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At least 1,369 records · Page 76

New Challenges in Model Checking

In the last 25 years, the notion of performing software verification with logic model checking techniques has evolved from intellectual curiosity to accepted technology with significant potential for broad practical application. In this paper we look back at the main steps in this evolution and illustrate how the challenges have changed over the years, as we sharpened our theories and tools. Next we discuss a typical challenge in software verification that we face today - and that perhaps we can look back on in another 25 years as having inspired the next logical step towards a broader integration of model checking into the software development process.

software verification↗

Modernization efforts for the R -Matrix code SAMMY [Abstract]

The R-Matrix code SAMMY is a widely used nuclear data evaluation code focused on the resolved range, which includes corrections for experimental effects. The code is still mostly written in Fortran 77, and uses a memory management system suitable for the time of its initial writing (1984). A modernization effort is under way to bring the code in-line with modern software development practices. A continuous-integration testing framework was added, automating the large existing set of test cases. It is run on every commit. The memory management was updated to current standard practices suitable for modern software analysis tools. The code can be obtained from https://code.ornl.gov/RNSD/SAMMY. The resonance parameters and covariance information are now stored in C++ objects shared by SAMMY and AMPX, the processing code that generates nuclear data libraries for SCALE. This allows for easier maintenance and access to the resonance parameters inside and outside of SAMMY. This feature is already used by accessing and changing parameters in memory in the Bayesian Monte Carlo Evaluation Framework for Cross Sections Nuclear Data and Integral Benchmark Experiments project, Further plans include the switch to the ENDF reading and writing routines in AMPX, as these routines are more robust, easier to maintain, and support more features. Of note here is support for the new GNDS format. Previously it wasn’t easy to share the full covariance matrix for evaluations containing more than one isotope due to limitations on the ENDF format; this is now supported in GNDS. The data are currently available in a binary SAMMY format and can be exported to GNDS to make them more widely available and sharable. The next step will be to use the same resonance processing code at 0K in AMPX and SAMMY as one of the available Reich-Moore R-Matrix formalism. The first step toward this goal is to isolate the reconstruction into a module that takes resonance parameters as its input and does not depend on SAMMY global parameters. This goal has been achieved and it should now be possible to more easily change the resonance formalism and add enhancements as the Phenomenological R-Matrix parameterization of direct, doorway, and compound nuclear reactions discussed elsewhere on this conference. This concerted modernization and enhancement effort provides multiple advantages to the nuclear data community. It will allow parameter optimization using enhanced formalisms, including experimental effects, that better match complex experimental data. Then those evaluated parameters can immediately be passed off to AMPX to be reconstructed with the exact same cross section model and be put into a data library for subsequent testing using SCALE and the Valid Benchmark suite or other suitable benchmark suites.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Parallel LU Factorization on GPU Cluster

This paper describes our progress in developing softwarefor performing parallel LU factorization of a large dense matrix on a GPU cluster. Three approaches, with increasing software complexity, are considered: (i) a naive “thunking” approach that links the existing parallel ScaLAPACK software library with cuBLAS through a software emulation layer; (ii) a more intrusive magmaBLAS implementation integrated into the LU solver in the High-Performance Linpack software; and (iii) a left-looking out-of-core algorithm for solving problems that are larger than the available memory on GPU devices. Comparison of the performance gains versus the current ScaLAPACK PZGETRF are provided.

