Primeur weekly 2016-11-14

Exascale supercomputing

Berkeley Lab to lead AMR co-design centre for DOE's Exascale Computing Project ...

Exascale Computing Project announces $48 million to establish Exascale co-design centres ...

US Exascale Computing Project awards $34 million for software development ...

Quantum computing

Breakthrough in the quantum transfer of information between matter and light ...

Focus on Europe

European Commission reveals its forthcoming call for energy efficient, high performance processors ...

World-leading HPC centres partner to form accelerated computing institute ...

Atos Bull to boost Dutch research at SURFsara with first Bull sequana supercomputer installed ...

Middleware

Allinea tools yield a 50% speed up for genome applications at the Earlham Institute ...

NERSC's 'Shifter' scales up to more than 9,000 Cori KNL processors ...

DDN's Big Data storage provides Aalto University ample capacity and fast access to vital research data ...

DDN unveils industry's fastest multi-level security Lustre solution ...

DDN delivers new burst buffer appliance and updates block and file appliances, completing total product line refresh ...

Atos Bull tackles storage bottlenecks for High Performance Computing ...

Cycle Computing debuts the newest version of its groundbreaking CycleCloud ...

Hardware

University of Toronto selects CoolIT Systems to liquid cool signal processor for CHIME project ...

CoolIT Systems optimizes Trade and Match solution with custom closed-loop liquid cooling ...

SDSC to host high-speed, large data transfer experiment at SC16 Show ...

Cray XC40 "Theta" supercomputer accepted at Argonne National Laboratory ...

Cray launches next-generation supercomputer: the Cray XC50 ...

Cray reports third quarter 2016 financial results ...

Mellanox drives Virtual Reality to new levels with breakthrough performance ...

Mellanox announces 200Gb/s HDR InfiniBand solutions enabling record levels of performance and scalability ...

Computers made of genetic material? ...

CoolIT Systems to showcase best-in-class HPC liquid cooling offering at SC16 ...

Applications

BoschDoc, AHCODA-DB and OpenML winners of the Data Prize 2016 ...

Blue Waters simulates largest membrane channel made of DNA origami ...

Cray joins iEnergy, the oil and gas industry's foremost community for exploration and production ...

Large-scale computer simulations reveal biological growth processes ...

NASA science and technology advancements demonstrated at Supercomputing Conference ...

Unlocking big genetic datasets ...

Accelerating cancer research with deep learning ...

System opens up high-performance programming to non-experts ...

Studying structure to understand function within 'material families' ...

Chury is much younger than previously thought ...

TOP500

Global supercomputing capacity creeps up as Petascale systems blanket Top 100 ...

InfiniBand chosen by nearly 4x more end-users versus proprietary offerings in 2016 as shown on the TOP500 supercomputers list ...

The Cloud

SURFnet selects eight Cloud providers for Dutch education and research ...

Primeur magazine

Edition: weekly - Issue: 2016-11-14

Exascale supercomputing

Berkeley Lab will lead one of four co-design centres under the Department of Energy's Exascale Computing Project (ECP). The Block-Structured Adaptive Mesh Refinement (AMR) Co-Design Center will be led by John Bell of the lab's Computational Research Division, with support from Argonne National Laboratory and the National Renewable Energy Laboratory. The centre will be funded at $3 million a year for four years. Read further...
The Department of Energy's Exascale Computing Project (ECP) has selected four co-design centres as part of a four-year, $48 million funding award. The first year is funded at $12 million, and is to be allocated evenly among the four award recipients. The ECP is responsible for the planning, execution, and delivery of technologies necessary for a capable exascale ecosystem to support the USA's exascale imperative including software, applications, hardware, and early testbed platforms. Read further...
The Department of Energy's Exascale Computing Project (ECP) has selected 35 software development proposals representing 25 research and academic organisations. The awards for the first year of funding total $34 million and cover many components of the software stack for exascale systems, including programming models and runtime libraries, mathematical libraries and frameworks, tools, lower-level system software, data management and I/O, as well as in situ visualization and data analysis. Read further...

