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At least 901 records · Page 50

System Architecture Directions for Post-SoC/32-bit Networked Sensors

The emergence of low-power 32-bit Systems-on-Chip (SoCs), which integrate a 32-bit MCU, radio, and flash, presents an opportunity to re-examine design points and trade-offs at all levels of the system architecture of networked sensors. To this end, we develop a post-SoC/32-bit design point called Hamilton, showing that using integrated components enables a ~$7 core and shifts hardware modularity to design time. We study the interaction between hardware and embedded operating systems, identifying that (1) post-SoC motes provide lower idle current (5.9 μA) than traditional 16-bit motes, (2) 32-bit MCUs are a major energy consumer (e.g., tick increases idle current >50 times), comparable to radios, and (3) thread-based concurrency is viable, requiring only 8.3 μs of context switch time. We design a system architecture, based on a tickless multithreading operating system, with cooperative/adaptive clocking, advanced sensor abstraction, and preemptive packet processing. Its efficient MCU control improves concurrency with ~30% less energy consumption. Together, these developments set the system architecture for networked sensors in a new direction.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication

Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs' high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Tan, Nigel↗

T-FSM: A Scalable Distributed Task-Based System for Frequent Subgraph Pattern Mining from a Big Graph

Finding frequent subgraph patterns in a big graph is an important problem with many applications such as classifying chemical compounds and building indexes to speed up graph queries. Since this problem is NP-hard, some recent parallel and distributed systems have been developed to accelerate the mining. However, they often have a huge memory cost, very long running time, suboptimal load balancing, poor scale-out capability, and possibly inaccurate results. In this article, we propose an efficient system called T-FSM for parallel mining of frequent subgraph patterns in a big graph. T-FSM supports a new anti-monotonic frequentness measure called Fraction-Score, which is more accurate than the widely used MNI measure. The execution engine of T-FSM supports both intra-machine parallelism and inter-machine parallelism. For intra-machine parallelism, T-FSM adopts a novel task-based execution model to ensure high multithreading concurrency, bounded memory consumption, and effective load balancing. For inter-machine parallelism, T-FSM ensures good scale-out performance with a lightweight pattern rebalancing approach that reduces workload skewness of pattern evaluations among machines. To avoid recomputing the contexts for migrated patterns, we design a novel context cache table to support concurrent and asynchronous requesting and caching of remote context data, which can timely evict and garbage collect used pattern contexts that are no longer needed to keep memory consumption bounded. Extensive experiments show that T-FSM is orders of magnitude faster than existing state-of-the-art parallel systems (more than 10×, 51×, 131×, 55× speedup over ScaleMine, DistGraph, Pangolin and Peregrine, respectively) and distributed systems (more than 42× and 88× over ScaleMine and DistGraph, respectively) for frequent subgraph pattern mining, and it scales out satisfactorily to 512 CPU cores on the Polaris supercomputer at Argonne National Laboratory.

97 MATHEMATICS AND COMPUTING↗

Evolution of Friction and Permeability in a Propped Fracture under Shear

We explore the evolution of friction and permeability of a propped fracture under shear. We examine the effects of normal stress, proppant thickness, proppant size, and fracture wall texture on the frictional and transport response of proppant packs confined between planar fracture surfaces. The proppant-absent and proppant-filled fractures show different frictional strength. For fractures with proppants, the frictional response is mainly controlled by the normal stress and proppant thickness. The depth of shearing-concurrent striations on fracture surfaces suggests that the magnitude of proppant embedment is controlled by the applied normal stress. Under high normal stress, the reduced friction implies that shear slip is more likely to occur on propped fractures in deeper reservoirs. The increase in the number of proppant layers, from monolayer to triple layers, significantly increases the friction of the propped fracture due to the interlocking of the particles and jamming. Permeability of the propped fracture is mainly controlled by the magnitude of the normal stress, the proppant thickness, and the proppant grain size. Permeability of the propped fracture decreases during shearing due to proppant particle crushing and related clogging. Proppants are prone to crushing if the shear loading evolves concurrently with the normal loading.

