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Development of ISO connection-oriented/correctionless gateways

The project had two goals, establishment of a gateway between French and U.S. academic networks and studies of issues related to the development of ISO connection-oriented/connectionless (CO/CL) gateways. The first component involved installation of a 56K bps line between Princeton Univ. and INRIA in France. The end-points of these lines were connected by Vitalink link level bridges. The Princeton end was then connected to the NSFNET via the John Von Neumann Supercomputer Center. The French end was connected to Transpac, the French X.25 public data network and to the French IP research internet. U.S. users may communicate with users of the French internet by e-mail and may access computational and data resources in France by use of remote login and file transfer. The connection to Transpac enables U.S. users to access the SIMBAD astronomical database outside of Paris. Access to this database from the U.S. can be via TCP/IP or DECNET (via a DECNET to TCP/IP gateway) protocols utilizing a TCP/IP to X.25 gateway developed and operated by INRIA. The second component of the project involved experiments aimed at understanding the issues involved is ISO CO/CL gateways. An experimental gateway was developed at Wisconsin and a preliminary report was prepared. Because of the need to devote most resources to the first component of the project, work in this area did not go beyond development of a prototype gateway.

Landweber, Lawrence H.↗

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing. The PRIMA Project

The growing number of cores provided by today’s high-­end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Juelich Supercomputing Centre of Forschungszentrum Juelich (FZJ) develop the performance analysis tools TAU and Scalasca, respectively, which allow high-­performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensively across HPC centers in the U.S., Germany, and around the world. The TAU and Scalasca groups share a heritage of parallel performance tool research and partnership throughout the past fifteen years. Indeed, the close interactions of the two groups resulted in a cross-­fertilization of tool ideas and technologies that pushed TAU and Scalasca to what they are today. It also produced two performance systems with an increasing degree of functional overlap. While each tool has its specific analysis focus, the tools were implementing measurement infrastructures that were substantially similar. Because each tool provides complementary performance analysis, sharing of measurement results is valuable to provide the user with more facets to understand performance behavior. However, each measurement system was producing performance data in different formats, requiring data interoperability tools to be created. A common measurement and instrumentation system was needed to more closely integrate TAU and Scalasca and to avoid the duplication of development and maintenance effort. The PRIMA (Performance Refactoring of Instrumentation, Measurement, and Analysis) project was proposed over three years ago as a joint international effort between UO and FZJ to accomplish these objectives: (1) refactor TAU and Scalasca performance system components for core code sharing and (2) integrate TAU and Scalasca functionality through data interfaces, formats, and utilities. As presented in this report, the project has completed these goals. In addition to shared technical advances, the groups have worked to engage with users through application performance engineering and tools training. In this regard, the project benefits from the close interactions the teams have with national laboratories in the United States and Germany. We have also sought to enhance our interactions through joint tutorials and outreach. UO has become a member of the Virtual Institute of High-­Productivity Supercomputing (VI-­HPS) established by the Helmholtz Association of German Research Centres as a center of excellence, focusing on HPC tools for diagnosing programming errors and optimizing performance. UO and FZJ have conducted several VI-­HPS training activities together within the past three years.

97 MATHEMATICS AND COMPUTING↗

Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations

The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CRADA Final Report: Weld Predictor App

