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At least 1,657 records · Page 92

Information Management for a Large Multidisciplinary Project

In 1989, NASA's Langley Research Center (LaRC) initiated the High-Speed Airframe Integration Research (HiSAIR) Program to develop and demonstrate an integrated environment for high-speed aircraft design using advanced multidisciplinary analysis and optimization procedures. The major goals of this program were to evolve the interactions among disciplines and promote sharing of information, to provide a timely exchange of information among aeronautical disciplines, and to increase the awareness of the effects each discipline has upon other disciplines. LaRC historically has emphasized the advancement of analysis techniques. HiSAIR was founded to synthesize these advanced methods into a multidisciplinary design process emphasizing information feedback among disciplines and optimization. Crucial to the development of such an environment are the definition of the required data exchanges and the methodology for both recording the information and providing the exchanges in a timely manner. These requirements demand extensive use of data management techniques, graphic visualization, and interactive computing. HiSAIR represents the first attempt at LaRC to promote interdisciplinary information exchange on a large scale using advanced data management methodologies combined with state-of-the-art, scientific visualization techniques on graphics workstations in a distributed computing environment. The subject of this paper is the development of the data management system for HiSAIR.

Kennie H Jones↗

Experiences readying applications for Exascale

The advent of Exascale computing invites an assessment of existing best practices for developing application readiness on the world's largest supercomputers. This work details observations from the last four years in preparing scientific applications to run on the Oak Ridge Leadership Computing Facility's (OLCF) Frontier system. This paper addresses a range of topics in software including programmability, tuning, and portability considerations that are key to moving applications from existing systems to future installations. A set of representative workloads provides case studies for general system and software testing. We evaluate the use of early access systems for development across several generations of hardware. Finally, we discuss how best practices were identified and disseminated to the community through a wide range of activities including user-guides and trainings. We conclude with recommendations for ensuring application readiness on future leadership computing systems.

Gottiparthi, Kalyan↗

ESnet-JLab FPGA Accelerated Transport (data plane) [EJFAT (udplb)] v1.0

The ESnet-JLab FPGA Accelerated Transport system is a solution for streaming high-speed scientific measurement data from Data Acquisition Systems (DAQs) to high-performance computing facilties. It is generally compatible with many science workflows, and makes no assumptions about the specifics of any particular experiment. This program (udplb) implements the data plane portion of the EJFAT system. It is an FPGA design that rewrites and forwards data packets from a UDP-based scientific workflow to high-performance compute nodes. It depends on another program (udplbd, disclosed separately) to implement the control system.

Bengough, Peter [Malleable Networks, Inc.]↗

Anomaly detection in scientific data using joint statistical moments

We propose an anomaly detection method for multi-variate scientific data based on analysis of high-order joint moments. Using kurtosis as a reliable measure of outliers, we suggest that principal kurtosis vectors, by analogy to principal component analysis (PCA) vectors, signify the principal directions along which outliers appear. The inception of an anomaly, then, manifests as a change in the principal values and vectors of kurtosis. Obtaining the principal kurtosis vectors requires decomposing a fourth order joint cumulant tensor for which we use a simple, computationally less expensive approach that involves performing a singular value decomposition (SVD) over the matricized tensor. We demonstrate the efficacy of this approach on synthetic data, and develop an algorithm to identify the occurrence of a spatial and/or temporal anomalous event in scientific phenomena. The algorithm decomposes the data into several spatial sub-domains and time steps to identify regions with such events. Feature moment metrics, based on the alignments of the principal kurtosis vectors, are computed at each sub-domain and time step for all features to quantify their relative importance towards the overall kurtosis in the data. Accordingly, spatial and temporal anomaly metrics for each sub-domain are proposed using the Hellinger distance of the feature moment metric distribution from a suitable nominal distribution. Finally, we apply the algorithm to two turbulent auto-ignition combustion cases and demonstrate that the anomaly metrics reliably capture the occurrence of auto-ignition in relevant spatial sub-domains at the right time steps.

97 MATHEMATICS AND COMPUTING↗

Roadmap on methods and software for electronic structure based simulations in chemistry and materials

This Roadmap article provides a succinct, comprehensive overview of the state of electronic structure methods and software for molecular and materials simulations. Seventeen distinct sections collect insights by 51 leading scientists in the field. Each contribution addresses the status of a particular area, as well as current challenges and anticipated future advances, with a particular eye towards software related aspects and providing key references for further reading. Foundational sections cover density functional theory and its implementation in real-world simulation frameworks, Green's function based many-body perturbation theory, wave-function based and stochastic electronic structure approaches, relativistic effects and semiempirical electronic structure theory approaches. Subsequent sections cover nuclear quantum effects, real-time propagation of the electronic structure, challenges for computational spectroscopy simulations, and exploration of complex potential energy surfaces. The final sections summarize practical aspects, including computational workflows for complex simulation tasks, the impact of current and future high-performance computing architectures, software engineering practices, education and training to maintain and broaden the community, as well as the status of and needs for electronic structure based modeling from the vantage point of industry environments. Overall, the field of electronic structure software and method development continues to unlock immense opportunities for future scientific discovery, based on the growing ability of computations to reveal complex phenomena, processes and properties that are determined by the make-up of matter at the atomic scale, with high precision.

