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Center of Excellence in Space Data and Information Sciences

This report summarizes the range of computer science-related activities undertaken by CESDIS for NASA in the twelve months from July 1, 1997 through June 30, 1998. These activities address issues related to accessing, processing, and analyzing data from space observing systems through collaborative efforts with university, industry, and NASA space and Earth scientists. The sections of this report which follow, detail the activities undertaken by the members of each of the CESDIS branches. This includes contributions from university faculty members and graduate students as well as CESDIS employees. Phone numbers and e-mail addresses appear in Appendix E (CESDIS Personnel and Associates) to facilitate interactions and new collaborations.

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Center of Excellence in Space Data and Information Sciences

This report summarizes the range of computer science-related activities undertaken by CESDIS for NASA in the twelve months from July 1, 1996 through June 30, 1997. These activities address issues related to accessing, processing, and analyzing data from space observing systems through collaborative efforts with university, industry,and NASA space and Earth scientists. The sections of this report which follow, detail the activities undertaken by the members of each of the CESDIS branches. This includes contributions from university faculty members and graduate students as well as CESDIS employees. Phone numbers and e-mail addresses appear in Appendix D (CESDIS Personnel and Associates) to facilitate interactions and new collaborations.

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S'COOL Provides Research Opportunities and Current Data for Today's Technological Classroom

NASA's Students' Cloud Observations On-Line (S'COOL) project, a hands-on educational project, was an innovative idea conceived by the scientists in the Radiation Sciences Branch at NASA Langley Research Center, Hampton, Virginia, in 1996. It came about after a local teacher expressed the idea that she wanted her students to be involved in real-life science. S'COOL supports NASA's Clouds and the Earth's Radiant Energy System (CERES) instrument, which was launched on the Tropical Rainforest Measuring Mission (TRMM) in November, 1997, as part of NASA's Earth Science Enterprise. With the S'COOL project students observe clouds and related weather conditions, compute data and note vital information while obtaining ground truth observations for the CERES instrument. The observations can then be used to help validate the CERES measurements, particularly detection of clear sky from space. In addition to meeting math, science and geography standards, students are engaged in using the computer to obtain, report and analyze current data, thus bringing modern technology into the realm of classroom, a paradigm that demands our attention.

Green, Carolyn J.↗

NASA Advanced Supercomputing Facility Expansion

The NASA Advanced Supercomputing (NAS) Division enables advances in high-end computing technologies and in modeling and simulation methods to tackle some of the toughest science and engineering challenges facing NASA today. The name "NAS" has long been associated with leadership and innovation throughout the high-end computing (HEC) community. We play a significant role in shaping HEC standards and paradigms, and provide leadership in the areas of large-scale InfiniBand fabrics, Lustre open-source filesystems, and hyperwall technologies. We provide an integrated high-end computing environment to accelerate NASA missions and make revolutionary advances in science. Pleiades, a petaflop-scale supercomputer, is used by scientists throughout the U.S. to support NASA missions, and is ranked among the most powerful systems in the world. One of our key focus areas is in modeling and simulation to support NASA's real-world engineering applications and make fundamental advances in modeling and simulation methods.

NASA↗

Machine Learning Toolkit for Extreme Scale

Support Vector Machines (SVM) is a popular machine learning technique, which has been applied to a wide range of domains such as science, finance, and social networks for supervised learning. MaTEx undertakes the challenge of designing a scalable parallel SVM training algorithm for large scale systems, which includes commodity multi-core machines, tightly connected supercomputers and cloud computing systems. Several techniques are proposed for improved speed and memory space usage including adaptive and aggressive elimination of samples for faster convergence , and sparse format representation of data samples. Several heuristics for earliest possible to lazy elimination of non-contributing samples are considered in MaTEx. In many cases, where an early sample elimination might result in a false positive, low overhead mechanisms for reconstruction of key data structures are proposed. The proposed algorithm and heuristics are implemented and evaluated on various publicly available datasets

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Accelerating Science with the NERSC Burst Buffer Early User Program

NVRAM-based Burst Buffers are an important part of the emerging HPC storage landscape. The National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory recently installed one of the first Burst Buffer systems as part of its new Cori supercomputer, collaborating with Cray on the development of the DataWarp software. NERSC has a diverse user base comprised of over 6500 users in 700 different projects spanning a wide variety of scientific computing applications. The use-cases of the Burst Buffer at NERSC are therefore also considerable and diverse. We describe here performance measurements and lessons learned from the Burst Buffer Early User Program at NERSC, which selected a number of research projects to gain early access to the Burst Buffer and exercise its capability to enable new scientific advancements. To the best of our knowledge this is the first time a Burst Buffer has been stressed at scale by diverse, real user workloads and therefore these lessons will be of considerable benefit to shaping the developing use of Burst Buffers at HPC centers.

