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At least 1,009 records · Page 56

Direct numerical simulations of reacting flows with detailed chemistry using many-core/GPU acceleration

A new direct numerical simulation (DNS) code for multi-component gaseous reacting flows has been developed at KAUST, with the state-of-the-art programming model for next generation high performance computing platforms. The code, named KAUST Adaptive Reacting Flows Solver (KARFS), employs the MPI+X programming, and relies on Kokkos for “X” for performance portability to multi-core, many-core and GPUs, providing innovative software development while maintaining backward compatibility with established parallel models and legacy code. The capability and potential of KARFS to perform DNS of reacting flows with large, detailed reaction mechanisms is demonstrated with various model problems involving ignition and turbulent flame propagations with varying degrees of chemical complexities.

Computer Science↗

Inference-Engine v0.1.0

Given a pre-trained neural network, Inference-Engine performs maps network inputs to outputs by executing the forward pass through the provided network. Although the predominant programming language for machine-learning is Python, most high-performance computing (HPC) applications are written in Fortran, C, or C++. Inference-Engine aims to support HPC programs and is written in Fortran, a language with a large feature set supporting interoperability with C. This software exposes concurrency in a portable way by using standard language features that some modern Fortran compilers can exploit with various optimizations, including offloading computation to a Graphics Processing Unit (GPU). In particular, this software makes extensive use of Fortran's "do concurrent" parallel loop construct, implicitly parallel array statements, and pure procedures that can be invoked inside "do concurrent" blocks. Inference-Engine also supports dynamic choice of inference methods at runtime. Two current options include one method that uses Fortran's "dot_product" intrinsic function inside "do concurrent" blocks and another method that instead uses Fortran' "matmul" array intrinsic function. We plan to investigate automatic compiler offloading of "do concurrent" calculations to GPUs and compile-time substitution of optimized libraries such as the Basic Linear Algebra Library (BLAS) for "matmul" invocations. We also envision the potential for the choice of which method to use could happen at program launch based on in situ performance measurements on any given platform.

Rouson, Damian↗

Simulating the dynamic interaction of a robotic arm and the Space Shuttle remote manipulator system

Industrial robots are usually attached to a rigid base. Placing the robot on a compliant base introduces dynamic coupling between the two systems. The Vehicle Emulation System (VES) is a six DOF platform that is capable of modeling this interaction. The VES employs a force-torque sensor as the interface between robot and base. A computer simulation of the VES is presented. Each of the hardware and software components is described and Simulink is used as the programming environment. The simulation performance is compared with experimental results to validate accuracy. A second simulation which models the dynamic interaction of a robot and a flexible base acts as a comparison to the simulated motion of the VES. Results are presented that compare the simulated VES motion with the motion of the VES hardware using the same admittance model. The two computer simulations are compared to determine how well the VES is expected to emulate the desired motion. Simulation results are given for robots mounted to the end effector of the Space Shuttle Remote Manipulator System (SRMS). It is shown that for fast motions of the two robots studied, the SRMS experiences disturbances on the order of centimeters. Larger disturbances are possible if different manipulators are used.

Garrahan, Steven L.↗

The ezSpectra suite: An easy‐to‐use toolkit for spectroscopy modeling

Abstract A molecule's spectrum encodes information about its structure and electronic properties. It is a unique fingerprint that can serve as a molecular ID. Quantum chemistry calculations provide key ingredients for interpreting spectra, but modeling the spectra rarely ends there; it requires additional steps that entail combined treatments of electronic and nuclear degrees of freedom and account for specifics of the experimental setup (light energy, polarization, averaging over molecular orientations, temperature, etc.). This Software Focus article describes the ezSpectra suite, which currently comprises two stand‐alone open‐source codes: ezFCF and ezDyson . ezFCF calculates Franck–Condon factors, which yield vibrational progressions for polyatomic molecules, within the double‐harmonic approximation. ezDyson calculates absolute cross‐sections for photodetachment/photoionization processes and photoelectron angular distributions using Dyson orbitals computed by a quantum chemistry program. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy Software > Simulation Methods

