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At least 1,549 records · Page 86

Minimizing Error Potential Using Computer Applications - 18498

Many Savannah River Site (SRS) liquid waste facility operations depend upon repetitive engineering calculations and operator actions. Although these calculations and actions are formalized in technical reports and paper procedures, they can still be vulnerable to data entry errors, calculation errors, equipment alignment errors, and occasional changes caused by different people performing these activities. Savannah River Remediation (SRR) is using computer automation to reduce these error precursors by standardizing repetitive calculations and by performing plant alignment checks for repetitive operation processes. Data entry can be automated, calculation methodologies can be standardized, and computers can check to see that predefined plant conditions exist before equipment operation. In addition to improving quality, the time required for these activities to generate technical reports, to perform independent reviews, and to perform equipment alignment checks can be significantly reduced. In the case of operator-performed calculations, error precursors involve distractions that can occur over a multi-page paper procedure, confusing displays and controls from equipment, mathematical errors, complacency, and unfamiliarity with the procedure among many others. Repetitive engineering calculations suffer from similar error precursors and are often compounded by high workloads, lack of proficiency, lack of standard methodology, mental shortcuts, and biases. Web-based computer applications can eliminate many of these precursors through standardization. Calculation methods are fixed, inputs are fixed, and computer checks can highlight potentially wrong inputs and outputs. Automated calculations are performed almost instantaneously once input is provided. Operators and engineers can spend more time focusing on the results than on the process to achieve the results. Similarly, when operators use repetitive procedures involving equipment manipulation, the same error precursors apply. Automated operation sequences and equipment checks can be programmed into the distributed control system to provide standard operating processes that reduce and eliminate error precursors. This paper describes how SRR incorporates Human Performance Improvement (HPI) principles when automating calculations and operation processes. Computer applications will be reviewed in detail, highlighting the software development life-cycle that includes requirements gathering, prototyping, design, development, testing, and implementation. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

PHANOTATE: a novel approach to gene identification in phage genomes

Motivation: Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path. Results: We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank’s non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes. Availability and implementation: https://github.com/deprekate/PHANOTATE. Supplementary information: Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Large Eddy Simulations for a Helical Coil Steam Generator

The desire for scalable power plants in remote locations and specialized applications has brought forth the small modular reactor (SMR). Now, smaller light water reactors are seen as viable means for meeting global energy requirements. Generally, straight or U-shape tubes are used to exchange heat from the primary to secondary coolant; however this is not ideal when size is a criterion. Helical coil steam generators (HCSGs) are advantageous for SMRs due to their enhanced heat transfer in compact spaces. Still, there is the concern of safety as steam generator tubes could rupture due to vibrations and fatigue on the material. Understanding flow characteristics and quantifying pressures for these tubes are important components for the design of safety and efficiency in these steam generators. The current study uses the spectral element computational fluid dynamic (CFD) code, Nek5000, to develop large eddy simulations (LES) for validation against experiments that will be conducted at Texas A and M University. Time-averaged pressure data will be compared with pressure tap readings, and velocity profile with particle image velocimetry (PIV) measurements. The presented preliminary results investigate the differences between 5.-, 7.-, and 9.-order polynomial simulations. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

NEAMS Update: Quarterly report for January - March 2012

Quarterly highlights are: (1) The integration of Denovo and AMP was demonstrated in an AMP simulation of the thermo-mechanics of a complete fuel assembly; (2) Bison was enhanced with a mechanistic fuel cracking model; (3) Mechanistic algorithms were incorporated into various lower-length-scale models to represent fission gases and dislocations in UO2 fuels; (4) Marmot was improved to allow faster testing of mesoscale models using larger problem domains; (5) Component models of reactor piping were developed for use in Relap-7; (6) The mesh generator of Proteus was updated to accept a mesh specification from Moose and equations were formulated for the intermediate-fidelity Proteus-2D1D module; (7) A new pressure solver was implemented in Nek5000 and demonstrated to work 2.5 times faster than the previous solver; (8) Work continued on volume-holdup models for two fuel reprocessing operations: voloxidation and dissolution; (9) Progress was made on a pyroprocessing model and the characterization of pyroprocessing emission signatures; (10) A new 1D groundwater waste transport code was delivered to the used fuel disposition (UFD) campaign; (11) Efforts on waste form modeling included empirical simulation of sodium-borosilicate glass compositions; (12) The Waste team developed three prototypes for modeling hydride reorientation in fuel cladding during very long-term fuel storage; (13) A benchmark demonstration problem (fission gas bubble growth) was modeled to evaluate the capabilities of different meso-scale numerical methods; (14) Work continued on a hierarchical up-scaling framework to model structural materials by directly coupling dislocation dynamics and crystal plasticity; (15) New 'importance sampling' methods were developed and demonstrated to reduce the computational cost of rare-event inference; (16) The survey and evaluation of existing data and knowledge bases was updated for NE-KAMS; (17) The NEAMS Early User Program was launched; (18) The Nuclear Regulatory Commission (NRC) Office of Regulatory Research was introduced to the NEAMS program; (19) The NEAMS overall software quality assurance plan (SQAP) was revised to version 1.5; and (20) Work continued on NiCE and its plug-ins and other utilities, such as Cubit and VisIt.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

