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NASA NTRS1988

Software reuse environment user's guide

This document describes the services provided by the prototype Software Reuse Environment, which was developed by CTA for NASA Goddard Space Flight Center, Code 520. This is one of three guides delivered by CTA as part of the environment. The other two guides are: Software Generation and Installation Guide; and SEMANTX--Defining the Schema. The Software Generation and Installation Guide describes the software source modules that make up the Reuse Environment, with instructions on how to generate and install an executable system from the source code. SEMANTX--Defining the Schema describes how a reuse database is created. Actually this guide is more general than the reuse database, as it describes how to generate a SEMANTX database. SEMANTX is an off-the-shelf tool that we have used to implement the reuse database. It is a product of Semantyk Systems, Inc. The Software Reuse Environment is built upon SEMANTX as well as on the IDE Structured Analysis Integrated Environment. (IDE is Interactive Development Environments, Inc.) SEMANTX itself is built on top of the Unify Database Management System. To use the Software Reuse Environment you should have the User's Manuals for SEMANTX, for Unify, and for the IDE software. CTA has provided all of these with the environment.

Source record↗

NASA NTRS2016

ROS Hexapod

As an intern project for NASA Johnson Space Center (JSC), my job was to familiarize myself and operate a Robotics Operating System (ROS). The project outcome will convert existing software assets into ROS using nodes, enabling a robotic Hexapod to communicate and to be functional and controlled by an existing PlayStation 3 (PS3) controller. Existing control algorithms and current libraries have no ROS capabilities within the Hexapod C++ source code. Conversion of C++ codes to ROS will enable existing code to be compatible with ROS, and will be controlled using existing PS3 controller. Furthermore, my job description is to design ROS messages and script programs which will enable assets to participate in the ROS ecosystem. In addition, an open source software (IDE) Arduino board will be integrated in the ecosystem with designing circuitry on a breadboard to add additional behavior with push buttons, potentiometers and other simple elements in the electrical circuitry. Other projects with the Arduino will be a GPS module digital clock that will run off 22 satellites to show accurate real time using a GPS signal and internal patch antenna to communicate with satellites.

Davis, Kirsch↗

DOE OSTI2020

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Code Coverage Status of ARC Code-DIF3D

The Argonne Reactor Code (ARC) software system supports users in their fast reactor design goals by providing neutronic, thermal-hydraulic, and structural analysis capabilities. DIF3D plays a pivotal role in the ARC system as the primary homogenized assembly neutronic calculation methodology for fast reactor problems. Over its 40 years history, ARC software usage with DIF3D has been applied to numerous fast and thermal spectrum reactor analysis projects with good to excellent comparison against experiments. With continued improvement of computation resources, many of the geometry modeling capabilities in DIF3D that were primarily used in low order schemes are not really needed anymore. Today, the diffusion and transport capabilities of DIF3D-VARIANT are primarily used in the reactor design process with some scattered usage of DIF3D-FD and DIF3D-Nodal. In recent work, the DIF3D software verification was completed for DIF3D-FD and DIF3D-VARIANT on the geometry options used in the Versatile Test Reactor project. While we can be confident that these capabilities of DIF3D are well used and thus trusted, it does not demonstrate that all possible input options of DIF3D are actually working, but just those that were tested as part of VTR are and that they are correct. Thus, the purpose of the present work is to identify a set of test problems for DIF3D and assess the code coverage of DIF3D for those test problems. The goal is to document what parts of the existing DIF3D code are touched by the set of test problems and which are not. Because the verification work done on DIF3D-VARIANT and DIF3D-FD was focused on the most common uses of DIF3D for fast reactor analysis, the code coverage assessment of those capabilities is the highest priority. This will ensure that nothing is being missed by the existing verification test problems that DIF3D relies upon. The DIF3D-Nodal capability will also be inspected for code coverage as part of this work to further ensure that regular regression testing of DIF3D will trap any likely errors the end user might experience with the DIF3D software. The code coverage analysis of DIF3D was performed with the Code Coverage Tool of the Intel Fortran compiler which requires modifications to the compilation of DIF3D. The detailed coverage tables are given for each submodule of DIF3D separately, and for the submodules which are primarily developed for DIF3D, most of the source files could be at least partially touched. Most of the uncovered parts/files could be easily ignored, because they are either for error message and debugging output or obviously not needed by DIF3D. Out of the entire source codes of DIF3D, only a few uncovered modules deserve further investigation.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Code Coverage Status of the ARC Code DIF3D

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Portable Software Environment for Ultrahigh-Resolution ELM Development on GPUs

