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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

A software for managing chemical processes in a multi-user laboratory

Here, we report a software for logging chemical processes in a multi-user laboratory, which implements a work flow designed to reduce hazardous situations associated with the disposal of chemicals in incompatible waste containers. The software allows users to perform only those processes displayed in their list of authorized chemical processes and provides the location and label code of waste containers, among other useful information. The software has been used for six years in the cleanroom of the Center for Functional Nanomaterials at Brookhaven National Laboratory and has been an important factor for the excellent safety record of the Center.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Make safety awareness a priority: Use a login software in your research facility

We report on a facility login software, whose objective is to improve safety in multi-user research facilities. Its most important safety features are: 1) blocks users from entering the lab after being absent for more than a predetermined number of days; 2) gives users a random safety quiz question, which they need to answer satisfactorily in order to use the facility; 3) blocks unauthorized users from using the facility afterhours; and 4) displays the current users in the facility. Besides restricting access to unauthorized users, the software keeps users mindful of key safety concepts. In addition, integration of the software with a door controller system can convert it into an effective physical safety mechanism. Depending on DOE approval, the code may be available as open source.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

Development and performance evaluation of a novel γ-γ coincidence analysis software

Processing of large amounts of data from a γ-γ coincidence system is a practical challenge in trace-level radionuclide measurements. Given the benefits and growing number of multidimensional gamma spectrometers worldwide, this is a major restriction in wide-spread applicability of coincidence techniques. This study demonstrates a novel γ-γ coincidence analysis software developed at Pacific Northwest National Laboratory, USA. The software utilizes advanced search techniques and Python libraries to readily identify coincidence signatures in the large data. Further, using both synthetic and experimental data, the study uncovers various strategies/libraries employed during software’s development. This work aims to provide a reference document in handling large data routinely encountered in trace-level measurements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

Traleika Glacier: A hardware-software co-designed approach to exascale computing

The move from current petascale machines to future exascale machines will need both hardware improvements and software changes. Hardware will need to evolve to focus primarily on features that lower energy consumption: near-threshold voltage operation, fine-grained power and clock management and heterogeneity. Software will also need to evolve and be able to express more parallelism, become more dynamic and adaptable in order to be able to operate on a much more variable hardware. Here, we present Traleika Glacier, an effort that seeks to evaluate radical design changes to meet the constraints, both in terms of power and cost, of exascale computing. The salient features of the hardware design presented in the work include a) a use of heterogeneous cores, b) a redesign of the memory system that centers around hierarchical scratchpads and a global address space, c) the hardware acceleration of certain memory and network operations through specialized engines and, d) very fine-grained control and monitoring capabilities. On the software side, we describe a task-based runtime system, the Open Community Runtime (OCR) which aims to express a wide range of higher-level programming models with a very limited set of core concepts: event-driven tasks for computation, events for synchronization and relocatable data-blocks for data management.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Protocol to detect dilution cycles in chemostat experiments and estimate growth rate slopes with linear modeling with R software chemostat_regression

Chemostat growth chambers measure optical density over time and require manual calculation of growth rates. Here, we present chemostat_regression, R software that enables users to automatically identify chemostat cycles and estimate growth rate using a linear regression approach. We describe steps for creating requisite software environment(s), formatting input data, executing the software via command line/RStudio/R-Shiny, interpreting results, assessing the validity of results, and modifying input parameters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Using geometric simulation software ‘GASP’ to model conformational flexibility in a family of zinc metal–organic frameworks

