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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

mRNA SARS-CoV-2 Immunization Confers Robust Antibody Response in Occupational Healthcare Workers and Fosters Workplace Safety

Immunization against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a major step in protecting the healthcare worker beyond standard pandemic precautions and infection control measures. Healthcare workers (HCW) are at high risk for SARS-CoV-2 exposure and infection placing burden on the workplace. Hence, reducing SARS-CoV-2 infection of HCWs serves multiple goals in the occupational health arena. These include protecting the health and safety of the HCW as well as reducing transmission of Coronavirus Disease 2019 (COVID-19) in the clinic and the larger workplace it serves. Furthermore, when HCWs demonstrate appropriate pandemic precautions and health practices, they serve as strategic models for other workers. Here, this modeling represents leadership which can inspire optimism and hope in a workforce beleaguered by the pandemic.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Developing MiniApps on Modern Platforms Using Multiple Programming Models, In: 2015 IEEE International Conference on Cluster Computing

We have developed a set of reduced, proxy applications ("MiniApps") based on large-scale application codes supported at the Oak Ridge Leadership Computing Facility (OLCF). The MiniApps are designed to encapsulate the details of the most important (i.e. the most time-consuming and/or unique) facets of the applications that run in production mode on the OLCF. In each case, we have produced or plan to produce individual versions of the MiniApps using different specific programming models (e.g., OpenACC, CUDA, OpenMP). We describe some of our initial observations regarding these different implementations along with estimates of how closely the MiniApps track the actual performance characteristics (in particular, the overall scalability) of the large-scale applications from which they are derived.

Computer Science↗
DOE OSTI2015

Exploring Memory Hierarchy to Improve Scientific Data Read Performance, In: 2015 IEEE International Conference on Cluster Computing

Improving read performance is one of the major challenges with speeding up scientific data analytic applications. Utilizing the memory hierarchy is one major line of researches to address the read performance bottleneck. Related methods usually combine solide-state-drives(SSDs) with dynamic random-access memory(DRAM) and/or parallel file system(PFS) to mitigate the speed and space gap between DRAM and PFS. However, these methods are unable to handle key performance issues plaguing SSDs, namely read contention that may cause up to 50% performance reduction. In this paper, we propose a framework that exploits the memory hierarchy resource to address the read contention issues involved with SSDs. The framework employs a general purpose online read algorithm that able to detect and utilize memory hierarchy resource to relieve the problem. To maintain a near optimal operating environment for SSDs, the framework is able to orchastrate data chunks across different memory layers to facilitate the read algorithm. Compared to existing tools, our framework achieves up to 50% read performance improvement when tested on datasets from real-world scientific simulations.

Computer Science↗
DOE OSTI2015

Fast Fault Injection and Sensitivity Analysis for Collective Communications, In: 2015 IEEE International Conference on Cluster Computing

The collective communication operations, which are widely used in parallel applications for global communication and synchronization are critical for application's performance and scalability. However, how faulty collective communications impact the application and how errors propagate between the application processes is largely unexplored. One of the critical reasons for this situation is the lack of fast evaluation method to investigate the impacts of faulty collective operations. The traditional random fault injection methods relying on a large amount of fault injection tests to ensure statistical significance require a significant amount of resources and time. These methods result in prohibitive evaluation cost when applied to the collectives. In this paper, we introduce a novel tool named Fast Fault Injection and Sensitivity Analysis Tool (FastFIT) to conduct fast fault injection and characterize the application sensitivity to faulty collectives. The tool achieves fast exploration by reducing the exploration space and predicting the application sensitivity using Machine Learning (ML) techniques. A basis for these techniques are implicit correlations between MPI semantics, application context, critical application features, and application responses to faulty collective communications. The experimental results show that our approach reduces the fault injection points and tests by 97% for representative benchmarks (NAS Parallel Benchmarks (NPB)) and a realistic application (Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)) on a production supercomputer. Further, we statistically generalize the application sensitivity to faulty collective communications for these workloads, and present correlation between application features and the sensitivity.

