pyRS: a user-friendly package for the reduction and analysis of neutron diffraction data measured at
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Fancher, Chris M.↗
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On the memory attribution problem: A solution and case study using MPI
As parallel applications running on large–scale computing systems become increasingly memory constrained, the ability to attribute memory usage to the various components of the application is becoming increasingly important. We present the design and implementation of memnesia, a novel memory usage profiler for parallel and distributed message–passing applications. Our approach captures both application– and message–passing library–specific memory usage statistics from unmodified binaries dynamically linked to a message–passing communication library. Using microbenchmarks and proxy applications, we evaluated our profiler across three Message Passing Interface (MPI) implementations and two hardware platforms. Furthermore, the results show that our approach and the corresponding implementation can accurately quantify memory resource usage as a function of time, scale, communication workload, and software or hardware system architecture, clearly distinguishing between application and MPI library memory usage at a per–process level. With this new capability, we show that job size, communication workload, and hardware/software architecture influence peak runtime memory usage. In practice, this tool provides a potentially valuable source of information for application developers seeking to measure and optimize memory usage.
97 MATHEMATICS AND COMPUTING↗
Turbo-Turtle v0.12.1
A collection of solid body modeling tools for 2D sketched, 2D axisymmetric, and 3D revolved models. It also contains general purpose meshing and image generation utilities appropriate for any model, not just those created with this package. Implemented for Abaqus and Cubit as backend modeling and meshing software. Orginal implementation targeted Abaqus so most options and descriptions use Abaqus modeling concepts and language. Turbo-Turtle makes a best effort to maintain common behaviors and features across each third-party software’s modeling concepts. As much as possible, the work for each subcommand is performed in Python 3 to minimize solution approach duplication in third-party tools. The third-party scripting interface is only accessed when creating the final tool specific objects and output. The tools contained in this project can be expanded to drive other meshing utilities in the future, as needed by the user community. This project derives its name from the origins as a sphere partitioning utility following the turtle shell (or soccer ball) pattern.s.
Brindley, Kyle↗
CiteSoft_Py
There is a need to provide a way for dev-users (Scientists, Engineers, and other Software Developers) to get credit (citations) when they contribute to an important software package - particularly a large package that is already established. Various solutions (including cross package) solutions do exist, but a simple standard format that can work between multiple packages and multiple languages in a modular way is not widely available. CiteSoft_py is a python implementation of CiteSoft. CiteSoft is a plain text standard consisting of a format and a protocol that exports the citations for the end-users for whichever softwares they have used. CiteSoft has been designed so that software dev-users can rely upon it regardless of coding language or platform, and even for cases where multiple codes are working in a coupled manner. The CiteSoft_py implementation includes python decorators to make wrappers for facile use. The purpose is that when dev-users (scientists, engineers and professional programmers) contribute to a collaborative software project, that the appropriate citations (e.g., journal article, conference proceeding) are provided to the end-user. The end-user does not need to know how to use a command line interface, API, etc.
Savara, Aditya↗
Interactive Web Application for Traffic Simulation Data Management and Visualization
As traffic simulation software becomes more effective for realistically simulating and analyzing traffic dynamics and vehicle interactions on the mesoscopic and microscopic level, the management, dissemination, and collaborative visualization of traffic simulation results produced by individual transportation planners presents a significant challenge. Existing online content management systems have a very limited capability in allowing users to query specific traffic simulation scenarios and geospatially visualize simulation results through shareable and interactive web interfaces. This paper presents a web-based application for promoting the archiving, sharing, and visualization of large-scale traffic simulation outputs. The application is developed to enhance cyber-physical controls, communications, and public education for collaborative transportation planning. Unique features of the web application include: (a) allowing users to upload their new traffic simulation scenarios (parameters and outputs), as well as search existing scenarios using easily accessible interfaces; (b) optimizing simulation output files with heterogeneous data formats and projected coordinate systems for web-based storage and management using a scalable and searchable data/metadata standard; (c) standardizing user-uploaded simulation outputs using web interfaces and data processing libraries with parallel computing capacity; and (d) providing shareable web visual interfaces for visualizing the traffic flow and signal information stored in simulation outputs (e.g., regional traffic patterns and individual vehicle interactions) and visually comparing multiple simulation outputs both spatially and temporally. Furthermore, the paper presents the conceptual design and implementation of this application, and demonstrates the application’s performance for sharing, comparing, and visualizing simulation outputs from VISSIM and SUMO, two commonly used traffic simulation software programs.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
On a Simplified Approach to Achieve Parallel Performance and Portability Across CPU and GPU Architectures
This paper presents software advances to easily exploit computer architectures consisting of a multi-core CPU and CPU+GPU to accelerate diverse types of high-performance computing (HPC) applications using a single code implementation. The paper describes and demonstrates the performance of the open-source C++ matrix and array (MATAR) library that uniquely offers: (1) a straightforward syntax for programming productivity, (2) usable data structures for data-oriented programming (DOP) for performance, and (3) a simple interface to the open-source C++ Kokkos library for portability and memory management across CPUs and GPUs. The portability across architectures with a single code implementation is achieved by automatically switching between diverse fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. The MATAR library solves many longstanding challenges associated with easily writing software that can run in parallel on any computer architecture. This work benefits projects seeking to write new C++ codes while also addressing the challenges of quickly making existing Fortran codes performant and portable over modern computer architectures with minimal syntactical changes from Fortran to C++. We demonstrate the feasibility of readily writing new C++ codes and modernizing existing codes with MATAR to be performant, parallel, and portable across diverse computer architectures.
