2011 Annual Report Ernest Orlando Lawrence Berkeley National Laboratory 1 Cyclotron Road, Berkeley, CA 94720-8148
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Complexed Adsorbed H3 L2 L7 H3 HP1 HP1 L2 L7 National Energy Research Scientific Computing Center 2011 Annual Report Ernest Orlando Lawrence Berkeley National Laboratory 1 Cyclotron Road, Berkeley, CA 94720-8148 This work was supported by the Director, Office of Science, Office of Advanced Scientific Computing Research of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. National Energy Research Scientific Computing Center 2011 Annual Report Table of Contents 6 The Year in Perspective 10 Research News 10 New Mathematical Method Reveals Where Genes Switch On or Off 12 Small Particles Have Big Impact 14 Detailed Model Changes View of Ancient Climate Change 16 A Better Way to Find Extreme Weather Events in Climate Modeling Data 18 Turning Grass into Gas for Less 20 Bubbles Help Break Energy Storage Record for Lithium–Air Batteries 22 New Anode Boosts Capacity of Lithium–Ion Batteries 24 Speeding Up Design of Organic Semiconductors 26 Solving the Mystery of LED “Droop” 28 Modeling the Bonds of Iron and Water 30 Discovering the Molecular Details of CO2 Reservoirs 32 Simulating Magnetic Instabilities in NSTX and ITER 34 Fusion PIC Code Optimization on Emerging Architectures 36 Proton Dripping Tests a Basic Force of Nature 38 Heaviest Antimatter Particle Detected with NERSC Help 40 Boosting the Next Wave of Accelerators 42 Supernova Caught in the Act Reveals First Direct Evidence of Its Progenitor System 44 Solar System’s Magnetic Edge More Turbulent Than Expected 46 Measuring the Distant Universe in 3D 48 NISE Program Encourages Innovative Research 52 Nobel Prize for Physics Leads List of Honors for NERSC Users in 2011 Table of Contents 5 54 The NERSC Center 54 Innovations 54 Petaflops Power to NERSC 56 Accelerating Advanced Materials Development 57 Supporting Diverse Workloads on HPC Platforms 59 Increasing Scientific Productivity by Tracking Data 60 Safeguarding Data with Parallel Incremental Backups 61 Data Transfer Nodes Facilitate Scientific Collaborations 62 Increasing NERSC’s Energy Efficiency 64 User Support and Outreach 64 Providing Rapid, Quality Front-Line User Support 65 NERSC Users Welcome Expanded Training Efforts 65 Comparing Compilers to Improve Code Performance 66 Learning How to Use Hopper’s Multi-Core Nodes Effectively 66 Facilitating Statistical Computing and Graphics Generation with Parallel R 67 Visualizing Electronic Structures from Quantum Monte Carlo Simulations 67 Improving Access to X-Windows-Based Tools and Applications 68 Improving the Efficiency of a User Code 69 Improving Account Support 69 Providing Comprehensive Support for an ALCC Project 70 Software Support for Third-Party Applications 71 New Website Makes Information More Easily Accessible 72 Research and Development by NERSC Staff 72 Magellan Answers Questions about Cloud Computing for Science 74 X-Ray Image Bank Open for Business 74 NERSC Staff Publications 82 Appendix A: NERSC User Statistics 84 Appendix B: NERSC Users Group Executive Committee 85 Appendix C: Office of Advanced Scientific Computing Research 86 Appendix D: Advanced Scientific Computing Advisory Committee 87 Appendix E: Acronyms and Abbreviations 6 NERSC 2011 Annual Report The Year in Perspective The year 2011 was unprecedented for scientific The year ended with the preparation of an in-depth report accomplishments at NERSC. Taking center stage was analyzing the results of our Magellan research effort on our support of cosmology. In October, Berkeley Lab’s cloud computing, which showed that NERSC’s HPC Saul Perlmutter was awarded the Nobel Prize in Physics systems substantially outperform standard commercial for his research that found that the Universe is continuing clouds in both runtime and cost while offering unique to expand and that the rate of expansion is gradually software and expertise for scientific computing. accelerating. A key component of this work was the simulation of 10,000 supernovae on NERSC supercomputers While these selected highlights illustrate the breadth of the a decade ago. And Peter Nugent, who performed those NERSC Center’s systems and support expertise, running simulations, made headlines around the world in August large-scale simulations day in and day out is the bread and when he discovered the closest supernova to Earth in 25 butter of NERSC computing. Over 40 percent of the time years, just as the star was beginning its explosive demise. used by jobs are spread over at least one eighth of the machine. Such capability jobs take advantage of the unique Our center again proved its leadership in scientific networks in these systems. At the same time, NERSC offers computing by moving Hopper, our first petaflops system, this singular capability to university researchers, who make into production and supporting a broad range of research up 65 percent of our users and typically don’t have access programs. Meanwhile, plans for the NERSC-7 system got to similar resources at their own institutions. underway, and NERSC staff, in