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At least 91 records · Page 5

Automated Instrumentation, Monitoring and Visualization of PVM Programs Using AIMS

We present views and analysis of the execution of several PVM codes for Computational Fluid Dynamics on a network of Sparcstations, including (a) NAS Parallel benchmarks CG and MG (White, Alund and Sunderam 1993); (b) a multi-partitioning algorithm for NAS Parallel Benchmark SP (Wijngaart 1993); and (c) an overset grid flowsolver (Smith 1993). These views and analysis were obtained using our Automated Instrumentation and Monitoring System (AIMS) version 3.0, a toolkit for debugging the performance of PVM programs. We will describe the architecture, operation and application of AIMS. The AIMS toolkit contains (a) Xinstrument, which can automatically instrument various computational and communication constructs in message-passing parallel programs; (b) Monitor, a library of run-time trace-collection routines; (c) VK (Visual Kernel), an execution-animation tool with source-code clickback; and (d) Tally, a tool for statistical analysis of execution profiles. Currently, Xinstrument can handle C and Fortran77 programs using PVM 3.2.x; Monitor has been implemented and tested on Sun 4 systems running SunOS 4.1.2; and VK uses X11R5 and Motif 1.2. Data and views obtained using AIMS clearly illustrate several characteristic features of executing parallel programs on networked workstations: (a) the impact of long message latencies; (b) the impact of multiprogramming overheads and associated load imbalance; (c) cache and virtual-memory effects; and (4significant skews between workstation clocks. Interestingly, AIMS can compensate for constant skew (zero drift) by calibrating the skew between a parent and its spawned children. In addition, AIMS' skew-compensation algorithm can adjust timestamps in a way that eliminates physically impossible communications (e.g., messages going backwards in time). Our current efforts are directed toward creating new views to explain the observed performance of PVM programs. Some of the features planned for the near future include: (a) ConfigView, showing the physical topology of the virtual machine, inferred using specially formatted IP (Internet Protocol) packets; and (b) LoadView, synchronous animation of PVM-program execution and resource-utilization patterns.

Mehra, Pankaj↗

Constructing Space-Time Views from Fixed Size Statistical Data: Getting the Best of both Worlds

Many performance monitoring tools are currently available to the super-computing community. The performance data gathered and analyzed by these tools fall under two categories: statistics and event traces. Statistical data is much more compact but lacks the probative power event traces offer. Event traces, on the other hand, can easily fill up the entire file system during execution such that the instrumented execution may have to be terminated half way through. In this paper, we propose an innovative methodology for performance data gathering and representation that offers a middle ground. The user can trade-off tracing overhead, trace data size vs. data quality incrementally. In other words, the user will be able to limit the amount of trace collected and, at the same time, carry out some of the analysis event traces offer using space-time views for the entire execution. Two basic ideas arc employed: the use of averages to replace recording data for each instance and formulae to represent sequences associated with communication and control flow. With the help of a few simple examples, we illustrate the use of these techniques in performance tuning and compare the quality of the traces we collected vs. event traces. We found that the trace files thus obtained are, in deed, small, bounded and predictable before program execution and that the quality of the space time views generated from these statistical data are excellent. Furthermore, experimental results showed that the formulae proposed were able to capture 100% of all the sequences associated with 11 of the 15 applications tested. The performance of the formulae can be incrementally improved by allocating more memory at run-time to learn longer sequences.

Schmidt, Melisa↗

Design of fiber optic probes for laser light scattering

A quantitative analysis is presented of the role of optical fibers in laser light scattering. Design of a general fiber optic/microlens probe by means of ray tracing is described. Several different geometries employing an optical fiber of the type used in lightwave communications and a graded index microlens are considered. Experimental results using a nonimaging fiber optic detector probe show that due to geometrical limitations of single mode fibers, a probe using a multimode optical fiber has better performance, for both static and dynamic measurements of the scattered light intensity, compared with a probe using a single mode fiber. Fiber optic detector probes are shown to be more efficient at data collection when compared with conventional approaches to measurements of the scattered laser light. Integration of fiber optic detector probes into a fiber optic spectrometer offers considerable miniaturization of conventional light scattering spectrometers, which can be made arbitrarily small. In addition static and dynamic measurements of scattered light can be made within the scattering cell and consequently very close to the scattering center.