42 ENGINEERING↗

The Wind Forecast Improvement Project (WFIP): A Public–Private Partnership Addressing Wind Energy Forecast Needs

The Wind Forecast Improvement Project (WFIP) is a public–private research program, the goal of which is to improve the accuracy of short-term (0–6 h) wind power forecasts for the wind energy industry. WFIP was sponsored by the U.S. Department of Energy (DOE), with partners that included the National Oceanic and Atmospheric Administration (NOAA), private forecasting companies (WindLogics and AWS Truepower), DOE national laboratories, grid operators, and universities. WFIP employed two avenues for improving wind power forecasts: first, through the collection of special observations to be assimilated into forecast models and, second, by upgrading NWP forecast models and ensembles. The new observations were collected during concurrent year-long field campaigns in two high wind energy resource areas of the United States (the upper Great Plains and Texas) and included 12 wind profiling radars, 12 sodars, several lidars and surface flux stations, 184 instrumented tall towers, and over 400 nacelle anemometers. Results demonstrate that a substantial reduction (12%–5% for forecast hours 1–12) in power RMSE was achieved from the combination of improved numerical weather prediction models and assimilation of new observations, equivalent to the previous decade’s worth of improvements found for low-level winds in NOAA/National Weather Service (NWS) operational weather forecast models. Data-denial experiments run over select periods of time demonstrate that up to a 6% improvement came from the new observations. Ensemble forecasts developed by the private sector partners also produced significant improvements in power production and ramp prediction. Based on the success of WFIP, DOE is planning follow-on field programs.

17 WIND ENERGY↗

Quantification of the Radiative Effect of Aerosol–Cloud Interactions in Shallow Continental Cumulus Clouds

The indirect radiative effect of aerosol variability on shallow cumulus clouds is realized in nature with considerable concurrent meteorological variability. Large-eddy simulations constrained by observations at a continental site in Oklahoma are performed to represent the variability of different meteorological states on days with different aerosol conditions. The total radiative effect of this natural covariation between aerosol and other meteorological drivers of total cloud amount and albedo is quantified. The changes to these bulk quantities are used to understand the response of the cloud radiative effect to aerosol–cloud interactions (ACI) in the context of concurrent processes, as opposed to attempting to untangle the effect of individual processes on a case-by-case basis. Mutual information (MI) analysis suggests that meteorological variability masks the strength of the relationship between cloud drop number concentration and the cloud radiative effect. This is shown to be mostly due to variation in solar zenith angle and cloud field horizontal heterogeneity masking the relationship between cloud drop number and cloud albedo. By combining MI and more traditional differential analyses, a framework to identify important modes of covariation between aerosol, clouds, and meteorological conditions is developed. This shows that accounting for solar zenith angle variation and implementing an albedo bias correction increases the detectability of the radiative effects of ACI in simulations of shallow cumulus.

54 ENVIRONMENTAL SCIENCES↗

Contributions of Different Combinations of the IPO and AMO to Recent Changes in Winter East Asian Jets

Recent concurrent shifts of the East Asian polar-front jet (EAPJ) and the East Asian subtropical jet (EASJ) in the boreal winter have raised concerns, since they could result in severe weather events over East Asia. However, the possible mechanisms are not fully understood. In this study, the roles of the interdecadal Pacific oscillation (IPO) and the Atlantic multidecadal oscillation (AMO) are investigated by analyzing reanalysis data and model simulations. Results show that combinations of opposite phases of the IPO and AMO can result in significant shifts of the two jets during 1920–2014. This relationship is particularly evident during 1999–2014 and 1979–98 in the reanalysis data. A combination of a negative phase of the IPO (-IPO) and a positive phase of the AMO (+AMO) since the late 1990s has enhanced the meridional temperature gradient and the Eady growth rate and thus westerlies over the region between the two jets, but weakened them to the south and north of the region, thereby contributing to the equatorward and poleward shifts of the EAPJ and EASJ, respectively. Atmospheric model simulations are further used to investigate the relative contribution of -IPO and +AMO to the jet shifts. The model simulations show that the combination of -IPO and +AMO favors the recent jet changes more than the individual -IPO or +AMO. Finally, under a concurrent -IPO and +AMO, the meridional eddy transport of zonal momentum and sensitive heat strengthens, and more mean available potential energy converts to the eddy available potential energy over the region between the two jets, which enhances westerly winds there.

