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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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DOE OSTI2020

Multi-genome Phage Annotation Toolkit and Evaluator

Summary: To address the need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of the multiPhATE code, multiPhATE2 includes comparative genomics codes for gene matching among sets of input bacteriophage genomes, and scales well to large input data sets due to incorporation of multiprocessing in the functional annotation and comparative genomics subsystems. Furthermore, additional search algorithms and databases have been added to the functional annotation subsystem. MultiPhATE2 was implemented in Python 3.7, and runs as a command-line code under Linux or MAC-OS.

Kimbrel, JeffreyA.↗

DOE OSTI2022

MEASUR - Manufacturing Energy Assessment Software for Utility Reduction

MEASUR your energy savings with the free DOE MEASUR software The Department of Energy (DOE), with Oak Ridge National Laboratory (ORNL), released version 1.0 of their energy efficiency software tool MEASUR (Manufacturing Energy Assessment Software for Utility Reduction). MEASUR has been available for several years as a beta version, being tested by industry experts and real users, and will continue to be updated and improved in the coming years. It is an integrated suite of tools to aid manufacturers in improving the efficiency of energy systems and equipment within a plant, including motors, pumps, fans, process heating, steam, and compressed air. Additionally, there are modules for wastewater energy analysis and to help perform energy treasure hunts. Several calculators are also included, allowing users to independently perform smaller calculations and analyses (such as estimating pump head, performing a fan traverse analysis, estimating waste heat recovery potential, and cataloging compressed air leaks). The MEASUR modules are based on previous DOE software tools that have been used by industry since the early 2000s (such as MotorMaster, AirMaster+, PSAT, PHAST, and FSAT). The original tools only ran on Windows operating systems, and by Windows 10, most of them were inoperable. DOE started their energy efficiency software tool revitalization effort in 2016, first with PSAT (for pumps), then began to integrate the other tools and expand their functionality and utility. The new MEASUR suite provides an extensively more user-friendly, modern, and versatile set of tools. All the assessment modules and most of the calculators have several visual components and graphs and detailed help text for every user input. To help reach international users, the tool utilizes Google translate and users can easily change unit systems, even converting existing user inputs if desired. The assessment files can be organized within the internal file system and easily shared to other users, regardless of their operating system. The entire suite is free, open-source, and can be downloaded on Windows, Mac, or Linux operating systems.

Accawi, Gina [Oak Ridge National Lab. (ORNL), Oak ↗

DOE OSTI2022

ornladios/ADIOS2

ADIOS 2: The Adaptable Input Output (I/O) System version 2 is an open-source framework that addresses scientific data management challenges, e.g. scalable parallel I/O, as we approach the exascale era in high-performance computing (HPC). ADIOS 2 bindings are available in C++, C, Fortran, Python and can be used on supercomputers, personal computers, and cloud systems running on Linux, macOS and Windows. ADIOS 2 has out-of-the-box support for MPI and serial environments.

ECP↗

DOE OSTI2022

LLNL/cyme-launcher

Utility to help run CYME in an HPC environment. Ensures sufficient licenses are available for running CYME in as part of a batch job, and helps start CYME running under WINE on Linux.

Mast, Ryan [Lawrence Livermore National Lab. (LLNL↗

DOE OSTI2022

BESTEST-GSR (Building Energy Simulation Test - Generation Simulation and Reporting) 2023 [SWR 18-23]

Building Energy Simulation Test (BESTEST) is an NREL-developed method to validate the qualitative performance of different whole building simulations engines relative to each other. https://www.nrel.gov/docs/legosti/old/6231.pdf The purpose of this repository is to generate BESTEST test case models, run simulations, and populate data for ASHRAE Standard 140 reporting spreadsheets for EnergyPlus® based whole building simulation tools. It was originally setup for 2014 version of Standard 140. In May of 2022 it was updated to the 2020 version of Standard 140. This update included updates and additions to existing test suites, the bulk of which was in Section 5.2 (Building Thermal Envelope and Fabric Load Tests). We did not add Section 5.5 Airside HVAC Equipment Performance, but we hope to add that later in 2022. At some point we also hope to add Section 5.2.4 ground modeling, which is currently excluded. Supported Tools The default IDF generation is based on the OpenStudio® CLI, but the workflow supports a 'Bring your own IDF' use case. Additionally, for non-EnergyPlus® based tools the post processing scripts can be used if simulation results are provided as a CSV file.The scripts on this repository should work on Mac, Windows, and Linux. Dependencies Install OpenStudio® 3.4.0 make sure command line can recognize the 'openstudio' command This includes EnergyPlus® 22.1 Install Ruby on your system if it isn't already setup. 2.7 is used for development but other versions may work Since OpenStudio has its own embedded Ruby, which is used for running measures, you don't necessarily have to use a version of Ruby supported by OpenStudio. Install RubyXL Ruby gem This is used to modify Microsoft Excel spreadsheets Install Parallel Ruby gem This allows the CLI to run simulations in parallel

