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At least 1,423 records · Page 79

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Sparse Linear Algebra Toolkit for Computational Aerodynamics

Finding solutions to sparse linear systems of equations is an essential step in Computational Engineering applications of interest to NASA. Linear systems of equations are composed and solved in almost every computational engineering application. The characteristics of linear systems vary greatly from one application to another. Accordingly, there are a wide variety of methods for the solution of linear systems of equations. The operations and methods prepared by the authors are focused on linear systems of interest to NASA, primarily those associated with Computational Fluid Dynamics (CFD), Aeroelasticity, and Aeroacoustics. The Sparse Linear Algebra Toolkit (SLAT) is a coordinated collection of software featuring operations, methods, and data structures that are useful when solving sparse linear systems of equations on modern computer architectures. The implemented operations and methods are designed and tuned for parallelism in shared memory, in distributed memory, and across the hybrid combination of distributed-shared memory. The toolkit includes novel methods and implementations for modern architectures and facilitates development of new approaches for meeting NASA’s evolving computational engineering challenges using evolving computer architectures that are not available in vendor libraries. In this paper, significant features and interfaces within SLAT are presented and verified for simulations performed with NASA’s CFD solver, FUN3D. The runtime and scaling performance of the Generalized Minimum Residual (GMRES) method implemented in SLAT is analyzed for the linear subproblems within the solution of turbulent Navier-Stokes equations employed in the simulation of high-lift configurations. Prior to this work, the SPARSKIT GMRES implementation was the only Krylov subspace method available within FUN3D. A strong scaling study shows the SLAT GMRES implementation facilitates accurate Reynolds-averaged Navier-Stokes CFD solutions between 15% and 56% faster than the SPARSKIT GMRES implementation.

Stephen L Wood↗

NASA NTRS2004

Polymer-carbon black composite sensors in an electronic nose for air-quality monitoring

An electronic nose that uses an array of 32 polymer-carbon black composite sensors has been developed, trained, and tested. By selecting a variety of chemical functionalities in the polymers used to make sensors, it is possible to construct an array capable of identifying and quantifying a broad range of target compounds, such as alcohols and aromatics, and distinguishing isomers and enantiomers (mirror-image isomers). A model of the interaction between target molecules and the polymer-carbon black composite sensors is under development to aid in selecting the array members and to enable identification of compounds with responses not stored in the analysis library.

NASA Discipline Life Sciences Technologies↗

DOE OSTI2021

Adiabatic quantum linear regression

Abstract A major challenge in machine learning is the computational expense of training these models. Model training can be viewed as a form of optimization used to fit a machine learning model to a set of data, which can take up significant amount of time on classical computers. Adiabatic quantum computers have been shown to excel at solving optimization problems, and therefore, we believe, present a promising alternative to improve machine learning training times. In this paper, we present an adiabatic quantum computing approach for training a linear regression model. In order to do this, we formulate the regression problem as a quadratic unconstrained binary optimization (QUBO) problem. We analyze our quantum approach theoretically, test it on the D-Wave adiabatic quantum computer and compare its performance to a classical approach that uses the Scikit-learn library in Python. Our analysis shows that the quantum approach attains up to $${2.8 \times }$$ 2.8 × speedup over the classical approach on larger datasets, and performs at par with the classical approach on the regression error metric. The quantum approach used the D-Wave 2000Q adiabatic quantum computer, whereas the classical approach used a desktop workstation with an 8-core Intel i9 processor. As such, the results obtained in this work must be interpreted within the context of the specific hardware and software implementations of these machines.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2016

Towards a Methodology and Tooling for Model-Based Probabilistic Risk Assessment (PRA)