collaboration with DOE program managers and users, completed the last of six Large-scale simulation is the foundation of computing workshops to map out future computing requirements for at NERSC, but we are seeing a move toward scientific the program offices in the Office of Science. The bottom workflows with very large numbers of jobs and data analysis line indicates that demand for NERSC computing is 10 involving massive datasets. To help people understand times greater than the resources we expect to have NERSC’s role in these ongoing and complex changes, I’ve available in the next few years. recently been discussing three trends: “science at scale,” “science through volume” and “science in data.” And as One way that NERSC is leveraging its resources to serve described below, these three trends are closely intertwined. a broader community is by building “science gateways” 2011 saw huge growth in science through volume and to share both results and raw data with other researchers. science in data. This annual report provides examples of Of particular note in 2011 was the launch of the Materials NERSC’s contributions to all three trends. Project, which is a “Google of material properties” and is being shared with industry and academia. The Materials Science at Scale Project database currently contains the structural and energetic properties of more than 28,000 inorganic Science at scale is what supercomputers are best known compounds, and up to hundreds more are added every for—using thousands of processor cores to perform massive day. This gateway opens the door for more research in calculations that simulate complex phenomena. These support of the Materials Genome Initiative announced simulations can lead to new understanding and even the by the White House in June 2011. discovery of new phenomena. The Year in Perspective 7 Large-scale simulations can also challenge long-held codes effectively on Hopper’s multi-core nodes. Berkeley assumptions. One example is modeling of an event that Lab’s Computational Research and Theory Facility will be coincided with the abrupt climate change that took place the most energy efficient computing facility in DOE, about 8,200 years ago, when a massive ice sheet that capable of supporting two exascale systems. covered much of Hudson Bay in arctic Canada melted and broke through an ice dam, suddenly dumping thousands Science through Volume of cubic kilometers of fresh water into the Atlantic Ocean. Geoscientists had assumed that this flood covered the Unlike science at scale, which involves small numbers surface of the Labrador and Greenland Seas, slowing the of heroically large simulations, science through volume Gulf Stream and ocean convection. But a new model, which involves large numbers—up to tens of thousands—of has 10 to 20 times higher resolution than previous models smaller jobs, sometimes referred to as high-throughput and runs on 1,800 computer cores, suggests the freshwater computing. At NERSC, research groups in several science flood actually flowed much farther south on the continental domains are using high-throughput computing to create shelf into the subtropical North Atlantic. This finding, large databases that serve as public resources for bolstered by observational evidence, challenges not just researchers. As noted above, one such database is used our understanding of ancient climate change but also the for screening properties of materials. assumptions built into ocean and sea ice models that we use to project our future climate. New materials are crucial to building a clean energy economy—for everything from batteries to photovoltaics An example of how science at scale can guide experimentation to lighter weight vehicles—but today the development is the discovery of fluorine-14, an exotic, short-lived nucleus cycle is too slow: around 18 years from conception to that was first predicted in simulations and then detected commercialization. To cut this gap in half, researchers experimentally, increasing our understanding of the strong from Berkeley Lab and MIT teamed up to develop a new force. The simulation of fluorine-14 was made possible by computational screening tool, called the Materials Project, decades of code development and optimization of the which was launched in October 2011 using NERSC’s science code to improve performance and mathematical precision gateway infrastructure. The team is using NERSC systems on petascale computers. to characterize the properties of inorganic compounds, such as their stability, voltage, capacity and oxidation state. Today, petascale computers—capable of 1 quadrillion (1015) The results are then organized into a database with a floating point operations per second (flops)—are state of user-friendly web interface that gives the entire research the art. But NERSC is collaborating to research the path to community free and easy access and search capabilities. exascale—1 quintillion (1018) flops—which we hope to see The purpose is not designing materials, but picking the within the next decade. NERSC will help vendors transition interesting ones for more detailed research.