36 MATERIALS SCIENCE↗

Federated Access from DOE Labs to Distributed Storage in the EIC Era of Computing

The Electron Ion Collider (EIC) collaboration and future experiment is a unique scientific ecosystem within Nuclear Physics as the experiment starts right off as a crosscollaboration between Brookhaven National Lab (BNL) & Jefferson Lab (JLab). As a result, this muti-lab computing model tries at best to provide services accessible from anywhere by anyone who is part of the collaboration. While the computing model for the EIC is not finalized, it is anticipated that the computational and storage resources will be made accessible to a wide range of collaborators across the world. The use of federated ID seems to be a critical element to the strategy of providing such services, allowing seamless access to each lab site computing resources. However, providing Federated access to a Federated storage is not a trivial matter and has its share of technical challenges. In this contribution, we focus on the steps we took towards the deployment of a distributed object storage system that integrates with Amazon S3 and Federated ID. We will first cover for and explain the first stage storage solutions provided to the EIC during the detector design phase. Our initial test deployment consisted of Lustre storage using MinIO, hence providing an S3 interface. High Availability load balancers were added later to provide the initial scalability it lacked. Performance of that system will be shown. While this embryonic solution worked well, it had many limitations. Looking ahead, the Ceph object storage is considered a top-of-the-line solution in the storage community - since the Ceph Object Gateway is compatible with the Amazon S3 API out of the box, our next phase will use a native S3 storage. Our Ceph deployment will consist of erasure coded storage nodes to maximize storage potential along with multiple Ceph Object Gateways for redundant access. We will compare performance of our next stage implementations. Finally, we will present how to leverage OpenID Connect with the Ceph Object Gateway’s to enable Federated ID access. We hope this contribution will serve the community needs as we move forward with cross-lab collaborations and the need for Federated ID access to distributed compute facilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Enabling On-Demand Scientific Workflows on a Federated Cloud

The Fermilab Grid and Cloud Computing Department and the KISTI Global Science experimental Data hub Center are working on a multi-year Collaborative Research and Development Agreement.With the knowledge developed in the first year on how to provision and manage a federation of virtual machines through Cloud management systems. In this second year, we expanded the work on provisioning and federation, increasing both scale and diversity of solutions, and we started to build on-demand services on the established fabric, introducing the paradigm of Platform as a Service to assist with the execution of scientific workflows. We have enabled scientific workflows of stakeholders to run on multiple cloud resources at the scale of 1,000 concurrent machines. The demonstrations have been in the areas of (a) Virtual Infrastructure Automation and Provisioning, (b) Interoperability and Federation of Cloud Resources, and (c) On-demand Services for ScientificWorkflows.

97 MATHEMATICS AND COMPUTING↗

Two new SciDAC institutes promote mathematical tools and software technology for high-performance computing

Bigger is often said to be better, and the newest extreme-scale computers certainly are bigger, with millions of processing units. Moreover, the breadth of science performed on the U.S. Department of Energy (DOE) computing facilities is expanding, with new technology such as artificial intelligence emerging. These advances are exciting, creating new opportunities for scientific discovery; however, they also raise new questions for scientists who want to exploit these advances for tackling more complex problems. Will my simulation code be able to utilize the accelerators in extreme-scale computing systems? Can I take advantage of the deepening memory hierarchy in heterogeneous processors? Is there a way around bottlenecks caused by the widening ratio of peak floating-point operations per second to I/0 bandwidth? How can I manage my huge amounts of data effectively? Can I analyze data in situ, or must I transfer it to offline storage for later analysis? To address such questions, DOE announced that it is providing $57.5 million over the next five years for two multidisciplinary teams — FASTMath and RAPIDS2 — to develop new tools and techniques to harness supercomputers for scientific discovery. The teams, called SciDAC Institutes, are part of the Scientific Discovery through Advanced Computing program.