Welding is an important manufacturing process used in a broad range of industries and market sectors, including automotive, aerospace, heavy manufacturing, medical, and defense. During welded fabrication, high localized heat input and subsequent rapid cooling result in the creation of residual stresses and distortion. These residual stresses can significantly affect the fatigue resistance, cracking behavior, and load-carrying capacity of welded structures during service. Further, additional fitting and tacking time is often required to fit distorted subassemblies together, resulting in non-value added cost. Using trial-and-error methods to determine which welding parameters, welding sequences, and fixture designs will most effectively reduce distortion is a time-consuming and expensive process. For complex structures with many welds, this approach can take several months. For this reason, efficient and accurate methods of mitigating distortion are in-demand across all industries where welding is used. Analytical and computational methods and commercial software tools have been developed to predict welding-induced residual stresses and distortion. Welding process parameters, fixtures, and tooling can be optimized to reduce the HAZ softening and minimize weld residual stress and distortion, improving performance and reducing design, fabrication and testing costs. However, weld modeling technology tools are currently accessible only to engineers and designers with a background in finite element analysis (FEA) who work with large manufacturers, research institutes, and universities with access to high-performance computing (HPC) resources. Small and medium enterprises (SMEs) in the US do not typically have the human and computational resources needed to adopt and utilize weld modeling technology. To allow an engineer with no background in FEA and SMEs to gain access to this important design tool, EWI and the Ohio Supercomputer Center (OSC) developed the online weld application software tool “WeldPredictor” ( https://eweldpredictor.ewi.org ). About 1400 users have tested this application. This project marked the beginning of development on the next version of WeldPredictor that addresses many outstanding features of the original, including 3D models, allow more material hardening laws, model material phase transformation, and uses open source finite element solvers to quickly solve problems (as opposed to expensive commercial tools).

42 ENGINEERING↗

Computational Aeroscience at NAS and Future Trends in High Performance Computing

NASA's Numerical Aerodynamic Simulation (NAS) program provides a unique world class supercomputing capability which is readily accessed by the U.S. aeronautics community and offers them the opportunity to perform high speed computations and simulations for a broad range of aerospace research applications. In addition, the NAS program performs on-going research and advanced technology development to ensure the innovative application of newly emerging technologies to computational fluid dynamics and other important aeroscience disciplines. The NAS system and its interaction with industry are described. Furthermore, the results of an analysis of current and future technologies and their potential impact on high performance computing are also presented.

Cooper, David M.↗

Exploring Electric Polarization Mechanisms in Multiferroic Oxides

Multiferroic oxides are a class of systems which exhibit coupling between the electrical polarization and the magnetization. These materials show promise to lead to devices in which ferromagnetic memory can be written with magnetic fields or magnetic bits can be written by an electric field. The work conducted in our research focuses on single phase materials. We studied the detailed coupling of the spin and lattice correlations in these systems. In the first phase of the proposal, we explored the complex spin spiral systems and low temperature behavior of hexagonal layered REMnO 3 (RE= rare earth, Y and Sc) system following the detailed structural changes which occurred on crossing into the magnetic states. The techniques were applied to other layered materials such as superconductors and thermoelectric where the same layered motif exists. The second phase of the proposal focused on understanding the mechanisms involved in the onset high temperature ferroelectricity ion hexagonal REMnO 3 and at low temperature in E-Type magnetic ordered perovskite REMnO 3 . We wsynthesized preovskite small A site multiferroics by high pressure and high temperature methods. Detailed measurement of the structural properties and dynamics were conducted over a range of length scales from atomic to mesoscopic scale using, x-ray absorption spectroscopy, x-ray diffuse scattering, x-ray and neutron pair distribution analysis and high resolution x-ray diffraction. Changes in vibration modes which occur with the onset of polarization were probed with temperature and pressure dependent infrared absorption spectroscopy. In addition the orthorhombic system (small radius RE ions) which is believed to exhibit electronically driven ferroelectricity and is also not understood was examined. The multiple length scale synchrotron based measurements may assist in developing more detailed models of these materials and possibly lead to device applications. The experimental work was complemented by density functional methods to determine the magnetic ground states and ab initio molecular dynamics methods (AIMD) to determine the high temperature structures. Simulation were carried out on supercomputers at the National Energy Research Scientific Computing Center (NERSC). An important contribution of this work was the training of graduate students and postdoctoral researchers in materials synthesis, high pressure methods and synchrotron based spectroscopy and x-ray scattering techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Job Management with mpi_jm

