid cells within each area they wish to simulate.

    They use load-balancing to divide the simulations and then parallelize using OpenMP. Finally, they vectorize the code to parallelize through the supercomputer’s cores.

    Even so, simulation datasets range from 1 to 100 terabytes, depending on how often they save the simulations, and require anywhere between 500 – 100,000 cores, possibly beyond, on Hazel Hen.

    “We are continuously making algorithmic improvements in the code, making new optimizations, and utilizing the latest advances in HPC to improve the efficiency of the calculations all the time,” says Palmroth.

    Taking off into the future

    In addition to advancing our knowledge of space weather, Vlasiator also helps scientists to better understand plasma physics. Until now, most fundamental plasma physical phenomena have been discovered from space because it’s the best available laboratory.

    But the universe is comprised of 99.9 percent plasma, the fourth state of matter. In order to understand the universe, you need to understand plasma physics. For scientists undertaking any kind of matter research, Vlasiator’s capacity to simulate the near-Earth space is significant.

    “As a scientist, I’m curious about what happens in the world,” says Palmroth. “I can’t really draw a line beyond which I don’t want to know what happens.”

    Significantly, Vlasiator has recently helped to explain some features of ultra-low frequency waves in the earth’s foreshock that have perplexed scientists for decades.

    A collaboration with NASA in the US helped validate those results with the THEMIS spacecraft, a constellation of five identical probes designed to gather information about large-scale space physics.

    Exchanging information with her colleagues at NASA allows Palmroth to get input from THEMIS’s direct observation of space phenomena and to exchange modeling results with the observational community.

    “The work we are doing now is important for the next generation,” says Palmroth. “We’re learning all the time. If future generations build upon our advances, their understanding of the universe will be on much more certain ground.”

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 9:48 am on May 25, 2017 Permalink | Reply
    Tags: , , Science Node,   

    From Science Node: “More than meets the eye” 

    Science Node bloc
    Science Node

    22 Mar, 2017 [Where has this been?]
    Tristan Fitzpatrick

    1
    Courtesy Innovega.

    Hold on tight, because an NSF-funded contact lens and eyewear combo is about to plunge us all into the Metaverse.

    7

    Augmented reality (AR) has been steadily making inroads into society. Sure the gaming is fun, but when you consider fields like medical training and remote site access for safety inspectors and science teachers, AR offers a lot of promise.

    However, many head mounted displays (HMD) are clunky and cumbersome and continue to restrict wide scale adoption of AR. What’s more, continual access to the digital world while navigating the real world presents a safety challenge.


    Close encounter. A smart investment by the NSF, eMacula puts augmented reality in a contact lens.

    So what’s the remedy that will vault us in to the Metaverse?

    “Contact lenses appear to be an optimal solution, but only if the user experience can deliver on the promise in comfort, real functionality, and a price point that consumers can afford,” says Chris Collins, founder and technical lead for the Center for Simulations and Virtual Environments Research (UCSIM) at the University of Cincinnati.

    “A product that meets all of those challenges could be a game-changer and bring us that much closer to a seamless immersive experience.”

    Virtual freedom

    Finally, scientists have come up with a way to free users from HMD and bring the virtual world closer than ever before.

    To better integrate the two worlds, Seattle-based startup Innovega has developed eMacula.

    “Allowing a user to have their digital media within their normal and unobstructed field of view means that people will stop staring at their phones and devices and start looking at each other again,” says Jay Marsh, vice president of engineering at Innovega.

    “It means that bio-metric health monitoring can be truly ‘real time, all the time’ and with driving/navigation directions painted on the road in front of you, you will never be distracted with a gaze shift to your mobile devices for guidance.”

    Funded in part by Small Business Innovation Research grants from the US National Science Foundation, Innovega has developed a filtered lens in a hybrid style contact lens along with lightweight and stylish eyewear.

    Pairing the glasses with a contact lens significantly reduces the burdens previously associated with HMD.

    “NSF was a critical player in the development of our current soft lens technology,” says Marsh.

    3
    Double trouble. Augmented reality has been held back by cumbersome interfaces and uncomfortable user experience. Courtesy David Hoffman, et al.

    Troubled technology

    With traditional AR, a problem known as vergence-accommodation conflict arises since our eyes try to focus on the screen in front of them, but end up converging at a farther distance. Often eyestrain, headaches, and nausea result.

    The contact lenses circumvent this problem because the media on the lenses is in focus while the eyes converge on the glasses behind.

    Merging the real and virtual worlds has broad implications for many professions, Marsh says. Doctors and technicians that need both hands to execute their work while also needing access to critical information will find great use in merging the virtual and real worlds.

