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Understanding and Improving High-Performance I/O Subsystems

This research program has been conducted in the framework of the NASA Earth and Space Science (ESS) evaluations led by Dr. Thomas Sterling. In addition to the many important research findings for NASA and the prestigious publications, the program has helped orienting the doctoral research program of two students towards parallel input/output in high-performance computing. Further, the experimental results in the case of the MasPar were very useful and helpful to MasPar with which the P.I. has had many interactions with the technical management. The contributions of this program are drawn from three experimental studies conducted on different high-performance computing testbeds/platforms, and therefore presented in 3 different segments as follows: 1. Evaluating the parallel input/output subsystem of a NASA high-performance computing testbeds, namely the MasPar MP- 1 and MP-2; 2. Characterizing the physical input/output request patterns for NASA ESS applications, which used the Beowulf platform; and 3. Dynamic scheduling techniques for hiding I/O latency in parallel applications such as sparse matrix computations. This study also has been conducted on the Intel Paragon and has also provided an experimental evaluation for the Parallel File System (PFS) and parallel input/output on the Paragon. This report is organized as follows. The summary of findings discusses the results of each of the aforementioned 3 studies. Three appendices, each containing a key scholarly research paper that details the work in one of the studies are included.

El-Ghazawi, Tarek A.↗

Rhamnogalacturonan I is a recalcitrant pectin domain during Clostridium thermocellum -mediated deconstruction of switchgrass biomass

Background Liquid fuels from lignocellulosic feedstocks are required for transition to a sustainable bioeconomy. However, the recalcitrance of carbon-containing feedstock cell walls to deconstruction poses a barrier to cost effective biological conversion of plant biomass to biofuels. One-step consolidated bioprocessing (CBP) in which anaerobic thermophilic bacteria convert lignocellulosic biomass into liquid fuels is a platform for overcoming the recalcitrance of plant biomass. Results The amounts of hemicellulosic and pectic polysaccharides, two complex cell wall glycans that contribute to plant biomass recalcitrance and that are partially solubilized during CBP of switchgrass aerial biomass by Clostridium thermocellum were evaluated in the liquor, solid residues and residue washate recovered during a 120-h CBP process. After 120 h, 24% of milled switchgrass was solubilized in the C. thermocellum CBP platform. Higher concentrations of arabinose, xylose, galactose, and glucose accumulated in the CBP-fermentation liquor and washate compared to fermentation controls without C. thermocellum, indicating that C. thermocellum solubilized hemicelluloses, but did not fully metabolize them. After five days of fermentation, the relative amount of rhamnose in the solid residues increased by 16% compared to controls, and CBP solid residues had more than 23% increased reactivity against RG-I reactive monoclonal antibodies, indicating that the pectic polymer rhamnogalacturonan I (RG-I) was not effectively solubilized from switchgrass biomass by C. thermocellum CBP. Similarly, the amount of mannose (Man) in the CBP solid residues increased by 7% and reactivity against galactomannan reactive antibodies increased by greater than 14%, indicating that the hemicellulosic polymer galactomannan was also resistant to degradation by C. thermocellum during CBP fermentation. Conclusions These findings show that C. thermocellum is unable to effectively degrade RG-I pectic and galactomannan hemicellulosic components in switchgrass biomass. Targeting these polymers for improved solubilization could enhance the efficiency of conversion of grass biomass to biofuels.

09 BIOMASS FUELS↗

Experimental Evaluation of Verification and Validation Tools on Martian Rover Software

