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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Toward more mechanistic representations of biogeochemical processes in river networks: Implementation and demonstration of a multiscale model

A recently introduced multiscale model for representing the effects of small-scale hyporheic-zone biogeochemical processes is extended from the reach scale to river network scales. The model uses advection-dispersion-reaction equations for the channel network and one-dimensional advection-reaction subgrid models for the hyporheic zone. We summarize implementation in the integrated surface/subsurface hydrology modeling system Amanzi-ATS. The extension uses topologically defined meshes to represent stream/river networks and associates a hyporheic subgrid model with each channel grid cell. Biogeochemical reaction modeling capability residing in community software is accessed through an application programming interface. The implementation is verified against independent numerical solutions on a single reach. Mesh convergence studies show that commonly used semi-distributed representations can introduce significant spatial discretization error. Denitrification of farm runoff in a subbasin of the Portage River Basin in Ohio, USA is used to demonstrate the general-purpose reactive transport capability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird’s eye view” of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry data sets showed that TopMG outperformed existing methods in identifying complex proteoforms.

Dynamic Programming↗
DOE OSTI2018

Safety Requirement Management System (SRMS) - Improved Documented Safety Analyses Implementation - 18476

Savannah River Remediation (SRR) developed a new software application, Safety Requirement Management System (SRMS), to improve Documented Safety Analysis (DSA) safety requirement implementation in the Savannah River Site's Liquid Waste facilities. Technical Safety Requirement (TSR) Limited Conditions of Operations (LCOs) and related surveillances were previously tracked using four different applications. Due to their differences and their age, the applications introduced a number of operational challenges and vulnerabilities, including outdated platforms, usage demands beyond original design, and different organizational work processes. SRMS was developed to resolve these issues by using a single web-based approach that provides consistency, wider accessibility, simpler maintenance, and a platform for additional functionality. Other SRS facilities are evaluating the application for its applicability as a standard practice across the site. The new SRMS application decreased the administrative overhead for application maintenance, provided the needed TSR change management functionality, and reduced error precursors with the following advantages: - Consistent process/application across all SRR facilities - More efficient way to track and communicate compliance with DSA time-related requirements (i.e., TSR LCOs and surveillances). - Web-based search capability for LCO entries/exits and a record of surveillance performances. - TSR change management and independent reviews through electronic approvals. For example, the application provides the ability to bundle and stage LCO and surveillance changes associated with a TSR revision. The approval process involves multiple roles from the facility to ensure validity. - Formal configuration management program, fully supported by software life cycle documents. SRMS was implemented at Defense Waste Processing Facility (DWPF) in June 2017, with implementation in all Liquid Waste facilities expected by the end of 2017. Next, SRR plans to expand SRMS functionality to include a linking document database (LDD) to support the DSA requirements. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

The ATLAS experiment software on ARM

With an increased dataset obtained during the Run 3 of the LHC at CERN and the even larger expected increase of the dataset by more than one order of magnitude for the HL-LHC, the ATLAS experiment is reaching the limits of the current data processing model in terms of traditional CPU resources based on x86_64 architectures and an extensive program for software upgrades towards the HL-LHC has been set up. The ARM architecture is becoming a competitive and energy efficient alternative. Some surveys indicate its increased presence in HPCs and commercial clouds, and some WLCG sites have expressed their interest. Chip makers are also developing their next generation solutions on ARM architectures, sometimes combining ARM and GPU processors in the same chip. Consequently it is important that the ATLAS software embraces the change and is able to successfully exploit this architecture. We report on the successful porting to ARM of the Athena software framework, which is used by ATLAS for both online and offline computing operations. Furthermore we report on the successful validation of simulation workflows running on ARM resources. For this we have set up an ATLAS Grid site using ARM compatible middleware and containers on Amazon Web Services (AWS) ARM resources. The ARM version of Athena is fully integrated in the regular software build system and distributed in the same way as other software releases. In addition, the workflows have been integrated into the HEPscore benchmark suite which is the planned WLCG wide replacement of the HepSpec06 benchmark used for Grid site pledges. In the overall porting process we have used resources on AWS, Google Cloud Platform (GCP) and CERN. A performance comparison of different architectures and resources will be discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

SU-E-T-235: Data Mining for Evaluating Treatment Performances Over a Large Quantity of Data to Monitor and Improve SBRT Workflow

Purpose: To quality assure a large quantity of retrospective treatment cases for treatment performances by randomly sampling is inefficient. Here we provide a method to efficiently monitor and investigate the QA of SBRT workflow over Mosaiq. Methods: The code developed with Microsoft SQL Server Management Studio 2008R2 and VBA was used for retrieving and sorting data from Mosaiq (version 2.3–2.6 during 2012–2015). SBRT patients were filtered by fractional dose over 350cGy and total fraction number less than 6, which SBRT prescriptions were defined. The quality assurance on the SBRT workflow was focused on the treatment deliveries such as patient positioning setup, CBCT indicated offsets and couch shifted corrections. The treatment delivery were done by Varian Truebeam systems and the record/verify by Mosaiq. Results: Total 82 SBRT patients corresponding to 103 courses and 854 CBCT images were found by the retrieval query. Most centers record daily pre-treatment (Pre-Tx: before treatment shift) image-guided shifts along treatment course for inter-fraction motion record, and it is useful to also verify it with post-treatment imaging (Post-Tx: after treatment CBCT verification) to verify intra-fraction motion. Analyzing the details of daily recorded shifts can reveals the information of patient-setup and staff’s record/verify behaviors. 3 examples were provided as solid evidences and on-going rectification for preventing future mistakes. Conclusions: The report gave feasible examples for inspector to verify a large amount of data during site investigation. This program can also be extended to a scheduled data mining with software to periodical analyze the timely records in Mosaiq, for example, a various control charts for different QA purposes. As the current trend of automation in radiation therapy field, the data mining would be a necessary tool in the future, just as the automatic plan quality evaluation has been under development in Eclipse.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

