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Soft Real-Time PID Control on a VME Computer

microPID (uPID) is a computer program for real-time proportional + integral + derivative (PID) control of a translation stage in a Fourier-transform ultraviolet spectrometer. microPID implements a PID control loop over a position profile at sampling rate of 8 kHz (sampling period 125microseconds). The software runs in a strippeddown Linux operating system on a VersaModule Eurocard (VME) computer operating in real-time priority queue using an embedded controller, a 16-bit digital-to-analog converter (D/A) board, and a laser-positioning board (LPB). microPID consists of three main parts: (1) VME device-driver routines, (2) software that administers a custom protocol for serial communication with a control computer, and (3) a loop section that obtains the current position from an LPB-driver routine, calculates the ideal position from the profile, and calculates a new voltage command by use of an embedded PID routine all within each sampling period. The voltage command is sent to the D/A board to control the stage. microPID uses special kernel headers to obtain microsecond timing resolution. Inasmuch as microPID implements a single-threaded process and all other processes are disabled, the Linux operating system acts as a soft real-time system.

Karayan, Vahag

The Development of the Puerto Rico Lightning Detection Network for Meteorological Research

A land-based Puerto Rico Lightning Detection Network (PR-LDN) dedicated to the academic research of meteorological phenomena has being developed. Five Boltek StormTracker PCI-Receivers with LTS-2 Timestamp Cards with GPS and lightning detectors were integrated to Pentium III PC-workstations running the CentOS linux operating system. The Boltek detector linux driver was compiled under CentOS, modified, and thoroughly tested. These PC-workstations with integrated lightning detectors were installed at five of the University of Puerto Rico (UPR) campuses distributed around the island of PR. The PC-workstations are left on permanently in order to monitor lightning activity at all times. Each is networked to their campus network-backbone permitting quasi-instantaneous data transfer to a central server at the UPR-Bayam n campus. Information generated by each lightning detector is managed by a C-program developed by us called the LDN-client. The LDN-client maintains an open connection to the central server operating the LDN-server program where data is sent real-time for analysis and archival. The LDN-client also manages the storing of data on the PC-workstation hard disk. The LDN-server software (also an in-house effort) analyses the data from each client and performs event triangulations. Time-of-arrival (TOA) and related hybrid algorithms, lightning-type and event discriminating routines are also implemented in the LDN-server software. We also have developed software to visually monitor lightning events in real-time from all clients and the triangulated events. We are currently monitoring and studying the spatial, temporal, and type distribution of lightning strikes associated with electrical storms and tropical cyclones in the vicinity of Puerto Rico.

Legault, Marc D.

Robotics On-Board Trainer (ROBoT)

ROBoT is an on-orbit version of the ground-based Dynamics Skills Trainer (DST) that astronauts use for training on a frequent basis. This software consists of two primary software groups. The first series of components is responsible for displaying the graphical scenes. The remaining components are responsible for simulating the Mobile Servicing System (MSS), the Japanese Experiment Module Remote Manipulator System (JEMRMS), and the H-II Transfer Vehicle (HTV) Free Flyer Robotics Operations. The MSS simulation software includes: Robotic Workstation (RWS) simulation, a simulation of the Space Station Remote Manipulator System (SSRMS), a simulation of the ISS Command and Control System (CCS), and a portion of the Portable Computer System (PCS) software necessary for MSS operations. These components all run under the CentOS4.5 Linux operating system. The JEMRMS simulation software includes real-time, HIL, dynamics, manipulator multi-body dynamics, and a moving object contact model with Tricks discrete time scheduling. The JEMRMS DST will be used as a functional proficiency and skills trainer for flight crews. The HTV Free Flyer Robotics Operations simulation software adds a functional simulation of HTV vehicle controllers, sensors, and data to the MSS simulation software. These components are intended to support HTV ISS visiting vehicle analysis and training. The scene generation software will use DOUG (Dynamic On-orbit Ubiquitous Graphics) to render the graphical scenes. DOUG runs on a laptop running the CentOS4.5 Linux operating system. DOUG is an Open GL-based 3D computer graphics rendering package. It uses pre-built three-dimensional models of on-orbit ISS and space shuttle systems elements, and provides realtime views of various station and shuttle configurations.

Johnson, Genevieve

The TSO Logic and G2 Software Product

This internship assignment for spring 2014 was at John F. Kennedy Space Center (KSC), in NASAs Engineering and Technology (NE) group in support of the Control and Data Systems Division (NE-C) within the Systems Hardware Engineering Branch. (NEC-4) The primary focus was in system integration and benchmarking utilizing two separate computer software products. The first half of this 2014 internship is spent in assisting NE-C4s Electronics and Embedded Systems Engineer, Kelvin Ruiz and fellow intern Scott Ditto with the evaluation of a newly piece of software, called G2. Its developed by the Gensym Corporation and introduced to the group as a tool used in monitoring launch environments. All fellow interns and employees of the G2 group have been working together in order to better understand the significance of the G2 application and how KSC can benefit from its capabilities. The second stage of this Spring project is to assist with an ongoing integration of a benchmarking tool, developed by a group of engineers from a Canadian based organization known as TSO Logic. Guided by NE-C4s Computer Engineer, Allen Villorin, NASA 2014 interns put forth great effort in helping to integrate TSOs software into the Spaceport Processing Systems Development Laboratory (SPSDL) for further testing and evaluating. The TSO Logic group claims that their software is designed for, monitoring and reducing energy consumption at in-house server farms and large data centers, allows data centers to control the power state of servers, without impacting availability or performance and without changes to infrastructure and the focus of the assignment is to test this theory. TSOs Aaron Rallo Founder and CEO, and Chris Tivel CTO, both came to KSC to assist with the installation of their software in the SPSDL laboratory. TSOs software is installed onto 24 individual workstations running three different operating systems. The workstations were divided into three groups of 8 with each group having its own operating system. The first group is comprised of Ubuntus Debian -based Linux the second group is windows 7 Professional and the third group ran Red Hat Linux. The highlight of this portion of the assignment is to compose documentation expressing the overall impression of the software and its capabilities.