97 MATHEMATICS AND COMPUTING↗

Methods and Experiences for Developing Abstractions for Data-intensive, Scientific Applications

Developing software for scientific applications that require the integration of diverse types of computing, instruments, and data present challenges that are distinct from commercial software. These applications require scale, and the need to integrate various programming and computational models with evolving and heterogeneous infrastructure. Pervasive and effective abstractions for distributed infrastructures are thus critical; however, the process of developing abstractions for scientific applications and infrastructures is not well understood. While theory-based approaches for system development are suited for well-defined, closed environments, they have severe limitations for designing abstractions for scientific systems and applications. The design science research (DSR) method provides the basis for designing practical systems that can handle real-world complexities at all levels. In contrast to theory-centric approaches, DSR emphasizes both practical relevance and knowledge creation by building and rigorously evaluating all artifacts. In this work, we show how DSR provides a well-defined framework for developing abstractions and middleware systems for distributed systems. Specifically, we address the critical problem of distributed resource management on heterogeneous infrastructure over a dynamic range of scales, a challenge that currently limits many scientific applications. We use the pilot-abstraction, a widely used resource management abstraction for high-performance, high throughput, big data, and streaming applications, as a case study for evaluating the DSR activities. For this purpose, we analyze the research process and artifacts produced during the design and evaluation of the pilot-abstraction. We find DSR provides a concise framework for iteratively designing and evaluating systems. Finally, we capture our experiences and formulate different lessons learned.

97 MATHEMATICS AND COMPUTING↗

Building the Scientific Modeling Assistant: An interactive environment for specialized software design

The construction of scientific software models is an integral part of doing science, both within NASA and within the scientific community at large. Typically, model-building is a time-intensive and painstaking process, involving the design of very large, complex computer programs. Despite the considerable expenditure of resources involved, completed scientific models cannot easily be distributed and shared with the larger scientific community due to the low-level, idiosyncratic nature of the implemented code. To address this problem, we have initiated a research project aimed at constructing a software tool called the Scientific Modeling Assistant. This tool provides automated assistance to the scientist in developing, using, and sharing software models. We describe the Scientific Modeling Assistant, and also touch on some human-machine interaction issues relevant to building a successful tool of this type.

Keller, Richard M.↗

Genetic algorithm based task reordering to improve the performance of batch scheduled massively parallel scientific applications

The growth in size of networked high performance computers along with novel accelerator-based node architectures has further emphasized the importance of communication efficiency in high performance computing. The world's largest high performance computers are usually operated as shared user facilities due to the costs of acquisition and operation. Applications are scheduled for execution in a shared environment and are placed on nodes that are not necessarily contiguous on the interconnect. Furthermore, the placement of tasks on the nodes allocated by the scheduler is sub-optimal, leading to performance loss and variability. Here, we investigate the impact of task placement on the performance of two massively parallel application codes on the Titan supercomputer, a turbulent combustion flow solver (S3D) and a molecular dynamics code (LAMMPS). Benchmark studies show a significant deviation from ideal weak scaling and variability in performance. The inter-task communication distance was determined to be one of the significant contributors to the performance degradation and variability. A genetic algorithm-based parallel optimization technique was used to optimize the task ordering. This technique provides an improved placement of the tasks on the nodes, taking into account the application's communication topology and the system interconnect topology. As a result, application benchmarks after task reordering through genetic algorithm show a significant improvement in performance and reduction in variability, therefore enabling the applications to achieve better time to solution and scalability on Titan during production.

97 MATHEMATICS AND COMPUTING↗

DIRAQ: scalable in situ data- and resource-aware indexing for optimized query performance

Scientific data analytics in high-performance computing environments has been evolving along with the advancement of computing capabilities. With the onset of exascale computing, the increasing gap between compute performance and I/O bandwidth has rendered the traditional post-simulation processing a tedious process. Despite the challenges due to increased data production, there exists an opportunity to benefit from "cheap" computing power to perform query-driven exploration and visualization during simulation time. To accelerate such analyses, applications traditionally augment, post-simulation, raw data with large indexes, which are then repeatedly utilized for data exploration. However, the generation of current state-of-the-art indexes involves a compute- and memory-intensive processing, thus rendering them inapplicable in an in situ context. In this paper we propose DIRAQ, a parallel in situ, in network data encoding and reorganization technique that enables the transformation of simulation output into a query-efficient form, with negligible runtime overhead to the simulation run. DIRAQ's effective core-local, precision-based encoding approach incorporates an embedded compressed index that is 3---6 $$\times $$ ? smaller than current state-of-the-art indexing schemes. Its data-aware index adjustmentation improves performance of group-level index layout creation by up to 35 % and reduces the size of the generated index by up to 27 %. Moreover, DIRAQ's in network index merging strategy enables the creation of aggregated indexes that speed up spatial-context query responses by up to $$10\times $$ 10 ? versus alternative techniques. DIRAQ's topology-, data-, and memory-aware aggregation strategy results in efficient I/O and yields overall end-to-end encoding and I/O time that is less than that required to write the raw data with MPI collective I/O.