About this book: This book constitutes the refereed post-conference proceedings of 13 workshops held at the 33rd International ISC High Performance 2018 Conference, in Frankfurt, Germany, in June 2018: HPC I/O in the Data Center, HPC-IODC 2018; Workshop on Performance and Scalability of Storage Systems, WOPSSS 2018; 13th Workshop on Virtualization in High­-Performance Cloud Computing, VHPC 2018; Third International Workshop on In Situ Visualization, WOIV 2018; 4th International Workshop on Communication Architectures for HPC, Big Data, Deep Learning and Clouds at Extreme Scale, ExaComm 2018; International Workshop on OpenPOWER for HPC, IWOPH 2018; IXPUG Workshop: Many-Core Computing on Intel Processors; Workshop on Sustainable Ultrascale Computing Systems; Approximate and Transprecision Computing on Emerging Technologies, ATCET 2018; First Workshop on the Convergence of Large-Scale Simulation and Artificial Intelligence; Third Workshop for Open Source Supercomputing, OpenSuCo 2018; First Workshop on Interactive High-Performance Computing; Workshop on Performance Portable Programming Models for Accelerators, P^3MA 2018. The 53 full papers included in this volume were carefully reviewed and selected from 80 submissions. They cover all aspects of research, development, and application of large-scale, high performance experimental and commercial systems. Topics include HPC computer architecture and hardware; programming models, system software, and applications; solutions for heterogeneity, reliability, power efficiency of systems; virtualization and containerized environments; big data and cloud computing; and artificial intelligence.

Berkowitz, Evan↗

3-D Deformable Grid Electomagnetic PIC for Parallel Computers

We have developed a three-dimensional non-orthogonal grid electromagnetic PIC code for parallel supercomputers. The numerical formulation is based on hexahedral cells which are logically connected cubic cells but distorted to body-fit complex geometries in physical space. An outstanding area of research is to improve the accuracy of the electromagnetic field solve on distorted meshes.

3D deformable non-orthogonal grid code PIC codes p↗

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.

59 BASIC BIOLOGICAL SCIENCES↗

Los Alamos works on a biologically realistic computer network

Brain neuroscientists and computer scientists call this field neuromimetic computing—building computers inspired by how the cerebral cortex of the brain works. Its cortical processes rely on billions of small biological “switches,” called neurons. To learn, they store and process information. Using an approach called neural networks, researchers are developing computers that simulate neurons and their interconnections. Then computers can learn about their surroundings, interpret data, and make predictions based on it. In practice, however, researchers attempting to simulate neural processing at anything close to the scale and complexity of the brain’s cortical circuits have been stymied by limitations on computer memory and computational power. All that has changed with the new Trinity supercomputer at Los Alamos, which became fully operational in mid-2017. Trinity has unique capabilities designed for the stockpile stewardship mission, which includes highly complex nuclear simulations that have replaced the testing of nuclear weapons. All this capability means Trinity allows a fundamentally different approach to large-scale cortical simulations, enabling an unprecedented leap in the ability to model neural processing. To test that capability on a limited-scale problem, computer scientists and neuroscientists at Los Alamos created a “sparse prediction machine” that runs on a neural network on Trinity. A sparse prediction machine is designed to work like the brain: researchers expose it to data—in this case, various videos of a car driving down a road—without labeling the data in any way. Then the program sorts through that data frame by frame, focuses on the important information, and develops a prediction about the car’s motion. With Trinity’s power, the Los Alamos team simulates the way a brain handles information in its neurons but uses the fewest neurons at any given moment to explain the information at hand. That’s the “sparse” part, and it makes the brain very efficient—and, hopefully, a computer more efficient, too.