Computer Science↗
DOE OSTI2015

TRIO: Burst Buffer Based I/O Orchestration, In: 2015 IEEE International Conference on Cluster Computing

The growing computing power on leadership HPC systems is often accompanied by ever-escalating failure rates. Checkpointing is a common defensive mechanism used by scientific applications for failure recovery. However, directly writing the large and bursty checkpointing dataset to parallel file systems can incur significant I/O contention on storage servers. Such contention in turn degrades bandwidth utilization of storage servers and prolongs the average job I/O time of concurrent applications. Recently burst buffers have been proposed as an intermediate layer to absorb the bursty I/O traffic from compute nodes to storage backend. But an I/O orchestration mechanism is still desirable to efficiently move checkpointing data from burst buffers to storage backend. In this paper, we propose a burst buffer based I/O orchestration framework, named TRIO, to intercept and reshape the bursty writes for better sequential write traffic to storage servers. Meanwhile, TRIO coordinates the flushing orders among concurrent burst buffers to alleviate the contention on storage server. Our experimental results demonstrated that TRIO could efficiently utilize storage bandwidth and reduce the average job I/O time by 37% on average for data-intensive applications in typical checkpointing scenarios.

Computer Science↗
DOE OSTI2015

An Approach to Selecting Thread + Process Mixes for Hybrid MPI + OpenMP Applications, In: 2015 IEEE International Conference on Cluster Computing

Hybrid MPI + OpenMP is a popular means of programming modern machines that feature substantial parallelism both off-node and on-node. Determining the right mix of the two programming models to use, however, is not as straightforward as simply using exclusively OpenMP on-node and limiting MPI to only inter-node communication. We present a step-by-step methodology to help make the decision of which mix of the two programming models to use. It starts with an estimate of the performance of a generic hybrid application on a given machine and incorporates additional available information about the specific application and the machine to provide guidance for selecting effective mixes of MPI processes and OpenMP threads to use when running that application on the machine in question. We validate our approach on four different applications on an IBM Blue Gene/Q, a Cray XK7, and a Cray XC30.

Computer Science↗
DOE OSTI2015

Understanding and Exploiting Spatial Properties of System Failures on Extreme-Scale HPC Systems, In: 2015 45th Annual IEEE/IFIP International Conference on Dependable Systems and Networks

As we approach exascale, the scientific simulations are expected to experience more interruptions due to increased system failures. Designing better HPC resilience techniques requires understanding the key characteristics of system failures on these systems. While temporal properties of system failures on HPC systems have been well-investigated, there is limited understanding about the spatial characteristics of system failures and its impact on the resilience mechanisms. Therefore, we examine the spatial characteristics and behavior of system failures. We investigate the interaction between spatial and temporal characteristics of failures and its implications for system operations and resilience mechanisms on large-scale HPC systems. We show that system failures have "spatial locality" at different granularity in the system, study impact of different failure-types, and investigate the correlation among different failure-types. Finally, we propose a novel scheme that exploits the spatial locality in failures to improve application and system performance. Our evaluation shows that the proposed scheme significantly improves the system performance in a dynamic and production-level HPC system.

Computer Science↗
DOE OSTI2015

Resident Block-Structured Adaptive Mesh Refinement on Thousands of Graphics Processing Units, In: 2015 44th International Conference on Parallel Processing

Block-structured adaptive mesh refinement (AMR) is a technique that can be used when solving partial differential equations to reduce the number of cells necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a resident GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an 8 node cluster, and 4,196 nodes of Oak Ridge National Laboratory's Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and is scalable on 4,196 K20x GPUs using a combination of MPI and CUDA.

Computer Science↗
DOE OSTI2015

Spatial Locality-Aware Cache Partitioning for Effective Cache Sharing, In: 2015 44th International Conference on Parallel Processing

In modern multi-core processors, last-level caches (LLCs) are typically shared among multiple cores. Previous works have shown that such sharing is beneficial as different workloads have different needs for cache capacity, and logical partitioning of capacity can improve system performance. However, what is missing in previous works on partitioning shared LLCs is that the heterogeneity in spatial locality among workloads has not been explored. In other words, all the cores use the same block/line size in shared LLCs. In this work, we highlight that exploiting spatial locality enables much more effective cache sharing. The fundamental reason is that for many memory intensive workloads, their cache capacity requirements can be drastically reduced when a large block size is employed, therefore they can effectively donate more capacity to other workloads. To leverage spatial locality for cache partitioning effectively, we first propose a simple yet effective mechanism to measure both spatial and temporal locality at run-time. The locality information is then used to determine both the proper block size and the capacity assigned to each workload. Our experiments show that our Spatial Locality-aware Cache Partitioning (SLCP) significantly outperforms the previous works. We also present several case studies that dissect the effectiveness of SLCP compared to the existing approaches.