42 ENGINEERING↗

Hydrogen Selective Exfoliated Zeolite Membranes

The objective of this project was to develop and evaluate an innovative membrane technology at process conditions that would be representative of Integrated Gasification Combined Cycle (IGCC) advanced power generation with pre-combustion capture of carbon dioxide (CO 2 ). This research focused on hydrogen (H 2 )-selective zeolite membranes that could be utilized to separate conditioned syngas into H 2 -rich and CO 2 -rich components. Both experiments and process design and optimization calculations were performed to evaluate the concept of ultra-thin membranes made from zeolites nanosheets. In this work, efforts in the laboratory were made to tackle two fundamental challenges in application of zeolite membranes in harsh industrial environments, namely, membrane thickness and membrane stability. Conventional zeolite membranes have thicknesses in the micron range, limiting their performance. In this research, we developed a method for fabrication of ultimately thin zeolite membranes based on zeolite nanosheets. A range of layered zeolites (MWW, RWR, NSI structure types) suitable for hydrogen separation was successfully exfoliated to their constituent nanosheets. Further, membranes were made from one of these zeolites, MWW, to demonstrate the potential of this group of materials. Moreover, long-term steam stability of these zeolites (up to 6 months) was investigated in high concentrations of steam (35 mol% and 95 mole%), high pressure (10 barg), and high temperatures (350 °C and 600 °C) relevant to conditions of water-gas-shift and steam methane reforming reactions. It was found that certain nanosheets are stable, and that stability depends on the concentration of structural defects. Additionally, models that represent a water-gas-shift (WGS) membrane reactor equipped with the zeolite membrane were developed for systems studies. These studies had the aim of analyzing the effect of the membrane reactor integration into IGCC plants in terms of performance and economic aspects of the plants. Specifically, simulation and design optimization studies were performed using the developed stand-alone membrane reactor models to identify the membrane selectivity and permeance characteristics necessary to achieve desired targets of CO 2 capture and H 2 recovery, as well as guide the selection of the optimal reactor design that minimizes the membrane cost as a function of its surface area required. The isothermal membrane reactor model was also integrated into IGCC system models using both the MATLAB and Aspen software platforms and techno-economic analyses of the integrated plants have been carried out to evaluate the feasibility of replacing current technologies for pre-combustion capture by the proposed novel approach in terms of satisfying stream constraints and achieving the DOE target goal of 90% CO 2 capture. The results of the performed analyses based on present value of annuity calculations showed break even costs for the membrane reactor within the feasible range for membrane fabrication. However, the predicted membrane performance used in these simulations exceeded the performance achieved experimentally. Therefore, further work is required to improve membrane performance.

01 COAL, LIGNITE, AND PEAT↗

Parallel LU Factorization on GPU cluster

This paper describes our progress in developing software for performing parallel LU factorization of a large dense matrix on a GPU cluster. Three approaches, with increasing software complexity, are considered: (i) a naive 'thunking' approach that links the existing parallel ScaLAPACK software library with cuBLAS through a software emulation layer; (ii) a more intrusive magmaBLAS implementation integrated into the LU solver in the High-Performance Linpack software; and (iii) a left-looking out-of-core algorithm for solving problems that are larger than the available memory on GPU devices. Comparison of the performance gains versus the current ScaLAPACK PZGETRF are provided.

99 GENERAL AND MISCELLANEOUS↗

Mapping analysis and planning system for the John F. Kennedy Space Center

Environmental management, impact assessment, research and monitoring are multidisciplinary activities which are ideally suited to incorporate a multi-media approach to environmental problem solving. Geographic information systems (GIS), simulation models, neural networks and expert-system software are some of the advancing technologies being used for data management, query, analysis and display. At the 140,000 acre John F. Kennedy Space Center, the Advanced Software Technology group has been supporting development and implementation of a program that integrates these and other rapidly evolving hardware and software capabilities into a comprehensive Mapping, Analysis and Planning System (MAPS) based in a workstation/local are network environment. An expert-system shell is being developed to link the various databases to guide users through the numerous stages of a facility siting and environmental assessment. The expert-system shell approach is appealing for its ease of data access by management-level decision makers while maintaining the involvement of the data specialists. This, as well as increased efficiency and accuracy in data analysis and report preparation, can benefit any organization involved in natural resources management.

Hall, C. R.↗

Use of Dynamic Models and Operational Architecture to Solve Complex Navy Challenges

The United States Navy established 8 Maritime Operations Centers (MOC) to enhance the command and control of forces at the operational level of warfare. Each MOC is a headquarters manned by qualified joint operational-level staffs, and enabled by globally interoperable C41 systems. To assess and refine MOC staffing, equipment, and schedules, a dynamic software model was developed. The model leverages pre-existing operational process architecture, joint military task lists that define activities and their precedence relations, as well as Navy documents that specify manning and roles per activity. The software model serves as a "computational wind-tunnel" in which to test a MOC on a mission, and to refine its structure, staffing, processes, and schedules. More generally, the model supports resource allocation decisions concerning Doctrine, Organization, Training, Material, Leadership, Personnel and Facilities (DOTMLPF) at MOCs around the world. A rapid prototype effort efficiently produced this software in less than five months, using an integrated process team consisting of MOC military and civilian staff, modeling experts, and software developers. The work reported here was conducted for Commander, United States Fleet Forces Command in Norfolk, Virginia, code N5-0LW (Operational Level of War) that facilitates the identification, consolidation, and prioritization of MOC capabilities requirements, and implementation and delivery of MOC solutions.

Grande, Darby↗

An Integrated Analysis-Test Approach

This viewgraph presentation provides an overview of a project to develop a computer program which integrates data analysis and test procedures. The software application aims to propose a new perspective to traditional mechanical analysis and test procedures and to integrate pre-test and test analysis calculation methods. The program also should also be able to be used in portable devices and allows for the 'quasi-real time' analysis of data sent by electronic means. Test methods reviewed during this presentation include: shaker swept sine and random tests, shaker shock mode tests, shaker base driven model survey tests and acoustic tests.