To achieve its science objectives in deep space exploration, NASA has a need for science platform vehicles to autonomously make control decisions in a time frame that excludes intervention from Earth-based controllers. Round-trip light-time is one significant factor motivating autonomy capability, another factor is the need to reduce ground support operations cost. An unsolved problem potentially impeding the adoption of autonomy capability is the verification and validation of such software systems, which exhibit far more behaviors (and hence distinct execution paths in the software) than is typical in current deepspace platforms. Hence the need for a study to benchmark advanced Verification and Validation (V&V) tools on representative autonomy software. The objective of the study was to access the maturity of different technologies, to provide data indicative of potential synergies between them, and to identify gaps in the technologies with respect to the challenge of autonomy V&V. The study consisted of two parts: first, a set of relatively independent case studies of different tools on the same autonomy code, second a carefully controlled experiment with human participants on a subset of these technologies. This paper describes the second part of the study. Overall, nearly four hundred hours of data on human use of three different advanced V&V tools were accumulated, with a control group that used conventional testing methods. The experiment simulated four independent V&V teams debugging three successive versions of an executive controller for a Martian Rover. Defects were carefully seeded into the three versions based on a profile of defects from CVS logs that occurred in the actual development of the executive controller. The rest of the document is structured a s follows. In section 2 and 3, we respectively describe the tools used in the study and the rover software that was analyzed. In section 4 the methodology for the experiment is described; this includes the code preparation, seeding of defects, participant training and experimental setup. Next we give a qualitative overview of how the experiment went from the point of view of each technology; model checking (section 5), static analysis (section 6), runtime analysis (section 7) and testing (section 8). The find section gives some preliminary quantitative results on how the tools compared.

Brat, Guillaume↗

Gains in operational flexibility, safety margins, and cost efficiencies via integrated Plant Reload Optimization platform

The U.S. Department of Energy Light Water Reactor Sustainability Program Risk-Informed Systems Analysis Pathway Plant Reload Optimization Project aims to develop an integrated, comprehensive framework offering an all-in-one solution for reload evaluations with a special focus on optimizing core design. Optimizing the fuel loading pattern is one of the most important considerations in reducing the amount of new fuel used in the core. Due to thousands of possible core configuration options, finding optimal solutions is an unachievable task for a human. The Plant ReLoad Optimization platform, which supports artificial-intelligence-based reactor core designing, is now fully capable of handling realistic problems. The Plant ReLoad Optimization platform development project aims to build a reactor core design tool that includes reactor safety and fuel performance analyses and uses artificial intelligence to support the optimization of core design solutions. The NSGA-II (Non-dominated Sorting Genetic Algorithm II) optimizer was developed and tested within RAVEN (Risk Analysis and Virtual ENvironment) to handle many constraints by using an augmented objectives methodology. The demonstration was performed with constrained multiobjective optimization of a 17 × 17 pressurized-water reactor core loading patterns to minimize fuel cost and maximize fuel cycle length.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Atmo-ecometabolomics: A novel atmospheric particle chemical characterization methodology for ecological research

Aerosol particles play important roles in processes controlling the composition of the atmosphere and function of ecosystems. A better understanding of the composition of aerosol particles is beginning to be recognized as critical for ecological research to further comprehend the link between aerosols and ecosystems. While chemical characterization of aerosols has been practiced in the atmospheric science community, detailed methodology tailored to the needs of ecological research does not exist yet. In this study, we describe an efficient methodology (atmo-ecometabolomics), in step-by-step details, from the sampling to the data analyses, to characterize the chemical composition of aerosol particles, namely atmo-metabolome. This method employs mass spectrometry platforms such as liquid and gas chromatography mass spectrometries (MS) and Fourier transform ion cyclotron resonance MS (FT-ICR-MS). For methodology evaluation, we analyzed aerosol particles collected during two different seasons (spring and summer) in a low-biologicalactivity ecosystem. Additionally, to further validate our methodology, we analyzed aerosol particles collected in a more biologically active ecosystem during the pollination peaks of three different representative tree species. Our statistical results showed that our sampling and extraction methods are suitable for characterizing the atmo-ecometabolomes in these two distinct ecosystems with any of the analytical platforms. Datasets obtained from each mass spectrometry instrument showed overall significant differences of the atmo-ecometabolomes between spring and summer as well as between the three pollination peak periods. Furthermore, we have identified several metabolites that can be attributed to pollen and other plant-related aerosol particles.We additionally provide a basic guide of the potential use ecometabolomic techniques on different mass spectrometry platforms to accurately analyze the atmoecometabolomes for ecological studies. Our method represents an advanced novel approach for future studies in the impact of aerosol particle chemical compositions on ecosystem structure and function and biogeochemistry.