CCAMP: An Integrated Translation and Optimization Framework for OpenACC and OpenMP

Heterogeneous computing and exploration into specialized accelerators are inevitable in current and future supercomputers. Although this diversity of devices is promising for performance, the array of architectures presents programming challenges. High-level programming strategies have emerged to face these challenges, such as the OpenMP offloading model and OpenACC. The varying levels of support for these standards, however, within vendor-specific and open-source tools, as well as the lack of performance portability across devices, have prevented the standards from achieving their goals. To address these shortcomings, we present CCAMP, an OpenMP and OpenACC interoperable framework. CCAMP provides two primary facilities: language translation between the two standards and device-specific directive optimization within each standard. We show that by using the CCAMP framework, programmers can easily transplant non-portable code into new ecosystems for new architectures. Additionally, by using CCAMP device-specific directive optimizations, users can achieve optimized performance across architectures using a single source code.

Lambert, Jacob↗

Visualization techniques for the gyrokinetic tokamak simulation code

Gyrokinetic simulations of plasma microturbulence in tokamaks are challenging to visualize because the compute grid follows the magnetic field lines that spiral around the torus. We have overcome this challenge by developing three new approaches that improve visualization of gyrokinetics. Our techniques work directly with the topology of magnetic flux surfaces where the simulation stores variables in concentric rings on poloidal planes (vertical cross sections of the torus). Our visualization preview step triangulates each consecutive pair of rings to display the data on a poloidal plane. The second visualization technique follows spiral field lines around the torus and constructs polygons to visualize a flux surface. Third, the poloidal triangles are connected between planes to form prisms that compose a 3-D model of the entire torus. The visualization workflow produces detailed geometry that matches the high resolution, irregular compute grid for every time step. The surface and solid models are displayed in scientific visualization programs to effectively explore and communicate the results, including fluctuation of electron density, ion temperature, and electrostatic potential. Highly detailed renderings verify plasma behavior along magnetic field lines over time.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Hierarchical computation in the SPMD programming model

Large-scale parallel machines are programmed mainly with the single program, multiple data (SPMD) model of parallelism. While this model has advantages of scalability and simplicity, it does not fit well with divide-and-conquer parallelism or hierarchical machines that mix shared and distributed memory. In this paper, we define the recursive single program, multiple data model (RSPMD) that extends SPMD with a hierarchical team mechanism to support hierarchical algorithms and machines. We implement this model in the Titanium language and describe how to eliminate a class of deadlocks by ensuring alignment of collective operations. We present application case studies evaluating the RSPMD model, showing that it enables divide-and-conquer algorithms such as sorting to be elegantly expressed and that team collective operations increase performance of conjugate gradient by up to a factor of two. The model also facilitates optimizations for hierarchical machines, improving scalability of particle in cell by 8x and performance of sorting and a stencil code by up to 40% and 14%, respectively.

Kamil, A↗

Report for the ASC CSSE L2 Milestone (4873) - Demonstration of Local Failure Local Recovery Resilient Programming Model.

Recovery from process loss during the execution of a distributed memory parallel application is presently achieved by restarting the program, typically from a checkpoint file. Future computer system trends indicate that the size of data to checkpoint, the lack of improvement in parallel file system performance and the increase in process failure rates will lead to situations where checkpoint restart becomes infeasible. In this report we describe and prototype the use of a new application level resilient computing model that manages persistent storage of local state for each process such that, if a process fails, recovery can be performed locally without requiring access to a global checkpoint file. LFLR provides application developers with an ability to recover locally and continue application execution when a process is lost. This report discusses what features are required from the hardware, OS and runtime layers, and what approaches application developers might use in the design of future codes, including a demonstration of LFLR-enabled MiniFE code from the Matenvo mini-application suite.