Goldwasser, David↗

DOE OSTI2023

HoneProject/Linux-Sensor

Correlate packets to the responsible processes in Linux systems. Diagnose connections by adding process information.

Griswold, Richard↗

DOE OSTI2023

HONE Sensor Wireshark Shim

The Hone sensors are packet-process correlation engines that log the relationships between applications and the communications they are responsible for. Hone sensors are available for a variety of platforms including Linux, Windows, and MacOSX

Fink, Glenn↗

DOE OSTI2024

spot_bt v.0.1.1

SAND2024-08430O spot_bt allows users to easily construct complex, autonomous behaviors without having to overly rely on Boston Dynamic’s Spot robot software development kit. Using a form-of-state machine called a "behavior tree," the software develops and applies different "leaves" or actions to the robot. Attaching multiple actions in sequence creates a "branch," and a series of these make up the "tree." The software works on any x86 or aarch64 hardware but must run on a Linux OS. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525

Kakish, Zahi↗

DOE OSTI2025

Accessible Content Optimization for Research Needs (ACORN)

ACORN employs a set of automated processes for informing and/or enforcing defined content schemas to create standardized and highly structured data. Because of its standardized data source, ACORN easily applies computer automation to generate communication assets such as PDFs, Powerpoint presentations, and web pages. Built using the memory-safe Rust programming language, ACORN is portable and accessible for use on any Windows, Mac, or Linux machine.

Wohlgemuth, JasonHoward [Oak Ridge National Labora↗

DOE OSTI2025

t9p

A lightweight 9P2000.L client and file system driver for RTEMS and Linux. t9p is designed to operate on performance constrained systems with as little as 16MB of memory and a single core.

Lorelli, Jeremy [SLAC National Accelerator Laborat↗

DOE OSTI2023

SALSA_python (SALSython) v1

SALSA_python (Semi-Analytical Leakage Solutions for Aquifers) is a software that computed semi-analytical solutions for hydraulic head and brine leakage in multilayered aquifer–aquitard systems with geologic pressure forcing. It can simulate brine leakage into aquifers in a multi-aquifer-aquitard system with multiple injection and leaky wells. This situation is encountered in underground CO2 storage wherein brine leakage from pressurized reservoirs into aquifers is of concern. SALSA_python calls the original SALSA[1] subroutines in python by using the salsa2.so library. This enables the incorporation and coupling of SALSA computations into existing python-based codes and tools. SALSA_python is available for Linux and Mac operating systems. [1] Cihan, A., Oldenburg, C. M., & Birkholzer, J. T. (2022). Leakage from coexisting geologic forcing and injection-induced pressurization: A semi-analytical solution for multilayered aquifers with multiple wells. Water Resources Research, 58, e2022WR032343.

Bhuvankar, Pramod↗

DOE OSTI2025

pseudopod

Pseudopod is a software tool that makes it easier and safer to build and run Linux containers without needing additional system privileges. It is designed to work with the open-soruce Podman container runtime. Pseudopod also provides and implements small library named libpseudo that provides the core functionality for tracking and emulating identity related system calls with low performance overhead. This allows complex tools, such as package managers and build systems, to run in a familiar way within a container while preserving the security of the host system and networks.

