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At least 595 records · Page 33

Effective Vectorization with OpenMP 4.5

This paper describes how the Single Instruction Multiple Data (SIMD) model and its extensions in OpenMP work, and how these are implemented in different compilers. Modern processors are highly parallel computational machines which often include multiple processors capable of executing several instructions in parallel. Understanding SIMD and executing instructions in parallel allows the processor to achieve higher performance without increasing the power required to run it. SIMD instructions can significantly reduce the runtime of code by executing a single operation on large groups of data. The SIMD model is so integral to the processor s potential performance that, if SIMD is not utilized, less than half of the processor is ever actually used. Unfortunately, using SIMD instructions is a challenge in higher level languages because most programming languages do not have a way to describe them. Most compilers are capable of vectorizing code by using the SIMD instructions, but there are many code features important for SIMD vectorization that the compiler cannot determine at compile time. OpenMP attempts to solve this by extending the C++/C and Fortran programming languages with compiler directives that express SIMD parallelism. OpenMP is used to pass hints to the compiler about the code to be executed in SIMD. This is a key resource for making optimized code, but it does not change whether or not the code can use SIMD operations. However, in many cases critical functions are limited by a poor understanding of how SIMD instructions are actually implemented, as SIMD can be implemented through vector instructions or simultaneous multi-threading (SMT). We have found that it is often the case that code cannot be vectorized, or is vectorized poorly, because the programmer does not have sufficient knowledge of how SIMD instructions work.

97 MATHEMATICS AND COMPUTING↗

Evaluation of the FIR Example using Xilinx Vivado High-Level Synthesis Compiler

Compared to central processing units (CPUs) and graphics processing units (GPUs), field programmable gate arrays (FPGAs) have major advantages in reconfigurability and performance achieved per watt. This development flow has been augmented with high-level synthesis (HLS) flow that can convert programs written in a high-level programming language to Hardware Description Language (HDL). Using high-level programming languages such as C, C++, and OpenCL for FPGA-based development could allow software developers, who have little FPGA knowledge, to take advantage of the FPGA-based application acceleration. This improves developer productivity and makes the FPGA-based acceleration accessible to hardware and software developers. Xilinx Vivado HLS compiler is a high-level synthesis tool that enables C, C++ and System C specification to be directly targeted into Xilinx FPGAs without the need to create RTL manually. The white paper [1] published recently by Xilinx uses a finite impulse response (FIR) example to demonstrate the variable-precision features in the Vivado HLS compiler and the resource and power benefits of converting floating point to fixed point for a design. To get a better understanding of variable-precision features in terms of resource usage and performance, this report presents the experimental results of evaluating the FIR example using Vivado HLS 2017.1 and a Kintex Ultrascale FPGA. In addition, we evaluated the half-precision floating-point data type against the double-precision and single-precision data type and present the detailed results.

97 MATHEMATICS AND COMPUTING↗

2018 Annual Site Environmental Report

Los Alamos National Laboratory’s (the Laboratory’s) annual site environmental reports are prepared annually by the Laboratory’s environmental organizations, as required by U.S. Department of Energy Order 231.1B, Administrative Change 1, Environment, Safety, and Health Reporting, and Order 458.1, Administrative Change 3, Radiation Protection of the Public and the Environment. The following chapters in this report discuss our success in complying with environmental laws, regulations, and orders (Chapter 2, Compliance Summary); how we manage the Laboratory’s environmental performance (Chapter 3, Environmental Programs); how we monitor for air emissions of radioactive materials and climate conditions (Chapter 4, Air Quality); how we monitor for effects of Laboratory operations on groundwater quality (Chapter 5, Groundwater Monitoring); how we monitor the movement of chemicals and radionuclides by storm water runoff and the levels of chemicals and radionuclides in deposited sediment (Chapter 6, Watershed Quality); how we monitor for the presence, levels, and effects of chemicals and radionuclides in plants, animals, soil, and vegetation (Chapter 7, Ecosystem Health); and finally, what radionuclide dose or risk from chemical exposure members of the public may experience as a result of Laboratory operations (Chapter 8, Public Dose and Risk Assessment). This report follows plain language guidelines, as required for federal agencies by the Plain Language Act of 2010. More information about plain language can be found at http://www.plainlanguage.gov/index.cfm. You will notice we have substantially reduced the use of acronyms and abbreviations and are using active voice and personal pronouns. We hope you find this report useful. If you have suggestions for improving this report, additional questions, or want a copy of this report, please contact us at envoutreach@lanl.gov, or call the Communications Office at 505-665-7000. This report, its supplemental tables, and the 2018 Annual Site Environmental Report Summary are available at http://www.lanl.gov/environment/environmental-report.php. Note: This document has been revised since it was initially published on September 23, 2019. The revisions included corrections to figure and table references, changes in heading levels, adding blank pages where appropriate, and changes of an editorial nature.