97 MATHEMATICS AND COMPUTING↗

FOX: A Fault Oblivious Extreme-Scale Execution Environment

The FOX project, funded under the ASCR X-stack I program, developed systems software and runtime libraries for a new approach to the data and work distribution for massively parallel, fault oblivious application execution. Our work was motivated by the premise that exascale computing systems will provide a thousand-fold increase in parallelism and a proportional increase in failure rate relative to today’s machines. To deliver the capability of exascale hardware, the systems software must provide the infrastructure to support existing applications while simultaneously enabling efficient execution of new programming models that naturally express dynamic, adaptive, irregular computation; coupled simulations; and massive data analysis in a highly unreliable hardware environment with billions of threads of execution. Our OS research has prototyped new methods to provide efficient resource sharing, synchronization, and protection in a many-core compute node. We have experimented with alternative task/dataflow programming models and shown scalability in some cases to hundreds of thousands of cores. Much of our software is in active development through open source projects. Concepts from FOX are being pursued in next generation exascale operating systems. Our OS work focused on adaptive, application tailored OS services optimized for multi → many core processors. We developed a new operating system NIX that supports role-based allocation of cores to processes which was released to open source. We contributed to the IBM FusedOS project, which promoted the concept of latency-optimized and throughput-optimized cores. We built a task queue library based on distributed, fault tolerant key-value store and identified scaling issues. A second fault tolerant task parallel library was developed, based on the Linda tuple space model, that used low level interconnect primitives for optimized communication. We designed fault tolerance mechanisms for task parallel computations employing work stealing for load balancing that scaled to the largest existing supercomputers. Finally, we implemented the Elastic Building Blocks runtime, a library to manage object-oriented distributed software components. To support the research, we won two INCITE awards for time on Intrepid (BG/P) and Mira (BG/Q). Much of our work has had impact in the OS and runtime community through the ASCR Exascale OS/R workshop and report, leading to the research agenda of the Exascale OS/R program. Our project was, however, also affected by attrition of multiple PIs. While the PIs continued to participate and offer guidance as time permitted, losing these key individuals was unfortunate both for the project and for the DOE HPC community.

97 MATHEMATICS AND COMPUTING↗

Modeling I/O Performance Variability Using Conditional Variational Auto Encoders

Storage system performance modeling is crucial for efficient use of heterogeneous shared resources on leadership class computers. Variability in application performance, particularly variability arising from concurrent applications sharing I/O resources, is a major hurdle in the development of accurate performance models. We adopt a deep learning approach based on conditional variational auto encoders (CVAE) for I/O performance modeling, and use it to quantify performance variability. We illustrate our approach using the data collected on Edison, a production supercomputing system at the National Energy Research Scientific Computing Center (NERSC). The CVAE approach is investigated by comparing it to a previously proposed sensitivity-based Gaussian process (GP) model. We find that the CVAE model performs slightly better than the GP model in cases where training and testing data come from different applications, since CVAE can inherently leverage the whole data from multiple applications whereas GP partitions the data and builds separate models for each partition. Hence, the CVAE offers an alternative modeling approach that does not need preprocessing; it has enough flexibility to handle data from a wide variety of applications without changing the inference approach.

I/O perfornance variability↗

Computer Simulation of Aircraft Aerodynamics

The role of Ames Research Center in conducting basic aerodynamics research through computer simulations is described. The computer facilities, including supercomputers and peripheral equipment that represent the state of the art, are described. The methodology of computational fluid dynamics is explained briefly. Fundamental studies of turbulence and transition are being pursued to understand these phenomena and to develop models that can be used in the solution of the Reynolds-averaged Navier-Stokes equations. Four applications of computer simulations for aerodynamics problems are described: subsonic flow around a fuselage at high angle of attack, subsonic flow through a turbine stator-rotor stage, transonic flow around a flexible swept wing, and transonic flow around a wing-body configuration that includes an inlet and a tail.

Inouye, Mamoru↗

CFD-Guided Combustion System Optimization of a Gasoline Range Fuel in a Heavy-Duty Compression Ignition Engine Using Automatic Piston Geometry Generation and a Supercomputer

A computational fluid dynamics (CFD) guided combustion system optimization was conducted for a heavy-duty diesel engine running with a gasoline fuel that has a research octane number (RON) of 80. The goal was to optimize the gasoline compression ignition (GCI) combustion recipe (piston bowl geometry, injector spray pattern, in-cylinder swirl motion, and thermal boundary conditions) for improved fuel efficiency while maintaining engine-out NO x within a 1-1.5 g/kW-hr window. The numerical model was developed using the multi-dimensional CFD software CONVERGE. A two-stage design of experiments (DoE) approach was employed with the first stage focusing on the piston bowl shape optimization and the second addressing refinement of the combustion recipe. For optimizing the piston bowl geometry, a software tool, CAESES, was utilized to automatically perturb key bowl design parameters. This led to the generation of 256 combustion chamber designs evaluated at several engine operating conditions. The second DoE campaign was conducted to optimize injector spray patterns, fuel injection strategies and in-cylinder swirl motion for the best performing piston bowl designs from the first DoE campaign. This comprehensive optimization study was performed on a supercomputer, Mira, to accelerate the development of an optimized fuel-efficiency focused design. Compared to the production combustion system in the baseline engine, the new combustion recipe from this study showed significantly improved closed-cycle fuel efficiency across key engine operating points while meeting the engine-out NO x targets. Optimized piston bowl designs and injector spray patterns were predicted to provide enhanced in-cylinder air utilization and more rapid mixing-controlled combustion, thereby leading to a fuel efficiency improvement. In addition, shifting the engine thermal boundary conditions toward leaner operation was also key to the improved fuel efficiency.