97 MATHEMATICS AND COMPUTING↗

Scientific and Technical Basis of Application of Nanostructured Materials Science and Nanoelectronics in Systems of Electromechanical Energy Converters for Special Purposes

We consider the current state of a completely new area of science; microsystem electromechanics. Тhe wide spectra of its practical applications and prospects for further development are analyzed. We discuss in detail two main directions of creating micro- and nanoelectromechanical converters as basic elements of microsystem electromechanics: “top down” and “down top.” We also describe the main technological methods in constructing basic functional elements of microsystem electromechanics, areas of their application in traditional and new technologies (information and computer technologies, medicine, aerospace, rocket and artillery systems, etc.). At the same time, we discuss some key issues of generalized physical and mathematical modeling of microelectromechanical and nanoelectromechanical systems (MEMS and NEMS). A new generalized approach is proposed to study dynamic and energy characteristics of MEMS and NEMS as complex dynamic systems with binary conjugate subsystems. Based on proposed theoretical principles and models, the possibilities of studying electrophysical characteristics of biological nanostructures have been considered.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Nonlinear Modeling of Macroscopic Plasma Dynamics Final Scientific Report May 1, 2006 – April 30, 2018

The project entitled, "Nonlinear Modeling of Macroscopic Plasma Dynamics," applied numerical computation to solve mathematical models of plasma behavior in laboratory systems. Plasma is the state of matter with sufficiently large internal energy density such that electrons dissociate from atoms to form gas of electrically charged particles. It occurs naturally in stars, planetary magnetospheres, and interstellar and intergalactic media. It is also used for industrial purposes and in lighting. Fusion energy science seeks to create and sustain plasma conditions where atomic nuclei fuse to create energy that can be captured for power production. Many laboratory experiments for this effort use magnetic field to contain plasma and to thermally insulate it from its surroundings. Possible plasma dynamics in magnetized systems include collective behavior over spatial scales that are comparable to the configuration size, and these dynamics often include evolution of the magnetic field that is used for confinement. Solving the mathematical models that describe these dynamics in specific experiments often requires computer simulations, as done in this project. This project analyzed plasma magnetic relaxation dynamics in the laboratory configurations known as the reversed-field pinch (RFP), the spheromak, and the spherical torus (ST). It also developed capabilities for modeling disruptive plasma dynamics in the tokamak, which has achieved the highest performance for magnetized plasma and is the design of the large international ITER experiment (https://www.iter.org) that is under construction and is expected to be the first to achieve self-heating conditions. Dynamic evolution to states of low energy, the aforementioned magnetic relaxation, is known to be important for generating the RFP and spheromak configurations. Nonlinear computational modeling with the Non-Ideal Magnetohydrodynamics with Rotation, Open Discussion code (NIMROD, https://nimrodteam.org) was applied to understand specific aspects of magnetic relaxation in RFPs, spheromaks, and STs. The RFP study considered how the nonlinear transfer of power among different fluctuation harmonics is altered due to the application of pulses of electric field, as done experimentally in the Madison Symmetric Torus RFP device at the University of Wisconsin-Madison. It also investigated the separation of electron and ion dynamics, known as two-fluid effects, including effects on the evolution of the plasma flow profile. The spheromak study considered the influence of these two-fluid effects in conditions relevant to the Sustained Spheromak Experiment (SSPX), formerly at Lawrence Livermore National Laboratory. Our study found that two-fluid effects enhance stability with respect to interchange in SSPX-relevant conditions, but having a complete model with two-fluid effects in separate electron and ion temperature equations is important. The study for STs focused on plasma startup in the Pegasus Toroidal Experiment at UW-Madison, which uses DC voltage applied through a small plasma gun. The simulations show how the resulting helical current stream relaxes through repetitive merging, forming current rings that accumulate into a tokamak-like configuration. Analytical theory was also developed to help explain behavior that was observed in the RFP and spheromak computations. Although the tokamak configuration has outperformed other magnetic confinement configurations, it has a tendency to undergo discharge-terminating dynamics that release energy onto plasma-facing surfaces and exert electromechanical forces on magnetic coils and structures. Our efforts have improved NIMROD's capabilities to model tokamak disruption by incorporating a resistive wall model that can be applied to axisymmetric, as well as asymmetric, distortions of the magnetic field configuration. Computations addressed whether mathematical conditions applied to plasma flow at the wall influence disruptive dynamics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Global Sensitivity Analysis Using the Ultra‐Low Resolution Energy Exascale Earth System Model