Gozem, Samer↗

Quantum Computing and Visualization: A Disruptive Technological Change Ahead

The focus of this Visualization Viewpoints article is to provide some background on quantum computing (QC), to explore ideas related to how visualization helps in understanding QC, and examine how QC might be useful for visualization with the growth and maturation of both technologies in the future. In a quickly evolving technology landscape, QC is emerging as a promising pathway to overcome the growth limits in classical computing. In some cases, QC platforms offer the potential to vastly outperform the familiar classical computer by solving problems more quickly or that may be intractable on any known classical platform. As further performance gains for classical computing platforms are limited by diminishing Moore’s Law scaling, QC platforms might be viewed as a potential successor to the current field of exascale-class platforms. Importantly, while present-day QC hardware platforms are still limited in scale, the field of quantum computing is robust and rapidly advancing in terms of hardware capabilities, software environments for developing quantum algorithms, and educational programs for training the next generation of scientists and engineers. After a brief introduction to QC concepts, the focus of this article is to explore the interplay between the fields of visualization and QC. First, visualization has played a role in QC by providing the means to show representations of the quantum state of single-qubits in superposition states and multiple-qubits in entangled states. Second, there are a number of ways in which the field of visual data exploration and analysis may potentially benefit from this disruptive new technology though there are challenges going forward.

97 MATHEMATICS AND COMPUTING↗

Software For Clear-Air Doppler-Radar Display

System of software developed to present plan-position-indicator scans of clear-air Doppler radar station on color graphical cathode-ray-tube display. Designed to incorporate latest accepted standards for equipment, computer programs, and meteorological data bases. Includes use of Ada programming language, of "Graphical-Kernel-System-like" graphics interface, and of Common Doppler Radar Exchange Format. Features include portability and maintainability. Use of Ada software packages produced number of software modules reused on other related projects.

Johnston, Bruce W.↗

Predicting Accumulations of Ice on Aerodynamic Surfaces

LEWICE is a computer program that predicts the accumulation of ice on two-dimensional aerodynamic surfaces under conditions representative of the flight of an aircraft through an icing cloud. The software first calculates the airflow surrounding the body of interest, then uses the airflow to compute the trajectories of water droplets that impinge on the surface of the body. The droplet trajectories are also used to compute impingement limits and local collection efficiencies, which are used in subsequent ice-growth calculations and are also useful for designing systems to protect against icing. Next, the software predicts the shape of accumulating ice by modeling transfers of mass and energy in small control volumes. The foregoing computations are repeated over several computational time steps until the total icing exposure time is reached. Results of computations by LEWICE have been compared with an extensive database of measured ice shapes obtained from experiments, and have been shown to closely approximate those shapes under most conditions of interest to the aviation community.

Bidwell, Colin↗

RAVEN Theory Manual

RAVEN is a software framework able to perform parametric and stochastic analysis based on the response of complex system codes. The initial development was aimed at providing dynamic risk analysis capabilities to the thermohydraulic code RELAP-7, currently under development at Idaho National Laboratory (INL). Although the initial goal has been fully accomplished, RAVEN is now a multi-purpose stochastic and uncertainty quantification platform, capable of communicating with any system code. In fact, the provided Application Programming Interfaces (APIs) allow RAVEN to interact with any code as long as all the parameters that need to be perturbed are accessible by input files or via python interfaces. RAVEN is capable of investigating system response and explore input space using various sampling schemes such as Monte Carlo, grid, or Latin hypercube. However, RAVEN strength lies in its system feature discovery capabilities such as: constructing limit surfaces, separating regions of the input space leading to system failure, and using dynamic supervised learning techniques. The development of RAVEN started in 2012 when, within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the need to provide a modern risk evaluation framework arose. RAVEN’s principal assignment is to provide the necessary software and algorithms in order to employ the concepts developed by the Risk Informed Safety Margin Characterization (RISMC) program. RISMC is one of the pathways defined within the Light Water Reactor Sustainability (LWRS) program. In the RISMC approach, the goal is not just to identify the frequency of an event potentially leading to a system failure, but the proximity (or lack thereof) to key safety-related events. Hence, the approach is interested in identifying and increasing the safety margins related to those events. A safety margin is a numerical value quantifying the probability that a safety metric (e.g. peak pressure in a pipe) is exceeded under certain conditions. Most of the capabilities, implemented having RELAP-7 as a principal focus, are easily deployable to other system codes. For this reason, several side activates have been employed (e.g. RELAP5-3D, any MOOSE-based App, etc.) or are currently ongoing for coupling RAVEN with several different software. The aim of this document is to provide a set of commented examples that can help the user to become familiar with the RAVEN code usage.