Heroux, Michael Allen↗

HFIRCON Version 1.0.5 User Guide

The High Flux Isotope Reactor (HFIR) Controller (HFIRCON) code is a collection of python routines and C plugins that automate the workflow for fuel and single- or multicycle target depletion analyses for HFIR at Oak Ridge National Laboratory (ORNL). This code calls the LAVAMINT (LAVA Model Interrogator) parallel (MCNP) Monte Carlo N-Particle model interrogator to stochastically calculate cell volumes and bounding boxes, the ADVANTG (Automatic Variance Reduction Generation) code package for all variance reduction and source biasing calculations, the ORNL-Transformative Neutronics/MCNP5 transport solver for all transport solutions, and the MSX_DEPLETE module to perform all depletion calculations via the ORIGEN (Oak Ridge Isotope Generation) application programming interface. It also performs a robust set of postprocessing functions to automatically provide summaries of several key metrics that are common to a wide variety of typical HFIR design and safety-basis analyses.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

The ASC-V&V Program [Slides]

The fundamental goal of the ASC-V&V Program is to obtain a quantitative understanding of our customers’ needs and priorities, and use it to assess applicability of numerical models of physical phenomena to physics questions, sensitivity of physics questions to physical phenomena, fidelity of a numerical implementation to the theory, the bounds of validity of theories, fidelity and coverage of experimental data relative to regimes of interest for physics questions, in order to warn users of IC codes and PEM data when simulations may lead to unsupported conclusions, and provide estimates of uncertainties on figures of merit calculated by the simulations.

97 MATHEMATICS AND COMPUTING↗

The History of Monte Carlo and MCNP at Los Alamos [Slides]

The Monte Carlo method for radiation particle transport has its origins at LANL dating back to the 1940’s. The creators of these methods were Drs. Stanislaw Ulam, John von Neumann, Robert Richtmyer, and Nicholas Metropolis. Monte Carlo methods for particle transport have been driving computational developments since the beginning of modern computers; this continues today. In the 1950’s and 1960’s, these new methods were organized into a series of special-purpose Monte Carlo codes, including MCS, MCN, MCP, and MCG. These codes were able to transport neutrons and photons for specialized LANL applications. In 1977, these separate codes were combined to create the LANL Monte Carlo N-Particle (MCNP) radiation particle transport code. In 1983, MCNP3 was released for public distribution to the Radiation Safety Information Computational Center (RSICC). MCNP6.3 will be released late in 2021. Each year, LANL has ~100 MCNP new users and RSICC ~1250 new licenses distributed. This talk will review the Los Alamos history of the development of the modern Monte Carlo method and MCNP.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

MCNP ® Code Version 6.3.0 Verification & Validation Testing

This report describes the verification and validation testing performed on MCNP ® code version 6.3.0. The purpose of this report is to act as a compendium of test suite descriptions and results. Accordingly the document is divided into two parts. Part I (this part) describes each test suite in the following sections. Part II provides the results of testing each suite and comparisons to experimental and/or alternative computational results, as appropriate.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Modbus RTU for Embedded Cyber Secure Inverter Controller

The Modbus communication protocol is a widely adopted communication standard in industrial control systems. This communication protocol is known for being reliable and straightforward to implement while being versatile in terms of its operating parameters while supporting multiple formats over various hardware infrastructures and architectures. Many intelligent devices such as Programmable Logic Controllers (PLCs), Human-Machine Interfaces (HMIs), Internet-of-Things (IoT), and various Operational Technologies (OT) utilize Modbus for their communication systems. These types of systems must communicate with each other through a standardized and central communication process. To support the integration of these modular systems, a Field-Programmable Gate Array (FPGA) can act as an embedded central routing fabric for this communication to take place. Embedded systems are versatile enough to interface with various devices and systems to accomplish various goals. Additionally, embedded systems require relatively small physical designs to minimize the required resources to facilitate the intended application by providing low-level system access. This minimization of system resources goes hand in hand with reducing the financial cost of a proposed solution or system. As remotely collaborating researchers often use FPGAs to prototype designs that are required to have a method for data transmission among systems, it is imperative to provide a baseline standard for communications among devices and systems. A typical method of implementing the Modbus RTU communication protocol in an embedded environment is using integrated logic architectures within the FPGA called “Intellectual Property (IP) cores.” IP cores can be designed using integrated logic or circuit designs to function as an embedded processor. These IP cores can then perform the required computational actions to support the Modbus RTU communication protocol by utilizing high-level programming languages such as the C programming language. The hardware description language of Very High-Speed Integrated Circuit Hardware Description Language (VHDL) allows for the control of real hardware at the logic gate and signal level. These logic gates and signals can be designed and controlled to perform desired actions based on the system design. Programming an FPGA using VHDL allows an individual to access the lowest abstraction level of the system during FPGA development. This level of abstraction is referred to as the register-transfer level (RTL), which gives access to manipulating values and variables at the register level. This register-level manipulation provides precision over creating the logical circuit within the FPGA, thus minimizing the required code to perform desired operations. The Modbus RTU communication protocol can be implemented within an FPGA using VHDL programming to establish a standardized and embedded serial communication pathway. This implementation provides a standardized communication protocol to streamline research efforts among researchers, thus increasing the efficiency of research efforts. Additionally, this Modbus RTU implementation requires fewer resources when compared to typical communication protocol implementations that utilize an IP core, reducing the hardware requirement for effective research efforts.