Rivas-Ubach, Albert (ORCID:0000000312937127)↗

Common Cause Failure Evaluation of High Safety-significant Safety-related Digital Instrumentation and Control Systems

Digital instrumentation and control (DI&C) systems in nuclear power plants (NPPs) have many advantages over analog systems but also pose different engineering and technical challenges, such as potential threats due to common cause failures (CCFs). This paper proposes a Platform for Risk Assessment of DI&C (PRADIC) developed by Idaho National Laboratory for dealing with potential software CCFs in DI&C systems of NPPs. The methodology development of PRADIC on the quantitative evaluation of software CCFs in high safety-significant safety-related DI&C systems in NPPs is illustrated in this paper. In PRADIC, qualitative hazard analysis and quantitative reliability and consequence analysis are successively implemented to obtain quantitative risk information, compare with respective risk evaluation acceptance criteria, and provide suggestions for risk reduction and design optimization. A comprehensive case study was also performed and documented in this paper. Results show that PRADIC can effectively identify potential digital-based CCFs, estimate their failure probabilities, and evaluate their impacts to system and plant safety.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

PLATFORM for Product Launch

Pecan Street Inc. (PSI) and its partners set out in 2017 to validate the PLATFORM for Product Launch, a new model for improving the effectiveness of investments in clean energy technologies and accelerating market entry of disruptive technologies. In partnership with a newly formed Innovation Advisory Council, PSI recruited fourteen companies with new hardware-based technologies that enable or create clean energy opportunities. Pecan Street carried out product evaluations and conducted market research with stakeholders and target customers to develop recommendations on product optimization opportunities for all companies, and created third party performance evaluation reports that include environmental metrics, such as water and energy savings potential, to assist in creating investment confidence and to unlock additional sources of funding, such as impact investments. Pecan Street set-up the product testing environment, performed small-batch field testing, and provided a verified third-party performance report on the product of twelve companies. PSI Street and its partners leveraged the performance evaluations and insights from the newly formed PRI toolkit to raise over $1.5M across five companies, and garner interest for private sector adoption of the PLATFORM for Product Launch.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Flight results from a study of aided inertial navigation applied to landing operations

An evaluation is presented of the approach and landing performance of a Kalman filter aided inertial navigation system using flight data obtained from a series of approaches and landings of the CV-340 aircraft at an instrumented test area. A description of the flight test is given, in which data recorded included: (1) accelerometer signals from the platform of an INS; (2) three ranges from the Ames-Cubic Precision Ranging System; and (3) radar and barometric altimeter signals. The method of system evaluation employed was postflight processing of the recorded data using a Kalman filter which was designed for use on the XDS920 computer onboard the CV-340 aircraft. Results shown include comparisons between the trajectories as estimated by the Kalman filter aided system and as determined from cinetheodolite data. Data start initialization of the Kalman filter, operation at a practical data rate, postflight modeling of sensor errors and operation under the adverse condition of bad data are illustrated.

Mcgee, L. A.↗

Adaptive filtering of biodynamic stick feedthrough in manipulation tasks on board moving platforms

A novel approach to suppress the effects of biodynamic interference is presented. An adaptive noise canceling technique is employed for substracting the platform motion correlated components from the control stick output. The effects of biodynamic interference and its suppression by adaptive noise cancellation has been evaluated in a series of tracking tasks performed in a moving base simulator. Simulator motions were in pitch, roll and combined pitch and roll. Human operator performance was assessed from the mean square values of the tracking error and the control activity. The tracking error and the total stick output signal were found to increase significantly with motion and to diminish substantially with adaptive noise cancellation, thus providing a considerable improvement in tracking performance under conditions in which platform motion were present. The adaptive filter was found to cause a significant increase in the cross-over frequency and decrease in the phase margin. Moreover, the adaptive filter was found to significantly improve the human operator visual motor response. This improvement is manifested as an increased human operator gain, a smaller time delay and lower pilot workload.

