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All sources NASA NTRS DOE OSTI

DOE OSTI2024

ReactionMechanismSimulator.jl: A modern approach to chemical kinetic mechanism simulation and analysis

Abstract We present ReactionMechanismSimulator.jl (RMS), a modern differentiable software for the simulation and analysis of chemical kinetic mechanisms, including multiphase systems. RMS has already been applied to problems in combustion, pyrolysis, polymers, pharmaceuticals, catalysis, and electrocatalysis. RMS is written in Julia, making it easy to develop and allowing it to take advantage of Julia's extensive numerical computing ecosystem. In addition to its extensive library of optimized analytic Jacobians, RMS can generate and use Jacobians computed using automatic differentiation and symbolically generated analytic Jacobians. RMS is demonstrated to be faster than Cantera and Chemkin in several benchmarks. RMS also implements an extensive set of features for analyzing chemical mechanisms, including a library of easy‐to‐call plotting functions, molecular structure resolved flux diagram generation, crash analysis, traditional sensitivity analysis, transitory sensitivity analysis, and an automatic mechanism analysis toolkit. RMS implements efficient adjoint and parallel forward sensitivity analyses. We also demonstrate the ease of adding new features to RMS.

Johnson, Matthew S.↗

DOE OSTI2017

Occupant behavior models: A critical review of implementation and representation approaches in building performance simulation programs

Occupant behavior (OB) in buildings is a leading factor influencing energy use in buildings. Quantifying this influence requires the integration of OB models with building performance simulation (BPS). This study reviews approaches to representing and implementing OB models in today’s popular BPS programs, and discusses weaknesses and strengths of these approaches and key issues in integrating of OB models with BPS programs. Two of the key findings are: (1) a common data model is needed to standardize the representation of OB models, enabling their flexibility and exchange among BPS programs and user applications; the data model can be implemented using a standard syntax (e.g., in the form of XML schema), and (2) a modular software implementation of OB models, such as functional mock-up units for co-simulation, adopting the common data model, has advantages in providing a robust and interoperable integration with multiple BPS programs. Such common OB model representation and implementation approaches help standardize the input structures of OB models, enable collaborative development of a shared library of OB models, and allow for rapid and widespread integration of OB models with BPS programs to improve the simulation of occupant behavior and quantification of their impact on building performance.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2017

Design and Implementation of Papyrus: Parallel Aggregate Persistent Storage

A surprising development in recently announced HPC platforms is the addition of, sometimes massive amounts of, persistent (nonvolatile) memory (NVM) in order to increase memory capacity and compensate for plateauing I/O capabilities. However, there are no portable and scalable programming interfaces using aggregate NVM effectively. This paper introduces Papyrus: a new software system built to exploit emerging capability of NVM in HPC architectures. Papyrus (or Parallel Aggregate Persistent -YRU- Storage) is a novel programming system that provides features for scalable, aggregate, persistent memory in an extreme-scale system for typical HPC usage scenarios. Papyrus mainly consists of Papyrus Virtual File System (VFS) and Papyrus Template Container Library (TCL). Papyrus VFS provides a uniform aggregate NVM storage image across diverse NVM architectures. It enables Papyrus TCL to provide a portable and scalable high-level container programming interface whose data elements are distributed across multiple NVM nodes without requiring the user to handle complex communication, synchronization, replication, and consistency model. We evaluate Papyrus on two HPC systems, including UTK Beacon and NERSC Cori, using real NVM storage devices.

Kim, Jungwon↗

DOE OSTI2022

ESnet SmartNIC v1.0

The ESnet SmartNIC is a collection of Verilog based FPGA design software, as well as drivers to interact with the FPGA. It provides an infrastructure framework for FPGA based hardware acceleration of network packet use cases. Different research and production applications can be easily written for the SmartNIC. Its advantage is that it reduces the development time for new applications by providing a pre-existing shell library for common functions.

Mah, Bruce↗

DOE OSTI2022

Caffeine: CoArray Fortran Framework of Efficient Interfaces to Network Environments

This paper provides an introduction to the CoArray Fortran Framework of Efficient Interfaces to Network Environments (Caffeine), a parallel runtime library built atop the GASNet-EX exascale networking library. Caffeine leverages several non-parallel Fortran features to write type- and rank-agnostic interfaces and corresponding procedure definitions that support parallel Fortran 2018 features, including communication, collective operations, and related services. One major goal is to develop a runtime library that can eventually be considered for adoption by LLVM Flang, enabling that compiler to support the parallel features of Fortran. The paper describes the motivations behind Caffeine's design and implementation decisions, details the current state of Caffeine's development, and previews future work. We explain how the design and implementation offer benefits related to software sustainability by lowering the barrier to user contributions, reducing complexity through the use of Fortran 2018 C-interoperability features, and high performance through the use of a lightweight communication substrate.