This paper presents our endeavors in developing the large-scale, ultra-high-resolution E3SM Land Model (uELM), specifically designed for exascale computers furnished with accelerators such as Nvidia GPUs. The uELM is a sophisticated code that substantially relies on High-Performance Computing (HPC) environments, necessitating particular machine and software configurations. To facilitate community-based uELM developments employing GPUs, we have created a portable, standalone software environment preconfigured with uELM input datasets, simulation cases, and source code. This environment, utilizing Docker, encompasses all essential code, libraries, and system software for uELM development on GPUs. It also features a functional unit test framework and an offline model testbed for comprehensive numerical experiments. From a technical perspective, the paper discusses GPU-ready container generations, uELM code management, and input data distribution across computational platforms. Lastly, the paper demonstrates the use of environment for functional unit testing, end-to-end simulation on CPUs and GPUs, and collaborative code development.

E3SM Land Model↗

NASA NTRS1998

Advanced x-ray imaging spectrometer

An x-ray spectrometer that also provides images of an x-ray source. Coded aperture imaging techniques are used to provide high resolution images. Imaging position-sensitive x-ray sensors with good energy resolution are utilized to provide excellent spectroscopic performance. The system produces high resolution spectral images of the x-ray source which can be viewed in any one of a number of specific energy bands.

Callas, John L.↗

DOE OSTI2023

Evaluating Portable Parallelization Strategies for Heterogeneous Architectures in High Energy Physics

High-energy physics (HEP) experiments have developed millions of lines of code over decades that are optimized to run on traditional x86 CPU systems. However, we are seeing a rapidly increasing fraction of floating point computing power in leadership-class computing facilities and traditional data centers coming from new accelerator architectures, such as GPUs. HEP experiments are now faced with the untenable prospect of rewriting millions of lines of x86 CPU code, for the increasingly dominant architectures found in these computational accelerators. This task is made more challenging by the architecture-specific languages and APIs promoted by manufacturers such as NVIDIA, Intel and AMD. Producing multiple, architecture-specific implementations is not a viable scenario, given the available person power and code maintenance issues. The Portable Parallelization Strategies team of the HEP Center for Computational Excellence is investigating the use of Kokkos, SYCL, OpenMP, std::execution::parallel and alpaka as potential portability solutions that promise to execute on multiple architectures from the same source code, using representative use cases from major HEP experiments, including the DUNE experiment of the Long Baseline Neutrino Facility, and the ATLAS and CMS experiments of the Large Hadron Collider. This cross-cutting evaluation of portability solutions using real applications will help inform and guide the HEP community when choosing their software and hardware suites for the next generation of experimental frameworks. We present the outcomes of our studies, including performance metrics, porting challenges, API evaluations, and build system integration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2014

Preliminary Results of a New Deterministic Iterative Image Reconstruction Algorithm - Paper 117

Iterative reconstruction techniques have become the standard for Single Photon Emission Computed Tomography (SPECT). Advances in computing have allowed these techniques to incorporate more and more detail; however, computation time must be balanced against increased detail. Monte Carlo methods are generally used for modeling the physics of a SPECT study, but can have long computation times. Advances in Monte Carlo-based scatter correction have shown reasonable results, but scatter estimation by measuring narrow energy windows remains more common. An iterative reconstruction technique using a deterministic transport code has been proposed as an alternative. This paper presents preliminary results of the new technique in which the TITAN deterministic code completes the forward projection step in a maximum likelihood expectation maximization (ML-EM) reconstruction of SPECT data. The effectiveness of the deterministic algorithm is examined for a 2-dimensional phantom. This work demonstrates the feasibility of using the TITAN code in an iterative reconstruction algorithm. The appropriate deterministic parameters were chosen by comparing sinograms produced with different mesh sizes, quadrature sets, and anisotropic scattering orders. The TITAN code was then successfully used as the forward projection step in an iterative reconstruction algorithm with a 2-dimensional homogeneous phantom. The impact of deterministic parameters on reconstruction quality is being investigated, along with the incorporation of a smoothing filter. The TITAN source code is being modified to include the ML-EM algorithm and iteration steps. This will significantly improve computation time by eliminating the repeated reading and writing of files for each iteration and allowing some steps to be completed in parallel. Further testing of the new reconstruction algorithm for more realistic phantoms is also underway. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2026

