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At least 235 records · Page 13

MATAR: A performance portability and productivity implementation of data-oriented design with Kokkos

There is a need for simple, fast, and memory-efficient multidimensional data structures for dense and sparse storage that arise with numerical methods and in software applications. The data structures must perform equally well across multiple computer architectures, including CPUs and GPUs. For this purpose, we developed MATAR, a C++ software library that allows for simple creation and use of intricate data structures that is also portable across disparate architectures using Kokkos. Here, the performance aspect is achieved by forcing contiguous memory layout (or as close to contiguous as possible) for multidimensional and multi-size dense or sparse MATrix and ARray (hence, MATAR) types. Our results show that MATAR has the capability to improve memory utilization, performance, and programmer productivity in scientific computing. This is achieved by fitting more work into the available memory, minimizing memory loads required, and by loading memory in the most efficient order. This document describes the purpose of the work, the implementation of each of the data types, and the resulting performance both in some simple baseline test cases and in an application code.

97 MATHEMATICS AND COMPUTING↗

Spiner: Performance Portable Routines for Generic, Tabulated, Multi-Dimensional Data

We present Spiner, a new, performance-portable library for working with tabulated data. Spiner provides efficient routines for multi-dimensional interpolation and indexing on both CPUs and GPUs—as well as more exotic hardware—including interwoven interpolation and indexing access patterns, as needed for radiation transport. Importantly, Spiner defines a data format, based on HDF5, that couples the tabulated data to the information required to interpolate it, which Spiner can read and move to GPU.

97 MATHEMATICS AND COMPUTING↗

Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION

As countries with endemic canine rabies progress towards elimination by 2030, it will become necessary to employ techniques to help plan, monitor, and confirm canine rabies elimination. Sequencing can provide critical information to inform control and vaccination strategies by identifying genetically distinct virus variants that may have different host reservoir species or geographic distributions. However, many rabies testing laboratories lack the resources or expertise for sequencing, especially in remote or rural areas where human rabies deaths are highest. We developed a low-cost, high throughput rabies virus sequencing method using the Oxford Nanopore MinION portable sequencer. A total of 259 sequences were generated from diverse rabies virus isolates in public health laboratories lacking rabies virus sequencing capacity in Guatemala, India, Kenya, and Vietnam. Phylogenetic analysis provided valuable insight into rabies virus diversity and distribution in these countries and identified a new rabies virus lineage in Kenya, the first published canine rabies virus sequence from Guatemala, evidence of rabies spread across an international border in Vietnam, and importation of a rabid dog into a state working to become rabies-free in India. Taken together, our evaluation highlights the MinION’s potential for low-cost, high volume sequencing of pathogens in locations with limited resources.

59 BASIC BIOLOGICAL SCIENCES↗

EMPIRE-PIC: A Performance Portable Unstructured Particle-in-Cell Code

In this study we introduce EMPIRE-PIC, a finite element method particle-in-cell (FEM-PIC) application developed at Sandia National Laboratories. The code has been developed in C++ using the Trilinos library and the Kokkos Performance Portability Framework to enable running on multiple modern compute architectures while only requiring maintenance of a single codebase. EMPIRE-PIC is capable of solving both electrostatic and electromagnetic problems in two- and three-dimensions to second-order accuracy in space and time. In this paper we validate the code against three benchmark problems — a simple electron orbit, an electrostatic Langmuir wave, and a transverse electromagnetic wave propagating through a plasma. We demonstrate the performance of EMPIRE-PIC on four different architectures: Intel Haswell CPUs, Intel's Xeon Phi Knights Landing, ARM Thunder-X2 CPUs, and NVIDIA Tesla V100 GPUs attached to IBM POWER9 processors. This analysis demonstrates scalability of the code up to more than two thousand GPUs, and greater than one hundred thousand CPUs.