Velger, M.↗

Voltage Regulation Performance Evaluation of Distributed Energy Resource Management via Advanced Hardware-in-the-Loop Simulation

This paper evaluates the performance of coordinated control across advanced distribution management systems (ADMS), distributed energy resources (DERs), and distributed energy resource management systems (DERMS) using an advanced hardware-in-the-loop (HIL) platform. This platform provides a realistic laboratory testing environment, including accurate dynamic modeling of a real-world distribution system from a utility partner, real controllers (ADMS and DERMS), physical power hardware (DERs), and standard communications protocols. One grid service—voltage regulation—is evaluated to show the performance of the coordinated grid automation system. The testing results demonstrate that the coordinated DERMS and ADMS system can effectively regulate system voltages within target operation limits using DERs. The realistic laboratory HIL testing results give utilities confidence in adopting the grid automation systems to manage DERs to achieve system-level control and operation objectives (e.g., voltage regulation). This helps utilities mitigate potential risks (e.g., instability) prior to field deployment.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Enabling power measurement and control on Astra: The first petascale Arm supercomputer

Astra, deployed in 2018, was the first petascale supercomputer to utilize processors based on the ARM instruction set. The system was also the first under Sandia's Vanguard program which seeks to provide an evaluation vehicle for novel technologies that with refinement could be utilized in demanding, large-scale HPC environments. In addition to ARM, several other important first-of-a-kind developments were used in the machine, including new approaches to cooling the datacenter and machine. Here we document our experiences building a power measurement and control infrastructure for Astra. While this is often beyond the control of users today, the accurate measurement, cataloging, and evaluation of power, as our experiences show, is critical to the successful deployment of a large-scale platform. While such systems exist in part for other architectures, Astra required new development to support the novel Marvell ThunderX2 processor used in compute nodes. In addition to documenting the measurement of power during system bring up and for subsequent on-going routine use, we present results associated with controlling the power usage of the processor, an area which is becoming of progressively greater interest as data centers and supercomputing sites look to improve compute/energy efficiency and find additional sources for full system optimization.

97 MATHEMATICS AND COMPUTING↗

Quantitative encapsulation and retention of 227 Th and decay daughters in core–shell lanthanum phosphate nanoparticles

Targeted alpha therapy (TAT) offers great promise for treating recalcitrant tumors and micrometastatic cancers. One drawback of TAT is the potential damage to normal tissues and organs due to the relocation of decay daughters from the treatment site. As such, the present study evaluates La( 227 Th)PO 4 core (C) and core +2 shells (C2S) nanoparticles (NPs) as a delivery platform of 227 Th to minimize systemic distribution of decay daughters, 223 Ra and 211 Pb. In vitro retention of decay daughters within La( 227 Th)PO 4 C NPs was influenced by the concentration of reagents used during synthesis, in which the leakage of 223 Ra was between 0.4 ± 0.2% and 20.3 ± 1.1% in deionized water. Deposition of two nonradioactive LaPO 4 shells onto La( 227 Th)PO 4 C NPs increased the retention of decay daughters to >99.75%. The toxicity of the nonradioactive LaPO 4 C and C2S NP delivery platforms was examined in a mammalian breast cancer cell line, BT-474. No significant decrease in cell viability was observed for a monolayer of BT-474 cells for NP concentrations below 233.9 μg mL –1 , however cell viability decreased below 60% when BT-474 spheroids were incubated with either LaPO 4 C or C2S NPs at concentrations exceeding 29.2 μg mL –1 . La( 227 Th)PO 4 C2S NPs exhibit a high encapsulation and in vitro retention of radionuclides with limited contribution to cellular cytotoxicity for TAT applications.

07 ISOTOPE AND RADIATION SOURCES↗

Cooperative On-Ramp Merging with Time-Varying Vehicle-to-Vehicle Communication Delay Compensation via a Model-Free Approach

Cooperative merging strategies enabled by vehicle-to-vehicle (V2V) communication have shown promise in addressing congestion, fuel inefficiency, and collision risks. However, their performance can be severely degraded by time-varying and uncertain communication delays-an issue often overlooked in existing research, which primarily focuses on merging sequence determination and trajectory planning. Furthermore, practical considerations such as heterogeneous vehicle dynamics, varying road conditions, and real-time implementation complexities are frequently neglected. This paper presents a model-free, online planning framework for cooperative on-ramp merging of connected and automated vehicles (CAVs), explicitly accounting for time-varying V2V communication delays. Without relying on detailed vehicle dynamics, the proposed method introduces a data-driven delay compensation scheme. A co-simulation platform integrating high-fidelity vehicle dynamics, traffic simulation (SUMO), and V2V communication within MATLAB/Simulink is developed to evaluate the proposed method. Simulation results demonstrate that unaddressed V2V communication delays significantly impair merging performance. In contrast, the proposed framework enhances intervehicle distance tracking and maintains low CO2 emissions and fuel consumption, under communication delay across different communication frequencies. In conclusion, its lightweight design also facilitates real-time implementation, making it well-suited for deployment in practical CAV systems.