Abstract For decades, Arctic temperatures have increased twice as fast as average global temperatures. As a first step toward quantifying parametric uncertainty in Arctic climate, we performed a variance‐based global sensitivity analysis (GSA) using a fully coupled, ultra‐low resolution (ULR) configuration of version 1 of the U.S. Department of Energy's Energy Exascale Earth System Model (E3SMv1). Specifically, we quantified the sensitivity of six quantities of interests (QOIs), which characterize changes in Arctic climate over a 75 year period, to uncertainties in nine model parameters spanning the sea ice, atmosphere, and ocean components of E3SMv1. Sensitivity indices for each QOI were computed with a Gaussian process emulator using 139 random realizations of the random parameters and fixed preindustrial forcing. Uncertainties in the atmospheric parameters in the Cloud Layers Unified by Binormals (CLUBB) scheme were found to have the most impact on sea ice status and the larger Arctic climate. Our results demonstrate the importance of conducting sensitivity analyses with fully coupled climate models. The ULR configuration makes such studies computationally feasible today due to its low computational cost. When advances in computational power and modeling algorithms enable the tractable use of higher‐resolution models, our results will provide a baseline that can quantify the impact of model resolution on the accuracy of sensitivity indices. Moreover, the confidence intervals provided by our study, which we used to quantify the impact of the number of model evaluations on the accuracy of sensitivity estimates, have the potential to inform the computational resources needed for future sensitivity studies.

54 ENVIRONMENTAL SCIENCES↗

NASA Virtual Glovebox: An Immersive Virtual Desktop Environment for Training Astronauts in Life Science Experiments

The International Space Station will soon provide an unparalleled research facility for studying the near- and longer-term effects of microgravity on living systems. Using the Space Station Glovebox Facility - a compact, fully contained reach-in environment - astronauts will conduct technically challenging life sciences experiments. Virtual environment technologies are being developed at NASA Ames Research Center to help realize the scientific potential of this unique resource by facilitating the experimental hardware and protocol designs and by assisting the astronauts in training. The Virtual GloveboX (VGX) integrates high-fidelity graphics, force-feedback devices and real- time computer simulation engines to achieve an immersive training environment. Here, we describe the prototype VGX system, the distributed processing architecture used in the simulation environment, and modifications to the visualization pipeline required to accommodate the display configuration.

Twombly, I. Alexander↗

The Ability of Soil Pore Network Metrics to Predict Redox Dynamics Is Scale Dependent

Variations in microbial community structure and metabolic efficiency are governed in part by oxygen availability, which is a function of water content, diffusion distance, and oxygen demand; for this reason, the volume, connectivity, and geometry of soil pores may exert primary controls on spatial metabolic diversity in soil. Here, we combine quantitative pore network metrics derived from X-ray computed tomography (XCT) with measurements of electromotive potentials to assess how the metabolic status of soil depends on variations of the overall pore network architecture. Contrasting pore network architectures were generated using a Mollisol—A horizon, and compared to intact control samples from the same soil. Mesocosms from each structural treatment were instrumented with Pt-electrodes to record available energy dynamics during a regimen of varying moisture conditions. We found that volume-based XCT-metrics were more frequently correlated with metrics describing changes in available energy than medial-axis XCT-metrics. An abundance of significant correlations between pore network metrics and available energy parameters was not only a function of pore architecture, but also of the dimensions of the sub-sample chosen for XCT analysis. Pore network metrics had the greatest power to statistically explain changes in available energy in the smallest volumes analyzed. Our work underscores the importance of scale in observations of natural systems.

59 BASIC BIOLOGICAL SCIENCES↗

SU-E-J-254: Utility of Pinnacle Dynamic Planning Module Utilizing Deformable Image Registration in Adaptive Radiotherapy

Purpose For certain highly conformal treatment techniques, changes in patient anatomy due to weight loss and/or tumor shrinkage can result in significant changes in dose distribution. Recently, the Pinnacle treatment planning system added a Dynamic Planning module utilizing Deformable Image Registration (DIR). The objective of this study was to evaluate the effectiveness of this software in adapting to altered anatomy and adjusting treatment plans to account for it. Methods We simulated significant tumor response by changing patient thickness and altered chin positions using a commercially-available head and neck (H and N) phantom. In addition, we studied 23 CT image sets of fifteen (15) patients with H and N tumors and eight (8) patients with prostate cancer. In each case, we applied deformable image registration through Dynamic Planning module of our Pinnacle Treatment Planning System. The dose distribution of the original CT image set was compared to the newly computed dose without altering any treatment parameter. Result was a dose if we did not adjust the plan to reflect anatomical changes. Results For the H and N phantom, a tumor response of up to 3.5 cm was correctly deformed by the Pinnacle Dynamic module. Recomputed isodose contours on new anatomies were within 1 mm of the expected distribution. The Pinnacle system configuration allowed dose computations resulting from original plans on new anatomies without leaving the planning system. Original and new doses were available side-by-side with both CT image sets. Based on DIR, about 75% of H and N patients (11/15) required a re-plan using new anatomy. Among prostate patients, the DIR predicted near-correct bladder volume in 62% of the patients (5/8). Conclusions The Dynamic Planning module of the Pinnacle system proved to be an accurate and useful tool in our ability to adapt to changes in patient anatomy during a course of radiotherapy.