Kaufman, Daniel↗

A Strawman for an HPC PowerStack

The landscape of High-Performance Computing (HPC) is changing as we enter the exascale era and power and energy management are key design points for any next generation of supercomputers. Efficiently utilizing procured power and optimizing performance of scientific applications under power and energy constraints is challenging due to several reasons including dynamic phase behavior, processor manufacturing variability and increasing heterogeneity of node-level components. Extending the scope from the node- and application-level up to the system-level introduces further challenges on top of power-unaware job scheduling, which is known to be NP-hard on its own. While there exists several individual efforts across the community to research automatic techniques for managing power and energy better, the majority of these techniques have been specialized to meet the needs of a specific HPC center or specific optimization goals and provide little support to connect them to each other. Some projects, most notably the PowerAPI efforts [1], discuss interfaces that form a good starting point for full stack integration, but these interfaces still need to be hooked up to the wide range of software components offered by academic partners, developers or vendors. Furthermore, a recent survey conducted by the EE HPC WG concluded that the majority of such techniques have lacked the application-awareness required to achieve the best system performance and throughput. Other observations were that each technique tended to target management of power and energy for a different subset of the site or system hardware and that the different techniques tended to perform management at different (and often conflicting) granularities. Unfortunately, the existing techniques have not been designed to coexist simultaneously on one site and cooperate on management in an integrated manner [2]. The lack of application-awareness, lack of coordinated management across different granularities, and the lack of widely accepted interfaces and consequent limited connectivity between modules, can result in substantially underutilized Watts and FLOPS. To address these gaps, the HPC community needs a holistic stack for power and energy management and none currently exists. In our view, a holistic stack is one that is extensible enough to support the present and anticipated future needs of various different HPC centers, one that achieves best system performance and throughput through application-awareness, one that is designed to coordinate management at different granularities, and one that enables the seamless integration of software components from different developers and vendors. In this seminar, our goal is bring together experts from academia, research laboratories, and industry in order to take stock of existing approaches, design points and power management concepts and requirements at the various participant’s institutions, and to design concepts for a holistic power and energy management stack, which we refer to as the HPC PowerStack. Further, we hope to take steps toward defining the interfaces necessary for providing a complete prototype shared among many groups. The intention is to align development and research efforts across the community so that we may share development resources, avoid duplicating effort, agree on common interfaces and reap the rewards together as a community. The intended final outcome of this collaboration will be a holistic, flexible and extensible concept of a software stack ecosystem that allows us to combine product-grade open-source software components to enable runtime optimization of system power, energy, and performance.

97 MATHEMATICS AND COMPUTING↗

Domain specific software design for decision aiding

McDonnell Aircraft Company (MCAIR) is involved in many large multi-discipline design and development efforts of tactical aircraft. These involve a number of design disciplines that must be coordinated to produce an integrated design and a successful product. Our interpretation of a domain specific software design (DSSD) is that of a representation or framework that is specialized to support a limited problem domain. A DSSD is an abstract software design that is shaped by the problem characteristics. This parallels the theme of object-oriented analysis and design of letting the problem model directly drive the design. The DSSD concept extends the notion of software reusability to include representations or frameworks. It supports the entire software life cycle and specifically leads to improved prototyping capability, supports system integration, and promotes reuse of software designs and supporting frameworks. The example presented in this paper is the task network architecture or design which was developed for the MCAIR Pilot's Associate program. The task network concept supported both module development and system integration within the domain of operator decision aiding. It is presented as an instance where a software design exhibited many of the attributes associated with DSSD concept.

Keller, Kirby↗

SEPAC software configuration control plan and procedures, revision 1

SEPAC Software Configuration Control Plan and Procedures are presented. The objective of the software configuration control is to establish the process for maintaining configuration control of the SEPAC software beginning with the baselining of SEPAC Flight Software Version 1 and encompass the integration and verification tests through Spacelab Level IV Integration. They are designed to provide a simplified but complete configuration control process. The intent is to require a minimum amount of paperwork but provide total traceability of SEPAC software.

Source record↗

A Data Exchange Interface for a Standards Based Data Integration Platform

The modern electrical grid is a complex and a data rich system, requiring several sub-systems to provide the capability and support needed to perform functions such as distributed energy resource management, outage management, and fault location and isolation, to name a few. There is a need to develop software solutions and platforms that provide an integrated infrastructure to allow interoperability between these subsystems, while leveraging the abundant data available from today’s grid. In this paper, we present the development and deployment of an application service to integrate GridAPPS-D which is an open source, standards-based software platform with SurvalentONE, a commonly used DNP3 based ADMS platform that allows operation, monitoring, analysis, restoration, and optimization of network operations. We present details of the integration architecture, including its implementation, and provide results from functional testing of the architecture on a 13 bus IEEE system. The results validate that the integration is successful and is able to provide a two-way exchange of communication and translation between different communication protocols.