54 ENVIRONMENTAL SCIENCES↗

Northern Hemisphere Winter Air Temperature Patterns and Their Associated Atmospheric and Ocean Conditions

The Northern Hemisphere (NH) has experienced winter Arctic warming and continental cooling in recent decades, but the dominant patterns in winter surface air temperature (SAT) are not well understood. Here, a self-organizing map (SOM) analysis is performed to identify the leading patterns in winter daily SAT fields from 1979 to 2018, and their associated atmospheric and ocean conditions are also examined. Three distinct winter SAT patterns with two phases of nearly opposite signs and a time scale of 7–12 days are found: one pattern exhibits concurrent SAT anomalies of the same sign over North America (NA) and northern Eurasia, while the other two patterns show SAT anomalies of opposite signs between, respectively, NA and the Bering Sea, and the Kara Sea and East Asia (EA). Winter SAT variations may arise from changes in the SOM frequencies. Specifically, the observed increasing trends of winter cold extremes over NA, central Eurasia, and EA during 1998–2013 can be understood as a result of the increasing occurrences of some specific SAT patterns. These SOMs are closely related to poleward advection of midlatitude warm air and equatorward movements of polar cold airmass. These meridional displacements of cold and warm airmasses cause concurrent anomalies over different regions not only in SAT but also in water vapor and surface downward longwave radiation. Anomalous sea surface temperatures in the tropical Pacific, midlatitude North Pacific, and North Atlantic and anomalous Arctic sea ice concentrations also concur to support and maintain the anomalous atmospheric circulation that causes the SAT anomalies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Online data analysis and reduction: An important co-design motif for extreme-scale computers

A growing disparity between supercomputer computation speeds and I/O rates means that it is rapidly becoming infeasible to analyze supercomputer application output only after that output has been written to a file system. Instead, data-generating applications must run concurrently with data reduction and/or analysis operations, with which they exchange information via high-speed methods such as interprocess communications. The resulting parallel computing motif, online data analysis and reduction (ODAR), has important implications for both application and HPC systems design. Here we introduce the ODAR motif and its co-design concerns, describe a co-design process for identifying and addressing those concerns, present tools that assist in the co-design process, and present case studies to illustrate the use of the process and tools in practical settings.

Data Analysis↗

Enabling off-highway diesel engine downsizing and performance improvement using electrically assisted turbocharging

Internal combustion engine (ICE) downsizing through various turbocharging configurations is generally known by the powertrain design community as an effective means to reduce frictional losses, increase waste heat recovery, and improve fuel efficiency while increasing engine power density. However, often is the case that turbocharging strategies, including variable geometry turbochargers, and regulated two-stage turbochargers, incur the performance tradeoff between transient response and fuel economy (pumping losses) at high engine speeds. For off-highway vehicles having particularly transient and high-powered duty cycles, efforts to improve this tradeoff and increase operational flexibility have turned to evaluating various electrified air system architectures. In this study, a 4.5 L diesel-ICE configured with an electrically driven compressor (eBooster ® ) is placed in series with a conventional turbocharger and integrated into a 48 V mild-hybrid powertrain architecture. The objective of this powertrain configuration is to enable engine downsizing by 34%, replacing the current 6.8 L ICE platform with the hybridized 4.5 L ICE concept. The commercial 1-D simulation software GT-SUITE is used for powertrain system development and system optimization. Development and validation of the GT-SUITE model and air system controls is concurrently supported through experimental data collection. The simulation model development includes using machine learning methods for optimizing exhaust gas dilution, injection timing, and eBooster ® power to improve steady-state and transient brake-specific fuel consumption while minimizing criteria pollutant emissions. It was found that total specific fluid consumption over the standardized non-road transient engine duty cycle could be reduced by 18% over the current 6.8 L engine by using an optimized eBoosted 4.5 L engine. The hybridized 4.5 L engine concept concurrently showed sufficient transient response capability and nearly an order of magnitude reduction in duty cycle total soot production.

25 ENERGY STORAGE↗

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses

We currently understand the carbon cycle in methanogenic environments as trophic interactions revolving around interspecies H 2 transfer between organotrophs and methanogens. However, many H 2 -generating processes are thermodynamically sensitive to H 2 accumulation and can be inhibited by high H 2 concentrations produced by other metabolisms. To uncover how anaerobes combat this H 2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology – methanogenic bioreactors. Through analysis of 15 anaerobic digesters, we recover 1343 high-quality metagenome-assembled genomes (MAGs) and corresponding gene expression profiles for diverse uncultured lineages spanning 66 phyla and reconstruct their individual metabolic capacities. We discover that diverse uncultured organotrophic populations can drive H 2 -sensitive degradation through (i) metabolic coupling with concurrent H 2 -tolerant catabolism, (ii) unprecedented shifts from H 2 generation to CO 2 -reducing formate transfer and cytochrome/pili-mediated direct interspecies electron transfer for avoiding thermodynamic conflict, and (iii) integration of low-concentration O 2 as an ancillary thermodynamics-enhancing electron sink. Archaeal populations in situ support the above processes through novel metabolisms distinct from conventional methanogenesis – high-affinity H 2 oxidation driven by methyl-reducing methanogenesis and concomitant uptake of formate, electrons, and acetate from HS metabolism by Methanothrix. In total, synthesis of omics analyses and eco-thermodynamics reveals overlooked metabolic behavior and interactions of uncultured organisms that address a central issue in methanogenic carbon cycling, thermodynamic conflict among diverse concurrent metabolic processes.