60 APPLIED LIFE SCIENCES↗

Materials perspective on Casimir and van der Waals interactions

Interactions induced by electromagnetic fluctuations, such as van der Waals and Casimir forces, are of universal nature present at any length scale between any types of systems. In such interactions these are important not only for the fundamental science of materials behavior, but also for the design and improvement of micro- and nanostructured devices. In the past decade, many new materials have become available, which has stimulated the need for understanding their dispersive interactions. The field of van der Waals and Casimir forces has experienced an impetus in terms of developing novel theoretical and computational methods to provide new insights into related phenomena. The understanding of such forces has far reaching consequences as it bridges concepts in materials, atomic and molecular physics, condensed-matter physics, high-energy physics, chemistry, and biology. Our review summarizes major breakthroughs and emphasizes the common origin of van der Waals and Casimir interactions. Progress related to novel ab initio modeling approaches and their application in various systems, interactions in materials with Dirac-like spectra, force manipulations through nontrivial boundary conditions, and applications of van der Waals forces in organic and biological matter are examined. Finally, the outlook of the review is to give the scientific community a materials perspective of van der Waals and Casimir phenomena and stimulate the development of experimental techniques and applications.

36 MATERIALS SCIENCE↗

System-independent characterization of materials using dual-energy computed tomography

In this study, we present a new decomposition approach for dual-energy computed tomography (DECT) called SIRZ that provides precise and accurate material description, independent of the scanner, over diagnostic energy ranges (30 to 200 keV). System independence is achieved by explicitly including a scanner-specific spectral description in the decomposition method, and a new X-ray-relevant feature space. The feature space consists of electron density, ρ e , and a new effective atomic number, Z e , which is based on published X-ray cross sections. Reference materials are used in conjunction with the system spectral response so that additional beam-hardening correction is not necessary. The technique is tested against other methods on DECT data of known specimens scanned by diverse spectra and systems. Uncertainties in accuracy and precision are less than 3% and 2% respectively for the (ρ e , Z e ) results compared to prior methods that are inaccurate and imprecise (over 9%).

42 ENGINEERING↗

Review of SPECT collimator selection, optimization, and fabrication for clinical and preclinical imaging

In single photon emission computed tomography, the choice of the collimator has a major impact on the sensitivity and resolution of the system. Traditional parallel-hole and fan-beam collimators used in clinical practice, for example, have a relatively poor sensitivity and subcentimeter spatial resolution, while in small-animal imaging, pinhole collimators are used to obtain submillimeter resolution and multiple pinholes are often combined to increase sensitivity. This paper reviews methods for production, sensitivity maximization, and task-based optimization of collimation for both clinical and preclinical imaging applications. New opportunities for improved collimation are now arising primarily because of (i) new collimator-production techniques and (ii) detectors with improved intrinsic spatial resolution that have recently become available. These new technologies are expected to impact the design of collimators in the future. The authors also discuss concepts like septal penetration, high-resolution applications, multiplexing, sampling completeness, and adaptive systems, and the authors conclude with an example of an optimization study for a parallel-hole, fan-beam, cone-beam, and multiple-pinhole collimator for different applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Scientific machine learning benchmarks

Deep learning has transformed the use of machine learning technologies for the analysis of large experimental datasets. In science, such datasets are typically generated by large-scale experimental facilities, and machine learning focuses on the identification of patterns, trends and anomalies to extract meaningful scientific insights from the data. In upcoming experimental facilities, such as the Extreme Photonics Application Centre (EPAC) in the UK or the international Square Kilometre Array (SKA), the rate of data generation and the scale of data volumes will increasingly require the use of more automated data analysis. Furthermore, at present, identifying the most appropriate machine learning algorithm for the analysis of any given scientific dataset is a challenge due to the potential applicability of many different machine learning frameworks, computer architectures and machine learning models. Historically, for modelling and simulation on high-performance computing systems, these issues have been addressed through benchmarking computer applications, algorithms and architectures. Extending such a benchmarking approach and identifying metrics for the application of machine learning methods to open, curated scientific datasets is a new challenge for both scientists and computer scientists. Here, we introduce the concept of machine learning benchmarks for science and review existing approaches. As an example, we describe the SciMLBench suite of scientific machine learning benchmarks.

42 ENGINEERING↗