Singh, Alka↗

Software modifications to the Demonstration Advanced Avionics Systems (DAAS)

Critical information required for the design of integrated avionics suitable for generation aviation is applied towards software modifications for the Demonstration Advanced Avionics System (DAAS). The program emphasizes the use of data busing, distributed microprocessors, shared electronic displays and data entry devices, and improved functional capability. A demonstration advanced avionics system (DAAS) is designed, built, and flight tested in a Cessna 402, twin engine, general aviation aircraft. Software modifications are made to DAAS at Ames concurrent with the flight test program. The changes are the result of the experience obtained with the system at Ames, and the comments of the pilots who evaluated the system.

Nedell, B. F.↗

A Scalable Software Architecture Booting and Configuring Nodes in the Whitney Commodity Computing Testbed

The Whitney project is integrating commodity off-the-shelf PC hardware and software technology to build a parallel supercomputer with hundreds to thousands of nodes. To build such a system, one must have a scalable software model, and the installation and maintenance of the system software must be completely automated. We describe the design of an architecture for booting, installing, and configuring nodes in such a system with particular consideration given to scalability and ease of maintenance. This system has been implemented on a 40-node prototype of Whitney and is to be used on the 500 processor Whitney system to be built in 1998.

Fineberg, Samuel A.↗

Development of an Integrated Rocket Thrust Chamber Assembly Analysis and Design Toolkit (TCAT)

There are many individual computational tools and methods used to analyze and design components of a rocket engine thrust chamber assembly (TCA) 11,21. To analyze and design a thrust chamber assembly these tools are usually used in sequence while communication of information between these tools is usually done manually. Each component of a TCA is usually designed and optimized individually with limited considerations on system optimized design. This approach is often iterative and can be prone to error. Also at present, expert knowledge of each tool is required. The objective of this software development effort is to select, integrate and automate the best tools into an easy-to-use computational package, the Thrust Chamber Analysis Toolkit (TCAT). This tool will provide a seamless process to analyze and design all or individual components of a thrust chamber assembly. This paper describes the current status of the MAT software development. The selected component codes and their capabilities are briefly described. User and module interfaces and integration status are presented. MAT pre- and post-processing added options are presented and overall MAT capabilities are demonstrated with the results of sample cases. Ongoing and planned model validation efforts are also described. Finally, the MAT future plan options are discussed.

Farhangi, S.↗

Guidance, Navigation, and Control Program

The Rendezvous and Proximity Operations Program (RPOP) is real-time guidance, navigation, and control (GN&C) domain piloting-aid software that provides 3D Orbiter graphics and runs on the Space Shuttle's Criticality-3 Payload and General Support Computer (PGSC) in the crew cockpit. This software provides the crew with Situational Awareness during the rendezvous and proximity operations phases of flight. RPOP can be configured from flight to flight, accounting for mission-specific flight scenarios and target vehicles, via initialization load (I-load) data files. The software provides real-time, automated, closed-loop guidance recommendations and the capability to integrate the crew s manual backup techniques. The software can bring all relative navigation sensor data, including the Orbiter's GPC (general purpose computer) data, into one central application to provide comprehensive situational awareness of the rendezvous and proximity operations trajectory. RPOP also can separately maintain trajectory estimates (past, current, and predicted) based on certain data types and co-plot them, in order to show how the various navigation solutions compare. RPOP s best estimate of the relative trajectory is determined by a relative Kalman filter processing data provided by the sensor suite s most accurate sensor, the trajectory control sensor (TCS). Integrated with the Kalman filter is an algorithm that identifies the reflector that the TCS is tracking. Because RPOP runs on PC laptop computers, the development and certification lifecycles are more agile, flexible, and cheaper than those that govern the Orbiter FSW (flight software) that runs in the GPC. New releases of RPOP can be turned around on a 3- to 6-month template, from new Change Request (CR) to certification, depending on the complexity of the changes.

Hinkel, Heather↗

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗

The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix

Abstract Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo‐electron microscopy data. The Phenix software suite has AlphaFold predictions integrated into an automated pipeline that can start with an amino acid sequence and data, and automatically perform model‐building and refinement to return a protein model fitted into the data. Due to the steep technical requirements of running AlphaFold efficiently, we have implemented a Phenix‐AlphaFold webservice that enables all Phenix users to run AlphaFold predictions remotely from the Phenix GUI starting with the official 1.21 release. This webservice will be improved based on how it is used by the research community and the future research directions for Phenix.

Poon, Billy K.↗