59 BASIC BIOLOGICAL SCIENCES↗

Combined near- and far-field high-energy diffraction microscopy dataset for Ti-7Al tensile specimen elastically loaded in situ

High-energy diffraction microscopy (HEDM) constitutes a suite of combined X-ray characterization methods, which hold the unique advantage of illuminating the microstructure and micromechanical state of a material during concurrent in situ mechanical deformation. The data generated from HEDM experiments provides a heretofore unrealized opportunity to validate meso-scale modeling techniques, such as crystal plasticity finite element modeling (CPFEM), by explicitly testing the accuracy of these models at the length scales where the models predict their response. Combining HEDM methods with in situ loading under known and controlled boundary conditions represents a significant challenge, inspiring the recent development of a new high-precision rotation and axial motion system for simultaneously rotating and axially loading a sample. In this paper, we describe the initial HEDM dataset collected using this hardware on an alpha-titanium alloy (Ti-7Al) under in situ tensile deformation at the Advanced Photon Source, Argonne National Laboratory. We present both near-field HEDM data that maps out the grain morphology and intragranular crystallographic orientations and far-field HEDM data that provides the grain centroid, grain average crystallographic orientation, and grain average elastic strain tensor for each grain. Finally, we provide a finite element mesh that can be utilized to simulate deformation in the volume of this Ti-7Al specimen.

36 MATERIALS SCIENCE↗

Evaluating the Rate of Upgrade to Invasive Breast Cancer and/or Ductal Carcinoma In Situ Following a Core Biopsy Diagnosis of Non-classic Lobular Carcinoma In Situ

Background: A diagnosis of non-classic lobular carcinoma in situ (NC-LCIS) encompasses a variety of lesions with poorly characterized natural history. We evaluated upgrade rates and factors associated with upgrade to malignancy following a core biopsy diagnosis of NC-LCIS, and its natural history. Methods: Upon Institutional Review Board approval, pathology databases were searched for NC-LCIS core biopsy diagnoses (carcinoma in situ [CIS], CIS with ductal and lobular features [CIS/DLF], pleomorphic LCIS [P-LCIS], variant LCIS [V-LCIS], LCIS with necrosis). Cases with available core and excision pathology were included, while cases with concurrent ipsilateral invasive carcinoma (IC), ductal carcinoma in situ (DCIS), and/or atypical ductal hyperplasia were excluded. Results: Overall, 121 NC-LCIS cases were identified from 1998 to 2017. We excluded 46 cases with concurrent cancer; 75 patients with 76 NC-LCIS core biopsy diagnoses followed by excision formed our study cohort. Median age was 56 years (range 41–83), and all imaging findings were classified as Breast Imaging Reporting and Data System 4; calcifications were the most common biopsy indication (80%). Excision yielded malignancy in 27 (36%) patients (IC 17, 63%; DCIS alone 10, 37%). We were unable to identify radiologic or pathologic features predictive of upgrade. Of 49 pure NC-LCIS cases, 15 (31%) had mastectomy, 9 (18%) had excision and radiation, and 25 (51%) had excision alone. At a median follow-up of 58 months (range 1–224), 1/25 (4%) patients with excision alone developed ipsilateral DCIS 14 months later. Conclusions: In this series of NC-LCIS, 36% of cases were upgraded, supporting routine excision. We were unable to identify predictors of upgrade. Among 25 patients with pure NC-LCIS, only one patient developed a future ipsilateral cancer. Further study of the natural history of NC-LCIS is warranted.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Radiological Staging for Distant Metastases in Breast Cancer Patients with Confirmed Local and/or Locoregional Recurrence: How Useful are Current Guideline Recommendations?