communication↗

International fuel performance study of fresh fuel experiments for PCMI effects during RIA experiments

This paper presents the results of High-burnup Experiments for Reactivity-initiated Accident (HERA) Modeling & Simulation (M&S) exercise. The HERA project under the Nuclear Energy Agency (NEA) Second Framework for Irradiation Experiments (FIDES-II) program is focused on studying Light Water Reactor (LWR) fuel behavior during Reactivity-Initiated Accident (RIA) conditions. The Part I M&S cases are based on a series of tests in the Transient Reactor Test (TREAT) facility in the United States and the Nuclear Safety Research Reactor (NSRR) in Japan. The purpose of this work is to evaluate the test design to accomplish its goals in establishing clearer understanding of the effects of power pulse width during RIA conditions. Further, the blind predictions using various computational tools have been performed and compared amongst to interpret the behaviors of high burnup fuels during RIA. While many international participants evaluate the thermal–mechanical behavior of fuel rod under different conditions, a considerable scatter of outputs comes out for the cases due to the disparity between codes in predicting mechanical behaviors. In general, however, the results of thermal–mechanical analysis elaborate that nominal design conditions the shorter pulse width tests in NSRR should cause cladding failures while the TREAT tests appear to have more split prediction of failure or not. Furthermore, the sensitivity analysis varying key testing parameters reveals the considerable effect of power pulse width and total energy deposition on prediction of fuel rod failure.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Adoption of High Performance Computational (HPC) Modeling Software for Widespread Use in the Manufacture of Welded Structures

This report summarizes the final product developed for the US DOE Small Business Innovation Research (SBIR) Phase II grant made to Engineering Mechanics Corporation of Columbus (Emc 2 ) between April 16, 2014 and August 31, 2016 titled ‘Adoption of High Performance Computational (HPC) Modeling Software for Widespread Use in the Manufacture of Welded Structures’. Many US companies have moved fabrication and production facilities off shore because of cheaper labor costs. A key aspect in bringing these jobs back to the US is the use of technology to render US-made fabrications more cost-efficient overall with higher quality. One significant advantage that has emerged in the US over the last two decades is the use of virtual design for fabrication of small and large structures in weld fabrication industries. Industries that use virtual design and analysis tools have reduced material part size, developed environmentally-friendly fabrication processes, improved product quality and performance, and reduced manufacturing costs. Indeed, Caterpillar Inc. (CAT), one of the partners in this effort, continues to have a large fabrication presence in the US because of the use of weld fabrication modeling to optimize fabrications by controlling weld residual stresses and distortions and improving fatigue, corrosion, and fracture performance. This report describes Emc 2 ’s DOE SBIR Phase II final results to extend an existing, state-of-the-art software code, Virtual Fabrication Technology (VFT®), currently used to design and model large welded structures prior to fabrication - to a broader range of products with widespread applications for small and medium-sized enterprises (SMEs). VFT® helps control distortion, can minimize and/or control residual stresses, control welding microstructure, and pre-determine welding parameters such as weld-sequencing, pre-bending, thermal-tensioning, etc. VFT® uses material properties, consumable properties, etc. as inputs. Through VFT®, manufacturing companies can avoid costly design changes after fabrication. This leads to the concept of joint design/fabrication where these important disciplines are intimately linked to minimize fabrication costs. Finally service performance (such as fatigue, corrosion, and fracture/damage) can be improved using this product. Emc 2 ’s DOE SBIR Phase II effort successfully adapted VFT® to perform efficiently in an HPC environment independent of commercial software on a platform to permit easy and cost effective access to the code. This provides the key for SMEs to access this sophisticated and proven methodology that is quick, accurate, cost effective and available “on-demand” to address weld-simulation and fabrication problems prior to manufacture. In addition, other organizations, such as Government agencies and large companies, may have a need for spot use of such a tool. The open source code, WARP3D, a high performance finite element code used in fracture and damage assessment of structures, was significantly modified so computational weld problems can be solved efficiently on multiple processors and threads with VFT®. The thermal solver for VFT®, based on a series of closed form solution approximations, was extensively enhanced for solution on multiple processors greatly increasing overall speed. In addition, the graphical user interface (GUI) was re-written to permit SMEs access to an HPC environment at the Ohio Super Computer Center (OSC) to integrate these solutions with WARP3D. The GUI is used to define all weld pass descriptions, number of passes, material properties, consumable properties, weld speed, etc. for the structure to be modeled. The GUI was enhanced to make it more user-friendly so that non-experts can perform weld modeling. Finally, an extensive outreach program to market this capability to fabrication companies was performed. This access will permit SMEs to perform weld modeling to improve their competitiveness at a reasonable cost.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability, Dallas, TX, November 2018.