Here, a new tripodal tricarboxylic acid ligand, 4,4'-(4'-(4'-carboxy-[1,1'-biphenyl]-4-yl)-[2,2':6',2''-terpyridine]-5,5''-diyl)-dibenzoic acid (H 3 cbt ), was synthesised using a three-step convergent strategy. Subsequent reactions with zinc( II ) nitrate hexahydrate yielded three metal–organic frameworks (MOFs). The three MOFs, [Zn(H cbt )]·4DMF ( 1 ), [Zn(H cbt )]·4DMSO·1.5H 2 O·DMF ( 2 ), and [Zn(H cbt )]·2DMF·3H 2 O ( 3 ), each adopt flexible interdigitated 2D net topologies. Framework 1 has DMF-filled channels that retain porosity upon desolvation, with a measured BET surface area of 248 m 2 g -1 . Framework 2 possesses larger DMSO-containing channels that collapse upon desolvation, resulting in near-equivalent porosity values to framework 1 . In silico calculations and topological considerations determined using the geometric simulation software GASP dictate that framework 2 can feasibly alter conformation to approximate 1 , but cannot perfectly replicate the interdigitated motif. Framework 3 formed when wet solvents were used to synthesise 1 . Interestingly, the interdigitated structure of 3 contains a unique carboxylate binding mode that precludes its subsequent adoption by either 1 or 2 upon their exposure to water. This diverse array of structural considerations recommends this MOF family for modelling using GASP. Interrogating frameworks 1–3 using this software provided insights that justified experimentally observed conformational trends, as well as barriers to interconversion between members of this MOF family. In a broader sense, this work demonstrates the wider applicability of GASP software to modelling structural changes within flexible MOF materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

The Data Quality Monitoring Software for the CMS experiment at the LHC: past, present and future

The Data Quality Monitoring software is a central tool in the CMS experiment. It is used in the following key environments: (i) Online, for real-time detector monitoring; (ii) Offline, for the prompt-offline-feedback and final fine-grained data quality analysis and certification; (iii) Validation of all the reconstruction software production releases; (iv) Validation in Monte Carlo productions. Though the basic structure of the Run1 DQM system remains the same for Run2, between the Run1 and Run2 periods, the DQM system underwent substantial upgrades in many areas, not only to adapt to the surrounding infrastructure changes, but also to provide improvements to meet the growing needs of the collaboration with an emphasis on more sophisticated methods for evaluating data quality. We need to cope with the higher-energy and -luminosity proton-proton collision data, as well as the data from various special runs, such as Heavy Ion runs. In this contribution, we will describe the current DQM software, structure and workflow in the different environments. We then discuss the performance and our experiences with the DQM system in Run2. The main technical challenges which we have encountered and the solutions adopted during Run2 will also be discussed, including efficient use of memory in multithreading environments. Finally, we present the prospect of a future DQM upgrade with emphasis on functionality and long-term robustness for LHC Run3.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

EIC Software Overview

Development of the EIC project detector "ePIC" is now well underway and this includes the "single software stack" used for simulation and reconstruction. The stack combines several non-experiment-specific packages including ACTS, DD4hep, JANA2, and PODIO. The software stack aims to be forward looking in the era of AI/ML and heterogeneous hardware. A formal decision making process was implemented to choose the components that involved everyone in the collaboration that was interested. This talk will present an overview of the software stack currently used for development of the ePIC detector and on which we expect to execute the experiment.

Lawrence, David↗
DOE OSTI2024

Publication of the Belle II Software

The Belle II software was developed by a few hundred individual contributors over several years. Following the rising desire of making it publicly available, the collaboration established open source software policies and procedures. The political and technical challenges and their solutions at Belle II are discussed in this article. With the publication of the Belle II software, basf2, on GitHub and Zenodo in 2021 an important milestone towards open science was reached.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Using the ATLAS experiment software on heterogeneous resources

With the large dataset expected from 2030 onwards by the HL-LHC at CERN, the ATLAS experiment is reaching the limits of the current data processing model in terms of traditional CPU resources based on x86_64 architectures and an extensive program for software upgrades towards the HL-LHC has been set up. The ARM CPU architecture is becoming a competitive and energy efficient alternative. Accelerators like GPUs are available in any recent HPC. In the past years ATLAS has successfully ported its full data processing and simulation software framework Athena to ARM and has invested significant effort in porting parts of the reconstruction and simulation algorithms to GPUs. We report on the successful usage of the ATLAS experiment offline and online software framework Athena on ARM and GPUs through the PanDA workflow management system at various WLCG sites. Furthermore we report on performance optimizations of the builds for ARM CPUs and the GPU integration efforts. We will discuss performance comparisons of different ARM and x86_64 architectures on WLCG resources and Cloud compute providers like GCP and AWS using ATLAS productions workflows as used in the Hep-Score23 benchmark suite.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Tokamak-independent software analysis suite for multi-spectral line-polarization MSE diagnostics