Quantum computing

A paper titled "High-Fidelity and Ultrafast Initialization of a Hole-Spin Bound to a Te Isoelectronic Centre in ZnSe" was recently published by a team from Polytechnique Montréal and France's CNRS in the prestigious journalPhysical Review Letters. The creation of a qubit in zinc selenide, a well-known semi-conductor material, made it possible to produce an interface between quantum physics that governs the behaviour of matter on a nanometre scale and the transfer of information at the speed of light, thereby paving the way to producing quantum communications networks. Read further...

Focus on Europe

Speaking at the HiPEAC Autumn 2016 Computing Systems Week, Sandro D'Elia of the Directorate General for Communications Networks, Content and Technology of the European Commission has made clear the shift of focus of the next round of European funding for customised and low energy computing. Read further...
Leaders in hybrid accelerated high-performance computing (HPC) in the United States (U.S.), Japan, and Switzerland have signed a memorandum of understanding (MOU) establishing an international institute dedicated to common goals, the sharing of HPC expertise, and forward-thinking evaluation of computing architecture. Read further...
Atos, a global expert in digital services, has installed a Bull sequana supercomputer at SURFsara in the Netherlands to expand the capacity of the national supercomputer Cartesius. Bull sequana is an open range of supercomputers that is ready to support future exascale technologies - which will make it possible to process a billion billion operations per second. This extension future-proofs the system as Bull sequana can be expanded with the latest technologies, allowing researchers to execute extremely complex research, and SURFsara to fully leverage its investment and save substantial costs. Today the compute capacity of Cartesius has been increased by 18% to a total of 1.8 Pflops. It will be operational on the 1st of December 2016; the first Bull sequana to be operational worldwide. Read further...

Middleware

Allinea MAP, a profiling tool from Allinea Software, is speeding up applications for the Earlham Institute, a life science research centre based in Norwich, UK, which is applying computational science and biotechnology to help find the answers to pressing world food problems. Read further...
Shifter - the scalable software toolkit that leverages container-based computing to help supercomputer users run a wider range of software more easily and securely - is now better than ever. Developed at Berkeley Lab's National Energy Research Scientific Computing Center (NERSC) to improve the flexibility and usability of HPC systems for data-intensive workloads by leveraging container-based computing tools such as Docker, Shifter was originally released in 2015. Development of this open-source tool has been ongoing, and in October NERSC released Shifter 16.08.3. Read further...
Aalto University has deployed DDN's SFA12KX and Lustre storage solutions to support the fast-paced growth of its data-intensive research. Deployed with six Hewlett Packard Enterprise (HPE) ProLiant DL360 Gen9 servers, the joint DDN storage and HPE server solution delivers 4x more capacity and 5x more performance than the University's prior system. Read further...
DataDirect Networks has introduced the industry's fastest multi-level security solution for Lustre, aimed at addressing growing use cases for HPC workflows in markets that require HPC-level performance but with increased security requirements, such as financial services, genomics and government organisations. DDN's Multi-Level Security (MLS) Lustre Solution provides the performance, scale and openness needed in HPC and Big Data enterprises, while also allowing organisations to meet the highest multi-level security requirements. Read further...
DataDirect Networks has launched several new products, solutions and updates, completing a refresh to its entire product line that began in September with the announcement of a new, high-density, high-performance object storage appliance (WOS8460). The newest additions include a refresh of the DDN14K-based products (DDN SFA14KX, SFA14KXE, GS14KX and ES14KX), an updated operating system with new capabilities, a new Burst Buffer Appliance (IME240) based on commodity hardware, and the company's new Multi-Level Security (MLS) Solution for Lustre environments. Read further...
Atos, through its technology brand Bull, launches Bull Director for HPSS, first component of the future range of Bull Data Management software dedicated to High Performance Computing. Bull Director for HPSS optimizes current large scale storage solutions and frees up compute time for users. This launch confirms Atos strategic commitment to develop innovative solutions for High Performance Computing (HPC) and High Performance Data Analytics (HPDA). The beta version of Bull Director for HPSS is revealed at the SC16 Conference in Salt Lake City, Utah, USA, which takes place 14-17 November. Read further...
Cycle Computing, an expert in Cloud computing orchestration software for Big Compute and Big Data, has made available the newest version of its flagship offering CycleCloud. CycleCloud V6 makes multi-environment management easier than ever before and is designed to deliver greater flexibility in managing workloads, Cloud access, and cluster set-up. Read further...

