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At least 343 records · Page 19

Characterizing Output Bottlenecks of a Production Supercomputer: Analysis and Implications

This article studies the I/O write behaviors of the Titan supercomputer and its Lustre parallel file stores under production load. The results can inform the design, deployment, and configuration of file systems along with the design of I/O software in the application, operating system, and adaptive I/O libraries.We propose a statistical benchmarking methodology to measure write performance across I/O configurations, hardware settings, and system conditions. Moreover, we introduce two relative measures to quantify the write-performance behaviors of hardware components under production load. In addition to designing experiments and benchmarking on Titan, we verify the experimental results on one real application and one real application I/O kernel, XGC and HACC IO, respectively. These two are representative and widely used to address the typical I/O behaviors of applications.In summary, we find that Titan’s I/O system is variable across the machine at fine time scales. This variability has two major implications. First, stragglers lessen the benefit of coupled I/O parallelism (striping). Peak median output bandwidths are obtained with parallel writes to many independent files, with no striping or write sharing of files across clients (compute nodes). I/O parallelism is most effective when the application—or its I/O libraries—distributes the I/O load so that each target stores files for multiple clients and each client writes files on multiple targets in a balanced way with minimal contention. Second, our results suggest that the potential benefit of dynamic adaptation is limited. In particular, it is not fruitful to attempt to identify “good locations” in the machine or in the file system: component performance is driven by transient load conditions and past performance is not a useful predictor of future performance. For example, we do not observe diurnal load patterns that are predictable.

97 MATHEMATICS AND COMPUTING↗

The economic and environmental costs and benefits of the renewable fuel standard

Abstract Mandates, like the renewable fuel standard (RFS), for biofuels from corn and cellulosic feedstocks, impact the environment in multiple ways by affecting land use, nitrogen (N)-leakage, and greenhouse gas (GHG) emissions. We analyze the differing trade-offs these different types of biofuels offer among these multi-dimensional environmental effects and convert them to a monetized value of environmental damages (or benefits) that can be compared with the economic costs of extending these mandates over the 2016–2030 period. The discounted values of cumulative net benefits (or costs) are then compared to those with a counterfactual level of biofuels that would have been produced in the absence of the RFS over this period. We find that maintaining the corn ethanol mandate at 56 billion l till 2030 will lead to a discounted cumulative value of an economic cost of $199 billion over the 2016–2030 period compared to the counterfactual scenario; this includes $109 billion of economic costs and $85 billion of net monetized environmental damages. The additional implementation of a cellulosic biofuel mandate for 60 billion l by 2030 will increase this economic cost by $69 billion which will be partly offset by the net discounted monetized value of environmental benefits of $20 billion, resulting in a net cost of $49 billion over the 2016–2030 period. We explore the sensitivity of these net (economic and environmental) costs to alternative values of the social costs of carbon and nitrogen and other technological and market parameters. We find that, unlike corn ethanol, cellulosic biofuels can result in positive net benefits if the monetary benefits of GHG mitigation are valued high and those of N-damages are not very high.

54 ENVIRONMENTAL SCIENCES↗

HtPIP: High-throughput phage isolation platform increases diversity and reduces isolation time using multiple bacteria

Bacteriophages are ubiquitous in nature, but relatively few have been isolated and characterized compared to the number of bacterial strains. Phage biotechnology applications benefit from a diverse library of isolated phages to kill or transfer genetic material to a bacterium of interest. However, scaling up phage discovery for diverse bacterial hosts can be time-consuming and costly. Here, we developed an approach to capture novel phages for multiple bacterial strains in parallel from an environmental sample using commercially available 0.2-μM filter plates. Using this High-throughput Phage Isolation Platform (HtPIP), 12 novel phages were isolated spanning 9 diverse bacterial host genera. Eleven of the isolated phages define new phage species, with nine also defining new genera. The HtPIP was used to discover both DNA and RNA phages, including a Tectiviridae infecting Pseudomonas putida mt-2 and a Leviviricetes infecting a Microbacterium isolate, which represents the first cultured RNA phage infecting a host outside of Proteobacteria. Using a metagenomic approach, we demonstrate that the HtPIP captures a higher proportion of novel phages compared to traditional low-throughput methods.