A tokamak-independent analysis suite has been developed to process data from Motional Stark Effect (mse) diagnostics. The software supports multi-spectral line-polarization mse diagnostics which simultaneously measure emission at the mse σ and π lines as well as at two "background" wavelengths that are displaced from the mse spectrum by a few nanometers. This analysis accurately estimates the amplitude of partially polarized background light at the σ and π wavelengths even in situations where the background light changes rapidly in time and space, a distinct improvement over traditional "time-interpolation" background estimation. The signal amplitude at many frequencies is computed using a numerical-beat algorithm which allows the retardance of the mse photo-elastic modulators (pem's) to be monitored during routine operation. It also allows the use of summed intensities at multiple frequencies in the calculation of polarization direction, which increases the effective signal strength and reduces sensitivity to pem retardance drift. The software allows the polarization angles to be corrected for calibration drift using a system that illuminates the mse diagnostic with polarized light at four known polarization angles within ten seconds of a plasma discharge. As a result, the software suite is modular, parallelized, and portable to other facilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

A new Software Training Model at Belle II

The physics output of modern experimental HEP collaborations hinges not only on the quality of its software but also on the ability of the collaborators to make the best possible use of it. With the COVID-19 pandemic making in-person training impossible, the training paradigm at Belle II was shifted from periodic workshops towards guided self-study. To that end, the study material was rebuilt from scratch as a series of modular and hands-on lessons tightly integrated with the software documentation using Sphinx. Each lesson contains multiple exercises that are supplemented with hints and complete solutions. Rather than duplicating information, students are systematically taught to work with the technical reference documentation to find the important sections for themselves. Unit tests ensure that all examples work with different software versions, and feedback buttons make it easy to submit comments for improvements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

artdaq : DAQ software development made simple

For a few years now, the artdaq data acquisition software toolkit has provided numerous experiments with ready-to-use components which allow for rapid development and deployment of DAQ systems. Developed within the Fermilab Scientific Computing Division, artdaq provides data transfer, event building, run control, and event analysis functionality. This latter feature includes built-in support for the art event analysis framework, allowing experiments to run art modules for real-time filtering, compression, disk writing and online monitoring; as art, also developed at Fermilab, is also used for online analysis, a major advantage of artdaq is that it allows developers to easily switch between developing online and online software. artdaq continues to be improved. Support for an alternate mode of running whereby data from some subdetector components are only streamed if requested has been added; this option will reduce unnecessary DAQ throughput. Real-time reporting of DAQ metrics has been implemented, along with the flexibility to choose the format through which experiments receive the reports; these formats include the Ganglia, Graphite and syslog software packages, along with at ASCII files. Additionally, work has been performed investigating more flexible modes of online monitoring, including the capability of being able to run multiple online monitoring processes on different hosts, each running its own set of art modules. Finally, a web-based GUI interface through which users can configure details of their DAQ system has been implemented, increasing the ease of use of the system. Already successfully deployed on the LArIAT, DarkSide-50, DUNE 35ton and Mu2e experiments, artdaq will be employed for SBND and is a strong candidate for use on ICARUS and protoDUNE. With each experiment comes new ideas for how artdaq can be made more flexible and powerful; the above improvements will be described, along with potential ideas for the future.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

XACC: a system-level software infrastructure for heterogeneous quantum–classical computing

Quantum programming techniques and software have advanced significantly over the past five years, with a majority focusing on high-level language frameworks targeting remote REST library APIs. As quantum computing architectures advance and become more widely available, lower-level, system software infrastructures will be needed to enable tighter, co-processor programming and access models. In this work, we present XACC, a system-level software infrastructure for quantum–classical computing that promotes a service-oriented architecture to expose interfaces for core quantum programming, compilation, and execution tasks. Additionally, we detail XACC's interfaces, their interactions, and its implementation as a hardware-agnostic framework for both near-term and future quantum–classical architectures. We provide concrete examples demonstrating the utility of this framework with paradigmatic tasks. Our approach lays the foundation for the development of compilers, associated runtimes, and low-level system tools tightly integrating quantum and classical workflows.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein–protein interactions