Dhadwal, Harbans S.↗

Trace-based performance analysis for the petascale simulation code FLASH

Performance analysis of applications on modern high-end petascale systems is increasingly challenging due to the rising complexity and quantity of the computing units. This paper presents a performance-analysis study using the Vampir performance-analysis tool suite, which examines application behavior as well as the fundamental system properties. This study was carried out on the Jaguar system at Oak Ridge National Laboratory, the fastest computer on the November 2009 Top500 list. We analyzed the FLASH simulation code that is designed to be scaled with tens of thousands of CPU cores, which means that using existing performance-analysis tools is very complex. The study reveals two classes of performance problems that are relevant for very high CPU counts: MPI communication and scalable I/O. For both, solutions are presented and verified. Finally, the paper proposes improvements and extensions for event tracing tools in order to allow scalability of the tools towards higher degrees of parallelism.

Computer Science↗

Transcription Factors Controlling the Rhizobium–Legume Symbiosis: Integrating Infection, Organogenesis and the Abiotic Environment

Abstract Legume roots engage in a symbiotic relationship with rhizobia, leading to the development of nitrogen-fixing nodules. Nodule development is a sophisticated process and is under the tight regulation of the plant. The symbiosis initiates with a signal exchange between the two partners, followed by the development of a new organ colonized by rhizobia. Over two decades of study have shed light on the transcriptional regulation of rhizobium–legume symbiosis. A large number of transcription factors (TFs) have been implicated in one or more stages of this symbiosis. Legumes must monitor nodule development amidst a dynamic physical environment. Some environmental factors are conducive to nodulation, whereas others are stressful. The modulation of rhizobium–legume symbiosis by the abiotic environment adds another layer of complexity and is also transcriptionally regulated. Several symbiotic TFs act as integrators between symbiosis and the response to the abiotic environment. In this review, we trace the role of various TFs involved in rhizobium–legume symbiosis along its developmental route and highlight the ones that also act as communicators between this symbiosis and the response to the abiotic environment. Finally, we discuss contemporary approaches to study TF-target interactions in plants and probe their potential utility in the field of rhizobium–legume symbiosis.

Cell Biology↗

Privacy-Assured Aggregation Protocol for Smart Metering: A Proactive Fault-Tolerant Approach [Proactive Fault-Tolerant Aggregation Protocol for Privacy-Assured Smart Metering]

Smart meters are integral to demand response in emerging smart grids, by reporting the electricity consumption of users to serve application needs. But reporting real-time usage information for individual households raises privacy concerns. Existing techniques to guarantee differential privacy (DP) of smart meter users either are not fault tolerant or achieve (possibly partial) fault tolerance at high communication overheads. In this paper, we propose a fault-tolerant protocol for smart metering that can handle general communication failures while ensuring DP with significantly improved efficiency and lower errors compared with the state of the art. Our protocol handles fail-stop faults proactively by using a novel design of future ciphertexts, and distributes trust among the smart meters by sharing secret keys among them. We prove the DP properties of our protocol and analyze its advantages in fault tolerance, accuracy, and communication efficiency relative to competing techniques. We illustrate our analysis by simulations driven by real-world traces of electricity consumption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