A Probabilistic Risk Assessment (PRA) aims to identify and assess potential risks to system technical performance requirements for the purpose of furnishing risk insights into project decisions. PRAs have traditionally been conducted manually using software with an isolated data model. As system complexity rises it becomes difficult to ensure consistency between a PRA, the evolving system design, and other engineering analyses; the techniques for conducting PRAs must evolve to meet this challenge. This work presents progress towards a methodology and tooling for conducting a PRA by leveraging data in the system model, embedded for other purposes and analyses, to conduct a PRA. An approach for identifying the appropriate probabilistic equation for each risk scenario from a standard library is presented, which is a significant step towards the quantification of the likelihood of a risk scenario occurrence. The final calculation of the likelihood of occurrence is left as an item of future work. We also present the development of preliminary tooling to carry out the methodology on a well-formed system model. The information needed to conduct the PRA is embedded in a consistent manner in a system model, so the model-based PRA can be regularly executed as the system model changes. The ability to modify the PRA in concert with lifecycle evolution affords a project the opportunity to track the extent to which system modification impacts compliance with requirements. These aspects of this model-based PRA methodology make it capable of managing risk in increasingly complex technical systems.

Schreiner, Samuel S.↗

DOE OSTI2019

SUSPECT: MINLP special structure detector for Pyomo

We present SUSPECT, an open source toolkit that symbolically analyzes mixed-integer nonlinear optimization problems formulated using the Python algebraic modeling library Pyomo. We present the data structures and algorithms used to implement SUSPECT. SUSPECT works on a directed acyclic graph representation of the optimization problem to perform: bounds tightening, bound propagation, monotonicity detection, and convexity detection. We show how the tree-walking rules in SUSPECT balance the need for lightweight computation with effective special structure detection. SUSPECT can be used as a standalone tool or as a Python library to be integrated in other tools or solvers. Here, we highlight the easy extensibility of SUSPECT with several recent convexity detection tricks from the literature. We also report experimental results on the MINLPLib 2 dataset.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

ONIX: An open-source depletion code

Open Source software enables innovative, community-based software development. ONIX brings this concept to the field of depletion calculations. It is an open-source depletion software to be used for nuclear reactor simulations, for fissile material production analysis as well as for nuclear arms control applications. ONIX provides a module to solve the depletion equation using a Chebyshev Rational Approximation Method. For the generation of one-group cross sections, it includes a coupling interface for the open-source neutron transport code, OpenMC, as well as a module to read pre-computed values in a stand-alone mode. ONIX has special features to optimize nuclear data libraries, to update isomeric branching ratio during burnup, and to support automation of simulations for nuclear archaeology. In conclusion, ONIX has been validated against results from numerical and experimental benchmarks, and its results agree with other methods within expected error ranges.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

ExaTN

A challenging scientific problem that will benefit from exascale computing is predictive simulation of two- and three-dimensional quantum many-body Hamiltonians in condensed matter physics, together with the related strong entanglement problems in quantum chemistry and quantum computing. Efficient numerical simulations will require new insights into wavefunction compression algorithms that scale on extremely heterogeneous HPC architectures. To address this need, we propose to develop a scalable math library of parallel multi-linear algebraic numerical primitives for hierarchical tensor compression. Our library will subsequently be used for building an efficient, performance-portable HPC framework for simulating strongly correlated quantum systems. In particular, our will will be the first to deliver a massively parallel implementation of the multiscale entanglement renormalization ansatz (MERA), a hierarchical tensor decomposition quantum scheme capable of expressing local expectation values of strongly entangled higher-dimensional quantum systems efficiently. To address the extreme complexity and high computational cost of such schemes, we will automate their parallel implementation by delivering an integrated software framework, ExaTN (Exascale Tensor Networks), that will process hierarchical tensor representations on exascale HPC systems via an asymchronous task-based programming model. As a specific application, our framework will provide scientists with a capability of simulating strongly entangled quantum systems, thus positioning ORNL as a strategic leader in modeling of strongly correlated materials.