54 ENVIRONMENTAL SCIENCES↗

A software package for modeling and simulating fault graphs

This report describes a novel fault graph modeling language and a simulation tool for executing models specified in the language. The modeling language has three primary features that distinguish it from similar reliability analysis tools. These are (1) a random variable modeling several distinct outcomes of a single fault; (2) chains of faults in which one fault triggers another; and (3) time to fail sampled from probability distributions including positive normal, exponential, Weibull with a minimum, or immediate. These features are motivated by their use in a historical analysis of centrifuge reliability.

97 MATHEMATICS AND COMPUTING↗

DOE Express Quantum Computing Application Teams (QCAT FY20 Report)

The QCOR project consists of 4 main research tasks: 1) scientific applications and algorithm development for machine learning (ML) and quantum theories of condensed matter systems and lattice gauge theories; 2) high-level quantum-classical (HLQC) language and domain specific language (DSL) development; 3) compiler and interfaces development for the HLQC language; and 4) hardware-level control, optimization, and algorithms libraries. In the succeeding sections we report on progress towards our research tasks during the 2020 calendar year.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

S4PST: Sustainability for Programming Systems and Tools: May Workshop Report

The US Department of Energy (DOE) Exascale Computing Project (ECP) has fostered and strengthened the use of modern software engineering practices for developing applications and libraries, and this effort has resulted in the coordinated and interoperable E4S1 and xSDK2 ecosystems. Although this approach is cost-effective, it relies on robust programming systems and tools (PST) as the underlying foundation for our HPC software. At present, our primary PST stack consists of traditional high-performance computing (HPC) languages, namely Fortran, C, C++, and the popular Python language for data analysis and AI workflows. These languages support various programming frameworks and run-time abstractions that enable parallelism and concurrency across multiple node architectures and thousands of nodes through a variety of interconnect systems. However, to accommodate users’ diverse needs, certain aspects of the HPC ecosystem are delegated to vendor-specific or third-party implementations that extend beyond a particular scientific domain. This broader scope results in a multitude of specifications and variations, which leads to a complex orchestration of many-ecosystems. Unfortunately, this complexity in the ecosystem imposes additional overhead costs on consumers during the latter stages of the development cycle. In addition to the software ecosystem challenge, the upcoming conclusion of the ECP by December 2023 has raised significant concerns within the HPC programming systems community, from both the economic and social perspectives. The ECP has implemented a management structure for software development and funding decisions across all ECP participants by following a conventional hierarchical and centralized approach. However, this structure has prompted certain considerations within the community, particularly in anticipation of the Software Sustainability initiative by the DOE’s Advanced Scientific Computing Research Program (ASCR). For the success of this new initiative, it is of utmost importance to secure consistent funding and foster close engagement with researchers and core developers of existing programming-system products. This collaboration is vital to maintaining the critical capabilities of the current software during the transition phase while proactively adapting to future technology and workforce trends. The community recognizes the significance of adapting to emerging trends and is aware of the inherent fragility of the HPC software ecosystem, particularly in relation to programming systems that cater to all users. The ability to adapt and evolve is essential to staying relevant and effectively addressing these technical, economic, and social challenges. The S4PST team, which represents one of the six ASCR Software Sustainability seedling projects, is dedicated to tackling these challenges through community-based approaches that go beyond the scope of the DOE. This involves collaboration between national laboratories with academia, non-DOE institutions, hardware and system vendors, and international partners. By fostering these partnerships, we aim to create a robust and sustainable HPC software ecosystem that can effectively meet the needs of the community. This new community effort, driven by the eight DOE labs, will take on the responsibility of guiding funding decisions for programming-systems development and maintenance with transparency and consistency across all decisions. Additionally, the team will offer common technical services to the programming systems community, irrespective of their funding situations, and facilitate community-wide incubation to proactively nurture the software ecosystem. By actively engaging with stakeholders and employing a collaborative approach, we can collectively shape the future of programming systems and ensure a robust and thriving HPC software landscape. On May 11–12, 2023, the S4PST team conducted its inaugural kick-off workshop at the Innovative Computing Laboratory (ICL) in the University of Tennessee, Knoxville, hosted by Hartwig Anzt. The workshop encompassed various sessions dedicated to presentations and discussions, with the aim of comprehending the team members’ perspectives on the vision of software sustainability. Additionally, the workshop aimed to identify the technical, economic, and social requirements for sustaining the programming-systems community in the field of HPC. This report provides a summary of the S4PST effort by highlighting five major thrust areas discussed during the workshop: (i) community, (ii) technical support, (iii) training and diversity, (iv) verification, validation and correctness, and (v) emerging technologies. It also encompasses an overview of the presentations and discussions held throughout the event, our views and potential synergies with other seedling efforts, along with the outcomes and key takeaways from our initial discussions.