97 MATHEMATICS AND COMPUTING↗

Portable Software Environment for Ultrahigh-Resolution ELM Development on GPUs

This paper presents our endeavors in developing the large-scale, ultra-high-resolution E3SM Land Model (uELM), specifically designed for exascale computers furnished with accelerators such as Nvidia GPUs. The uELM is a sophisticated code that substantially relies on High-Performance Computing (HPC) environments, necessitating particular machine and software configurations. To facilitate community-based uELM developments employing GPUs, we have created a portable, standalone software environment preconfigured with uELM input datasets, simulation cases, and source code. This environment, utilizing Docker, encompasses all essential code, libraries, and system software for uELM development on GPUs. It also features a functional unit test framework and an offline model testbed for comprehensive numerical experiments. From a technical perspective, the paper discusses GPU-ready container generations, uELM code management, and input data distribution across computational platforms. Lastly, the paper demonstrates the use of environment for functional unit testing, end-to-end simulation on CPUs and GPUs, and collaborative code development.

E3SM Land Model↗

Portable Long-Wavelength Infrared Camera for Civilian Application

In this paper, we discuss the performance of this portable long-wavelength infrared camera in quantum efficiency, NEAT, minimum resolvable temperature differnce (MRTD), uniformity, etc. and its application in science, medicine and defense.

infrared wavelength portable↗

Reliability of the Danish Aerospace Corporation Portable Pulmonary Function System

Metabolic gas analysis is a critical component of investigations that measure cardio-pulmonary exercise responses during and after long-duration spaceflight. The primary purpose of the current study was to determine the reliability and intra-subject repeatability of a metabolic gas analysis device, the Portable Pulmonary Function System (PPFS), designed for use on the International Space Station (ISS). The second objective of this study was to directly compare PPFS measurements of expired oxygen and carbon dioxide (FEO2 and FECO2) to values obtained from a well-validated clinical metabolic gas analysis system (ParvoMedics TrueOne (c) [PM]). Eight subjects performed four peak cycle tests to maximal exertion. The first test was used to prescribe work rates for the subsequent test sessions. Metabolic gas analysis for this test was performed by the PM, but samples of FEO2 and FECO2 also were simultaneously collected for analysis by the PPFS. Subjects then performed three additional peak cycle tests, consisting of three 5-min stages designed to elicit 25%, 50%, and 75% maximal oxygen consumption (VO2max) followed by stepwise increases of 25 W/min until subjects reached volitional exhaustion. Metabolic gas analysis was performed using the PPFS for these tests. Intraclass correlation coefficients (ICC), within-subject standard deviations (WS SD), and coefficients of variation (CV%) were calculated for the repeated exercise tests. Mixed model regression analysis was used to compare paired FEO2 and FECO2 values obtained from the PPFS and the PM during the initial test. The ICC values for oxygen consumption (VO2), carbon dioxide production (VCO2), and ventilation (VE) indicate that the PPFS is highly reliable (0.79 to 0.99) for all exercise levels tested; however, ICCs for respiratory exchange ratio (RER) were low ( 0.11 - 0.51), indicating poor agreement between trials during submaximal and maximal exercise. Overall, CVs ranged from 1.6% to 6.7% for all measurements, a finding consistent with reported values that were obtained using other metabolic gas analysis techniques. The PPFS and PM produced comparable FEO2 data; however, there was less agreement between measures of FECO2 obtained from the two devices, particularly at lower CO2 concentrations. The PPFS appears, in practically all respects, to yield highly reliable metabolic gas analysis data. Lower reliability of RER measurements reported in the literature and likely is not a function of the PPFS device. Further examination of PPFS CO2 data is warranted to better understand the limitations of these PPFS measurements. Overall, the PPFS when used for repeated measures of cardio-pulmonary exercise should provide accurate and reliable data for studies of human adaptation to spaceflight.