    In an industry setting, Marsh foresees applications that allow for system level safety data to be provided to all operators in real time, and more refined information based on physical locations.

    The lenses are currently undergoing FDA approval and should be on the market later in 2017.

    It appears the next step in the digital mobile evolution of technology may be on the horizon, and the natural integration of the virtual world into our real experience is at hand.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 11:45 am on May 24, 2017 Permalink | Reply
    Tags: , , HPC heard around the world, Science Node   

    From Science Node: “HPC heard around the world” 

    Science Node bloc
    Science Node

    19 May, 2017
    Tristan Fitzpatrick

    A new advanced computing alliance indicates cooperation and collaboration are alive and well in the global research community.

    It was an international celebration in Barcelona, Spain, as representatives from three continents met at PRACEdays17 to sign a memorandum of understanding (MoU), formalizing a new era in advanced research computing.

    On hand to recognize the partnership were John Towns, principal investigator of the Extreme Science and Engineering Discovery Environment (XSEDE), Serge Bogaerts, managing director of the Partnership for Advanced Computing in Europe (PRACE), and Masahiro Seki, president of the Japanese Research Organization for Information Science and Technology (RIST).

    1

    “We are excited about this development and fully expect this effort will support the growing number of international collaborations emerging across all fields of scholarship,” says Towns.

    As steward of the US supercomputing infrastructure, XSEDE will share their socio-technical platform that integrates and coordinates the advanced digital services that support contemporary science across the country.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 1:14 pm on May 7, 2017 Permalink | Reply
    Tags: , , , , , Into the wild simulated yonder, Science Node   

    From Science Node: “Into the wild simulated yonder” 

    Science Node bloc
    Science Node

    28 Apr, 2017
    Tristan Fitzpatrick

    So much of our universe is known to us, but there is so much more we don’t know – yet.

    For example, normal matter that is easily observable (such as gas and rocks) makes up only four percent of the known mass-energy in the universe, according to the Canada-France Hawaii Lensing Survey (CFHTLenS).

    1
    Image: NASA/ESA



    CFHT Telescope, Mauna Kea, Hawaii, USA

    The other 96 percent is dark matter and energy. These two components are critical to science’s understanding of how the galaxy was formed, but there’s one problem: A combination of dark matter and energy can only be observed by how it affects the four percent of the universe scientists can measure.

    Telescopes don’t help much in observing these galactic effects, and this creates a challenge for scholars.

    Building a mystery

    One research project seeks to bring science one step closer to solving this cosmic mystery.

    Carnegie Mellon University associate professor Rachel Mandelbaum uses generative adversarial networks (GANs) to simulate galaxies warped by gravitational lensing – and takes science one step closer to solving the origins of our cosmos.

    Gravitational Lensing NASA/ESA


    Gravitational microlensing, S. Liebes, Physical Review B, 133 (1964): 835

    Gravitational lensing is a process by which mass bends light, an effect predicted by Albert Einstein’s theory of general relativity. The larger an object, the greater its gravitational field will be, and the greater its ability to bend light rays.

    ______________________________________________________________________

    Because light bending is sensitive to the strength of the gravitational field it goes through, observing the lensing effect can be used to measure dark matter.
    ______________________________________________________________________

    There are several difficulties with observing rays of light, however. According to Mandelbaum’s research [ScienceDirect], detector imperfections, telescopic blurring and distortion, atmospheric effects, and noise can all affect the quality of the data, making research challenging for scientists.

    Unlike GANs, a traditional neural network, for example, will detect the difference between different images, but only if these images have been tagged by people and include descriptions. Eventually, the artificial intelligence will learn to distinguish images by itself, but only after it first sorts through images manually one-by-one.

    GANs save resources compared to other neural networks because fewer people are needed to operate them and because a GAN does not include a tagging and descriptor process. An image generator produces fake and real images on its own, without outside help, and the network will eventually learn to tell the difference between the two.

    Astronomical implications

    Mandelbaum’s research has wide implications in astronomy, as it can serve as a useful starting point for astronomical image analysis when telescopic problems and other issues create obstacles for scientists.

    2
    A portion of Mandelbaum’s simulation of a focal plane on the Large Synoptic Survey Telescope [?Not built yet]. Courtesy Mandelbaum, et al.

    Astrophysicist Peter Nugent at the Computational Research Division of Lawrence Berkeley National Laboratory and his colleagues have researched a gravitationally lensed supernova using computer simulations, which will shed light on how matter is distributed throughout the galaxy.

    Discovering new ways to explore the unknown universe is just one of the many possibilities computational science offers.

    To learn more about gravitational lensing, visit the CFHTLenS website or check out Mandelbaum’s research paper.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
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