97 MATHEMATICS AND COMPUTING↗

Electric Vehicle Charging for Residential and Commercial Energy Codes: Technical Brief

Numerous studies show that sales of electric vehicles (EVs) have grown consistently over recent years in the U.S. The U.S. Energy Information Administration (EIA) estimated 3 million EVs were on the road in 2022, and the Edison Electric Institute (EEI) forecasts a total of 26.4 million EVs on the road by 2030. Based on this forecast, EEI projects the need for an additional 12.9 million EV charge ports by 2030. If EV charging infrastructure fails to keep pace with sales of EVs it could result in consumers stranded without options to power their vehicles. EVs are capable of providing substantial benefits to the consumers. EVs are less expensive to operate than conventional internal combustion engine vehicles, have lower maintenance costs, and have the convenience of fueling (charging) at home or work. Studies conducted in California show that costs associated with installing EV charging infrastructure can be substantially more expensive for retrofit scenarios compared to new construction, making inclusion of EV infrastructure in new construction codes a cost-effective policy option to increase infrastructure to meet growing demands. PNNL tracks adoption of mandatory EV provisions across the U.S. As of December 20, 2024, 12 states (California, Oregon, Washington, Colorado, New Mexico, Illinois, Maryland, Delaware, New Jersey, Rhode Island, Massachusetts and Vermont) and 53 local governments have added EV provisions to their building codes, local ordinances and zoning requirements. Originally published in 2022, this tech brief has been revised to align with recent model energy code committee discussions and published EV infrastructure code language. This technical brief summarizes market trends, costs and benefits, and provides sample code language for EV charging infrastructure for consideration to be included in model codes, such as the International Energy Conservation Code (IECC) and ANSI/ASHRAE/IES Standard 90.1, as well as directly by states and local governments in their building codes. The technical brief summarizes related efforts undertaken by states and local governments, and builds upon language considered during the 2021 and 2024 IECC development cycles.

2021 IECC↗

Compositional Reasoning for Hierarchical State Machines

Harel statecharts and its derivatives are popular graphical languages for specifying discrete control systems via hierarchical state machines. Separately, there has been a long line of work on specifying concurrent systems with process calculi which come equipped with an algebraic theory, the ability reason compositionally about various temporal properties, and strong type systems. While these two approaches to modeling systems are tantalizingly similar, the integrated reasoning principles that exist for process calculi have not been demonstrated in hierarchical state machines. A key issue is that operational theories for process calculi do not behave like control systems, and thus, there is virtually no tool support for modeling control systems with such languages. For a control system designer, bringing the integrated, more scalable reasoning from the process calculi to state-machine languages would enable the specification of more complex systems and a more modular systems development process. Our insight is that we can recover many important results from the process calculi in hierarchical state machines with local scope. We employ a structural operational semantics, which is ubiquitous in process and 𝜆-calculi but uncommon in hierarchical statemachine formalizations, to enable inductive reasoning about behavior. Taking inspiration from the structure of process calculi metatheories, we define a calculus of refinement and equivalence that we prove sound with respect to local notion of (bi)simulation. Furthermore, we prove that the calculus preserves the behavioral properties of reactivity, observational determinism, traces, and linear temporal properties. Our results are mechanized in the Rocq proof assistant.