Portable Pulmonary Function System (PPFS)↗

Evaluation of the Danish Aerospace Corporation Portable Pulmonary Function System

A research project designed to investigate changes in maximal oxygen consumption (VO2max) during and following long duration flight on the International Space Station (ISS) has recently been completed. The device used to measure VO2 on board ISS, the Portable Pulmonary Function System (PPFS) manufactured by the Danish Aerospace Corporation (DAC), is based on previous-generation devices manufactured by DAC, but the PPFS has not been validated for analyzing metabolic gases or measuring cardiac output (Qc). The purpose of the present evaluation is to compare PPFS metabolic gas analysis measurements to measurements obtained using a clinically-validated system (ParvoMedics TrueOne(c) 2400 system; Parvo). In addition, Qc data collected with the PPFS were compared to Qc measurements from echocardiography. METHODS: Ten subjects completed three cycle exercise tests to maximal exertion. The first test was conducted to determine each subject's VO2max and set the work rates for the second and third (comparison) tests. The protocol for the two comparison tests consisted of three 5-minute stages designed to elicit 25%, 50%, and 75% VO2max (based upon results from the initial test), followed by 1-minute stages of increasing work rate (25 watt/minute) until the subject reached maximal effort. During one of the two comparison tests, metabolic gases and Qc were assessed with the PPFS; metabolic gases and Qc were assessed with the Parvo and by echocardiography, respectively, during the other test. The order of the comparison tests was counterbalanced. VO2max and maximal work rate during the comparison tests were compared using t tests. Mixed-effects regression modeling was used to analyze submaximal data. RESULTS: All of the data were within normal physiological ranges. The PPFS-measured values for VO2max were 6% lower than values obtained with the Parvo (PPFS: 3.11 +/- 0.75 L/min; Parvo: 3.32 +/- 0.87 L/min; mean +/- standard deviation; P = 0.02); this difference is probably due to flow restriction imposed by the PPFS Qc accessories. Submaximal VO2 values were slightly lower when measured with the PPFS, although differences were not physiologically relevant. The PPFS-measured values of submaximal carbon dioxide production (VCO2) were lower than the data obtained from Parvo, which could be attributed to lower fractions of expired carbon dioxide measured by the PPFS. The PPFS Qc values tended to be lower than echocardiography-derived values. CONCLUSIONS: The results of the present study indicate a need to further examine the PPFS and to better quantify its reproducibility; however, none of the findings of the current evaluation indicate that the PPFS needs to be replaced or modified.

Portable Pulmonary Function System (PPFS)↗

A Portable High-Density Power Technology for Space, Lunar, and Planetary Applications

A new direct energy conversion concept called Nuclear Thermionic Avalanche Cell (NTAC) combined with a Metallic Junction Thermoelectric (MJ-TE) generator, both invented and patented by NASA, offers high specific power for portable applications. Estimates based on experimental results suggest superior performance compared to radioisotope thermoelectric generators (RTG) by up to two orders of magnitude for the NTAC and three to four times better for the MJ-TE generator for the same mass. The NTAC technology can use a variety of radioisotopes including nuclear waste to liberate a large number of intra-band(IB), inner shell electrons of atoms (105 C/cm3) by gamma-ray photons (100 keV to MeV). In contrast, conventional power generation has poor specific power because they only utilize the valence band electrons (3C/cm3) of the semiconductor or free electrons (8×103 C/cm3) of the conductor.

NTAC↗

Exploration Extravehicular Mobility Unit (xEMU): Electron Beam Welding of the Portable Life Support System (PLSS) Ti-6Al-4V Backplate with Integrated Cooling Channels

The Exploration Extravehicular Mobility Unit (xEMU) is the first clean sheet redesign of the astronaut spacesuit in approximately 40 years. NASA Langley Research Center’s electron beam welding team, of which the author is a member, is leading the development of the weld technology required to manufacture the backplate component of the Portable Life Support System (PLSS). This backplate will provide both structural support and integral cooling for the life support systems, communications, and other electronics inside the spacesuit.