ArborX 2.0

ArborX library tackles a problem of efficiently finding geometric objects that are close in space. Variations of this problem, such as finding the nearest neighbors of a point, or finding all objects within a certain distance, are inherent components of applications in many fields. The data may be large so that solving the problem efficiently may require significant computational resources, such as multiple processors or accelerators such as general purpose GPUs. ArborX' main advantage in its ability to solve large problems efficiently utilizing a combination of distributed and on-node parallelism. ArborX can be run efficiently on a wide variety of hardware, including GPUs from different vendors, which distinguishes it from other available libraries which typically choose only few of these. The other advantage is that it supports both types of user problems: spatial problems (useful for intersections and finding objects within certain distance), and nearest neighbor problems. ArborX also supports flexible interface in its interaction with a user. Particularly, it allows a user to call user's own function on a positive match, a functionality not rarely available in other libraries. ArborX implements construction and traversal algorithms using efficient tree structures, such as bounding volume hierarchy (BVH). At its core, ArborX uses linear BVH for its low construction cost and sufficient quality. ArborX implements both spatial and nearest-neighbor traversal algorithms. ArborX also provides several clustering algorithms (minimum spanning tree, DBSCAN, HDBSCAN*), interpolation using minimum least squares and ray tracing. ArborX is written using C++, and is parallelized using the message passing interface (MPI) for the distributed communication, and the Kokkos library for on-node parallelism. This approach allows ArborX to be run on a wide variety of hardware, from common laptops and desktops to supercomputers while using the same codebase.

Prokopenko, Andrey [Oak Ridge National Laboratory ↗

Dynamic object management for distributed data structures

In distributed-memory multiprocessors, remote memory accesses incur larger delays than local accesses. Hence, insightful allocation and access of distributed data can yield substantial performance gains. The authors argue for the use of dynamic data management policies encapsulated within individual distributed data structures. Distributed data structures offer performance, flexibility, abstraction, and system independence. This approach is supported by data from a trace-driven simulation study of parallel scientific benchmarks. Experimental data on memory locality, message count, message volume, and communication delay suggest that data-structure-specific data management is superior to a single, system-imposed policy.

Totty, Brian K.↗

Using Digital Trace Data to Identify Regions and Cities

A greater understanding of human dynamics as they play out in both physical space and through inter-personal communication is vital for the design and development of intelligent and resilient cities. Physical context provides insight in to the space-time distribution of population and their activity patterns, while inter-personal communication can, for the first time, be measured at scale through virtual interactions. The confluence of these two enables spatial social network analysis in the built environment for edge computing, knowledge discovery, and artificial intelligence activities. In this work, we propose a novel method to discover such dynamics. We use a dataset of 72 million tweets to develop a spatially embedded network of communication, and then use community detection algorithms to explore regional and urban delineation in the United States. We find that the broad spatial delineation of communities and community sub-structure is consistent with major United States socio-cultural regions, states, and major metropolitan areas. We describe how these methods could be extended to generate a measure of socially cohesive regions that can be consistently applied anywhere there is a sufficiently rich data source. We hope the proposed methods will generate new perspectives on smart and resilient cities.

Brelsford, Christa↗

Distributed Macroscopic Traffic Simulation with Open Traffic Models

This paper presents OTM-MPI, an extension of the Open Traffic Models platform (OTM) for running macroscopic traffic simulations in high-performance computing environments. OTM-MPI represents the first open-source, distributed-memory, macroscopic simulation model developed for modern high performance parallel machines and large networks. Macroscopic simulations are appropriate for studying regional traffic scenarios when aggregate trends are of interest, rather than individual vehicle traces. They are also appropriate for studying the routing behavior of classes of vehicles, such as app-informed vehicles. The network partitioning was performed with METIS. Inter-process communication was done with MPI (message-passing interface). Results are provided for two networks: one realistic network which was obtained from Open Street Maps for Chattanooga, TN, and another larger synthetic grid network. The software recorded a speedups of 198x using 256 cores for Chattanooga, and 475x with 1,024 cores for the synthetic network.

macro-scopic traffic simulation↗

Historics of the Space Tracking And Data Acquisition Network (STADAN), the Manned Space Flight Network (MSFN), and the NASA Communications Network (NASCOM)

The historical and technical aspects of the major networks which comprise the NASA tracking and data acquisition system are considered in a complete reference work which traces the origin and growth of STADAN, MSFN, and NASCOM up to mid-1971. The roles of these networks in both the Gemini and Apollo programs are discussed, and the separate developmental trends are identified for each network.