97 MATHEMATICS AND COMPUTING↗

Framework for Extensible, Asynchronous Task Scheduling (FEATS) in Fortran

Most parallel scientific programs contain compiler directives (pragmas) such as those from OpenMP, explicit calls to runtime library procedures such as those implementing the Message Passing Interface (MPI), or compiler-specific language extensions such as those provided by CUDA. By contrast, the recent Fortran standards empower developers to express parallel algorithms without directly referencing lower-level parallel programming models. Fortran’s parallel features place the language within the Partitioned Global Address Space (PGAS) class of programming models. When writing programs that exploit data-parallelism, application developers often find it straightforward to develop custom parallel algorithms. Problems involving complex, heterogeneous, staged calculations, however, pose much greater challenges. Such applications require careful coordination of tasks in a manner that respects dependencies prescribed by a directed acyclic graph. When rolling one’s own solution proves difficult, extending a customizable framework becomes attractive. The paper presents the design, implementation, and use of the Framework for Extensible Asynchronous Task Scheduling (FEATS), which we believe to be the first task-scheduling tool written in modern Fortran. We describe the benefits and compromises associated with choosing Fortran as the implementation language, and we propose ways in which future Fortran standards can best support the use case in this paper.

Richardson, Brad↗

AI-powered topic modeling: comparing LDA and BERTopic in analyzing opioid-related cardiovascular risks in women

Topic modeling is a crucial technique in natural language processing (NLP), enabling the extraction of latent themes from large text corpora. Traditional topic modeling, such as Latent Dirichlet Allocation (LDA), faces limitations in capturing the semantic relationships in the text document although it has been widely applied in text mining. BERTopic, created in 2022, leveraged advances in deep learning and can capture the contextual relationships between words. In this work, we integrated Artificial Intelligence (AI) modules to LDA and BERTopic and provided a comprehensive comparison on the analysis of prescription opioid-related cardiovascular risks in women. Opioid use can increase the risk of cardiovascular problems in women such as arrhythmia, hypotension etc. 1,837 abstracts were retrieved and downloaded from PubMed as of April 2024 using three Medical Subject Headings (MeSH) words: “opioid,” “cardiovascular,” and “women.” Machine Learning of Language Toolkit (MALLET) was employed for the implementation of LDA. BioBERT was used for document embedding in BERTopic. Eighteen was selected as the optimal topic number for MALLET and 23 for BERTopic. ChatGPT-4-Turbo was integrated to interpret and compare the results. The short descriptions created by ChatGPT for each topic from LDA and BERTopic were highly correlated, and the performance accuracies of LDA and BERTopic were similar as determined by expert manual reviews of the abstracts grouped by their predominant topics. The results of the t-SNE (t-distributed Stochastic Neighbor Embedding) plots showed that the clusters created from BERTopic were more compact and well-separated, representing improved coherence and distinctiveness between the topics. Our findings indicated that AI algorithms could augment both traditional and contemporary topic modeling techniques. In addition, BERTopic has the connection port for ChatGPT-4-Turbo or other large language models in its algorithm for automatic interpretation, while with LDA interpretation must be manually, and needs special procedures for data pre-processing and stop words exclusion. Therefore, while LDA remains valuable for large-scale text analysis with resource constraints, AI-assisted BERTopic offers significant advantages in providing the enhanced interpretability and the improved semantic coherence for extracting valuable insights from textual data.

Research & Experimental Medicine↗

SCIMON: Scientific Inspiration Machines Optimized for Novelty

We explore and enhance the ability of neu- ral language models to generate novel scien- tific directions grounded in literature. Work on literature-based hypothesis generation has traditionally focused on binary link prediction— severely limiting the expressivity of hypothe- ses. This line of work also does not focus on optimizing novelty. We take a dramatic depar- ture with a novel setting in which models use as input background contexts (e.g., problems, experimental settings, goals), and output natu- ral language ideas grounded in literature. We present SCIMON, a modeling framework that uses retrieval of “inspirations” from past scien- tific papers, and explicitly optimizes for novelty by iteratively comparing to prior papers and up- dating idea suggestions until sufficient novelty is achieved. Comprehensive evaluations reveal that GPT-4 tends to generate ideas with over- all low technical depth and novelty, while our methods partially mitigate this issue. Our work represents a first step toward evaluating and developing language models that generate new ideas derived from the scientific literature.