McCaskey, AlexanderJ↗

DOE OSTI2022

NISQ Benchmarking

Test suite of quantum algorithms for Noisy Intermediate Scale Quantum (NISQ) computers. The test suite includes benchmark-style code for quantum volume circuits (QV), fairness sampling circuits, quantum telecloning circuits, and other NISQ benchmark style algorithms on small problems (i.e., up to 100 qubits), such as Variational Quantum Eigensolver (VQE), Hamiltonian Simulation, and Grover unstructured search example circuits. These benchmark-style applications are implemented in quantum software packages, mostly IBM's QISKIT, but may include vendor-specific frameworks, such as PyQuil (for Rigetti) or Q\# for Microsoft, or CirQ (for Google) as the test suite grows with the vendor sample. The test suite also includes numerical simulation code for Quantum Alternating Operator Ansatz (QAOA) algorithms, VQE, Hamiltonian Simulation and search examples. Numerical simulation code simulates quantum computers on classical computers, which is only possible for small problem instances; the implementation framework of choice is typically within Python, using the numpy/scipy libraries as well as extensions to the Julia language.

Pelofske, Elijah↗

DOE OSTI2015

Coupling of Thermochemistry Solver THERMOCHIMICA with MOOSE/BISON

THERMOCHIMICA is a computational library for chemical thermodynamics. It determines a unique combination of phases and their compositions for a prescribed chemical composition, temperature and pressure. The solver and the underlying thermodynamic models can be used to estimate the chemical state and various constitutive and transport properties necessary for nuclear fuel performance modeling. Our NEAMS research project focuses on the development of nuclear fuel thermodynamics models and computational thermodynamics equilibrium solvers, and their implementation into Idaho National Laboratory (INL) nuclear fuel performance simulation system MOOSE/BISON. This report documents the software integration of THERMOCHIMICA with MOOSE/BISON using the current INL development framework GitLab. The THERMOCHIMICA implementation is demonstrated on modeling oxygen related phenomena in irradiated fuel, such as calculation of oxygen to metal ratio in the fluorite phase, oxygen partial pressure, oxygen chemical potential and oxygen transport. Experimental measurements from the open literature were used to validate the implemented models and illustrate functionality of the developed thermodynamics module. The calculations are based on chemical element inventory provided by neutronics, isotopic depletion, transmutation and decay calculations in the SCALE system. The burnup calculation in BISON can also be used for elemental composition although it provides only a limited set. Coupling of THERMOCHIMICA with other codes that can provide chemical composition of irradiated fuel for BISON simulations is currently being explored.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Initial Development of Fusion Magnet Simulation Capabilities for Performance and Safety Evaluation Using the MOOSE Framework

Fusion energy holds the promise of being a transformative technology as a carbon-neutral, sustainable source of energy. Whole device modeling and the development of fusion digital twins will be increasingly important for emerging fusion device concepts at both national laboratories and within the commercial fusion industry. However, meeting the challenge of whole device modeling of fusion energy devices requires robust, multiphysics, multiscale modeling and simulation technologies capable of running on large-scale supercomputers. Detailed analysis of individual systems at-scale is also required to ensure safe and efficient operation as well as provide the safety basis for future device designs and licensing activities. In a tokamak, toroidal and poloidal magnets confine and shape the fusion plasma to promote the fusion reaction. High plasma temperatures and high magnetic field requirements in modern design concepts (leading to high amounts of energy stored within each magnet) impose electrical, thermal, and mechanical loads on the magnet components, which in turn impacts the safety considerations of the magnet and their supporting systems. Idaho National Laboratory (INL) has a history of working in this space, including development and benchmarking of the Magnetic System Circuitry Analysis Program (MSCAP) and Magnet Arcing (MAGARC) codes to study magnet quench events; notably, MAGARC was used to study quenching during the ITER Engineering Design Activity. However, these legacy codes and capabilities are not parallel and scalable, and new tools are required for future advances in this area, which leads to the INL-developed Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. Developed originally for fission reactor systems under United States Department of Energy, Office of Nuclear Energy modeling and simulation programs, the MOOSE framework has been well-suited to multiscale, multiphysics modeling and simulation needs for nuclear systems. The framework is open-source, well-tested, under continuous development and deployment, and developed to a Nuclear Quality Assurance, Level 1 software quality standard. MOOSE has also been used in the fusion space previously in several projects: INL’s Tritium Migration Analysis Program, Version 8 (TMAP8) for tritium migration, UK Atomic Energy Authority’s A Unified Resource for OpenMC (fusion) Reactor Applications (AURORA) code for fusion thermo-mechanical and neutronics analysis, and Argonne National Laboratory’s Cardinal for high-fidelity computational fluid dynamics and neutronics. However, to model superconducting magnets, several MOOSE enhancements are required: additions to the current MOOSE electromagnetic capabilities, new material libraries for superconductors of interest (such as YBCO), as well as fusion-specific models for thermo-mechanics. This talk will discuss initial development activities to build these capabilities in MOOSE, focusing on initial validation and benchmarking activities. Proposed coupling workflows and future work to support the simulation of fusion magnets and magnet structural assemblies for performance and safety evaluation in MOOSE will also be discussed.