Framework for X-ray mirror surface shape fitting

For accurate characterization of grazing-incidence X-ray mirrors, we present a comprehensive framework to fit measured surface shapes (either slope or height) of X-ray mirrors used in synchrotron radiation and free-electron laser facilities. We summarize the closed-form expressions of some typical surface shapes of X-ray mirrors including elliptic cylinders, hyperbolic cylinders, ellipsoids, hyperboloids, and diaboloids. This framework is composed of four layers: definition of standard shapes with closed-form expressions, generation of theoretical surface with pose parameters (six degrees of freedom defining an object's position and orientation relative to a coordinate system), parameter optimization with the ability to select which parameters are fit and which are held constant, and the development of user-friendly fitting function wrappers for particular fitting tasks. A few practical fitting examples are demonstrated to verify the effectiveness of the proposed fitting framework. We discuss the physical meanings of the fitting parameters, and provide several examples using the elliptic cylinder and ellipsoid shapes to highlight some features of the framework. Moreover, we provide the presented framework as open-source codes (MATLAB and Python codes available at https://github.com/nsls2omf/xmf) to the community to encourage academic collaboration and further improvements.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5 Zr 35.5 , and pair correlation function of liquid Ni 3 Al. Our code scales well with the size of the simulating system on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Stellarator Design Exploration Using Symbolic-Regression Neutronics Surrogates

Systems codes require fast, simplified models to rapidly evaluate fusion power plant concepts, but neutronics analyses are often a computational bottleneck. Here, to address this, surrogate models for key neutronics responses have been developed using 3-D neutronics-ready models built with the open-source code ParaStell from a database of stellarator equilibria. Neutronics responses such as tritium breeding ratio (TBR), nuclear heating, and neutron-induced radiation damage displacements per atom (dpa) were simulated using OpenMC. Through sensitivity analysis and symbolic regression (SR), simple power-law formulas were derived connecting these neutronics responses to global stellarator parameters, including fusion power, plasma surface area, and plasma elongation. Validation shows these formulas can predict the simulation results with low error, enabling quick and accurate assessment of neutronics requirements in stellarator design exploration activities with systems codes.

Modeling↗

DOE OSTI2018

Modeling the Drying of a Mock Used Fuel Assembly with COBRA-SFS Cycle-4 - 18597

The processing and storage of nuclear fuel is an ever increasingly pressing issue. Around 70,000 tons of used fuel are currently in either dry or wet storage on site at nuclear power plants or at specified spent fuel storage facilities. Additionally, about 2,000 tons are added to that sum each year. To promote retrievability, limit degradation in the canister, and reduce potential for hydrogen generation, spent fuel that is initially in wet storage must be dried before moving to dry cask storage. Therefore, this research seeks to use a mock used fuel storage cask to replicate the conditions in the industry during the drying process of fuel being moved from storage pools. To simulate this, a mock storage cask has been constructed to closely resemble those used in industry such that any areas that tend to retain water are replicated effectively. It is able to hold one mock used fuel assembly. The assembly used is an AREVA 10A 10 x 10 assembly with 78 rods filled with depleted uranium, 12 heater rods to simulate decay heat, a 3 x 3 BWR water channel, and one interchangeable rod position for tests such as a simulated failed fuel rod, BWR water rod, and PWR guide tube tests. The industry standard procedure is used in drying the assembly which involves stepping the system pressure down and holding for certain periods until reaching 3 torr and holding for 30 minutes. This is believed to sufficiently dry the assembly. The goal is to record data throughout these tests that can provide the industry with a greater understanding of how well the process works. This data will also be used to develop and validate a computer model of the drying process. Mechanistic models are currently under development. Reduced order models are being investigated for incorporation into current related engineering codes such as COBRA-SFS. COBRA-SFS is a member of the COBRA family of codes which is mainly used in the evaluation of thermal hydraulic systems containing spent nuclear fuel. However, it does not currently have the capability to account for processes such as evaporation encountered during drying operations. Therefore, those physical models are to be added to the source code. At present a model of the experiment has been created using the COBRA-SFS Cycle-4 code. A number of steady state models along with transient models have been developed and presented. Each of these yield valuable results for comparison with the experiments conducted. In addition to comparison with experimental results, the data collected from COBRA-SFS is compared with that which has been generated from other computer models which utilize computational fluid dynamics. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)

Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.