Hardware

CoolIT Systems, a global expert in energy efficient liquid cooling solutions for the HPC, Cloud and Enterprise markets, has been selected by the University of Toronto to provide custom liquid cooling for its new signal processing back-end which will support Canada's largest radio telescope, the Canadian Hydrogen Intensity Mapping Experiment (CHIME), a joint project between the National Research Council of Canada (NRC) and three major Universities, McGill, Toronto, and the University of British Columbia (UCB). Read further...
CoolIT Systems Inc., a global expert in energy efficient liquid cooling solutions for the HPC, Cloud and Enterprise markets, has been selected to manufacture a Closed-Loop DCLC liquid cooling device for the latest Hewlett Packard Enterprise (HPE) Apollo 2000 Trade and Match Server Solution. This overclocked HPE server benefits immensely from the installed CoolIT liquid system by enabling greater CPU performance for the Financial Services industry, where computing milliseconds are essential. Read further...
Scientific discovery requires investigations of extremely large amounts of data, which must be transported at a high level of performance among multiple distributed collaborator sites. The Pacific Research Platform (PRP) initiative is addressing the many challenges of such large-scale transport by implementing network architecture and technology not common on general networks. Read further...
At the 2016 Supercomputing Conference in Salt Lake City, Utah, Cray Inc. announced it has achieved acceptance for "Theta", the Cray XC40 supercomputer, as well as a Cray Sonexion 3000 storage system, located at the Argonne Leadership Computing Facility (ALCF), a U.S. Department of Energy Office of Science User Facility at Argonne National Laboratory. The Theta system marks Cray and Intel's first acceptance for a large-scale supercomputer featuring the latest generation of Intel Xeon Phi processors formerly code named "Knights Landing". Read further...
At the 2016 Supercomputing Conference in Salt Lake City, Utah, Cray Inc. has launched the Cray XC50 supercomputer - the company's fastest supercomputer ever with a peak performance of one petaflop in a single cabinet. Read further...
Cray Inc. has issued financial results for the third quarter ended September 30, 2016. All figures are based on U.S. GAAP unless otherwise noted. Revenue for the third quarter of 2016 was $77.5 million, which compares with $191.4 million in the third quarter of 2015. Net loss for the third quarter of 2016 was $23.0 million, or $0.58 per diluted share, compared to net income of $10.9 million, or $0.27 per diluted share in the third quarter of 2015. Non-GAAP net loss was $19.5 million, or $0.49 per diluted share for the third quarter of 2016, compared to non-GAAP net income of $19.5 million, or $0.48 per diluted share for the same period of 2015. Read further...
Mellanox Technologies Ltd., a supplier of high-performance, end-to-end interconnect solutions for data centre servers and storage systems, will showcase a Virtual Reality over 100Gb/s EDR InfiniBand demonstration at the Supercomputing Conference, November 14-17, Salt Lake City. Read further...
Mellanox Technologies Ltd., a supplier of high-performance, end-to-end interconnect solutions for data centre servers and storage systems, has introduced the world's first 200Gb/s data center interconnect solutions. Mellanox ConnectX-6 adapters, Quantum switches and LinkX cables and transceivers together provide a complete 200Gb/s HDR InfiniBand interconnect infrastructure for the next generation of high performance computing, machine learning, Big Data, Cloud, web 2.0 and storage platforms. These 200Gb/s HDR InfiniBand solutions maintain Mellanox's generation-ahead leadership while enabling customers and users to leverage an open, standards-based technology that maximizes application performance and scalability while minimizing overall data center total cost of ownership. Mellanox 200Gb/s HDR solutions will become generally available in 2017. Read further...
Tinier than the AIDS virus - that is currently the circumference of the smallest transistors. The industry has shrunk the central elements of their computer chips to fourteen nanometers in the last sixty years. Conventional methods, however, are hitting physical boundaries. An alternative could be the self-organisation of components from molecules and atoms. Scientists at HZDR and Paderborn University have now made an important advance: the physicists conducted a current through gold-plated nanowires, which independently assembled themselves from single DNA strands. Read further...
CoolIT Systems Inc., a global expert in energy efficient liquid cooling technologies for HPC, Cloud and Enterprise markets, is returning to the Supercomputing Conference 2016 (SC16) in Salt Lake City, Utah for the fifth consecutive year as an exhibitor and host of a Birds-of-a-Feather panel session. Read further...