Ji, Heng↗

Comparing the Performance of Julia on CPUs versus GPUs and Julia-MPI versus Fortran-MPI: a case study with MPAS-Ocean (Version 7.1)

Abstract. Some programming languages are easy to develop at the cost of slow execution, while others are fast at runtime but much more difficult to write. Julia is a programming language that aims to be the best of both worlds – a development and production language at the same time. To test Julia's utility in scientific high-performance computing (HPC), we built an unstructured-mesh shallow water model in Julia and compared it against an established Fortran-MPI ocean model, the Model for Prediction Across Scales–Ocean (MPAS-Ocean), as well as a Python shallow water code. Three versions of the Julia shallow water code were created: for single-core CPU, graphics processing unit (GPU), and Message Passing Interface (MPI) CPU clusters. Comparing identical simulations revealed that our first version of the Julia model was 13 times faster than Python using NumPy, where both used an unthreaded single-core CPU. Further Julia optimizations, including static typing and removing implicit memory allocations, provided an additional 10–20× speed-up of the single-core CPU Julia model. The GPU-accelerated Julia code was almost identical in terms of performance to the MPI parallelized code on 64 processes, an unexpected result for such different architectures. Parallelized Julia-MPI performance was identical to Fortran-MPI MPAS-Ocean for low processor counts and ranges from 2× faster to 2× slower for higher processor counts. Our experience is that Julia development is fast and convenient for prototyping but that Julia requires further investment and expertise to be competitive with compiled codes. We provide advice on Julia code optimization for HPC systems.

54 ENVIRONMENTAL SCIENCES↗

Working memory, situation models, and synesthesia

Research on language comprehension suggests a strong relationship between working memory span measures and language comprehension. However, there is also evidence that this relationship weakens at higher levels of comprehension, such as the situation model level. The current study explored this relationship by comparing 10 grapheme–color synesthetes who have additional color experiences when they read words that begin with different letters and 48 normal controls on a number of tests of complex working memory capacity and processing at the situation model level. On all tests of working memory capacity, the synesthetes outperformed the controls. Importantly, there was no carryover benefit for the synesthetes for processing at the situation model level. This reinforces the idea that although some aspects of language comprehension are related to working memory span scores, this applies less directly to situation model levels. As a result, this suggests that theories of working memory must take into account this limitation, and the working memory processes that are involved in situation model construction and processing must be derived.

59 BASIC BIOLOGICAL SCIENCES↗

Sisal

Sisal (Streams and Iterations in a Single Assignment Language) was a general-purpose applicative language developed for shared-memory and vector supercomputer systems. It provided an hierarchical intermediate form, parallel runtime system, optimizing compiler, and programming environment. The language was strongly typed. It supported both array and stream data structures, and had both iterative and parallel loop constructs.

Feo, John T↗

Arion

Arion is a library and tool set that enables researchers to holistically define test system models. To define a complex system for testing an algorithm or control requires expertise across multiple domains. Simulating a complex system requires the integration of multiple simulators and test hardware, each with their own specification languages and concepts. This requires extensive set of knowledge and capabilities. Arion was developed to alleviate this challenge. Arion is a library of Java libraries that abstracts the concepts from supported simulators into a cohesive model language that allows someone to build models to their needed level of fidelity and expertise. Arion is also a software tool that translates the users model back into the specification languages of the simulators and test hardware needed for execution.

Source record↗

A Scalable Graph Analytics Framework for Programming with Big Data in R (pbdR)

Many disciplines such as biology, economics, engineering, physics, and the social sciences represent their data as graphs to capture patterns, trends, and associations. There are are many commercially available graph libraries in different programming languages to analyze these complex graphs. But there is no distributed graph library package in R - the popular statistical programming language to analyze graphs that bigger than a single machine's memory. Many domain experts prefer R over the numerous other alternatives. Towards this, we present a distributed graph analytics framework for R called programming with big graph using R (pBGR.) Our proposed framework leverages the Programming with Big Data in R (pbdR) ecosystem that provides scalable R packages for distributed computing in data science. We present an early prototype implementation of this framework using the distributed-memory parallel graph library CombBLAS and evaluate the framework's performance on leadership class computing platforms. Our experimental results demonstrate that the proposed framework is capable of performing large-scale parallel graph mining through the easyto-use R language. This enhanced graph processing capability coupled with other statistical tools already available in R, should be valuable to many domain experts.