Background: Breast cancer patients with local and/or locoregional recurrence (LR) are at higher risk of developing distant metastases (DM) at a later time. Once LR has been confirmed, some international interdisciplinary guidelines recommend performing radiological examinations for DM to determine the course of further therapy (curative or palliative approach). This study analyzed the metastatic patterns of patients with LR with particular regard to the frequency of concurrent diagnosis of LR and DM; in other words: are radiological staging procedures actually justified for DM at the time of diagnosis of LR? Methods: This study included all patients (n = 1368) who were diagnosed and treated for nonmetastatic breast cancer (Stage I–III) at the University Women’s Hospital Basel, Switzerland between 1990 and 2009. Results: In 137 patients, LR was diagnosed without a history of DM: in-breast/thoracic wall only, n = 90 (65.7%); involvement of axillary/supra-/infraclavicular lymph nodes, n = 47 (34.3%). DM was found at the time of diagnosis of LR in 44 patients (32.1%). Concurrent diagnosis of LR and DM occurred significantly more often in patients with lymph node recurrence compared with those with in-breast/chest wall recurrence (48.9% vs. 23.3%; p = 0.004). Conclusions: Approximately one-third of patients with a LR had synchronous DM at the time of their local/locoregional event. For this reason, routine systemic staging imaging at the time of LR should be an absolute requirement for planning further therapy. Confirmation of DM may spare the patients radical surgical interventions with questionable impact on survival in the face of an incurable disease.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Massively Parallel, Three-Dimensional Transport Solutions for the k-Eigenvalue Problem

We have implemented a new multilevel parallel decomposition in the Denovo dis- crete ordinates radiation transport code. In concert with Krylov subspace iterative solvers, the multilevel decomposition allows concurrency over energy in addition to space-angle, enabling scalability beyond the limits imposed by the traditional KBA space-angle partitioning. Furthermore, a new Arnoldi-based k-eigenvalue solver has been implemented. The added phase-space concurrency combined with the high- performance Krylov and Arnoldi solvers has enabled weak scaling to O(100K) cores on the Jaguar XK6 supercomputer. The multilevel decomposition provides sucient parallelism to scale to exascale computing and beyond.

Arnoldi↗

Reversion and T Cell Escape Mutations Compensate the Fitness Loss of a CD8+ T Cell Escape Mutant in Their Cognate Transmitted/Founder Virus

Immune escape mutations that revert back to the consensus sequence frequently occur in newly HIV-1-infected individuals and have been thought to render the viruses more fit. However, their impact on viral fitness and their interaction with other immune escape mutations have not been evaluated in the background of their cognate transmitted/founder (T/F) viral genomes. To precisely determine the role of reversion mutations, we introduced reversion mutations alone or together with CD8+ T cell escape mutations in their unmodified cognate T/F viral genome and determined their impact on viral fitness in primary CD4+ T cells. Two reversion mutations, V247I and I64T, were identified in Gag and Tat, respectively, but neither had measurable effect on the fitness of their cognate T/F virus. The V247I and G248A mutations that were detected before and concurrently with the potent T cell escape mutation T242N, respectively, were selected by early T cell responses. The V247I or the G248A mutation alone partially restored the fitness loss caused by the T242N mutation. Together they could fully restore the fitness of the T242N mutant to the T/F level. These results demonstrate that the fitness loss caused by a T cell escape mutation could be compensated by preexisting or concurrent reversion and other T cell escape mutations. Our findings indicate that the overall viral fitness is modulated by the complex interplay among T cell escape, compensatory and reversion mutations to maintain the balance between immune escape and viral replication capacity.

59 BASIC BIOLOGICAL SCIENCES↗

In Situ Visualization and Production of Extract Databases

Simulations running at high concurrency on HPC systems generate large volumes of data that are impractical to write to disk due to time and storage constraints. Applications often adapt by saving data infrequently, resulting in datasets with poor temporal resolution. This can make datasets difficult to interpret during post hoc visualization and analysis, or worse, it can lead to lost science. In Situ visualization and analysis can enable efficient production of small data products such as rendered images or surface extracts that consist of polygonal geometry plus fields. These data products are far smaller than their source data and can be processed much more economically in a traditional post hoc workflow using far fewer computational resources. We used the SENSEI and Libsim in situ infrastructures to implement rendering workflow and surface data extraction workflows in the AVF-LESLIE combustion code. Finally, these workflows were then demonstrated at high levels of concurrency and showed significant data reductions and limited impact on the simulation runtime.

97 MATHEMATICS AND COMPUTING↗

Preventing Run-Time Bugs at Compile-Time Using Advanced C++

When writing software, we develop algorithms that tell the computer what to do at run-time. Our solutions are easier to understand and debug when they are properly modeled using class hierarchies, enumerations, and a well-factored API. Unfortunately, even with these design tools, we end up having to debug our programs at run-time. Worse still, debugging an embedded system changes its dynamics, making it tough to find and fix concurrency issues. This paper describes techniques using C++ to detect run-time bugs *at compile time*. A concurrency library, developed at Fermilab, is used for examples in illustrating these techniques.

43 PARTICLE ACCELERATORS↗