Accounting↗

Intranasal Nanoparticle Vaccination Elicits a Persistent, Polyfunctional CD4 T Cell Response in the Murine Lung Specific for a Highly Conserved Influenza Virus Antigen That Is Sufficient To Mediate Protection from Influenza Virus Challenge

We report lung-localized CD4 T cells play a critical role in the control of influenza virus infection and can provide broadly protective immunity. However, current influenza vaccination strategies primarily target influenza hemagglutinin (HA) and are administered peripherally to induce neutralizing antibodies. We have used an intranasal vaccination strategy targeting the highly conserved influenza nucleoprotein (NP) to elicit broadly protective lung-localized CD4 T cell responses. The vaccine platform consists of a self-assembling nanolipoprotein particle (NLP) linked to NP with an adjuvant. We have evaluated the functionality, in vivo localization, and persistence of the T cells elicited. Our study revealed that intranasal vaccination elicits a polyfunctional subset of lung-localized CD4 T cells that persist long term. A subset of these lung CD4 T cells localize to the airway, where they can act as early responders following encounter with cognate antigen. Polyfunctional CD4 T cells isolated from airway and lung tissue produce significantly more effector cytokines IFN-γ and TNF-α, as well as cytotoxic functionality. When adoptively transferred to naive recipients, CD4 T cells from NLP:NP-immunized lung were sufficient to mediate 100% survival from lethal challenge with H1N1 influenza virus.

59 BASIC BIOLOGICAL SCIENCES↗

A massively parallel and scalable multi-CPU material point method

Harnessing the power of modern multi-GPU architectures, we present a massively parallel simulation system based on the Material Point Method (MPM) for simulating physical behaviors of materials undergoing complex topological changes, self-collision, and large deformations. Our system makes three critical contributions. First, we introduce a new particle data structure that promotes coalesced memory access patterns on the GPU and eliminates the need for complex atomic operations on the memory hierarchy when writing particle data to the grid. Second, we propose a kernel fusion approach using a new Grid-to-Particles-to-Grid (G2P2G) scheme, which efficiently reduces GPU kernel launches, improves latency, and significantly reduces the amount of global memory needed to store particle data. Finally, we introduce optimized algorithmic designs that allow for efficient sparse grids in a shared memory context, enabling us to best utilize modern multi-GPU computational platforms for hybrid Lagrangian-Eulerian computational patterns. We demonstrate the effectiveness of our method with extensive benchmarks, evaluations, and dynamic simulations with elastoplasticity, granular media, and fluid dynamics. In comparisons against an open-source and heavily optimized CPU-based MPM codebase [Fang et al. 2019] on an elastic sphere colliding scene with particle counts ranging from 5 to 40 million, our GPU MPM achieves over 100x per-time-step speedup on a workstation with an Intel 8086K CPU and a single Quadro P6000 GPU, exposing exciting possibilities for future MPM simulations in computer graphics and computational science. Moreover, compared to the state-of-the-art GPU MPM method [Hu et al. 2019a], we not only achieve 2x acceleration on a single GPU but our kernel fusion strategy and Array-of-Structs-of-Array (AoSoA) data structure design also generalizes to multi-GPU systems. Our multi-GPU MPM exhibits near-perfect weak and strong scaling with 4 GPUs, enabling performant and large-scale simulations on a 10243 grid with close to 100 million particles with less than 4 minutes per frame on a single 4-GPU workstation and 134 million particles with less than 1 minute per frame on an 8-GPU workstation.