70 - PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Analysis of Spectral Lines in Large Databases of Synthetic Spectra for Massive Stars

In this paper, we describe a program that identifies in the optical spectrum the main parameters of a spectral line, namely the initial and final wavelengths, and the line depth. Moreover, using numerical calculations, it identifies and removes adjacent lines. Next, the program calculates the equivalent width and the FWHM. The software was tested in a sample of 300 lines in two databases of synthetic spectra generated by the CMFGEN and PoWR codes, and 300 lines in observed spectra from the IACOB database, showing a Gaussian distribution of relative errors, from which it is inferred that 80% of the measured lines have errors less than 17% and only 5% of the lines have errors greater than 26%. The program was also run on the entire database of 45,000 CMFGEN and 202 POWR synthetic spectra, generating a library of H i, He i, and He ii lines necessary to feed the FITspec code for the derivation of stellar parameters: effective temperature, surface gravity, and luminosity.

47 OTHER INSTRUMENTATION↗

NASA NTRS1990

PAN AIR: A computer program for predicting subsonic or supersonic linear potential flows about arbitrary configurations using a higher order panel method. Volume 4: Maintenance document (version 3.0)

The Maintenance Document Version 3.0 is a guide to the PAN AIR software system, a system which computes the subsonic or supersonic linear potential flow about a body of nearly arbitrary shape, using a higher order panel method. The document describes the overall system and each program module of the system. Sufficient detail is given for program maintenance, updating, and modification. It is assumed that the reader is familiar with programming and CRAY computer systems. The PAN AIR system was written in FORTRAN 4 language except for a few CAL language subroutines which exist in the PAN AIR library. Structured programming techniques were used to provide code documentation and maintainability. The operating systems accommodated are COS 1.11, COS 1.12, COS 1.13, and COS 1.14 on the CRAY 1S, 1M, and X-MP computing systems. The system is comprised of a data base management system, a program library, an execution control module, and nine separate FORTRAN technical modules. Each module calculates part of the posed PAN AIR problem. The data base manager is used to communicate between modules and within modules. The technical modules must be run in a prescribed fashion for each PAN AIR problem. In order to ease the problem of supplying the many JCL cards required to execute the modules, a set of CRAY procedures (PAPROCS) was created to automatically supply most of the JCL cards. Most of this document has not changed for Version 3.0. It now, however, strictly applies only to PAN AIR version 3.0. The major changes are: (1) additional sections covering the new FDP module (which calculates streamlines and offbody points); (2) a complete rewrite of the section on the MAG module; and (3) strict applicability to CRAY computing systems.

Purdon, David J.↗

DOE OSTI2022

Noodles: Cooking Up Collaborative Visualization

NOODLES is a new cross-domain collaborative visualization and analysis capability being developed at NREL. The NOODLES specification is a minimal protocol that can tie different software packages and platforms together. As an example, a simulation code that speaks this protocol could stream iso-surfaces to an immersive VR space and a web browser. Another example is a team (with some members across the country) classifying and discovering features in a statistical data plot, driven from a researcher's existing Python-based workflow. In this talk, we will discuss some background on the problems that this protocol intends to solve, basic principles of the specification, the current state of supporting libraries, and some demonstrations of the protocol in action.