Rouson, Damian↗

NASA NTRS1988

Knowledge based programming environments: A perspective

Programming environments is an area of recent origin and refers to an integrated set of tools, such as program library, text editor, compiler, and debugger, in support of program development. Understanding of programs and programming has lead to automated techniques for program development. Knowledge based programming system using program transformations offer significant impact on future program development methodologies. A review of recent developments in the area of knowledge based programming environments, from the perspective of software engineering, is presented.

Amin, Ashok T.↗

NASA NTRS1989

Visualizing large data sets in the earth sciences

The authors describe the capabilities of McIDAS, an interactive visualization system that is vastly increasing the ability of earth scientists to manage and analyze data from remote sensing instruments and numerical simulation models. McIDAS provides animated three-dimensionsal images and highly interactive displays. The software can manage, analyze, and visualize large data sets that span many physical variables (such as temperature, pressure, humidity, and wind speed), as well as time and three spatial dimensions. The McIDAS system manages data from at least 100 different sources. The data management tools consist of data structures for storing different data types in files, libraries of routines for accessing these data structures, system commands for performing housekeeping functions on the data files, and reformatting programs for converting external data to the system's data structures. The McIDAS tools for three-dimensional visualization of meteorological data run on an IBM mainframe and can load up to 128-frame animation sequences into the workstations. A highly interactive version of the system can provide an interactive window into data sets containing tens of millions of points produced by numerical models and remote sensing instruments. The visualizations are being used for teaching as well as by scientists.

Hibbard, William↗

NASA NTRS1989

The KALI multi-arm robot programming and control environment

The KALI distributed robot programming and control environment is described within the context of its use in the Jet Propulsion Laboratory (JPL) telerobot project. The purpose of KALI is to provide a flexible robot programming and control environment for coordinated multi-arm robots. Flexibility, both in hardware configuration and software, is desired so that it can be easily modified to test various concepts in robot programming and control, e.g., multi-arm control, force control, sensor integration, teleoperation, and shared control. In the programming environment, user programs written in the C programming language describe trajectories for multiple coordinated manipulators with the aid of KALI function libraries. A system of multiple coordinated manipulators is considered within the programming environment as one motion system. The user plans the trajectory of one controlled Cartesian frame associated with a motion system and describes the positions of the manipulators with respect to that frame. Smooth Cartesian trajectories are achieved through a blending of successive path segments. The manipulator and load dynamics are considered during trajectory generation so that given interface force limits are not exceeded.

Backes, Paul↗

NASA NTRS1989

CONFIG - Adapting qualitative modeling and discrete event simulation for design of fault management systems

CONFIG is a modeling and simulation tool prototype for analyzing the normal and faulty qualitative behaviors of engineered systems. Qualitative modeling and discrete-event simulation have been adapted and integrated, to support early development, during system design, of software and procedures for management of failures, especially in diagnostic expert systems. Qualitative component models are defined in terms of normal and faulty modes and processes, which are defined by invocation statements and effect statements with time delays. System models are constructed graphically by using instances of components and relations from object-oriented hierarchical model libraries. Extension and reuse of CONFIG models and analysis capabilities in hybrid rule- and model-based expert fault-management support systems are discussed.

Malin, Jane T.↗

NASA NTRS2014

Robot Task Commander with Extensible Programming Environment

A system for developing distributed robot application-level software includes a robot having an associated control module which controls motion of the robot in response to a commanded task, and a robot task commander (RTC) in networked communication with the control module over a network transport layer (NTL). The RTC includes a script engine(s) and a GUI, with a processor and a centralized library of library blocks constructed from an interpretive computer programming code and having input and output connections. The GUI provides access to a Visual Programming Language (VPL) environment and a text editor. In executing a method, the VPL is opened, a task for the robot is built from the code library blocks, and data is assigned to input and output connections identifying input and output data for each block. A task sequence(s) is sent to the control module(s) over the NTL to command execution of the task.

Hart, Stephen W↗

DOE OSTI2014

LipidMiner: A Software for Automated Identification and Quantification of Lipids from Multiple Liquid Chromatography-Mass Spectrometry Data Files

We have developed a tool for automated, high-throughput analysis of LC-MS/MS data files, which greatly simplifies LC-MS based lipidomics analysis. Our results showed that LipidMiner is accurate and comprehensive in identification and quantification of lipid molecular species. In addition, the workflow implemented in LipidMiner is not limited to identification and quantification of lipids. If a suitable metabolite library is implemented in the library matching module, LipidMiner could be reconfigured as a tool for general metabolomics data analysis. It is of note that LipidMiner currently is limited to singly charged ions, although it is adequate for the purpose of lipidomics since lipids are rarely multiply charged,[14] even for the polyphosphoinositides. LipidMiner also only processes file formats generated from mass spectrometers from Thermo, i.e. the .RAW format. In the future, we are planning to accommodate file formats generated by mass spectrometers from other predominant instrument vendors to make this tool more universal.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2016