Wang, Xinlei↗

Autonomous Tools for Attack Surface Reduction (Final Report)

The electric power grid is a complex critical infrastructure that forms the lifeline of modern society, and its secure and reliable operation is of paramount importance to national security and economic wellbeing. However, recent findings documented in authoritative sources indicate the threat of cyber-based attacks growing in numbers and sophistication. However, securing the grid against stealthy cyberattacks is a challenging task due to legacy nature of the infrastructure coupled with dynamic nature of threat landscape and ever-growing sophistication of the adversaries. Additionally, the grid’s attack surface continues to grow with the increased dependence on digital communications and control that now extends to each consumer through smart meters and distributed energy resources. Unfortunately, this expansive surface increases the grid’s vulnerability and further exposes critical control systems in both substations and control centers. To respond to this emerging need, we had successfully assembled an interdisciplinary team with academic- industry partnership to successfully conduct research, development, evaluation, demonstration, and commercialization of attack surface reduction tools, whose goal was to significantly reduce the cyber attack surface in the North American power grid. Our proposed project was a synergistic collaborative effort leveraging the synergistic expertise of the team members across power systems, cyber security and CPS security, testbeds, field deployments and demonstration, and successful commercialization. The following are the specific tasks that have been successfully completed two phases (2016-2020). Phase I: Task 1: Developed and implemented a robust Project Management and Data Management Plan, coupled with a well thought out Risk Mitigation Plan. Task 2.1: Developed a comprehensive framework that continually assesses and autonomously reduces the attack surface for the power grid control environment spanning across substations, control center and the SCADA network to significantly reduce the risks of cyber attacks. Task 2.2: Developed attack surface analysis techniques, metrics, and tools that assess the attack surface at multiple levels including the control center, substations, and the SCADA network. Task 2.3: Developed attack surface reduction techniques and tools that dynamically reduce attack surface and hence increase attacker’s cost without interfering in the critical functions of the system. Task 2.4: Prototyped, implemented, and quantitatively evaluated/validated the techniques and tools on a realistic industrial CPS security testbed environment by leveraging the unique resources of the team. Task 3: Developed Commercialization plan to transition the developed tools into power system industry stakeholders for a broader adoption by leveraging the expertise of our industrial members. Phase II: Task 4: Successfully completed field demonstration, verification, and evaluation of the effectiveness of the attack surface analysis and reduction techniques on a realistic utility testbed environment. This also involved the development of realistic scenarios, sound metrics, data sets, evaluation criteria, and documentation. Technology integration & Field demonstration: The project had significantly advanced the state-of-the-art research and practice in improving the cybersecurity of our nation’s power grid infrastructure against cyber threats. In particular, the proposed, designed, and deployed attack surface analysis and reduction algorithms and tools have contributed to significantly reducing the exposure and risk of the devices, substations, and the integrated SCADA/EMS/ DMS grid environment to cyber threat. Strong demonstration and evaluation techniques have verified the feasibility of the developed techniques on realistic cyber-physical testbeds and utility partner's real grid environment, and collaborative research and evaluation of attack surface reduction techniques (for wide-are monitoring and control) within a vendor (GE) EMS platform. The Attack Host Analyzer (AHA) tool that was developed through this project was made available through GitHub.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Structural analysis for preliminary design of High Speed Civil Transport (HSCT)

In the preliminary design environment, there is a need for quick evaluation of configuration and material concepts. The simplified beam representations used in the subsonic, high aspect ratio wing platform are not applicable for low aspect ratio configurations typical of supersonic transports. There is a requirement to develop methods for efficient generation of structural arrangement and finite element representation to support multidisciplinary analysis and optimization. In addition, empirical data bases required to validate prediction methods need to be improved for high speed civil transport (HSCT) type configurations.

Bhatia, Kumar G.↗

Branch strategies - Modeling and optimization

The authors provide a common platform for modeling different schemes for reducing the branch-delay penalty in pipelined processors as well as evaluating the associated increased instruction bandwidth. Their objective is twofold: to develop a model for different approaches to the branch problem and to help select an optimal strategy after taking into account additional i-traffic generated by branch strategies. The model presented provides a flexible tool for comparing different branch strategies in terms of the reduction it offers in average branch delay and also in terms of the associated cost of wasted instruction fetches. This additional criterion turns out to be a valuable consideration in choosing between two strategies that perform almost equally. More importantly, it provides a better insight into the expected overall system performance. Simple compiler-support-based low-implementation-cost strategies can be very effective under certain conditions. An active branch prediction scheme based on loop buffers can be as competitive as a branch-target-buffer based strategy.

Dubey, Pradeep K.↗