Corliss, W. R.↗

Using Monte Carlo ray tracing simulations to model the quantum harmonic oscillator modes observed in uranium nitride

Recently an extended series of equally spaced vibrational modes was observed in uranium nitride (UN) by performing neutron spectroscopy measurements using the ARCS and SEQUOIA time-of- flight chopper spectrometers [A.A. Aczel et al, Nature Communications 3, 1124 (2012)]. These modes are well described by 3D isotropic quantum harmonic oscillator (QHO) behavior of the nitrogen atoms, but there are additional contributions to the scattering that complicate the measured response. In an effort to better characterize the observed neutron scattering spectrum of UN, we have performed Monte Carlo ray tracing simulations of the ARCS and SEQUOIA experiments with various sample kernels, accounting for the nitrogen QHO scattering, contributions that arise from the acoustic portion of the partial phonon density of states (PDOS), and multiple scattering. These simulations demonstrate that the U and N motions can be treated independently, and show that multiple scattering contributes an approximate Q-independent background to the spectrum at the oscillator mode positions. Temperature dependent studies of the lowest few oscillator modes have also been made with SEQUOIA, and our simulations indicate that the T-dependence of the scattering from these modes is strongly influenced by the uranium lattice.

Lin, J. Y. Y.↗

Active Pacific meridional overturning circulation (PMOC) during the warm Pliocene

An essential element of modern ocean circulation and climate is the Atlantic meridional overturning circulation (AMOC), which includes deep-water formation in the subarctic North Atlantic. However, a comparable overturning circulation is absent in the Pacific, theworld’s largest ocean,where relatively fresh surface waters inhibitNorth Pacific deep convection. We present complementary measurement and modeling evidence that the warm, ~400–ppmv (parts per million by volume) CO 2 world of the Pliocene supported subarctic North Pacific deep-water formation and a Pacific meridional overturning circulation (PMOC) cell. In Pliocene subarctic North Pacific sediments, we report orbitally paced maxima in calcium carbonate accumulation rate, with accompanying pigment and total organic carbon measurements supporting deep-ocean ventilation-driven preservation as their cause. Together with high accumulation rates of biogenic opal, these findings require vigorous bidirectional communication between surface waters and interior waters down to ~3 km in the western subarctic North Pacific, implying deep convection. Redoxsensitive trace metal data provide further evidence of higher Pliocene deep-ocean ventilation before the 2.73-Ma (million years) transition. This observational analysis is supported by climate modeling results, demonstrating that atmospheric moisture transport changes, in response to the reduced meridional sea surface temperature gradients of the Pliocene, were capable of eroding the halocline, leading to deep-water formation in the western subarctic Pacific and a strong PMOC. This second Northern Hemisphere overturning cell has important implications for heat transport, the ocean/atmosphere cycle of carbon, and potentially the equilibrium response of the Pacific to global warming.

54 ENVIRONMENTAL SCIENCES↗

Earth-Independent Medical Operations (EIMO) Concept of Operations

In contrast to the current crew health paradigm for low-Earth orbit and Lunar missions, which depends on real-time communication with Mission Control, deep-space exploration missions will require a significant shift in medical operations. This shift is driven by the constraints of operating at a considerable distance from Earth, such as resource limitations—lack of resupply, restricted mass, power, volume, and data—as well as communication delays and the inability to evacuate back to Earth during emergencies. To move toward a more self-reliant medical model, a strategy is needed to gradually increase space-based crew autonomy and reduce risks to mission success in the challenging environment of deep space. This transformative change, known as "Earth-Independent Medical Operations" (EIMO), explores the gradual transfer of medical care and decision-making from Earth-based support to space-based systems. The goal of this transition is to enhance astronaut health and performance while minimizing mission risks. EIMO requires the development of a medical system that integrates seamlessly with mission planning, vehicle and spacesuit design, and data architecture. This integration is crucial for building a robust medical infrastructure that not only safeguards astronaut well-being but also ensures overall mission success. The Human Research Program (HRP) Exploration Medical Capability (ExMC) Element has revised the EIMO model-based Concept of Operations (ConOps) which outlines an initial vision for EIMO. The ConOps, which is built on the stakeholders’ need, system goals, and objectives (NGOs), presents an array of in-mission scenarios that span a wide range of medical conditions demonstrating the system’s capabilities from basic to complex events. Developed by a multidisciplinary team of systems engineers, scientists, and clinicians within ExMC, the ConOps revision includes two new scenarios(Barotrauma and Self-Medical Management and Behavioral Health and Chronic Medical Care), and implementation of findings from EIMO technical interchange meetings that focused on data and training. The envisioned EIMO Medical System (MS) operates as a system of systems, gathering data from various sources such as reference databases, real-time wearable sensors, point-of-care diagnostics, and environmental controls. The MS also incorporates advanced training tools to support autonomous medical care, assisting the Crew Medical Officer (CMO) during medical events where Ground Support is either unavailable or communication-delayed beyond practicality. Furthermore, MS functions and capabilities were decomposed from the scenarios to establish foundational requirements for EIMO and traced to the NASA Spaceflight Human-System Standard(NASA-STD-3001, Volumes 1 and 2). These traces were performed to gain insights on the alignment of EIMO requirements with the NASA standard. This work serves as an initial recommendation to increase crew autonomy gradually and safely for Mars missions and future deep-space exploration.