High-throughput↗

Effects of additively manufactured surface roughness on small diameter plenums with multiple side discharges for high temperature gas turbine blade cooling applications

Combined heat and power (CHP) applications have significant environmental and economic benefits that are consistent with the goals of the U.S. Department of Energy (DOE). One area that is currently being studied includes the potential benefits of CHP turbine operation at higher turbine inlet temperatures. Internal cooling concepts enabled by additive manufacturing (AM) are of primary interest. Here, the effectiveness of internal cooling is hindered by many factors such as velocity distribution of the cooling air to the hot surface considering impingement cooling. To simulate cooling air exiting from a series of orifices for internal cooling in an airfoil, a straight smooth wall tubing with multiple side discharging orifices is used and compared to additively manufactured tubing (Ti6Al4V Grade 23) with orifice size and spacing as well as inner and outer diameters identical to the smooth wall tubing. Similar to flow discharging form perforated pipes, the flow discharged from individual orifices along the tubes in this study is found to be nonuniformly distributed, and the horizontal (axial direction) momentum can be observed from the experimental data. Discharge velocities have been measured with two-dimensional (2D) particle imaging velocimetry (PIV) and single element hot wire anemometry. Numerical analysis has also been conducted to predict the velocity distributions along the orifices in the smooth wall and additive manufacturing (AM) tubing, which are inherited with surface roughness. Numerical and measured results in this study are compared, presented, and discussed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Single Application of Compost Can Leave Lasting Impacts on Soil Microbial Community Structure and Alter Cross-Domain Interaction Networks

Our current understanding suggests that nutrient management strategies applied to agricultural soils over multiple years are required to cause major and stable shifts in soil microbial communities. However, some studies suggest that agricultural soils can benefit even from sporadic, single additions of organic matter. Here we investigate how single additions of high-quality organic matter can cause significant shifts in microbial soil communities over multiple cropping cycles. We grew radishes in a tropical Oxisol soil for six crop cycles after a single application of a high-nitrogen compost or urea. At planting and before biomass harvest, we sampled soils influenced by the radish rhizosphere and sequenced bacterial and archaeal 16S and fungal ITS rDNA marker genes. We measured microbial richness and diversity, community composition and structure, and constructed correlation networks to predict cross-domain microbial interactions. We found that a single application of compost, compared to urea or control, resulted in a persistent improved plant biomass response and led to sustained changes in the soil microbial community throughout the duration of the 227-day study. Compost altered the structure of both the fungal and prokaryotic microbial communities, introduced new microorganisms that persisted in the resident soil system, and altered soil microbial correlation network structure and hub taxa. In contrast, fertilization with urea did not significantly alter the structure of soil microbial communities compared to the control but reduced network complexity and altered hub taxa. This study highlights the significant impacts that high-quality organic matter fertilization can exert on agricultural soil microbiomes and adds to the growing body of knowledge on using organic fertilizers as a way to steer the soil microbiome toward a healthier soil.

Heisey, Steven↗

Scalable Data-Intensive Geocomputation: A Design for Real-Time Continental Flood Inundation Mapping