97 MATHEMATICS AND COMPUTING↗
Symmetry-mode analysis for local structure investigations using pair distribution function data
Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.
36 MATERIALS SCIENCE↗
Improving Frequency Stability and Minimizing Load Shedding Events by Adopting Grid-Scale Energy Storage with Grid Forming Inverters
The upward adoption trend of renewable generation not only means cleaner energy integrated into modern power grids, but also that most new generation sources are based on front-end inverter bridges, used as interfaces to most wind generation and all the solar PV. It is well known that due to their power electronics-based construction rather than rotational shafts, these sources do not provide inertia inherently, nor substantial amounts of short-circuit currents. However, stable energy such as what can be stored in energy storage systems, although interfaced via inverters, can be controlled to respond to system disturbances in a manner that emulates inertial behavior. This paper focuses on the application of such energy storage systems to augment inertia in the island of Puerto Rico. To do so, a user defined inverter model that contains grid forming capabilities and fast frequency response is modeled and integrated into the real transmission system in power flow and dynamics software. Energy storage is then connected to two selected areas so that it not only provides frequency regulation to avoid widespread load shedding events, but also other tangible benefits. The simulated cases suggest that even relatively small energy storage systems can avert load shedding events if adequately placed in the transmission network.
Grid-forming inverters, IBR, Inertia↗
Software-Defined Network for End-to-end Networked Science at the Exascale
Domain science applications and workflow processes are currently forced to view the network as an opaque infrastructure into which they inject data and hope that it emerges at the destination with an acceptable Quality of Experience. There is little ability for applications to interact with the network to exchange information, negotiate performance parameters, discover expected performance metrics, or receive status/troubleshooting information in real time. The work we presen here is motivated by a vision for a new smart network and smart application ecosystem that will provide a more deterministic and interactive environment for domain science workflows. The Software-Defined Network for End-to-end Networked Science at Exascale (SENSE) system includes a model-based architecture, implementation, and deployment which enables automated end-to-end network service instantiation across administrative domains. An intent based interface allows applications to express their high-level service requirements, an intelligent orchestrator and resource control systems allow for custom tailoring of scalability and real-time responsiveness based on individual application and infrastructure operator requirements. This allows the science applications to manage the network as a first-class schedulable resource as is the current practice for instruments, compute, and storage systems. Deployment and experiments on production networks and testbeds have validated SENSE functions and performance. Emulation based testing verified the scalability needed to support research and education infrastructures. Key contributions of this work include an architecture definition, reference implementation, and deployment. This provides the basis for further innovation of smart network services to accelerate scientific discovery in the era of big data, cloud computing, machine learning and artificial intelligence.
97 MATHEMATICS AND COMPUTING↗
Production Operations Management System
The Production Operations Management System (POMS) is a set of software tools which allows production teams and analysis groups across multiple Fermilab experiments to launch, modify and monitor large scale campaigns of related Monte Carlo or data processing jobs. POMS provides a web service interface that enables automated jobs submission on distributed resources according to customers’ requests and subsequent monitoring and recovery of failed submissions, debugging and record keeping. POMS interfaces with existing HEP data access, processing, movement and monitoring tools at Fermilab, including Jobsub, dCache, SAM, and FIFEmon, and in combination with them handles the creation and tracking of unique filenames for multistage campaigns. A flexible, interactive GUI interface exists as part of the system to visualize campaign stages, parallelization tracks and data flow. An important feature of POMS is a one-to-one connection between the GUI campaign visualizer and a text based representation of the complete campaign configuration. An extensible library of template campaign configurations is available. The templates are user modifiable and map cleanly to and from the GUI description of the campaign. Future releases of POMS will interface with Rucio for file movement.