Draco,Version 6.x.x

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

Thompson, Kelly↗

DOE OSTI2013

Alquimia

Alquimia provides a generic interface between flow and transport simulators (drivers) and biogeochemical reaction capabilities (engines). Alquimia consists of two parts: an application programming interface, API, and a wrapper library. The API describes in detail how information is exchanged between the driver and the engine. This includes the function call signatures and data structures required for implementing alquimia in a mixed language (C/C++/Fortran) programming environment. The library is an implementation of the documented API, providing an interface into the biogeochemistry routines supplied by other codes: Alquimia does not do any geochemical calculations. Version 1.0 provides interfaces to the open source codes (BSD) CrunchFlow/CrunchTope and (LGPL) PFLOTRAN. Version 1.0 meets the policies set forth by (and is part of) the Extreme-scale Scientific Software Development Kit, xSDK version 0.6.0.

Andre, Benjamin [Lawrence Berkeley National Lab. (↗

DOE OSTI2024

Web Based Beamline Control System (Bluesky Web) v0.1.0

Bluesky Web is a web based interface that provides beam line controls to the end user. It allows users to issue commands to various physical devices at a beam line end station like motors and cameras. It utilizes an open source Python library (Bluesky) as the controller. It uses Bluesky to also allow for running "plans" or a sequence of device operations that can be used when running an experiment. This program is different from other controls technologies because it is intended to be open source and can be accessed from a web browser, as opposed to other paid software that is run as a stand-alone application on a computer.

De Leon, Seij↗

DOE OSTI2020

Toward Resilient Heterogeneous Computing Workflow through Kokkos-DataSpaces Integration

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Design and Performance of Kokkos Staging Space toward Scalable Resilient Application Couplings

With the growing number of applications designed for heterogeneous HPC devices, application programmers and users are finding it challenging to compose scalable workflows as ensembles of these applications, that are portable, performant and resilient. The Kokkos C++ library has been designed to simplify this cumbersome procedure by providing an intra-application uniform programming model and portable performance. However, assembling multiple Kokkos-enabled applications into a complex workflow is still a challenge. Although Kokkos enables a uniform programming model, the inter-application data exchange still remains a challenge from both performance and software development cost perspectives. In order to address this issue, we propose Kokkos data staging memory space, an extension of Kokkos' data abstraction (memory space) for heterogeneous computing systems. This new abstraction allows to express data on a virtual shared-space for multiple Kokkos applications, thus extending Kokkos to support inter-application data exchange to build an efficient application workflow. Additionally, we study the effectiveness of asynchronous data layout conversions for applications requiring different memory access patterns for the shared data. Our preliminary evaluation with a synthetic benchmark indicate the effectiveness of this conversion adapted to three different scenarios representing access frequency and use patterns of the shared data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

SCALE Newsletter (Number 52, Spring 2020)

SCALE Newsletter is published by the Reactor and Nuclear Systems Division of the Oak Ridge National Laboratory. This issue, number 52 from Spring of 2020, holds information about the current state, planned updates, and previews of the SCALE system designed and maintained by ORNL staff. This issue contains employee spotlights for Dr. Kursat Bekar as well as Dr. Andrew M. Holcomb and displays data and charts from new/updated features of SCALE such as new data libraries, Fulcrum 3D visualizations, and interactions with ENDF/B-VIII.0 data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1997

Develop Advanced Nonlinear Signal Analysis Topographical Mapping System

During the development of the SSME, a hierarchy of advanced signal analysis techniques for mechanical signature analysis has been developed by NASA and AI Signal Research Inc. (ASRI) to improve the safety and reliability for Space Shuttle operations. These techniques can process and identify intelligent information hidden in a measured signal which is often unidentifiable using conventional signal analysis methods. Currently, due to the highly interactive processing requirements and the volume of dynamic data involved, detailed diagnostic analysis is being performed manually which requires immense man-hours with extensive human interface. To overcome this manual process, NASA implemented this program to develop an Advanced nonlinear signal Analysis Topographical Mapping System (ATMS) to provide automatic/unsupervised engine diagnostic capabilities. The ATMS will utilize a rule-based Clips expert system to supervise a hierarchy of diagnostic signature analysis techniques in the Advanced Signal Analysis Library (ASAL). ASAL will perform automatic signal processing, archiving, and anomaly detection/identification tasks in order to provide an intelligent and fully automated engine diagnostic capability. The ATMS has been successfully developed under this contract. In summary, the program objectives to design, develop, test and conduct performance evaluation for an automated engine diagnostic system have been successfully achieved. Software implementation of the entire ATMS system on MSFC's OISPS computer has been completed. The significance of the ATMS developed under this program is attributed to the fully automated coherence analysis capability for anomaly detection and identification which can greatly enhance the power and reliability of engine diagnostic evaluation. The results have demonstrated that ATMS can significantly save time and man-hours in performing engine test/flight data analysis and performance evaluation of large volumes of dynamic test data.

Jong, Jen-Yi↗