medical system↗

Scalable algorithms for domain decomposition of Monte Carlo neutral particle transport simulations on unstructured mesh

Monte Carlo simulations are the gold standard in particle transport simulations, for shielding and nuclear reactor simulations Full core simulations can require terabytes of memory for tracking pin-resolved (up to 50k pins), nuclide (200 tracked), axial (20-200 zones) reaction rates Domain decomposition, splitting the calculation and the memory storage, among several nodes is challenging as it involves communication of particles across domain boundaries We created a new MOOSE application, MaCaw, to study this problem Algorithms developed for ray tracing in MOOSE were adapted for simulating neutral particle transport Physics and tally routines in OpenMC, dynamically linked, are called from the application

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Modeling UV Radiation Feedback from Massive Stars. I. Implementation of Adaptive Ray-tracing Method and Tests [Modeling UV Radiation Feedback from Massive Stars: I. Implementation of Adaptive Ray Tracing Algorithm]

Here, we present an implementation of an adaptive ray-tracing (ART) module in the Athena hydrodynamics code that accurately and efficiently handles the radiative transfer involving multiple point sources on a three-dimensional Cartesian grid. We adopt a recently proposed parallel algorithm that uses nonblocking, asynchronous MPI communications to accelerate transport of rays across the computational domain. We validate our implementation through several standard test problems, including the propagation of radiation in vacuum and the expansions of various types of H II regions. Additionally, scaling tests show that the cost of a full ray trace per source remains comparable to that of the hydrodynamics update on up to $\sim {10}^{3}$ processors. To demonstrate application of our ART implementation, we perform a simulation of star cluster formation in a marginally bound, turbulent cloud, finding that its star formation efficiency is 12% when both radiation pressure forces and photoionization by UV radiation are treated. We directly compare the radiation forces computed from the ART scheme with those from the M 1 closure relation. Although the ART and M 1 schemes yield similar results on large scales, the latter is unable to resolve the radiation field accurately near individual point sources.

79 ASTRONOMY AND ASTROPHYSICS↗

Developing Concepts of Operations Using Multi-Step Tool Techniques With Large Language Models