Applications

This year the Dutch Data Prize goes to BoschDoc for humanities and social sciences, AHCODA-DB for medical and life sciences, and OpenML for exact and technical sciences. These prizes were awarded on November 9, 2016 by the chairman of the Dutch Data Prize 2016 jury, Prof. José van Dijck PhD, President of the Royal Netherlands Academy of Arts and Sciences. The winners went home with a Data Prize 2016 trophy and 5,000 euro to make their data set even more accessible. Read further...
What do you get when you cross an art form with something found in all living organisms? It may sound unusual, but DNA origami is something that has been explored in the scientific community for the last 10 years. DNA is a string of four nucleotide bases (A, T, G and C), each of which pairs only with one other base (A with T and G with C). In DNA origami, researchers take a long single strand of DNA - picture a ladder sawed in half vertically, and fold it into a shape using staple strands that have the corresponding bases. Everything from smiley faces to robots has been made using this method. While those are 2D, 3D shapes can also be made. Read further...
Cray Inc. has joined iEnergy, the rapidly growing exploration and production industry community brokered by Halliburton Landmark. iEnergy community members can now choose to run Landmark SeisSpace Seismic Processing Software on a Cray CS400 cluster supercomputer. Read further...
Researchers at CWI and AMC used large-scale computer simulations to discover how cell types work together to form new blood vessels. Understanding vascular growth is essential for understanding and manipulating processes such as tumour growth, wound healing, and a number of eye diseases. The results of the simulations were published in the online journalPLOS ONE. Read further...
Whether tracking climate patterns around the globe, improving aircraft safety or designing spacecraft to explore the mysteries of our galaxy, NASA is pushing the boundaries of science, discovery and technology for the benefit of humanity with help from its powerful supercomputers. Experts from five NASA centres and across the U.S. will present their latest research results and supercomputing achievements at SC16, the international high-performance computing conference, November 14-17 in Salt Lake City, Utah. Read further...
The same algorithms that personalize movie recommendations and extract topics from oceans of text could bring doctors closer to diagnosing, treating and preventing disease on the basis of an individual's unique genetic profile. In a study published on November 7 inNature Genetics, researchers at Columbia and Princeton universities describe a new machine-learning algorithm for scanning massive genetic data sets to infer an individual's ancestral make-up, which is key to identifying disease-carrying genetic mutations. Read further...
Despite steady progress in detection and treatment in recent decades, cancer remains the second leading cause of death in the United States, cutting short the lives of approximately 500,000 people each year. To better understand and combat this disease, medical researchers rely on cancer registry programs - a national network of organisations that systematically collect demographic and clinical information related to the diagnosis, treatment, and history of cancer incidence in the United States. The surveillance effort, coordinated by the National Cancer Institute (NCI) and the Centers for Disease Control and Prevention, enables researchers and clinicians to monitor cancer cases at the national, state, and local levels. Read further...
Dynamic programming is a technique that can yield relatively efficient solutions to computational problems in economics, genomic analysis, and other fields. But adapting it to computer chips with multiple "cores", or processing units, requires a level of programming expertise that few economists and biologists have. Read further...
Carbon, silicon, germanium, tin and lead are all part of a family that share the same structure of their outermost electrons, yet range from acting as insulators to semiconductors to metals.Is it possible to understand these and other trends within element families? InThe Journal of Chemical Physics, researchers describe probing the relationship between the structure - arrangement of atoms - and function - physical properties - of a liquid metal form of the element bismuth. Read further...
Based on computer simulations, astrophysicists at the University of Bern, Switzerland, conclude that the comet Chury did not obtain its duck-like form during the formation of our solar system 4.5 billion years ago. Although it does contain primordial material, they are able to show that the comet in its present form is hardly more than a billion years old. Read further...