Hasan, S M Shamimul↗

Integration of Data Analytics with Plant System Health Program

This report summarizes the R&D activities of the Plant Health Management (PHM) project during fiscal year 2020 (FY20). This project focuses on the development of methods that integrate component health data and propagate such information at the system level to evaluate system sources of risk. This project development lives in cooperation with the Risk Informed Asset Management (RIAM) project. The RIAM project, in fact, uses the reliability models and data generated by the PHM project to optimize plant operations (e.g., maintenance/replacement schedule, optimal maintenance posture). This year’s activities for the PHM project focused mainly on the development of two classes of models. The first one includes a series of component reliability models which include aging, testing and maintenance. The second class includes a series of system reliability models which focus on the secondary side of exiting U.S. reactors. These models are based on fault tree logic structures such that they can be used by existing plant PRA software. We also started to focus on the management of health data and we tackled this issue in two directions. The first one focuses on the integration of monitor data with simulation models to assess component health. This approach is moving from a classical data based to a model+data based approach with the goal of improving higher component health information. The second direction focuses on linking equipment reliability data (e.g., maintenance/failure reports, component monitoring data) directly to system reliability models using a safety margin based language rather than a probability based language. The main advantage of a safety margin based language is that it can provide to system engineers more tangible information on system/component health and how it propagates to the system level.

97 MATHEMATICS AND COMPUTING↗

Site-Specific Analyses for Demonstrating Compliance with 10 CFR 61 Performance Objectives - 12179

The U.S. Nuclear Regulatory Commission (NRC) is proposing to amend its regulations at 10 CFR Part 61 to require low-level radioactive waste disposal facilities to conduct site-specific analyses to demonstrate compliance with the performance objectives in Subpart C. The amendments would require licensees to conduct site-specific analyses for protection of the public and inadvertent intruders as well as analyses for long-lived waste. The amendments would ensure protection of public health and safety, while providing flexibility to demonstrate compliance with the performance objectives, for current and potential future waste streams. NRC staff intends to submit proposed rule language and associated regulatory basis to the Commission for its approval in early 2012. The NRC staff also intends to develop associated guidance to accompany any proposed amendments. The guidance is intended to supplement existing low-level radioactive waste guidance on issues pertinent to conducting site-specific analyses to demonstrate compliance with the performance objectives. The guidance will facilitate implementation of the proposed amendments by licensees and assist competent regulatory authorities in reviewing the site-specific analyses. Specifically, the guidance provides staff recommendations on general considerations for the site-specific analyses, modeling issues for assessments to demonstrate compliance with the performance objectives including the performance assessment, intruder assessment, stability assessment, and analyses for long-lived waste. This paper describes the technical basis for changes to the rule language and the proposed guidance associated with implementation of the rule language. The NRC staff, per Commission direction, intends to propose amendments to 10 CFR Part 61 to require licensees to conduct site-specific analyses to demonstrate compliance with performance objectives for the protection of public health and the environment. The amendments would require a performance assessment to demonstrate protection of the general population from releases of radioactivity, an assessment to demonstrate protection of a potential inadvertent intruder, and a long-term analysis to assess how the design of the facility considers the potential radiological impacts associated with disposal of long-lived waste streams. Concurrently, the NRC staff intends to propose associated guidance to facilitate the implementation of the requirements to conduct site-specific analyses. In proposing these amendments to the regulation and associated guidance, the NRC staff has conducted extensive public outreach since 2009 including three public meetings and four briefings of the NRC's Advisory Committee on Reactor Safeguards. The NRC staff plans to submit the proposed amendments to the regulations to the Commission in early 2012. Subsequently, the proposed amendments and associated guidance would be published in the Federal Register for public comment pending approval of the proposed amendments to the regulations by the Commission. Following the public comment period, NRC staff plans to address public comments and revise, as necessary, the regulations and associated guidance before publishing a final rule, which is anticipated in 2013. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