97 MATHEMATICS AND COMPUTING↗

Application of a personal computer for the uncoupled vibration analysis of wind turbine blade and counterweight assemblies

A research effort was undertaken to develop personal computer based software for vibrational analysis. The software was developed to analytically determine the natural frequencies and mode shapes for the uncoupled lateral vibrations of the blade and counterweight assemblies used in a single bladed wind turbine. The uncoupled vibration analysis was performed in both the flapwise and chordwise directions for static rotor conditions. The effects of rotation on the uncoupled flapwise vibration of the blade and counterweight assemblies were evaluated for various rotor speeds up to 90 rpm. The theory, used in the vibration analysis codes, is based on a lumped mass formulation for the blade and counterweight assemblies. The codes are general so that other designs can be readily analyzed. The input for the codes is generally interactive to facilitate usage. The output of the codes is both tabular and graphical. Listings of the codes are provided. Predicted natural frequencies of the first several modes show reasonable agreement with experimental results. The analysis codes were originally developed on a DEC PDP 11/34 minicomputer and then downloaded and modified to run on an ITT XTRA personal computer. Studies conducted to evaluate the efficiency of running the programs on a personal computer as compared with the minicomputer indicated that, with the proper combination of hardware and software options, the efficiency of using a personal computer exceeds that of a minicomputer.

White, P. R.↗

Portable computers as companions in space

The paper describes a Space Shuttle Program payload that uses a Macintosh portable computer to gather human performance data for a cursor control device experiment and to test prototype software applications for the Space Station Freedom (SSF). The payload is the first phase of a NASA research and development project to operationally test human-computer interface requirements and crew support applications for an advanced portable computer for the SSF.

Microgravity↗

Ensemble averaging of acoustic data

A computer program called Ensemble Averaging of Acoustic Data is documented. The program samples analog data, analyzes the data, and displays them in the time and frequency domains. Hard copies of the displays are the program's output. The documentation includes a description of the program and detailed user instructions for the program. This software was developed for use on the Ames 40- by 80-Foot Wind Tunnel's Dynamic Analysis System consisting of a PDP-11/45 computer, two RK05 disk drives, a tektronix 611 keyboard/display terminal, and FPE-4 Fourier Processing Element, and an analog-to-digital converter.

Stefanski, P. K.↗

Use of Faraday-rotation data from beacon satellites to determine ionospheric corrections for interplanetary spacecraft navigation

Faraday-rotation data from the linearly polarized 137-MHz beacons of the ATS-1, SIRIO, and Kiku-2 geosynchronous satellites are used to determine the ionospheric corrections to the range and Doppler data for interplanetary spacecraft navigation. The JPL operates the Deep Space Network of tracking stations for NASA; these stations monitor Faraday rotation with dual orthogonal, linearly polarized antennas, Teledyne polarization tracking receivers, analog-to-digital converter/scanners, and other support equipment. Computer software examines the Faraday data, resolves the pi ambiguities, constructs a continuous Faraday-rotation profile and converts the profile to columnar zenith total electron content at the ionospheric reference point; a second program computes the line-of-sight ionospheric correction for each pass of the spacecraft over each tracking complex. Line-of-sight ionospheric electron content using mapped Faraday-rotation data is compared with that using dispersive Doppler data from the Voyager spacecraft; a difference of about 0.4 meters, or 5 x 10 to the 16th electrons/sq m is obtained. The technique of determining the electron content of interplanetary plasma by subtraction of the ionospheric contribution is demonstrated on the plasma torus surrounding the orbit of Io.

Royden, H. N.↗

Multidisciplinary Optimization Branch Experience Using iSIGHT Software

The Multidisciplinary Optimization (MDO) Branch at NASA Langley Research Center is investigating frameworks for supporting multidisciplinary analysis and optimization research. An optimization framework call improve the design process while reducing time and costs. A framework provides software and system services to integrate computational tasks and allows the researcher to concentrate more on the application and less on the programming details. A framework also provides a common working environment and a full range of optimization tools, and so increases the productivity of multidisciplinary research teams. Finally, a framework enables staff members to develop applications for use by disciplinary experts in other organizations. Since the release of version 4.0, the MDO Branch has gained experience with the iSIGHT framework developed by Engineous Software, Inc. This paper describes experiences with four aerospace applications: (1) reusable launch vehicle sizing, (2) aerospike nozzle design, (3) low-noise rotorcraft trajectories, and (4) acoustic liner design. All applications have been successfully tested using the iSIGHT framework, except for the aerospike nozzle problem, which is in progress. Brief overviews of each problem are provided. The problem descriptions include the number and type of disciplinary codes, as well as all estimate of the multidisciplinary analysis execution time. In addition, the optimization methods, objective functions, design variables, and design constraints are described for each problem. Discussions on the experience gained and lessons learned are provided for each problem. These discussions include the advantages and disadvantages of using the iSIGHT framework for each case as well as the ease of use of various advanced features. Potential areas of improvement are identified.