The convergence of data-intensive and extreme-scale computing enables an integrated software and data ecosystem for scientific discovery. Developments in this realm will fuel transformative research in data-driven interdisciplinary domains. Geocomputation provides computing paradigms in Geographic Information Systems (GIS) for interactive computing of geographic data, processes, models, and maps. Because GIS is data-driven, the computational scalability of a geocomputation workflow is directly related to the scale of the GIS data layers, their resolution and extent, as well as the velocity of the geo-located data streams to be processed. Unique in high user interactivity and low end-to-end latency requirements, geocomputation applications will dramatically benefit from the convergence of high-end data analytics (HDA) and high-performance computing (HPC). The application level challenge, however, is to identify and eliminate computational bottlenecks that arise along a geocomputation workflow. Indeed, poor scalability at any of the workflow components is detrimental to the entire end-to-end pipeline. Here, we study a large geocomputation use case in flood inundation mapping that handles multiple national-scale geospatial datasets and targets low end-to-end latency. We discuss benefits and challenges for harnessing both HDA and HPC for data-intensive geospatial data processing and intensive numerical modeling of geographic processes. We propose an HDA+HPC geocomputation architecture design that couples HDA (e.g., Spark)-based spatial data handling and HPC-based parallel data modeling. Key techniques for coupling HDA and HPC to bridge the two different software stacks are reviewed and discussed.

Liu, Yan↗

Potential of water quality wetlands to mitigate habitat losses from agricultural drainage modernization

Given widespread biodiversity declines, a growing global human population, and demands to improve water quality, there is an immediate need to explore land management solutions that support multiple ecosystem services. Agricultural water quality wetlands designed to provide both water quality benefits and wetland and grassland habitat are an emerging restoration solution that may reverse habitat declines in intensive agricultural areas. Installation of water quality wetlands in the Upper Midwest, USA, when considered alongside the repair and modification of aging agricultural tile drainage infrastructure, is a likely scenario that may mitigate nutrient pollution exported from agricultural systems and improve crop yields. The capacity of water quality wetlands to provide habitat within the wetland pool and the surrounding grassland is not well-studied, particularly with respect to potential habitat changes resulting from drainage infrastructure upgrades. For the current study, we produced spatially explicit models of 37 catchments distributed throughout an important region for agriculture and biodiversity, the Des Moines Lobe of Iowa. Four scenarios were considered - with and without improved drainage and with and without water quality wetlands - to estimate the net potential habitat implications of these scenarios for amphibians, grassland birds, and wild bees. Model results indicate that drainage modification alone will likely result in moderate direct losses of suitable amphibian habitat and large declines in overall habitat quality. However, inclusion of water quality wetlands at the catchment scale may mitigate these amphibian habitat losses while also increasing grassland bird and pollinator habitat. In conclusion, the impacts of water quality wetlands and drainage modernization on waterfowl in the region require additional study.

54 ENVIRONMENTAL SCIENCES↗

Planarization of Rough (100) GaAs Substrates via Growth by Hydride Vapor Phase Epitaxy

Wafer reuse techniques help offset the cost of III-V growth substrates by using a single wafer for multiple growths, but costly re-polishing after device removal limits the end benefit. In this work, we present planarization growth by hydride vapor-phase epitaxy (HVPE), a potentially low-cost growth technique, as a method of smoothing rough substrates for subsequent high-quality device growth without the need for polishing. First, we show there is a threshold for allowable substrate roughness without device degradation by comparing devices grown by organometallic vapor-phase epitaxy (OMVPE) on epi-ready polished and pre-polished substrates that did not have the final epi-ready polish. We then demonstrate successful smoothing with HVPE growth on substrates with different surface morphologies, with features ranging from general roughness to large facets. Initial devices grown by HVPE on a pre-polished substate showed no degradation compared to a control wafer, indicating that planarizing rough substrates through HVPE growth is a promising path toward being able to use rough substrates directly for growth, without costly polishing steps.

