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All sources NASA NTRS DOE OSTI

DOE OSTI2025

A nonhydrostatic formulation for MPAS-Ocean

The Model for Prediction Across Scales-Ocean (MPAS-Ocean) is an open-source, global ocean model and is one component of a family of climate models within the MPAS framework, including atmosphere, sea-ice, and land-ice models. Here, in this work, a new formulation for the ocean model is presented that solves the nonhydrostatic, incompressible Boussinesq equations on an unstructured, staggered, z-level grid. The introduction of this nonhydrostatic capability is necessary for the resolution of internal wave dynamics and large eddy simulations. Compared to the standard, hydrostatic formulation, a nonhydrostatic pressure solver and a vertical momentum equation are added, where the PETSc (Portable Extensible Toolkit for Scientific Computation) library is used for the inversion of a large sparse system for the nonhydrostatic pressure. Numerical results on a stratified seiche, internal solitary wave, overflow and lock-exchange test cases are presented, and the parallel efficiency of the code is evaluated using up to 1024 processors.

3D Poisson equation↗

DOE OSTI2025

A nonhydrostatic formulation for MPAS-Ocean

3D Poisson equation↗

DOE OSTI2019

Energy Deposition, Radiological and Thermal Studies for Linac-to-Booster Transfer Line Beam Absorber

The PIP-II Linac-to-Booster transfer line will transport the beam from the end of the superconducting Linac to the Injection Girder of the Booster. The transfer line consists of two arcs and a straight section in between (see Fig. 1). The straight section splits into two separate lines: Beam Absorber and Mu2e experiment lines. In this paper, results of energy deposition studies for the Beam Absorber, performed with MARS15 Monte Carlo code for normal operation, are presented. Also, corresponding thermal analyses with ANSYS code are described. According to PIP-II design parameters, the beam energy as high as 1 GeV is considered. Two beam power options were studied: (i) 50 kW as a conservative estimate for a permanent absorber; (ii) 5 kW as an option for a portable absorber required for a commissioning stage.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

PETSc Users Manual (Revision 3.15)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms

The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept of a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

A Structural Design Approach Tailored for the Rapid Preliminary Design of Microreactor Components

High-temperature microreactors can play a role in developing reliable, portable energy sources for off-grid remote locations, microgrid concepts, and industrial process heat. Portability and passive safety criteria tend to skew microreactor structural component designs toward complex geometries, high thermal stresses, and design bases with large numbers of startup/shutdown cycles. Current design rules, as typified by Section III of the American Society of Mechanical Engineers (ASME) Boiler & Pressure Vessel Code, are less than optimal for these conditions, particularly for preliminary component designs where developers need to rapidly consider a large number of potential component configurations. This paper presents a design method targeted toward rapid, efficient evaluation of preliminary component designs using modern finite element analysis. The new method retains key connections with the ASME Code rules and design data while streamlining the design approach. This paper presents the design method, several verification examples illustrating the similarities and differences between the new method and the current ASME rules, and the application of the new approach to the evaluation of a test article mimicking key features of a heat pipe–cooled microreactor.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2015

Portable File Format (PFF) specifications

Created at Sandia National Laboratories, the Portable File Format (PFF) allows binary data transfer across computer platforms. Although this capability is supported by many other formats, PFF files are still in use at Sandia, particularly in pulsed power research. This report provides detailed PFF specifications for accessing data without relying on legacy code.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Omega_h

Omega_h is a C++11 library that implements tetrahedron and triangle mesh adaptativity, with a focus on scalable HPC performance using (optionally) MPI, OpenMP, or CUDA. It is intended to provided adaptive functionality to existing simulation codes. Mesh adaptivity allows one to minimize both discretization error and number of degrees of freedom live during the simulation, as well as enabling moving object and evolving geometry simulations. Omega_h will do this for you in a way that is fast, memory-efficient, and portable across many different architectures, including NVIDIA GPUs.

Ibanez, Daniel [Sandia National Laboratories] (000↗

DOE OSTI2021

HiPACE++ v0.1

Hipace++ is the new implementation of the DESY-LBNL code Hipace (not distributed nor licensed) for plasma acceleration, relying on the quasi-static particle-in-cell (PIC) method, enabling fast and accurate simulations of plasma accelerators for problems satisfying the quasi-static approximation. Plasma acceleration is a priority in the ATAP division, and such problems represent a wide range of parameters. Hipace++ is an HPC (high-performance computing) code running on supercomputers and it provides the first efficient implementation of the quasi-static PIC method on Graphic Processing Units (GPU), showing 10x speedup and using much less resources than CPU implementations for production simulations. It currently runs on Nvidia GPUs and will ultimately be portable to more accelerated HPC platforms. The porting strategy is novel, and can be adapted to other flavors of quasi-static PIC. Besides, Hipace++ aims at using mesh refinement for higher efficiency, thus enabling simulations unfeasible today. For this purpose, Hipace++ depends on the open-source library AMReX (Adaptive Mesh Refinement at EXascale) developed at LBNL.