Computer Science↗

Plot2Spectra: an automatic spectra extraction tool

Scientists cannot easily make use of numerical data encoded in plot images, such as of spectroscopy data, in scientific literature. Plot2Spectra was developed to use computer vision tools to automatically digitize plot images.

Jiang, Weixin↗

Evaluation of Low Dose Silicon Carbide Temperature Monitors

Thermocouples are generally used to provide real-time temperature indications in instrumented tests performed at materials and test reactors. Melt wires or paint spots are often included in such tests as an independent technique of detecting peak temperatures incurred during irradiation. In addition, less expensive static capsule tests, which have no leads attached for real-time data transmission, often rely on melt wires and paint spots as a post-irradiation technique for peak temperature indication. Unfortunately, these techniques are limited in that they can only detect whether a single temperature is or is not exceeded. Silicon carbide (SiC) monitors are advantageous because a single monitor can be used to determine the peak temperature reached within a relatively broad range (200 – 800°C). Although the use of SiC monitors was proposed more than five decades ago, the ultimate performance limits of this technique are not fully understood. The Nuclear Science User Facilities (NSUF) is the United States Department of Energy Office of Nuclear Energy's only designated nuclear energy user facility. Its mission is to provide nuclear energy researchers access to world-class capabilities and to facilitate the advancement of nuclear science and technology. This mission is supported by providing access to state-of-the-art experimental irradiation testing, post irradiation examination facilities, and high performance computing capabilities as well as technical and scientific assistance for the design and execution of projects. As part of an NSUF project, low dose silicon carbide monitors were irradiated in the Belgian Reactor 2 and were then evaluated both at the SCK•CEN and at Idaho National Laboratory's High Temperature Test Laboratory to determine their peak temperature achieved during irradiation. The technical significance of this work was that the monitors were irradiated to a dose that was significantly less than recommended in published literature. This paper will discuss the evaluation process, the irradiation test, and the performance of the low dose silicon carbide temperature monitors.

36 MATERIALS SCIENCE↗

On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer

We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for D{sub e} = − 16.1 ± 0.1 kcal/mol and for D{sub 0} = − 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of −14.22 ± 0.12 kcal/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nonintrusive manufactured solutions for ablation

The study of heat transfer and ablation plays an important role in many problems of scientific and engineering interest. As with the computational simulation of any physical phenomenon, the first step toward establishing credibility in ablation simulations involves code verification. Code verification is typically performed using exact and manufactured solutions. However, manufactured solutions generally require the invasive introduction of an artificial forcing term within the source code such that the code solves a modified problem for which the solution is known. In this paper, we present a nonintrusive method for manufacturing solutions for a non-decomposing ablation code, which does not require the addition of a source term.

42 ENGINEERING↗

A lightweight, user-configurable detector ASIC digital architecture with on-chip data compression for MHz X-ray coherent diffraction imaging

Today, most X-ray pixel detectors used at light sources transmit raw pixel data off the detector ASIC. With the availability of more advanced ASIC technology nodes for scientific application, more digital functionalities from the computing domains (e.g., compression) can be integrated directly into a detector ASIC to increase data velocity. In this paper, we describe a lightweight, user-configurable detector ASIC digital architecture with on-chip compression which can be implemented in 130 nm technologies in a reasonable area on the ASIC periphery. In addition, we present a design to efficiently handle the variable data from the stream of parallel compressors. The architecture includes user-selectable lossy and lossless compression blocks. The impact of lossy compression algorithms is evaluated on simulated and experimental X-ray ptychography datasets. This architecture is a practical approach to increase pixel detector frame rates towards the continuous 1 MHz regime for not only coherent imaging techniques such as ptychography, but also for other diffraction techniques at X-ray light sources.

47 OTHER INSTRUMENTATION↗

Simulations of subatomic many-body physics on a quantum frequency processor

Simulating complex many-body quantum phenomena is a major scientific impetus behind the development of quantum computing, and a range of technologies are being explored to address such systems. We present the results of the largest photonics-based simulation to date, applied in the context of subatomic physics. Using an all-optical quantum frequency processor, the ground-state energies of light nuclei including the triton ( 3 H), 3 He, and the alpha particle ( 4 He) are computed. Complementing these calculations and utilizing a 68-dimensional Hilbert space, our photonic simulator is used to perform subnucleon calculations of the two- and three-body forces between heavy mesons in the Schwinger model. Furthermore, this work is a first step in simulating subatomic many-body physics on quantum frequency processors—augmenting classical computations that bridge scales from quarks to nuclei.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