Highly-optimized parallel molecular dynamics programs have allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: a significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup, we assess key accelerating programming components of four different best-performing molecular dynamics programs - GROMACS, NAMD, LAMMPS and CP2K-- each having a particular scope of application, for contribution to performance and for portability. We use builds with and without these components, tested on HPC systems. We also analyze the code-bases to determine compliance with portability recommendations. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. This characterizes the performance efficiency that must be approached for good performance portability on a programmatic level, suggesting solutions to this difficult problem, which should come from developers, industry and funding institutions, and possibly new research in programming languages.

Computer Science↗

MO-F-CAMPUS-I-01: A System for Automatically Calculating Organ and Effective Dose for Fluoroscopically-Guided Procedures

Purpose: A system was developed that automatically calculates the organ and effective dose for individual fluoroscopically-guided procedures using a log of the clinical exposure parameters. Methods: We have previously developed a dose tracking system (DTS) to provide a real-time color-coded 3D- mapping of skin dose. This software produces a log file of all geometry and exposure parameters for every x-ray pulse during a procedure. The data in the log files is input into PCXMC, a Monte Carlo program that calculates organ and effective dose for projections and exposure parameters set by the user. We developed a MATLAB program to read data from the log files produced by the DTS and to automatically generate the definition files in the format used by PCXMC. The processing is done at the end of a procedure after all exposures are completed. Since there are thousands of exposure pulses with various parameters for fluoroscopy, DA and DSA and at various projections, the data for exposures with similar parameters is grouped prior to entry into PCXMC to reduce the number of Monte Carlo calculations that need to be performed. Results: The software developed automatically transfers data from the DTS log file to PCXMC and runs the program for each grouping of exposure pulses. When the dose from all exposure events are calculated, the doses for each organ and all effective doses are summed to obtain procedure totals. For a complicated interventional procedure, the calculations can be completed on a PC without manual intervention in less than 30 minutes depending on the level of data grouping. Conclusion: This system allows organ dose to be calculated for individual procedures for every patient without tedious calculations or data entry so that estimates of stochastic risk can be obtained in addition to the deterministic risk estimate provided by the DTS. Partial support from NIH grant R01EB002873 and Toshiba Medical Systems Corp.

60 APPLIED LIFE SCIENCES↗

Integration of Dynamical System Scaling to RAVEN and Facility Application

As part of the design optimization and model validation effort within the hybrid energy systems program, the research to implement dynamical system scaling (DSS) code to RAVEN is funded under the Integrated Energy System program in collaboration with the Digital Reactor Technology & Development department. The DSS data processing algorithm has been coded within the RAVEN framework along with other metrics and postprocessing models. The implemented code was tested using a gravity-driven draining tank draining case modeled in RELAP5-3D and generated data was successfully postprocessed based on the scaling analyses defined by DSS. Postprocessed data concluded less agreement for the tank exit velocity and indicated that the modeled input deck for RELAP5-3D requires modification to enforce minimal pressure differential effects to the draining process.

97 MATHEMATICS AND COMPUTING↗