74 ATOMIC AND MOLECULAR PHYSICS↗

NASA NTRS2001

HITEMP Material and Structural Optimization Technology Transfer

The feasibility of adding viscoelasticity and the Generalized Method of Cells (GMC) for micromechanical viscoelastic behavior into the commercial HyperSizer structural analysis and optimization code was investigated. The viscoelasticity methodology was developed in four steps. First, a simplified algorithm was devised to test the iterative time stepping method for simple one-dimensional multiple ply structures. Second, GMC code was made into a callable subroutine and incorporated into the one-dimensional code to test the accuracy and usability of the code. Third, the viscoelastic time-stepping and iterative scheme was incorporated into HyperSizer for homogeneous, isotropic viscoelastic materials. Finally, the GMC was included in a version of HyperSizer. MS Windows executable files implementing each of these steps is delivered with this report, as well as source code. The findings of this research are that both viscoelasticity and GMC are feasible and valuable additions to HyperSizer and that the door is open for more advanced nonlinear capability, such as viscoplasticity.

Collier, Craig S.↗

NASA NTRS2014

Using the NASA GRC Sectored-One-Dimensional Combustor Simulation

The document is a user manual for the NASA GRC Sectored-One-Dimensional (S-1-D) Combustor Simulation. It consists of three sections. The first is a very brief outline of the mathematical and numerical background of the code along with a description of the non-dimensional variables on which it operates. The second section describes how to run the code and includes an explanation of the input file. The input file contains the parameters necessary to establish an operating point as well as the associated boundary conditions (i.e. how it is fed and terminated) of a geometrically configured combustor. It also describes the code output. The third section describes the configuration process and utilizes a specific example combustor to do so. Configuration consists of geometrically describing the combustor (section lengths, axial locations, and cross sectional areas) and locating the fuel injection point and flame region. Configuration requires modifying the source code and recompiling. As such, an executable utility is included with the code which will guide the requisite modifications and insure that they are done correctly.

Combustion Stability↗

NASA NTRS1999

Visualization Co-Processing of a CFD Simulation

OVERFLOW, a widely used CFD simulation code, is combined with a visualization system, pV3, to experiment with an environment for simulation/visualization co-processing on a SGI Origin 2000 computer(O2K) system. The shared memory version of the solver is used with the O2K 'pfa' preprocessor invoked to automatically discover parallelism in the source code. No other explicit parallelism is enabled. In order to study the scaling and performance of the visualization co-processing system, sample runs are made with different processor groups in the range of 1 to 254 processors. The data exchange between the visualization system and the simulation system is rapid enough for user interactivity when the problem size is small. This shared memory version of OVERFLOW, with minimal parallelization, does not scale well to an increasing number of available processors. The visualization task takes about 18 to 30% of the total processing time and does not appear to be a major contributor to the poor scaling. Improper load balancing and inter-processor communication overhead are contributors to this poor performance. Work is in progress which is aimed at obtaining improved parallel performance of the solver and removing the limitations of serial data transfer to pV3 by examining various parallelization/communication strategies, including the use of the explicit message passing.

Vaziri, Arsi↗

NASA NTRSDate not supplied

Developing Open-Source Training Materials for AI/ML and Space Biological Sciences Using NASA Cloud-Based Data

Artificial Intelligence (AI) and Machine Learning (ML) has gained significant traction in the biological and biomedical research fields in the last two decades, in part thanks to an increasing culture of open data sharing and reuse. Due to its capability for identifying complex relationships and patterns, AI/ML methodology is particularly well suited to recognize and predict biological patterns from high-dimensional next-generation sequencing data (e.g. whole genome sequencing, transcriptomic sequencing), as well as from biological or medical imaging data (e.g. microscopy, computed tomography, ultrasound, magnetic resonance imaging, radiography). These methodologies hold particular promise for space biosciences research and automated space health monitoring systems. However, there are many key considerations for properly training, validating, and testing a machine learning model in biological research or clinical application. Even with the positive culture of Open Science and data sharing, inexperienced researchers working quickly without proper checks can produce models that perform poorly outside of the immediate training dataset. Lessons learned from biological AI/ML research indicate that Open Science principles such as data sharing and open-source code must go hand-in-hand with publicly available, high-quality training curricula in best practices, with modules centered on real-life scientific use cases and data so future AI/ML practitioners gain experience on real problems. Here we present the development of open-source training materials for AI/ML and space biosciences, as part of the NASA Transform to Open Science Training (TOPST) initiative. We develop 4 independent training programs, focused on the following topics: 1) Fundamentals of Machine Learning and Space Biosciences Domain, 2) Open Science, Artificial Intelligence, and Ethical Best Practices for Data Sharing and Analysis, 3) Using AI/ML Classification to Identify Gene Networks Affected By Space Exposure in Mouse Liver, and 4) Using Neural Networks to Find DNA Damage Patterns in Immune Cells after Radiation. All programs leverage cloud-based NASA biological datasets. The curriculum we present will enable worldwide access to training in AI/ML and scientific analysis.

James Andrew Casaletto↗