Green, ElenaN [Lawrence Livermore National Laborat↗

DOE OSTI2022

areaDetector/ADTimePix3

ADTimePix3 is an open‑source EPICS areaDetector driver for TimePix3 pixel detectors from Advanced Scientific Instruments (ASI). It provides a complete control and data‑acquisition interface between EPICS and the Serval server, supporting both real detectors (single‑chip and 2×2 quad configurations) and the TimePix3 emulator. The driver configures measurements via an HTTP/JSON REST API and acquires data through high‑rate TCP streams for raw events, images, and histograms. It offers real‑time preview and accumulated images, Time‑of‑Flight histogram processing, pixel masking (including Binary Pixel Configuration files and hot‑pixel tools), extensive health and status monitoring, and integration with standard areaDetector plugins for file saving and downstream analysis. ADTimePix3 is designed for Linux 64‑bit systems (tested on Ubuntu and RHEL) and is distributed under an MIT license with additional institutional disclaimers, enabling reuse and extension in photon science beamlines and other TimePix3‑based experimental facilities.

Gofron, Kaz↗

DOE OSTI2026

static-subid: Deterministic subordinate UID/GID assignment for unprivileged containers

static-subid calculates predictable subordinate UID and GID ranges for Linux users based on their UID, ensuring consistent ID mappings across multiple systems. Unlike shadow-utils' sequential allocation (which depends on creation order), static-subid uses a deterministic formula that guarantees the same user UID always receives the same subordinate ID range. Subordinate IDs enable user namespaces for unprivileged container runtimes (Podman, Docker rootless mode, LXC) by mapping container UIDs/GIDs to host subordinate IDs without requiring root privileges.

Riehecky, Pat [Fermi National Accelerator Laborato↗

DOE OSTI2026

Scientific Core Library Stack (SCLS) v2026

SCLS (Scientific Core Library Stack) is an opinionated build and packaging system for scientific computing libraries developed at Lawrence Berkeley National Laboratory. It produces a coherent, reproducible stack of numerical libraries — including BLAS/LAPACK, MPI, sparse direct and iterative solvers, graph partitioners, and parallel I/O libraries (e.g., PETSc, SLEPc, HDF5, NetCDF, MUMPS, OpenBLAS) — that work together without manual repair by downstream scientific software. From a single recipe-and-flavor model, SCLS produces native RPM packages for RHEL-family Linux, DEB packages for Debian/Ubuntu, direct Unix-style prefix installs for HPC and locked-down environments, and native macOS builds. Multiple build "flavors" (e.g., GCC+OpenBLAS, GCC+MKL, Intel+MKL, debug) coexist in distinct prefixes on the same host. Compared to general-purpose meta-build frameworks, SCLS is deliberately curated rather than infinitely configurable. It enforces deterministic, audit-friendly behavior: explicit build dependencies, no silent feature autodetection, a clear open-source license policy, and rpath-based runtime linkage so installs integrate cleanly with standard package-manager workflows.

Messe, Christian [Lawrence Berkeley National Labor↗

DOE OSTI2026

slac-epics/devLinuxAdc

EPICS device support for ADCs using the Linux industrial IO (IIO) subsystem

Lorelli, Jeremy [SLAC National Accelerator Laborat↗

DOE OSTI2024

UMap: An application-oriented user level memory mapping library

Exploiting the prominent role of complex memories in exascale node architecture, the UMap page fault handler offers new capabilities to access large memory-mapped data sets directly. UMap provides flexible configuration options to customize page handling to each application, including analysis of massive observational and simulation data sets. The high-performance design features I/O decoupling, dynamic load balancing, and application-level controls. Page faults triggered by application threads and processes accessing data mapped to a UMapp’ed region are handled via the Linux userfaultfd protocol, an asynchronous message-oriented kernel-user communication mechanism that avoids the context switch penalty of traditional signal fault handlers. UMap is fully open source. In this paper, we give an overview of the UMap library architecture, its extensible plugin architecture, and the use/performance of UMap in emerging heterogeneous memory hierarchies such as near-node Non-volatile Memory (NVM) and network attached memories. We highlight new capabilities in two pagefault management plugins, the NetworkStore and SparseStore. We demonstrate the integration between UMap and multiple ECP products including Caliper, Metall, ZFP, Mochi, and Ripples.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

59 BASIC BIOLOGICAL SCIENCES↗