electron beam welding↗

The SENSEI Generic In Situ Interface: Tool and Processing Portability at Scale [Book Chapter]

One key challenge when doing in situ processing is the investment required to add code to numerical simulations needed to take advantage of in situ processing. Such instrumentation code is often specialized, and tailored to a specific in situ method or infrastructure. Then, if a simulation wants to use other in situ tools, each of which has its own bespoke API [4], then the simulation code team will quickly become overwhelmed with having a different set of instrumentation APIs, one per in situ tool or method. In an ideal situation, such instrumentation need happen only once, and then the instrumentation API provides access to a large diversity of tools. In this way, a data producer’s instrumentation need not be modified if the user desires to take advantage of a different set of in situ tools. The SENSEI generic in situ interface addresses this challenge, which means that SENSEI-instrumented codes enjoy the benefit of being able to use a diversity of tools at scale, tools that include Libsim, Catalyst, Ascent, as well as user-defined methods written in C++ or Python. SENSEI has been shown to scale to greater than 1M-way concurrency on HPC platforms, and provides support for a rich and diverse collection of common scientific data models. Furthermore, this chapter presents the key design challenges that enable tool and processing portability at scale, some performance analysis, and example science applications of the methods.

Bethel, E. Wes↗

Proximity Portability and in Transit , M-to-N Data Partitioning and Movement in SENSEI [Book Chapter]

In high-performance parallel in situ processing, the term in transit processing refers to those configurations where data must move from a producer to a consumer that runs on separate resources. In the context of parallel and distributed computing on an HPC platform one of the central challenges is to determine a mapping of data from producer ranks to consumer ranks. This problem is complicated by the heterogeneity that arises in producer-consumer pairs, such as when producer and consumer codes have different levels of concurrency, different scaling characteristics, or different data models. The resulting mapping and movement of data from M producer to N consumer ranks can have a significant impact on aggregate application performance, particularly when the data consumer requires only a subset of the overall data for its task. This chapter focuses on the design considerations that underlie SENSEI’s implementation to this challenging problem. These design considerations extend the core SENSEI architecture and include ideas like the need to accommodate flexibility in the choice of different partitioning methods, the ability for a data consumer to request and receive only the subset of data needed for its particular operation, and the ability to leverage any of several different data transport tools. The idea of proximity portability, being able to use different data transport methods as part of an in transit workflow, is illustrated through the use of three different transport layers where switching from one transport tool to another is accomplished with only a configuration file change. Here, the chapter also includes a performance analysis summary showing the performance gains that are possible in terms of multiple metrics, such as memory footprint, time to solution, and amount of data moved, when using optimized partitioners in an in transit setting, gains that are made possible by the implementation shaped by specific design considerations.

Bethel, E. Wes↗

Sample screening of uranium ore concentrates using portable spectrophotometers: investigating the correlation between visible colors and chemical signatures

A research collaboration between the Japan Atomic Energy Agency and the Department of Energy’s National Nuclear Security Administration examined nuclear forensic signatures and analytical methods for tracing the origins of uranium ore concentrates (UOCs). Here, this study focuses on utilizing portable spectrophotometers capable of reflectance measurements in the visible light spectrum as a potential rapid screening tool for nuclear forensics analysis. Unlike laboratory-based near-infrared spectroscopy or digital image analysis, this research investigated the potential to correlate visible color measurements with key nuclear forensics signatures using seven types of UOC samples with known origins and three UOC certified reference materials. Results demonstrated that distinct color groups, quantified using CIELAB values, correlated with major uranium compounds. Furthermore, the findings indicated that trace elements can influence the UOC colors, providing additional insights into material characteristics. Although this approach requires further validation across a broader range of UOC species, this study demonstrated that simple colorimetric analysis using visible spectrophotometry, which does not require complex sample preparation or data processing, can serve as a practical and novel rapid tool for preliminary screening and attribution in nuclear forensics investigations.

and nuclear chemistry↗