LLVM Infrastructure and Tools Project Summary

This project works with the open source LLVM Compiler Infrastructure (http://llvm.org) to provide tools and capabilities that address needs and challenges faced by ECP community (applications, libraries, and other components of the software stack). Our focus is on providing a more productive development environment that enables (i) improved compilation times and code generation for parallelism, (ii) additional features/capabilities within the design and implementations of LLVM components for improved platform/performance portability and (iii) improved aspects related to composition of the underlying implementation details of the programming environment, capturing resource utilization, overheads, etc. -- including runtime systems that are often not easily addressed by application and library developers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Chemics-Reactors: A Preliminary Python Program for Implementing Network Models of Multiphase Reactors

We discuss the design and implementation of a preliminary software package written in Python 3 that is intended to represent complex multiphase reactors as networks of ideal continuous stirred tank reactors. This software also implements statistical design of experiments, uncertainty quantification, and global sensitivity analysis. These advanced features can provide important qualitative and quantitative insights into the effect of operating conditions and model parameters on predicted reactor performance. We demonstrate the utility of the program by modeling the vapor phase catalytic upgrading of bio-oil in a bubbling fluidized bed reactor.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Implementation and Demonstration of P4 Software for Improving ICS Protocol Visibility and Control [Slides]

No prior enabling funded work applicable to this proposal. Programming Protocol-independent Packet Processors (P4) is an open source, domain-specific programming language for network switching devices. P4 complements traditional Software Defined Networking (SDN) which is primarily concerned with the management of packets (e.g. routing/dropping decisions) rather than how each packet is processed. The introduction of P4 provided new capabilities (e.g. firewall, load balancing, enhanced security) but has primarily been deployed in data centers. This effort investigates ways to expand P4 into other niches such as ICS networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

HEP Software Foundation Community White Paper Working Group - Data Processing Frameworks

Data processing frameworks are an essential part of HEP experiments' software stacks. Frameworks provide a means by which code developers can undertake the essential tasks of physics data processing, accessing relevant inputs and storing their outputs, in a coherent way without needing to know the details of other domains. Frameworks provide essential core services for developers and help deliver a configurable working application to the experiments' production systems. Modern HEP processing frameworks are in the process of adapting to a new computing landscape dominated by parallel processing and heterogeneity, which pose many questions regarding enhanced functionality and scaling that must be faced without compromising the maintainability of the code. In this paper we identify a program of work that can help further clarify the key concepts of frameworks for HEP and then spawn R&D activities that can focus the community's efforts in the most efficient manner to address the challenges of the upcoming experimental program.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

A mathematical programming approach for the optimal placement of flame detectors in petrochemical facilities

Flame detectors provide an important layer of protection for personnel in petrochemical plants, but effective placement can be challenging. A mixed-integer nonlinear programming formulation is proposed for optimal placement of flame detectors while considering non-uniform probabilities of detection failure. We show that this approach allows for the placement of fire detectors using a fixed sensor budget and outperforms models that do not account for imperfect detection. In this study, we develop a linear relaxation to the formulation and an efficient solution algorithm that achieves global optimality with reasonable computational effort. We integrate this problem formulation into the Python package, Chama, and demonstrate the effectiveness of this formulation on a small test case and on two real-world case studies using the fire and gas mapping software, Kenexis Effigy.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Compiler-Driven FPGA Virtualization with SYNERGY

FPGAs are increasingly common in modern applications, and cloud providers now support on-demand FPGA acceleration in datacenters. Applications in datacenters run on virtual infrastructure, where consolidation, multi-tenancy, and workload migration enable economies of scale that are fundamental to the provider's business. However, a general strategy for virtualizing FPGAs has yet to emerge. While manufacturers struggle with hardware-based approaches, we propose a compiler/runtime-based solution called Synergy. We show a compiler transformation for Verilog programs that produces code able to yield control to software atsub-clock-tickgranularity according to the semantics of the original program. Synergy uses this property to efficiently support core virtualization primitives: suspend and resume, program migration, and spatial/temporal multiplexing, on hardware which is availabletoday.We use Synergy to virtualize FPGA workloads across a cluster of Intel SoCs and Xilinx FPGAs on Amazon F1. The workloads require no modification, run within 3--4x of unvirtualized performance, and incur a modest increase in FPGA fabric usage.

Computer Science↗
DOE OSTI2017

SIERRA/Aero User Manual (V.4.44)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

SIERRA/Aero User Manual Version 4.46.

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

SIERRA/Aero User Manual - Version 4.50

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

SIERRA/Aero User Manual - Version 4.48

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

SIERRA/Aero User Manual (V. 4.40)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.

42 ENGINEERING↗
DOE OSTI2016

SIERRA/Aero User Manual (V.4.42)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

SIERRA/Aero Theory Manual (V.4.54)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