97 MATHEMATICS AND COMPUTING↗
JUSTIFI: Open-Source Software for Identifying and Quantifying Non-Energy Benefits
The integration of Non-Energy Benefits (NEBs) into energy efficiency initiatives is essential for operational excellence in manufacturing. This presentation and software demonstration explore how quantifying NEBs such as improved safety, increased quality, and enhanced productivity, can strengthen business cases for energy investments, leading to better payback periods and alignment with organizational goals. We introduce JUSTIFI, a free, open-source software by the U.S. Department of Energy that aids in the measurement of NEBs and enhances understanding of their impact on Key Performance Indicators (KPIs) and return on investment (ROI). JUSTIFI features an intuitive interface for identifying NEBs, customizable reporting tools, and comprehensive system cataloging, empowering companies to effectively communicate the value of energy efficiency projects. By leveraging this innovative tool, organizations can better navigate energy efficiency assessments and drive support for their energy management initiatives.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Optimization of prefabricated component installation using a real-time evaluator (RTE) connection locating system
Prefabrication promises to industrialize the construction industry. By constructing elements within a manufacturing environment, producers can better control quality and maximize production efficiency. Since the major adoption of prefabrication, a wide variety of prefabricated components have been produced for varying applications such as new construction and exterior wall retrofits. While the production processes of these prefabricated components have seen much innovation, the installation process has remained relatively unchanged for decades. To innovate the installation process with modern technologies, a real-time evaluator (RTE) has been developed to reduce the installation cost of prefabricated components by reducing installation time, decreasing rework, and improving accuracy. The RTE uses developed software solutions with off-the-shelf hardware to assist erectors in completing an installation by measuring the real-time positions of connections and prefabricated components, providing installation guidance through a graphical user interface, and monitoring the accumulated installation errors. An overview of the RTE and proposed workflow is presented. A connection locating system that guides users in expediting the installation of connections is introduced. Laboratory experiments were conducted to determine the accuracy improvement and time savings of the RTE in installing connections for prefabricated components. RTE enabled a time saving of up to 37% compared to traditional connection installation methods using handheld measurement tools.
Hayes, Nolan↗
New controller for high voltage converter modulator at spallation neutron source
The Spallation Neutron Source (SNS) has developed a new control system for the High Voltage Convertor Modulator (HVCM) at the SNS to replace the original control system which is approaching obsolescence. The original system was based on controllers for similar high voltage systems that were already in use [1]. The new controller, based on National Instruments PXI/FlexRIO Field Programmable Gate Array (FPGA) platform, offers enhancements such as modular construction, flexibility and non-proprietary software. The new controller also provides new capabilities like various methods for modulator pulse flattening, waveform capture, and first fault detection. This paper will discuss the design of the system, including the human machine interface, based on lessons learned at the SNS and other projects. It will also discuss performance and other issues related to its operation in an accelerator facility which requires high availability. To date, 73% of the operational HVCMs have been upgraded to with the new controller, and the remainder are scheduled for completion by mid-2017.
Wezensky, Mark W↗
Continuous Test and Transition Infrastructure for Quantum Networking for Science Complex
We propose a network architecture with a separate quantum dataplane and a conventional control plane: (a) Quantum Data Plane: The Quantum Data plane consists of links of dark fibers connecting quantum switches and repeaters, which in turn, connect to quantum computers, memory and sensors. Since the current reach is limited to local areas, it will begin as a collection of site networks at laboratories, (b) Conventional Control Plane: The Control plane provides management access to quantum devices for configuration and provisioning via control nodes with firewall and encryption capabilities. Continuous Test and Transition Infrastructure: We propose an infrastructure with a control plane connecting multiple sites via encrypted tunnels over conventional networks consisting of the following: (a) Site Quantum Networks: Individual site networks supported by their fiber plants connect laboratories that house and connect to their quantum devices for testing and interoperability.(b) Site Control Planes: Sites are connected over individual control planes with control hosts with Software Defined Networking capabilities, which can be peered with other networks via ESnet.(c) Progressive Expansion: Initially, sites will develop individual data planes with their specific quantum devices and fiber connections, and mechanisms to interface with conventional networks. They progressively expand and interconnect, under a wide-area ecosystem of peered control planes for device testing, interoperability development and roll off into production environments.