3D↗

DOE OSTI2016

Profiling Production OpenSHMEM Applications, In: OpenSHMEM 2016: OpenSHMEM and Related Technologies. Enhancing OpenSHMEM for Hybrid Environments

Developing high performance OpenSHMEM applications routinely involves gaining a deeper understanding of software execution, yet there are numerous hurdles to gathering performance metrics in a production environment. Most OpenSHMEM performance profilers rely on the PSHMEM interface but PSHMEM is an optional and often unavailable feature. We present a tool that generates direct measurement performance profiles of OpenSHMEM applications even when PSHMEM is unavailable. The tool operates on dynamically linked and statically linked application binaries, does not require debugging symbols, and functions regardless of compiler optimization level. Integrated in the TAU Performance System, the tool uses automatically-generated wrapper libraries that intercept OpenSHMEM API calls to gather performance metrics with minimal overhead. Dynamically linked applications may use the tool without modifying the application binary in any way.

Computer Science↗

DOE OSTI2024

Exploring Architectural-Aware Affinity Policies in Modern HPC Runtimes

Modern commodity and High-Performance Computing (HPC) systems are evolving with complex CPU architectures. These architectures now feature higher core and NUMA domain counts and implement features such as hyperthreading. When considering significant differences in hardware configurations, library availability, and hardware-tailored system/software stacks, which could substantially vary from one system to another, performance portability is hard to achieve. Throughout the years, this trend resulted in an increasingly high burden on application developers to fine-tune their workloads for each architecture. This work explores how hardware-dependent aspects such as locality/process/thread affinity affect performance in modern CPU architectures. We focus our study on the Global Memory and Threading (GMT) distributed runtime system as a representative of Partitioned Global Address Space (PGAS) software stacks commonly adopted for productivity. In particular, to appreciate performance implications, we evaluate GMT’s thread affinity policies, and, introduce two new ones which exploit architectural awareness. Finally, we explore alternative NUMA configurations via different process bindings and perform a scalability study on three HPC clusters with varying CPU architectures and NUMA layouts. Our analysis indicates that more complex architectures are more affected by affinity and binding policies and highlights the importance of setting proper runtime configurations to achieve superior performance.

Di Dio Lavore, Ian↗

DOE OSTI2023

pynucastro: A Python Library for Nuclear Astrophysics

We describe pynucastro 2.0, an open-source library for interactively creating and exploring astrophysical nuclear reaction networks. We demonstrate new methods for approximating rates and use detailed balance to create reverse rates, show how to build networks and determine whether they are appropriate for a particular science application, and discuss the changes made to the library over the past few years. Finally, we demonstrate the validity of the networks produced and share how we use pynucastro networks in simulation codes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1989

Probabilistic structural analysis methods for select space propulsion system components

The Probabilistic Structural Analysis Methods (PSAM) project developed at the Southwest Research Institute integrates state-of-the-art structural analysis techniques with probability theory for the design and analysis of complex large-scale engineering structures. An advanced efficient software system (NESSUS) capable of performing complex probabilistic analysis has been developed. NESSUS contains a number of software components to perform probabilistic analysis of structures. These components include: an expert system, a probabilistic finite element code, a probabilistic boundary element code and a fast probability integrator. The NESSUS software system is shown. An expert system is included to capture and utilize PSAM knowledge and experience. NESSUS/EXPERT is an interactive menu-driven expert system that provides information to assist in the use of the probabilistic finite element code NESSUS/FEM and the fast probability integrator (FPI). The expert system menu structure is summarized. The NESSUS system contains a state-of-the-art nonlinear probabilistic finite element code, NESSUS/FEM, to determine the structural response and sensitivities. A broad range of analysis capabilities and an extensive element library is present.

Millwater, H. R.↗