Padula, S. L.↗

IGDS/TRAP Interface Program (ITIP). Software User Manual (SUM)

This specification establishes the requirements, concepts, and preliminary design for a set of software known as the IGDS/TRAP Interface Program (ITIP). This software provides the capability to develop at an Interactive Graphics Design System (IGDS) design station process flow diagrams for use by the NASA Coal Gasification Task Team. In addition, ITIP will use the Data Management and Retrieval System (DMRS) to maintain a data base from which a properly formatted input file to the Time-Line and Resources Analysis Program (TRAP) can be extracted. This set of software will reside on the PDP-11/70 and will become the primary interface between the Coal Gasification Task Team and IGDS, DMRS, and TRAP. The user manual for the computer program is presented.

Jefferys, S.↗

TChem v2.0 - A Software Toolkit for the Analysis of Complex Kinetic Models

TChem is an open source software library for solving complex computational chemistry problems and analyzing detailed chemical kinetic models. The software provides support for: complex kinetic models for gas-phase and surface chemistry; thermodynamic properties based on NASA polynomials; species production/consumption rates; stable time integrator for solving stiff time ordinary differential equations; and, reactor models such as homogenous gas-phase ignition (with analytical Jacobian matrices), continuously stirred tank reactor, plug-flow reactor. This toolkit builds upon earlier versions that were written in C and featured tools for gas-phase chemistry only. The current version of the software was completely refactored in C++, uses an object-oriented programming model, and adopts Kokkos as its portability layer to make it ready for the next generation computing architectures i.e., multi/many core computing platforms with GPU accelerators. We have expanded the range of kinetic models to include surface chemistry and have added examples pertaining to Continuously Stirred Tank Reactors (CSTR) and Plug Flow Reactor (PFR) models to complement the homogenous ignition examples present in the earlier versions. To exploit the massive parallelism available from modern computing platforms, the current software interface is designed to evaluate samples in parallel, which enables large scale parametric studies, e.g. for sensitivity analysis and model calibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A pervasive parallel framework for visualization: final report for FWP 10-014707

We are on the threshold of a transformative change in the basic architecture of highperformance computing. The use of accelerator processors, characterized by large core counts, shared but asymmetrical memory, and heavy thread loading, is quickly becoming the norm in high performance computing. These accelerators represent significant challenges in updating our existing base of software. An intrinsic problem with this transition is a fundamental programming shift from message passing processes to much more fine thread scheduling with memory sharing. Another problem is the lack of stability in accelerator implementation; processor and compiler technology is currently changing rapidly. This report documents the results of our three-year ASCR project to address these challenges. Our project includes the development of the Dax toolkit, which contains the beginnings of new algorithms for a new generation of computers and the underlying infrastructure to rapidly prototype and build further algorithms as necessary.

97 MATHEMATICS AND COMPUTING↗

TEAM Project Review, Year 2

This report summarizes our research activities within the TEAM project between December 2020 and December 2021, funded by the ASCR Advanced Research in Quantum Computing program. During the reporting period the LLNL-MSU team has made progress on several fronts. An overarching goal of the team is to provide a comprehensive suite of software tools that can be used for the Characterize-Optimize-Compute loop needed to implement and execute algorithms on quantum devices. We are concurrently developing lightweight solvers that can be used on desktop computers to find optimal control pulses and to characterize small quantum systems (consisting of a few transmons and cavities). However, desktop computers are insufficient for simulating and characterizing larger quantum systems. We have therefore also developed parallel, distributed memory, simulators and optimization solvers, both for open and closed quantum systems. These parallel solvers have, for example, been used to study quantum optimal control for pure-state preparation, utilizing 1000’s of cores on a modern high-performance computing (HPC) platform.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The parallelism motifs of genomic data analysis

Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

59 BASIC BIOLOGICAL SCIENCES↗