GaAs↗

Beyond the Hype: An Evaluation of Commercially Available Machine-Learning-Based Malware Detectors

There is a lack of scientific testing of commercially available malware detectors, especially those that boast accurate classification of never-before-seen (i.e., zero-day) files using machine learning (ML). Consequently, efficacy of malware detectors is opaque, inhibiting end users from making informed decisions and researchers from targeting gaps in current detectors. In this paper, we present a scientific evaluation of four prominent commercial malware detection tools to assist an organization with two primary questions: To what extent do ML-based tools accurately classify previously and never-before-seen files? Is purchasing a network-level malware detector worth the cost? To investigate, we tested each tool against 3,536 total files (2,554 or 72% malicious, 982 or 28% benign) of a variety of file types, including hundreds of malicious zero-days, polyglots, and APT-style files, delivered on multiple protocols. We present statistical results on detection time and accuracy, consider complementary analysis (using multiple tools together), and provide two novel applications of the recent cost-benefit evaluation procedure of Iannacone & Bridges. Although the ML-based tools are more effective at detecting zero-day files and executables, the signature-based tool might still be an overall better option. Both network-based tools provide substantial (simulated) savings when paired with either host tool, yet both show poor detection rates on protocols other than HTTP or SMTP. Our results show that all four tools have near-perfect precision but alarmingly low recall, especially on file types other than executables and office files—37% of malware, including all polyglot files, were undetected. Priorities for researchers and takeaways for end users are given. Code for future use of the cost model is provided.

97 MATHEMATICS AND COMPUTING↗

Implementation and Operation of Power Flow Control Solutions for Transmission Systems

Power-flow controls (PFCs) technologies provide a suite of alternatives to more-efficiently direct the flow of power on the grid, improving flexibility and enabling the grid to be more responsive and resilient. PFCs can be used in many cases to mitigate overloads and consequently defer the installation of grid-expansion projects. They can also be suitable options in situations where new transmission lines cannot be built because of environmental constraints, land use, or other types of restrictions. Other uses include mitigation of loop or unintended flows, forcing of contractual or scheduled flows, reduction of congestion, and mitigation solutions during large maintenance or construction projects. While many studies have demonstrated the potential economic benefits of PFC for different types of applications, the implementation implications of using multiple PFCs for system operation and reliability have not been analyzed in detail. The lack of information and practical experience on these aspects hinders adoption of this technology. One use case would be that multiple PFCs are required to coordinate congestion management. In such cases, multiple PFCs are deployed in a meshed power system to control power flows across a wide area. The challenges are associated with PFC interaction—namely, the self and mutual power-flow sensitivity of each PFC, which must be accounted for in the calculation of the respective operating setpoints. This report analyzes implementation and operation that must be considered in evaluating transmission solutions using PFCs. The report first analyzes attributes with which PFC-based solutions should comply, based on the objective and characteristics of each particular use case. It then describes different approaches for coordinated control of multiple PFC devices for different applications, including options to avoid adverse interactions and reduce risks due to inappropriate coordination. Control and operation are illustrated through case studies performed on both generic and actual power system models. This report provides insights for transmission planners and operation engineers about the implementation of PFC-based transmission solutions; consequently, it will help them make informed decisions about the adoption of the technology.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Implementation of a Coded Modulation for Deep Space Optical Communications

We present a field programmable gate array code (FPGA) implementation of a turbo-like decoder for a serially concatenated pulse-position modulation (SCPPM) code. NASA a developed this coded modulation scheme for deep space communications from Mars. Under a nominal mission condition, the decoder complexity by iteratively decoding the modulation and SCPPM coded system can operate within a one dB signal energy gap from capacity. The structure of SCPPM makes direct application of the conventional turbo decoding algorithm very inefficient. Here, we describe techniques to increase the throughput and performance of a hardware SCPPM decoder. using our optimizations, we demonstrate a 6 mega-bits per second (Mbps) decoder realization on a single FPGA. Extension toa higher data rate decoder using multiple FPGAs is readily achievable. Similar codes designed for the optical channel can benefit from our optimization techniques.

modulation↗

Advances in Digital Calibration Techniques Enabling Real-Time Beamforming SweepSAR Architectures