Vay, Jean-Luc↗

DOE OSTI2022

An Investigation of using FleCSI for Monte Carlo Radiation Transport

This document details the attempt to use FleCSI to provide MPI parallelization and domain decomposition for a Monte Carlo radiation transport application. FleCSI is a framework designed to support multi-physics application development with a focus on task-based parallelism and domain decomposition [1]. FleCSI also supports performance portability via a wrapper around a back-end performance portability layer. The goal of this work is to use FleCSI for domain decomposition and MPI parallelization inside of a Monte Carlo radiation transport application and document any pain points and shortcomings. The following section introduce the nomenclature used in FleCSI and its potential benefit for physics code developers, detail the code used to explore using FleCSI in a Monte Carlo radiation transport solver, and list the issues and concerns discovered during the work.

36 MATERIALS SCIENCE↗

DOE OSTI2023

The Kokkos OpenMPTarget Backend: Implementation and Lessons Learned

As the supercomputing landscape diversifies, solutions such as Kokkos to write vendor agnostic applications and libraries have risen in popularity. Kokkos provides a programming model designed for performance portability, which allows developers to write a single source implementation that can run efficiently on various architectures. At its heart, Kokkos maps parallel algorithms to architecture and vendor specific backends written in lower level programming models such as CUDA and HIP. Another approach to writing vendor agnostic parallel code is using OpenMP’s directives based approach, which lets developers annotate code to express parallelism. It is implemented at the compiler level and is supported by all major high performance computing vendors, as well as the primary Open Source toolchains GNU and LLVM. Since its inception, Kokkos has used OpenMP to parallelize on CPU architectures. In this paper, we explore leveraging OpenMP for a GPU backend and discuss the challenges we encountered when mapping the Kokkos APIs and semantics to OpenMP target constructs. As an exemplar workload we chose a simple conjugate gradient solver for sparse matrices. We find that performance on NVIDIA and AMD GPUs varies widely based on details of the implementation strategy and the chosen compiler. Furthermore, the performance of the OpenMP implementations decreases with increasing complexity of the investigated algorithms.

Gayatri, Rahulkumar↗

DOE OSTI2015

Extra-light gamma-ray imager for safeguards and homeland security

Gamma-ray imaging is the most important way to identify unknown gamma-ray emitting objects in decommissioning, security, overcoming accidents. Over the past two decades a system for producing of gamma images in these conditions became more or less portable devices. But in recent years these systems have become the hand-held devices. This is very important, especially in emergency situations, and measurements for safety reasons. We describe the first integrated hand-held instrument for emergency and security applications. The device is based on the coded aperture image formation, position sensitive gamma-ray (X-ray) detector Medipix2 (detectors produces by X-ray Imaging Europe) and tablet computer. The development was aimed at creating a very low weight system with high angular resolution. We present some sample gamma-ray images by camera. Main estimated parameters of the system are the following. The field of view video channel ∼ 490 deg. The field of view gamma channel ∼ 300 deg. The sensitivity of the system with a hexagonal mask for the source of Cs-137 (Eg = 662 keV), is in units of dose D ∼ 100 mR. This option is less then order of magnitude worse than for the heavy, non-hand-held systems (e.g., gamma-camera Cartogam, by Canberra.) The angular resolution of the gamma channel for the sources of Cs-137 (Eg = 662 keV) is about 1.20 deg. (authors)

42 ENGINEERING↗

DOE OSTI2011

Using the Global Arrays Toolkit to Reimplement NumPy for Distributed Computation

Global Arrays (GA) is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared memory programming interface to manipulate distributed defense arrays. Using a combination of GA and NumPy, we have reimplemented NumPy as a distributed drop-in replacement called Global Arrays in NumPy (GAiN). Scalability studies will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.

Global Arrays↗

DOE OSTI2013

Safety of Hydrogen Systems Installed in Outdoor Enclosures

The Hydrogen Safety Panel brings a broad cross-section of expertise from the industrial, government, and academic sectors to help advise the U.S. Department of Energy’s (DOE) Fuel Cell Technologies Office through its work in hydrogen safety, codes, and standards. The Panel’s initiatives in reviewing safety plans, conducting safety evaluations, identifying safety-related technical data gaps, and supporting safety knowledge tools and databases cover the gamut from research and development to demonstration and deployment. The Panel’s recent work has focused on the safe deployment of hydrogen and fuel cell systems in support of DOE efforts to accelerate fuel cell commercialization in early market applications: vehicle refueling, material handling equipment, backup power for warehouses and telecommunication sites, and portable power devices. This paper resulted from observations and considerations stemming from the Panel’s work on early market applications. This paper focuses on hydrogen system components that are installed in outdoor enclosures. These enclosures might alternatively be called “cabinets,” but for simplicity, they are all referred to as “enclosures” in this paper. These enclosures can provide a space where a flammable mixture of hydrogen and air might accumulate, creating the potential for a fire or explosion should an ignition occur. If the enclosure is large enough for a person to enter, and ventilation is inadequate, the hydrogen concentration could be high enough to asphyxiate a person who entered the space. Manufacturers, users, and government authorities rely on requirements described in codes to guide safe design and installation of such systems. Except for small enclosures used for hydrogen gas cylinders (gas cabinets), fuel cell power systems, and the enclosures that most people would describe as buildings, there are no hydrogen safety requirements for these enclosures, leaving gaps that must be addressed. This paper proposes that a technical basis be developed to enable code bodies to write requirements for the range of enclosures from the smallest to the largest.