TOP500

The 48th edition of the TOP500 list saw China and United States pacing each other for supercomputing supremacy. Both nations now claim 171 systems apiece in the latest rankings, accounting for two-thirds of the list. However, China has maintained its dominance at the top of the list with the same number 1 and 2 systems from six months ago: Sunway TaihuLight, at 93 petaflops, and Tianhe-2, at 34 petaflops. This latest edition of the TOP500 was announced on November 14, at the SC16 conference in Salt Lake City, Utah. Read further...
InfiniBand solutions were chosen in nearly four times more end-user projects in 2016 versus Omni-Path and five times more end-user projects versus other proprietary offerings as shown in the November release of the TOP500 list. This demonstrates an increase in both InfiniBand usage and market share. InfiniBand accelerates 65 percent of the total HPC systems on the list and 46 percent of the Petaflop infrastructures. Mellanox continues to connect the fastest supercomputer on the list, delivering highest scalability, performance and efficiency. Mellanox Ethernet solutions connect all of the 40 Gigabit Ethernet systems and the first 100 Gigabit Ethernet system. Read further...

The Cloud

In the coming months, SURFnet is set to sign contracts with eight providers that will provide Dutch education and research institutions with affordable and secure IaaS Cloud services. Amazon, CloudSigma, Dimension Data, Interoute Communications, KPN, Microsoft, NTT Europe and Vancis will all offer their Cloud services via SURFcumulus, SURFnet's hybrid IaaS service. Read further...

Primeur weekly 2016-11-14

Exascale supercomputing

Berkeley Lab to lead AMR co-design centre for DOE's Exascale Computing Project ...

Exascale Computing Project announces $48 million to establish Exascale co-design centres ...

US Exascale Computing Project awards $34 million for software development ...

Quantum computing

Breakthrough in the quantum transfer of information between matter and light ...

Focus on Europe

European Commission reveals its forthcoming call for energy efficient, high performance processors ...

World-leading HPC centres partner to form accelerated computing institute ...

Atos Bull to boost Dutch research at SURFsara with first Bull sequana supercomputer installed ...

Middleware

Allinea tools yield a 50% speed up for genome applications at the Earlham Institute ...

NERSC's 'Shifter' scales up to more than 9,000 Cori KNL processors ...

DDN's Big Data storage provides Aalto University ample capacity and fast access to vital research data ...

DDN unveils industry's fastest multi-level security Lustre solution ...

DDN delivers new burst buffer appliance and updates block and file appliances, completing total product line refresh ...

Atos Bull tackles storage bottlenecks for High Performance Computing ...

Cycle Computing debuts the newest version of its groundbreaking CycleCloud ...

Hardware

University of Toronto selects CoolIT Systems to liquid cool signal processor for CHIME project ...

CoolIT Systems optimizes Trade and Match solution with custom closed-loop liquid cooling ...

SDSC to host high-speed, large data transfer experiment at SC16 Show ...

Cray XC40 "Theta" supercomputer accepted at Argonne National Laboratory ...

Cray launches next-generation supercomputer: the Cray XC50 ...

Cray reports third quarter 2016 financial results ...

Mellanox drives Virtual Reality to new levels with breakthrough performance ...

Mellanox announces 200Gb/s HDR InfiniBand solutions enabling record levels of performance and scalability ...

Computers made of genetic material? ...

CoolIT Systems to showcase best-in-class HPC liquid cooling offering at SC16 ...

Applications

BoschDoc, AHCODA-DB and OpenML winners of the Data Prize 2016 ...

Blue Waters simulates largest membrane channel made of DNA origami ...

Cray joins iEnergy, the oil and gas industry's foremost community for exploration and production ...

Large-scale computer simulations reveal biological growth processes ...

NASA science and technology advancements demonstrated at Supercomputing Conference ...

Unlocking big genetic datasets ...

Accelerating cancer research with deep learning ...

System opens up high-performance programming to non-experts ...

Studying structure to understand function within 'material families' ...

Chury is much younger than previously thought ...

TOP500

Global supercomputing capacity creeps up as Petascale systems blanket Top 100 ...

InfiniBand chosen by nearly 4x more end-users versus proprietary offerings in 2016 as shown on the TOP500 supercomputers list ...

The Cloud

SURFnet selects eight Cloud providers for Dutch education and research ...