Real-time digital beamforming, combined with lightweight, large aperture reflectors, enable SweepSAR architectures, which promise significant increases in instrument capability for solid earth and biomass remote sensing. These new instrument concepts require new methods for calibrating the multiple channels, which are combined on-board, in real-time. The benefit of this effort is that it enables a new class of lightweight radar architecture, Digital Beamforming with SweepSAR, providing significantly larger swath coverage than conventional SAR architectures for reduced mass and cost. This paper will review the on-going development of the digital calibration architecture for digital beamforming radar instrument, such as the proposed Earth Radar Mission's DESDynI (Deformation, Ecosystem Structure, and Dynamics of Ice) instrument. This proposed instrument's baseline design employs SweepSAR digital beamforming and requires digital calibration. We will review the overall concepts and status of the system architecture, algorithm development, and the digital calibration testbed currently being developed. We will present results from a preliminary hardware demonstration. We will also discuss the challenges and opportunities specific to this novel architecture.

TR (Transmit/Receive)↗

GEO Disaster Risk Reduction Working Group

GEO is an international partnership of more than 100 national governments, 100 Participating Organizations and multiple Associate members working towards a future where decisions and actions for the benefit of humankind are informed by coordinated, comprehensive and sustained Earth observations.

David Borges↗

Comparing Low-Cost Sensors with Ground-Based and Airborne In-Situ and Column Observations of NO2 and HCHO during the FRAPPE Field Campaign in Colorado, USA

Even in the presence of more reliable air quality tools, low-cost sensors have the benefit of recording data on highly localized spatial and temporal scales, allowing for multiple measurements within a single satellite pixel and on pixel boundaries. However, they are less accurate than their regulatory-grade counterparts, requiring regular co-locations with accepted instruments to ensure their validity. Thus, the addition of low-cost sensors to a field campaign – where reference-grade air quality instruments are abundant – not only provides ample opportunities for low-cost sensor co-location and calibration, but also allows the low-cost instruments to be used for sub-pixel validation, covering more surface area than the regulatory instruments alone with a network of sensors. During the summer of 2014, our low-cost sensor network was deployed during the Front Range Air Pollution and Photochemistry Experiment (FRAPPÉ) campaign conducted to sample the composition of air at and above ground level in northeastern Colorado, USA. The low-cost sensor platform included a suite of gas-phase sensors, notably NO2 and two generalized volatile organic compound (VOC) sensors, which were leveraged together to quantify speciated hydrocarbons such as formaldehyde. These key pollutants were chosen for their impacts on human health and climate change, as well as their inclusion on the TEMPO satellite launching this year. Airborne campaign measurements included slant column optical observations of formaldehyde (HCHO), nitrogen dioxide (NO2), and ozone (O3). Myriad additional in-situ instruments described chemical composition up to approximately 5 km above surface level. Ground-based instrumentation included both stationary and mobile regulatory-grade instruments, which were used for sensor calibration. Machine learning techniques such as artificial neural networks (ANNs) were used to match the low-cost signals to that of the reference-grade instruments. Here, we compare calibrated low-cost sensor data collected at ground level in a variety of locations along Colorado’s Front Range to various data sources from the FRAPPÉ campaign to better understand how well airborne and regulatory ground-based measurements can be extrapolated to other locations. Further, as the slant column measurements act as satellite simulators, we explore how low-cost instruments can be used for satellite validation purposes. Comparisons among these different data types also have important implications in data fusion.

Kristen Okorn↗

In silico trials predict that combination strategies for enhancing vesicular stomatitis oncolytic virus are determined by tumor aggressivity