08 HYDROGEN↗

DOE OSTI2013

PoPLAR: Portal for Petascale Lifescience Applications and Research

Background: We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches–such as proteomics, genomics, metabolomics, and meta-genomics–drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge. Methods: The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community’s most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal. Results: This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences. Conclusions: This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Handheld Biosensor for COVID-19 Screening

We have made significant progress toward the development of an integrated nucleic acid amplification system for Autonomous Medical Devices Incorporated (AMDIs) Optikus handheld diagnostic device. In this effort, we developed a set of loop-mediated isothermal amplification (LAMP) primers for SARS-CoV-2 and then demonstrate amplification directly on a surface acoustic wave (SAW) sensor. We built associated hardware and developed a C-code to control the amplification process. The goal of this project was to develop a nucleic amplification assay that is compatible with SAW sensors to enable both nucleic and serological testing in a single handheld diagnostic device. Toward this goal, AMDI is collaborating Sandia National Laboratories to develop a rapid, portable diagnostic screening device that utilizes Sandias unique surface acoustic wave biosensor (SAW) for COVID-19 detection. Previously, the SANDIA- AMDI SAW sensor has successfully detected multiple high-profile bacteria viruses, including Ebola, HIV, Sin Nombre, and Anthrax. Over the last two years, AMDI and SANDIA have significantly improved the sensitivity and detection capability of the SAW biosensor and have also developed a modular hand-held, portable platform called the Optikus, which uses CD microfluidics and handheld instrumentation to automate all sample preparation, reagent introduction, sample delivery, and measurement for a number of different assay targets. We propose to use this platform for the development of a rapid (%3C30 minutes), point-of-care diagnostic test for detection of COVID-19 from nasal swab samples.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

Pixelated CZT Technology for the Detection, Identification, and Localization of Gamma-Ray Sources - 18311

Radioactive waste-management applications require good measurements to qualitatively and quantitatively characterize waste materials. Often these measurements must be done in situ, and the user wishes to learn something of the isotopic and spatial distribution of the source. Therefore, there is a need for a portable instrument that can map radioactive contamination and quantify sources. This presentation introduces several instruments that have been applied to this task, along with example measurements in relevant applications. All instruments are based on 3D-position-sensitive CdZnTe (CZT) detectors. This technology routinely achieves better than 1.1% FWHM energy resolution at 662 keV and operates at room temperature with a startup time under 2 minutes. All are packaged in portable enclosures with WiFi and Bluetooth capabilities for wireless communication. These capabilities allow the technology to be used in more advanced measurements in the field. A unique capability of these detectors is the ability to image the spatial distribution of gamma rays from a single stationary measurement. The first product, Polaris-H, has been in use at commercial nuclear power plants since 2013. The system, currently used at over 50% of the US nuclear-power fleet, integrates a 3D-position-sensitive CZT detector, associated readout electronics, an embedded computer, a battery with over 7-hour life, an optical camera, and a laser range finder in a portable water-proof enclosure. The system connects wirelessly to a tablet which displays a gamma-ray spectrum and isotope-specific images of the gamma-ray distribution in all directions in real time. The CZT detectors have a dynamic range from 50 keV up to 3 MeV. Coded aperture or pinhole imaging is used for energies below 250 keV, and Compton imaging is used for energies above 250 keV. List-mode data is saved to an external USB memory stick to enable more advanced analysis, including isotopic activity analysis, via H3D's post-processing software. Additional systems based on the same architecture have been developed to optimize the technology for other applications. These include Polaris-H Quad, which provides over 3 times the sensitivity for applications involving weaker sources, and Polaris-H Shield, which uses a collimator to provide images and isotope information over a narrower field of view in order to measure weaker sources in the presence of stronger sources of the same isotope. H3D has also developed custom systems that have been mounted on robots and drones that enable remote operation of the technology. Results from the measurements collected at commercial nuclear power plants and other applicable sites will be presented to show how these instruments can be used to detect, identify, and localize gamma-ray sources. Advanced analysis techniques to show the accurate quantification of the gamma-ray source will also be presented. Applications range from characterizing simple objects, to locating hottest points, estimating contamination distributions on an isotope-by-isotope basis, and differentiating scatter and direct emissions. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2013

Lightweight performance data collectors 2.0 with Eiger support.

We report on the use and design of a portable, extensible performance data collection tool motivated by modeling needs of the high performance computing systems co-design com- munity. The lightweight performance data collectors with Eiger support is intended to be a tailorable tool, not a shrink-wrapped library product, as pro ling needs vary widely. A single code markup scheme is reported which, based on compilation ags, can send perfor- mance data from parallel applications to CSV les, to an Eiger mysql database, or (in a non-database environment) to at les for later merging and loading on a host with mysql available. The tool supports C, C++, and Fortran applications.

Allan, Benjamin A.↗