33 ADVANCED PROPULSION SYSTEMS↗

Impact of I/O and Data Management in Ensemble Large Scale Climate Forecasting Using EC-Earth3

The EC-Earth climate model is a seamless Earth System Model (ESM) used to carry out climate research in 24 academic institutions and meteorological services from 11 countries in Europe. This model couples several components and it is continuously under development. In this work we present a study regarding the impact of the I/O and data management when using EC-Earth in well-known supercomputing environments. Most large-scale and long-term climate simulators have been developed bearing in mind the paramount importance of its scalability. However, the computational capabilities of the High Performance Computing (HPC) environments increase at so great speed that it is almost impossible to re-implement the whole models so that they are able to exploit efficiently the new features. Therefore, it is necessary to design different strategies to take advantage of them. In this work we present an operational framework to run ensemble simulations in HPC platforms. A set of experiments are presented in order to validate the suitability of this technique. Moreover, the derived impact regarding the I/O and data management aspects is analyzed.

97 MATHEMATICS AND COMPUTING↗

Center for Computing Research Highlights

Sandia has a legacy of leadership in the advancement of high performance computing (HPC) at extreme scales. First-of-a-kind scalable distributed-memory parallel platforms such as the Intel Paragon, ASCI Red (the world’s first teraflops computer), and Red Storm (co-developed with Cray) helped form the basis for one of the most successful supercomputer product lines ever: the Cray XT series. Sandia also has pioneered system software elements—including lightweight operating systems, the Portals network programming interface, advanced interconnection network designs, and scalable I/O— that are critical to achieving scalability on large computing systems.

97 MATHEMATICS AND COMPUTING↗

SIMBER: the Simula Berkeley Education and Research Collaboration (CRADA Final Report)

The SIMBER project is centered around advancing the state-of-the-art in the science of modelling of the human heart and leveraging the collaborations between leading research groups at the University of California Berkeley (UC Berkeley), the Lawrence Berkeley National Laboratory (Berkeley Lab), and Simula Research Laboratory (Simula). In particular, the following areas of expertise are shared and expanded through this project: “heart-on-chip” experimental systems from UC Berkeley, mathematical modelling of the heart from Simula, and supercomputing software from Simula and Berkeley Lab. This intersection of expertise is already enabling the development of novel tools and knowledge that produce more accurate models of the human heart in both health and disease, which in turn are leading to drug screening technologies that make cardiac drug development faster, cheaper and more humane.

Li, Xiaoye Sherry [Lawrence Berkeley National Labo↗

Automated Discovery for Emulytics

Sandia has an extensive background in cybersecurity research and is currently extending its state-of-the-art modeling via emulation capability. However, a key part of Sandia's modeling methodology is the discovery and specification of the information-system under study, and the ability to recreate that specification with the highest fidelity possible in order to extrapolate meaningful results. This work details a method to conduct information system discovery and develop tools to enable the creation of high-fidelity emulation models that can be used to enable assessment of our infrastructure information system security posture and potential system impacts that could result from cyber threats. The outcome are a set of tools and techniques to go from network discovery of operational systems to emulating complex systems. As a concrete usecase, we have applied these tools and techniques at Supercomputing 2016 to model SCinet, the world's largest research network. This model includes five routers and nearly 10,000 endpoints which we have launched in our emulation platform.

97 MATHEMATICS AND COMPUTING↗