Rao, Nageswara S.↗
Software-defined network for end-to-end networked science at the exascale
Domain science applications and workflow processes are currently forced to view the network as an opaque infrastructure into which they inject data and hope that it emerges at the destination with an acceptable Quality of Experience. There is little ability for applications to interact with the network to exchange information, negotiate performance parameters, discover expected performance metrics, or receive status/troubleshooting information in real time. The work presented here is motivated by a vision for a new smart network and smart application ecosystem that will provide a more deterministic and interactive environment for domain science workflows. The Software-Defined Network for End-to-end Networked Science at Exascale (SENSE) system includes a model-based architecture, implementation, and deployment which enables automated end- to-end network service instantiation across administrative domains. An intent based interface allows applications to express their high-level service requirements, an intelligent orchestrator and resource control systems allow for custom tailoring of scalability and real-time responsiveness based on individual application and infrastructure operator requirements. This allows the science applications to manage the network as a first-class schedulable resource as is the current practice for instruments, compute, and storage systems. Deployment and experiments on production networks and testbeds have validated SENSE functions and performance. Emulation based testing verified the scalability needed to support research and education infrastructures. Key contributions of this work include an architecture definition, reference implementation, and deployment. This provides the basis for further innovation of smart network services to accelerate scientific discovery in the era of big data, cloud computing, machine learning and artificial intelligence.
47 OTHER INSTRUMENTATION↗
Automation of Nanoparticle Synthesis Processes in a Plasma Environment Using LabVIEW
This work presents an automated control system for the synthesis of nanomaterials by plasma-enhanced chemical vapor deposition (PECVD), implemented using the LabVIEW software environment. The main objective of the study is to develop an integrated hardware-software platform that enables sequential control of the key stages of the PECVD process, including vacuum chamber preparation, pressure monitoring, working gas supply, plasma ignition, power matching, cyclic nanomaterial growth, and optical monitoring of nanoparticles in the plasma environment. The use of LabVIEW made it possible to integrate actuator control, experimental parameter acquisition, and realtime process visualization within a single automated system. The automated cycle begins with evacuation of the reaction chamber to a predefined base pressure. Transition to the next stage is permitted only after the specified pressure threshold has been reached, ensuring reproducible initial conditions for each experiment. The program then controls the supply of the working gas through mass flow controllers (MFCs). In this work, two gas-flow control modes were considered: analog control using a 0-5 V voltage signal and digital communication via RS-232 interface. It was shown that the analog approach requires accurate scaling of the control voltage, since applying 5 V corresponds to full-scale opening of the controller and results in the maximum gas flow. In contrast, the RS232 interface enables the gas flow rate to be specified directly in sccm, improving the accuracy, flexibility, and convenience of gas-environment control. After pressure stabilization, LabVIEW initiates RF plasma ignition and executes the RF matching algorithm aimed at minimizing reflected power and improving the stability of the plasma process. A separate software module implements the cyclic nanomaterial growth mode, in which the plasma-on time, plasma duration, and total number of synthesis cycles are predefined. This approach makes it possible to control material accumulation on the substrate and to correlate the process parameters with the morphological characteristics of the resulting nanostructures. The final module of the system is designed for optical monitoring of the nanoparticle cloud density in dusty plasma. For this purpose, the change in the intensity of laser radiation passing through the plasma region is recorded using a photodetector and a Keithley 2401 measuring unit connected to LabVIEW via RS-232 interface. The difference between the initial and modified optical signal intensity is used as a diagnostic parameter characterizing the formation and temporal evolution of nanoparticles. The developed system demonstrates that LabVIEW can be effectively applied not only for the automation of individual instruments, but also for the implementation of a complete digital control cycle for PECVD-based nanomaterial synthesis.
PECVD↗
H2Fills™ [SWR-19-67]
H2FillS: Hydrogen Filling Simulation The Hydrogen Filling Simulation (H2FillS) software is a thermodynamic model designed to track and report on the transient change in hydrogen temperature, pressure, and mass flow when filling a fuel cell electric vehicle (FCEV). H2FillS simulates gas flow from the hydrogen station to the FCEV storage system. Using empirical fueling data sets, the model has been validated over a range of fueling conditions to match common light-duty FCEV fill profiles. Overall, it provides significant benefits to the light-duty fueling market and fill knowledge gaps of the interaction between a hydrogen station and an FCEV. Capabilities Use the comprehensive H2FillS model to: Safely design and operate a hydrogen fueling station Support code refinement with readily available data Develop system and operational improvements to reduce capital or operating costs at hydrogen stations or on-board FCEVs. How It Works H2FillS uses a "drag-and-drop" graphical user interface to simulate station and vehicle systems with preset parameters for common hydrogen station components as default values. When needed, users can define their own parameters to create their own station or vehicle components. Download H2FillS in Two Steps Read the terms of the end user software license agreement. Register to download the software. There are two versions of the model: A full-station model starts the simulation at high-pressure ground storage, runs through a dispenser, and ends at a vehicle storage system. A partial-station model starts at the dispenser breakaway and consists solely of the dispenser components and the vehicle storage system. H2FillS will automatically output fill performance data from the vehicle by tracking pressure and temperature throughout the fill. Users can input their own fill profiles into the model to run a variety of simulations.
Peters, Michael↗
Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases
Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.
59 BASIC BIOLOGICAL SCIENCES↗