Computer Science↗
DOE OSTI2018

2018 IEEE International Conference on Probabilistic Methods Applied to Power Systems (PMAPS)

As hydroelectric utilities move toward probabilistic risk assessments that capture the increased degradation resulting from an increase in unit starts, there is a need to capture how reliably a hydroelectric facility is being operated. Traditional statistics like EAF and EFOR are still necessary but do not capture intra-facility decisions made on a yearly or sub-yearly time frame, as it is possible to operate in the least reliable dispatch case for small periods of time and still avoid major unit outages. Our proposed Reliability Index fills this need and provides asset management decision makers with another tool for benchmarking facilities.

Signore, Stephen R.↗
DOE OSTI2019

Oral immunization of mice with Lactococcus lactis expressing Shiga toxin truncate confers enhanced protection against Shiga toxins of Escherichia coli O157:H7 and Shigella dysenteriae

Regardless of the communal impact of Shiga toxins, till today neither a specific treatment nor licensed vaccine is available. Lactococcus lactis ( L. lactis ), generally regarded as safe organism, is well known to provide a valuable approach regarding the oral delivery of vaccines. This study was undertaken to evaluate the protective efficacy of Stx2a1 expressed in nisin‐inducible L. lactis, against Shiga toxins (Stx1, Stx2) in mouse model. Oral immunization of BALB/c mice with LL ‐ Stx2a1 elicited significant serum antibody titer with elevated fecal and serum IgA, along with minimized intestinal and kidney damage resulting in survival of immunized animals at 84% and 100% when challenged with 10 × LD 50 of Escherichia coli O157 and Shigella dysenteriae toxins, respectively. HeLa cells incubated with immune sera and toxin mixture revealed high neutralizing capacity with 90% cell survivability against both the toxins. Mice immunized passively with both toxins and antibody mixture survived the observation period of 15 days, and the controls administered with sham sera and toxins were succumbed to death within 3 days. Our results revealed protective efficacy and toxin neutralization ability of LL‐Stx2a1, proposing it as an oral vaccine candidate against Shiga toxicity mediated by E. coli O157 and S. dysenteriae .

Sreerohini, Sagi↗
DOE OSTI2017

Neuronal Rho GTPase Rac1 elimination confers neuroprotection in a mouse model of permanent ischemic stroke

Abstract The Rho GTPase Rac1 is a multifunctional protein involved in distinct pathways ranging from development to pathology. The aim of the present study was to unravel the contribution of neuronal Rac1 in regulating the response to brain injury induced by permanent focal cerebral ischemia (pMCAO). Our results show that pMCAO significantly increased total Rac1 levels in wild type mice, mainly through rising nuclear Rac1, while a reduction in Rac1 activation was observed. Such changes preceded cell death induced by excitotoxic stress. Pharmacological inhibition of Rac1 in primary neuronal cortical cells prevented the increase in oxidative stress induced after overactivation of glutamate receptors. However, this was not sufficient to prevent the associated neuronal cell death. In contrast, RNAi‐mediated knock down of Rac1 in primary cortical neurons prevented cell death elicited by glutamate excitotoxicity and decreased the activity of NADPH oxidase. To test whether in vivo down regulation of neuronal Rac1 was neuroprotective after pMCAO, we used tamoxifen‐inducible neuron‐specific conditional Rac1‐knockout mice. We observed a significant 50% decrease in brain infarct volume of knockout mice and a concomitant increase in HIF‐1α expression compared to littermate control mice, demonstrating that ablation of Rac1 in neurons is neuroprotective. Transmission electron microscopy performed in the ischemic brain showed that lysosomes in the infarct of Rac1‐ knockout mice were preserved at similar levels to those of non‐infarcted tissue, while littermate mice displayed a decrease in the number of lysosomes, further corroborating the notion that Rac1 ablation in neurons is neuroprotective. Our results demonstrate that Rac1 plays important roles in the ischemic pathological cascade and that modulation of its levels is of therapeutic interest.

