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All sources NASA NTRS DOE OSTI

NASA NTRS2017

Smoothing-Based Relative Navigation and Coded Aperture Imaging

This project will develop an efficient smoothing software for incremental estimation of the relative poses and velocities between multiple, small spacecraft in a formation, and a small, long range depth sensor based on coded aperture imaging that is capable of identifying other spacecraft in the formation. The smoothing algorithm will obtain the maximum a posteriori estimate of the relative poses between the spacecraft by using all available sensor information in the spacecraft formation.This algorithm will be portable between different satellite platforms that possess different sensor suites and computational capabilities, and will be adaptable in the case that one or more satellites in the formation become inoperable. It will obtain a solution that will approach an exact solution, as opposed to one with linearization approximation that is typical of filtering algorithms. Thus, the algorithms developed and demonstrated as part of this program will enhance the applicability of small spacecraft to multi-platform operations, such as precisely aligned constellations and fractionated satellite systems.

Relative positioning↗

DOE OSTI2012

Omics Tools

The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the omics.jar file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not contain Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on a server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the help command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTA stats, e.g. # bases, GC content pal : stem-loop motif detection by palindromic sequence search (code stub) randgrp : random subsample without replacement, of groups randgrpr : random subsample with replacement, of groups (fast) randsub : random subsample without replacement, of file lines For more help regarding a particular command, use: java -jar omics.jar command help Usage: java -jar omics.jar command args

Schaumberg, Andrew↗

DOE OSTI2022

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

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

Bethel, E. Wes↗

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↗

NASA NTRS1993

Digital Electronic Still Camera

Digital electronic still camera part of electronic recording, processing, tansmitting, and displaying system. Removable hard-disk drive in camera serves as digital electronic equivalent of photographic film. Images viewed, analyzed, or transmitted quickly. Camera takes images of nearly photographic quality and stores them in digital form. Portable, hand-held, battery-powered unit designed for scientific use. Camera used in conjunction with playback unit also serving as transmitting unit if images sent to remote station. Remote station equipped to store, process, and display images. Digital image data encoded with error-correcting code at playback/transmitting unit for error-free transmission to remote station.

Holland, Samuel D.↗

NASA NTRS1994

Towards a Comprehensive Computational Simulation System for Turbomachinery

The objective of this work is to develop algorithms associated with a comprehensive computational simulation system for turbomachinery flow fields. This development is accomplished in a modular fashion. These modules includes grid generation, visualization, network, simulation, toolbox, and flow modules. An interactive grid generation module is customized to facilitate the grid generation process associated with complicated turbomachinery configurations. With its user-friendly graphical user interface, the user may interactively manipulate the default settings to obtain a quality grid within a fraction of time that is usually required for building a grid about the same geometry with a general-purpose grid generation code. Non-Uniform Rational B-Spline formulations are utilized in the algorithm to maintain geometry fidelity while redistributing grid points on the solid surfaces. Bezier curve formulation is used to allow interactive construction of inner boundaries. It is also utilized to allow interactive point distribution. Cascade surfaces are transformed from three-dimensional surfaces of revolution into two-dimensional parametric planes for easy manipulation. Such a transformation allows these manipulated plane grids to be mapped to surfaces of revolution by any generatrix definition. A sophisticated visualization module is developed to al-low visualization for both grid and flow solution, steady or unsteady. A network module is built to allow data transferring in the heterogeneous environment. A flow module is integrated into this system, using an existing turbomachinery flow code. A simulation module is developed to combine the network, flow, and visualization module to achieve near real-time flow simulation about turbomachinery geometries. A toolbox module is developed to support the overall task. A batch version of the grid generation module is developed to allow portability and has been extended to allow dynamic grid generation for pitch changing turbomachinery configurations. Various applications with different characteristics are presented to demonstrate the success of this system.

Shih, Ming-Hsin↗

NASA NTRS2021

Harmonized Emissions Component (HEMCO) 3.0 as a Versatile Emissions Component for Atmospheric Models: Application in the GEOS-Chem, NASA GEOS, WRF-GC, CESM2, NOAA GEFS-Aerosol, and NOAA UFS Models

Emissions are a central component of atmospheric chemistry models. The Harmonized Emissions Component (HEMCO) is a software component for computing emissions from a user-selected ensemble of emission inventories and algorithms. It allows users to re-grid, combine, overwrite, subset, and scale emissions from different inventories through a configuration file and with no change to the model source code. The configuration file also maps emissions to model species with appropriate units. HEMCO can operate in offline stand-alone mode, but more importantly it provides an online facility for models to compute emissions at runtime. HEMCO complies with the Earth System Modeling Framework (ESMF) for portability across models. We present a new version here, HEMCO 3.0, that features an improved three-layer architecture to facilitate implementation into any atmospheric model and improved capability for calculating emissions at any model resolution including multiscale and unstructured grids. The three-layer architecture of HEMCO 3.0 includes (1) the Data Input Layer that reads the configuration file and accesses the HEMCO library of emission inventories and other environmental data, (2) the HEMCO Core that computes emissions on the user-selected HEMCO grid, and (3) the Model Interface Layer that re-grids (if needed) and serves the data to the atmospheric model and also serves model data to the HEMCO Core for computing emissions dependent on model state (such as from dust or vegetation). The HEMCO Core is common to the implementation in all models, while the Data Input Layer and the Model Interface Layer are adaptable to the model environment. Default versions of the Data Input Layer and Model Interface Layer enable straightforward implementation of HEMCO in any simple model architecture, and options are available to disable features such as re-gridding that may be done by independent couplers in more complex architectures. The HEMCO library of emission inventories and algorithms is continuously enriched through user contributions so that new inventories can be immediately shared across models. HEMCO can also serve as a general data broker for models to process input data not only for emissions but for any gridded environmental datasets. We describe existing implementations of HEMCO 3.0 in (1) the GEOS-Chem “Classic” chemical transport model with shared-memory infrastructure, (2) the high-performance GEOS-Chem (GCHP) model with distributed-memory architecture, (3) the NASA GEOS Earth System Model (GEOS ESM), (4) the Weather Research and Forecasting model with GEOS-Chem (WRF-GC), (5) the Community Earth System Model Version 2 (CESM2), and (6) the NOAA Global Ensemble Forecast System – Aerosols (GEFS-Aerosols), as well as the planned implementation in the NOAA Unified Forecast System (UFS). Implementation of HEMCO in CESM2 contributes to the Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICA) by providing a common emissions infrastructure to support different simulations of atmospheric chemistry across scales.

Haipeng Lin↗

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↗