Abstract Summary Batch yeast two-hybrid (Y2H) assays, leveraged with next-generation sequencing, have afforded successful innovations for the analysis of protein–protein interactions. NGPINT is a Conda-based software designed to process the millions of raw sequencing reads resulting from Y2H–next-generation interaction screens. Over time, increasing compatibility and dependency issues have prevented clean NGPINT installation and operation. A system-wide update was essential to continue effective use with its companion software, Y2H-SCORES. We present NGPINT V3, a containerized implementation built with both Singularity and Docker, allowing accessibility across virtually any operating system and computing environment. Availability and implementation This update includes streamlined dependencies and container images hosted on Sylabs (https://cloud.sylabs.io/library/schuyler/ngpint/ngpint) and Dockerhub (https://hub.docker.com/r/schuylerds/ngpint), facilitating easier adoption and integration into high-throughput and cloud-computing workflows. Full instructions and software can be also found in the GitHub repository https://github.com/Wiselab2/NGPINT_V3 and Zenodo https://doi.org/10.5281/zenodo.15256036.

Biochemistry & Molecular Biology↗
DOE OSTI2025

A Tale from the Trenches: Applying Metamorphic and Differential Testing to Bioinformatics Software

Metamorphic and differential testing have been proposed as best practices for testing software that is difficult to test, such as for programs in scientific domains. An assumption is that these approaches can be easily customized and applied to almost any domain. However, scientific software is often data-driven, and metamorphic relations may require significant domain knowledge to develop. In addition, tools are often written for ad-hoc experimentation by the scientists and often embed many assumptions about the importance and representation of different natural phenomena. In this paper, we present our experience applying both metamorphic and differential testing to a set of four computational biology tools that predict the growth of an organism. While our original goal was to evaluate these techniques to improve our system-level testing, we encountered multiple roadblocks along the way. Although we did find faults (some confirmed by developers), we also uncovered a set of challenges, including the considerable manual effort required for (a) defining domain-specific tests, (b) validating correctness, and (c) distinguishing between issues stemming from poor data and those arising from incorrect software.

Marsh, Alexis L [Iowa State University/Ames Labora↗
DOE OSTI2021

Virtual Framework for Development and Testing of Federation Software Stack

Softwarization of networked infrastructures combined with containerization of codes promises unprecedented computing capabilities distributed across the federations of computing systems and physical instruments. The development and testing of a software stack that implements these capabilities over an expensive physical production infrastructure is not cost-effective, and in the early stages, may potentially cause service disruptions. To address these aspects, we develop the Virtual Federated Science Instrument Environment (VFSIE), a digital twin of the physical infrastructure that emulates a multi-site federation. Each federated site is emulated using containers and virtual hosts that are connected over local-area networks, and the sites, in turn, are connected over an emulated wide-area network. We describe the framework design and implementation details. We also illustrate its application by emulating a federation of four laboratories that use Jupyter Notebook for computations and the EPICS software system for instrument control.

Al Najjar, Anees↗
DOE OSTI2023

Managing Software Provenance to Enhance Reproducibility in Computational Research

Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years, sustainable software development practices have made progress in being considered as an integral component of research. However, management of computation-based scientific studies is often left to individual researchers who design their computational experiments based on personal preferences and the nature of the study. Here, we believe that the quality, efficiency, and reproducibility of computation-based scientific research can be improved by explicitly creating an execution environment that allows researchers to provide a clear record of traceability. This is particularly relevant to complex computational studies in high-performance computing (HPC) environments. In this article, we review the documentation required to maintain a comprehensive record of HPC computational experiments for reproducibility. We also provide an overview of tools and practices that we have developed to perform such studies around Flash-X, a multiphysics scientific software.

97 MATHEMATICS AND COMPUTING↗