The National Aeronautics and Space Administration (NASA) Air Mobility Pathfinders (AMP) project is developing and evaluating concepts of operations (ConOps) for safe, secure, and scalable Urban Air Mobility (UAM) operations. The AMP project’s Operational Concepts, Architecture, and Requirements Integration (OCARI) Team is using a Model Based System Engineering (MBSE) approach for integration, interoperability, and traceability of Advanced Air Mobility (AAM) ecosystems centered around urban air taxi services. The team’s goal is to define structures and behaviors needed for system feasibility, readiness, and interoperability, establish a UAM knowledge base, and trace and validate assumptions and requirements relevant to AAM. NASA Langley Research Center (LaRC) is spearheading an innovative digital engineering approach to integrate, communicate, and facilitate the research of multi-modal transportation systems. The Knowledge-based Digital Platform (KbDP) is a concept being developed that ties the workflows of Project Managers (PM), Principal Investigators (PI), and System Engineers together across organizational boundaries. It does so through the management of an information database defined by mathematical, data science, and system engineering principles. Machine Learning (ML) algorithms play a key role in this concept by extracting meaningful knowledge from relational and graph databases, document repositories, and system artifacts, which the human user leverages to greatly improve the efficiency and effectiveness of their research. Recent advancements in the field of Large Language Models (LLMs), specifically models trained for tool use, such as Command-R , now allow for the reliable implementation of single-step and multi-step tool-centric systems. These techniques provide the LLM with a set of tools, in our case Python functions, that can be called on to answer a much wider range of questions compared to LLMs implemented using a traditional single-source or Retrieval Augmented Generation (RAG) approach. Through this method, the LLM can pull information from multiple data sources, such as relational or graph databases, document repositories, application programming interfaces (APIs), and SysML artifacts depending on the user’s question. The LLM can also output the information in a variety of different formats, using output generation tools, such as CSV, UML, or SysML artifacts. Additionally, tools can be assigned roles and can work together to provide answers to queries in an “agent” like approach, similar to that implemented by Microsoft’s AutoGen framework where different agents can converse with each other to accomplish tasks. Previously, our team developed a chatbot system with “agent like” functionality in the form of different “modes” the user could select from a user interface (UI), this architecture can be seen on the left in figure 1. Three different modes were implemented, the first mode allowed the LLM to utilize the structures and algorithms within a graph database to trace UAM requirements. The second mode gave the LLM access to a vector search capable of providing relevant information from thousands of document pages related to UAM ConOps and requirements. The third mode served as a general assistant where users could enter open-ended questions and custom prompts to utilize the LLM for different use-cases. This system improved the process surrounding generating and analyzing information related to UAM requirements, however, the implementation provided a clunky user experience. Users were required to know what mode to select within the UI in advance before entering their question to the selected tool. Moreover, the different tools were isolated from each other, they lacked bidirectional links that would allow for tools to collaborate to generate better responses. Our team is working on a new architecture, seen on the right in the below figure, with the goal to address many of the UX shortcomings of our original system while improving the accuracy and depth of responses from the LLM. This new system will automatically select the appropriate tool to use based off the user’s question. Each tool will be capable of calling on any of the other tools available to the LLM, resulting in a collaborative pipeline where tools can pass data between other tools until enough data is received to generate an answer to the user’s question. Using a locally deployed, open-source, LLM, the NASA OCARI team, in collaboration with Collins Aerospace, will implement a prototype application that will bridge knowledge across multiple sources to assist System Engineers (SEs) with requirements discovery and tracing, research question and use case identification, and assumption validation. Such a system will also allow SEs to more easily, and intuitively, explore the AAM ecosystem, ultimately improving the efficiency and effectiveness of the SE's research and decision-making processes surrounding ConOps development and validation. In this session, our team will provide a video demonstration of our new prototype architecture in action. We will also present an overview of our prototype system architecture and talk about its advantages over traditional LLM deployments along with how those advantages can provide additional value to the field of System Engineering.

systems engineering↗

Automated Performance Prediction of Message Passing Parallel Programs

As the trend toward massively parallel processing continues, the need for tools that can predict scalability trends becomes greater. While high level languages Eke HPF have come into greater use, explicit message-passing programs proliferate, and will probably do so for some time, thanks to the onslaught of standards such as MPI. Much work has been done to create simple models that represent important characteristics of parallel programs, such as latency, network contention, and communication volume. But many of these methods still require a substantial manual effort to represent an application in the model's format. The YAPP ("Yet Another Performance Predictor") tool is an attempt to automate the formation of first-order expressions for completion time, with a minimum of programmer assistance. The content of this paper is as follows: First, we explore the implementation details of YAPP, and illustrate with examples some of the reasons that automatic prediction is difficult. In the following sections, we present the results of four applications, using execution traces on the Intel i860, analyze the error in YAPP's predictions, explain the limitations of our implementation, and mention possible future additions. In particular, we illustrate techniques used to identify pipeline communication patterns, and demonstrate how compiler analysis and regression are combined to automate the prediction process.

Block, Robert J.↗