Background Immunotherapies, driven by immune-mediated antitumorigenicity, offer the potential for significant improvements to the treatment of multiple cancer types. Identifying therapeutic strategies that bolster antitumor immunity while limiting immune suppression is critical to selecting treatment combinations and schedules that offer durable therapeutic benefits. Combination oncolytic virus (OV) therapy, wherein complementary OVs are administered in succession, offer such promise, yet their translation from preclinical studies to clinical implementation is a major challenge. Overcoming this obstacle requires answering fundamental questions about how to effectively design and tailor schedules to provide the most benefit to patients. Methods We developed a computational biology model of combined oncolytic vaccinia (an enhancer virus) and vesicular stomatitis virus (VSV) calibrated to and validated against multiple data sources. We then optimized protocols in a cohort of heterogeneous virtual individuals by leveraging this model and our previously established in silico clinical trial platform. Results Enhancer multiplicity was shown to have little to no impact on the average response to therapy. However, the duration of the VSV injection lag was found to be determinant for survival outcomes. Importantly, through treatment individualization, we found that optimal combination schedules are closely linked to tumor aggressivity. We predicted that patients with aggressively growing tumors required a single enhancer followed by a VSV injection 1 day later, whereas a small subset of patients with the slowest growing tumors needed multiple enhancers followed by a longer VSV delay of 15 days, suggesting that intrinsic tumor growth rates could inform the segregation of patients into clinical trials and ultimately determine patient survival. These results were validated in entirely new cohorts of virtual individuals with aggressive or non-aggressive subtypes. Conclusions Based on our results, improved therapeutic schedules for combinations with enhancer OVs can be studied and implemented. Our results further underline the impact of interdisciplinary approaches to preclinical planning and the importance of computational approaches to drug discovery and development.

60 APPLIED LIFE SCIENCES↗

Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

Abstract Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

59 BASIC BIOLOGICAL SCIENCES↗

Consolidated Hydropower Data Repository: Value and Opportunities

Hydropower is one of several types of generating assets that provides energy, capacity, and services to electric power systems. It does so under rubrics and objectives—market driven and regulated, internal and external to asset and fleet owners—that address reliability, cost, price, and, increasingly, flexibility of output. The aggregation of data from multiple hydropower units can provide insights into asset operations and maintenance practices and needs and assist in meeting hydropower objectives. This paper examines the concept and potential benefits of aggregating hydropower asset data—primarily supervisory control and data acquisition (SCADA) information—with examples of insights developed from data aggregated by the Hydropower Research Institute (HRI). Data aggregation as discussed herein, and as implemented by the HRI, extends beyond multiple units in a powerhouse and beyond multiple hydropower facilities in an electric utility fleet or river system. Examples of research and analytics from such aggregated datasets range from unit load dependency analyses to modeling sensor measurements to detect and diagnose anomalies in assets. These examples showed the benefits of utilizing the entire dataset for insights into how the sensor layout of a single unit or set of units compares to the hydropower industry overall. Such insights include whether additional sensors are needed to complete analyses or to make decisions. In addition, utilizing multiple sensors of the same kind within a unit can provide an indication of possible current or upcoming problems with equipment. Although other analyses are possible, their use requires the development of complex models and, potentially, access to types of data that are currently not included with the example dataset used in this study. However, the examples studied herein confirmed the value of data aggregation in the fleet and unit contexts, and the value extends beyond multiple units in a powerhouse and beyond multiple hydropower facilities in an electric utility fleet or river system. The assessments also provided insights into potential extensions to the data aggregation concept that could further add to their value to the hydropower community, and these are included in this document as a set of recommendations.

13 HYDRO ENERGY↗

A Decision Support Framework for Feasibility Analysis of International Space Station (ISS) Research Capability Enhancing Options

The assembly and operation of the ISS has generated significant challenges that have ultimately impacted resources available to the program's primary mission: research. To address this, program personnel routinely perform trade-off studies on alternative options to enhance research. The approach, content level of analysis and resulting outputs of these studies vary due to many factors, however, complicating the Program Manager's job of selecting the best option. To address this, the program requested a framework be developed to evaluate multiple research-enhancing options in a thorough, disciplined and repeatable manner, and to identify the best option on the basis of cost, benefit and risk. The resulting framework consisted of a systematic methodology and a decision-support toolset. The framework provides quantifiable and repeatable means for ranking research-enhancing options for the complex and multiple-constraint domain of the space research laboratory. This paper describes the development, verification and validation of this framework and provides observations on its operational use.

Ortiz, James N.↗