Karabiyik, Cansu↗
DOE OSTI2016

Knockdown of a laccase in Populus deltoides confers altered cell wall chemistry and increased sugar release

Summary Plant laccases are thought to function in the oxidation of monolignols which leads to higher order lignin formation. Only a hand‐full of laccases in plants have been functionally evaluated, and as such little is known about the breadth of their impact on cell wall chemistry or structure. Here, we describe a previously uncharacterized laccase from Populus , encoded by locus Potri.008G064000, whose reduced expression resulted in transgenic Populus trees with changes in syringyl/guaiacyl ratios as well as altered sugar release phenotypes. These phenotypes are consistent with plant biomass exhibiting reduced recalcitrance. Interestingly, the transgene effect on recalcitrance is dependent on a mild pretreatment prior to chemical extraction of sugars. Metabolite profiling suggests the transgene modulates phenolics that are associated with the cell wall structure. We propose that this particular laccase has a range of functions related to oxidation of phenolics and conjugation of flavonoids that interact with lignin in the cell wall.

09 BIOMASS FUELS↗
DOE OSTI2018

Year 2 instrument status from the SPT-3G cosmic microwave background receiver (Conference Presentation)

The South Pole Telescope (SPT) is a millimeter-wavelength telescope surveying the cosmic microwave background (CMB). The SPT measures both the temperature and polarization of the CMB with a large aperture, resulting in high-resolution maps sensitive to signals across a wide range of angular scales on the sky. With these capabilities, the SPT has the potential to constrain inflationary gravitational waves as well as the effect of massive neutrinos on large-scale structure formation. The SPT was upgraded in late 2016 with a new receiver (SPT-3G) containing 16,0000 polarization-sensitive transition-edge sensor bolometers. Several key technological developments have enabled this large-format focal, including advances in detectors, readout electronics, and large millimeter-wavelength optics. We will discuss the implementation of these technologies in the SPT-3G receiver as well as the challenges they presented. In late 2017 the implementations of all three of these technologies were iterated to optimize total performance. Here, we present the current instrument status of the SPT-3G receiver.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Design and characterization of the SPT-3G receiver (Conference Presentation)

(On behalf of the SPT-3G collaboration)The SPT-3G receiver was commissioned in early 2017 on the 10-meter South Pole Telescope (SPT) to map the Cosmic Microwave Background (CMB) with arcminute resolution. The new instrument significantly improves on previous SPT camera designs, offering unprecedented sensitivity to the CMB’s temperature and polarization anisotropies while maintaining a tight control on systematic effects.A restructured optics chain features new secondary and tertiary mirrors to increase the receiver’s field of view by a factor of four in area, coupling light through a set of four cryogenic 720 mm alumina elements, which re-image the Gregorian focus inside the receiver. The broad-band (70-270 GHz) anti-reflective coated lenses are paired with a Lyot stop and cooled to 4 K using a dedicated two-stage pulse-tube cooler (PTC) to minimize in-band attenuation, internal radiative loading, and stray light on the considerably larger focal plane, which is populated with ~2,700 diffraction-limited pixels.Each independent pixel incorporates a lenslet-coupled broadband sinuous antenna, which routes signals through superconducting transmission lines and in-line band-defining filters to six transition-edge sensors, each measuring one of three bands (90, 150, and 220 GHz) and two polarizations, yielding a total of ~16,000 bolometers distributed across ten 150 mm monolithic wafers on a 430 mm image plane. A robust mechanical and thermal architecture supports and cools all detectors across this sizable focal plane to ~250 mK using a closed-cycle Helium adsorption refrigerator backed by a PTC, allowing a duty cycle greater than 90%.This order of magnitude increase in detector count relies on an improved digital frequency-domain SQUID readout system which integrates superconducting inductor-capacitor resonators wired in series with each bolometer to achieve a 68x multiplexing factor while mitigating noise and crosstalk effects.Cumulatively, SPT-3G’s new optics, detector, and readout strategies boast a potential factor of ~20 improvement in mapping speed over its predecessor, SPT-Pol, offering the potential to improve our understanding of inflationary physics, astroparticle physics, and growth of structure. We summarize the new receiver’s core design principles, outline technology characterization results, and report on plans for future upgrades.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