TSO Logic

Software Tool for Tracking & Mapping the NASA Orion AA-2 Test Flight Ejectable Data Recorders in Real Time

On 2 July 2019, the NASA Ascent Abort 2 flight took place off the Florida coast to test the emergency systems to separate the Orion Crew Module (CM) from the future Space Launch System rocket in the event of a malfunction. During this high-altitude test, instrumentation data was recorded on twelve customized buoyant Ejectable Data Recorders (EDRs) and subsequently jettisoned from the CM in mid-air. Upon release, the EDRs activated their GPS-Iridium beacon systems and began transmitting Short Burst Data (SBD) messages via the Iridium satellite network to relay their individual location and system health information. To locate, track and retrieve each EDR from the ocean surface in real-time, multiple open-source programming tools (Python and Linux shells) were developed for parsing the incoming Iridium binary SBD messages. For this, a Linux laptop was used to receive the Iridium-generated emails containing the SBD messages and autonomously execute the parsing tools. The received SBD data contained location, timestamp and health status information that was translated, saved, and subsequently used for simultaneously generating a continuously updated color-coded tabular display summary and unique KML files used with Google Earth to track their locations. Once their locations were known, dedicated recovery vessels retrieved all EDRs from the ocean. An additional tool was also developed in order to generate 5- and 10-minute geolocation predictions for each EDR by deriving the displacement distance, elapsed time, displacement heading and velocity based on the latest known information available. The recovery vessels were also tracked with the use of a separate commercial GPS beacon system. After jettison, 67% of the EDRs transmitted valid data by the time they were retrieved from the ocean. However, the real-time information presented by the plotting tool allowed for the ready depiction of EDR dispersal patterns and reference drift trajectories, which contributed to the recovery of all twelve EDRs and the AA-2 flight data. Lastly, the available data showed that the distance between the software’s reported drift/predicted locations and the recovery locations did not exceed 38 meters, therefore demonstrating the advantages of this software tool for supporting real-time tracking and recovery efforts of beacon devices.

Moxey, Lucas

TPSAS-NF1676L-33992-DND

The CERES Science Team integrates and fuses observations from 6 CERES instruments aboard the Terra, Aqua, S-NPP, and NOAA-20 missions with data from more than 20 other unique data sources. Following the November 2017 launch of CERES Flight Model 6 (FM6) onboard NOAA20, CERES has now amassed over 80 instrument-years of valuable Earth radiation budget data. The rapidly growing volume of CERES data coupled with the introduction of new data products alongside improvements to existing science algorithms fosters the requirement for faster, more flexible, and scalable data production and orchestration. New virtualized, cloud-centric compute hardware hosted by the NASA Langley Research Center’s (LaRC) Atmospheric Sciences Data Center (ASDC) provides an ideal environment for these ever-increasing data production demands for CERES. This poster discusses updates to the implementation of the CERES Data Management Team’s (DMT) CERES AuTomAted job Loading sYSTem (CATALYST), a custom data processing workflow engine for CERES, to use on-demand computing resources to perform automated CERES data production processing in a Linux-based container environment. Linux containers provide CERES the flexibility to build multiple production environments in containers tailored for specific workloads and allow effortless provisioning of resources based on the CERES Science Team’s data production requirements.

Thomas N. Hillyer

SEE Test Results for SAMA5D3

ARM processors power a class of high-performance, lower power system on a chip devices. In the absence of radiation effects, these devices are highly desirable for space use. The processor core architecture for ARM devices is licensed to provide computing on multiple hardware platforms. The A5 processor is in a unique pioneering space for providing detailed radiation response data to explore the baseline performance of these devices. These data can help set options for ARM processors and possibly impact design choices for the next generation of ARM fault tolerance capabilities. The SAMA5D3 was tested to establish general SEE performance for a relatively simple implementation of the ARM A5 core. This testing observed SRAM sensitivity starting at an LET of about 3 MeV-cm2/mg, with a saturated cross section of about 2x10-8cm2/bit, and this was determined by both active write and read of the caches, in addition to the use of a debugger to provide test results. Crash/SEFI data was collected using both Linux and bare metal C-code. The onset LET for crashes was about LET 1.5 MeV-cm2/mg, with saturated cross sections of about 2x10-5 cm2 for bare metal (low utilization), and 2x10-4cm2 for Linux (high utilization) tests.

Daniel, Andrew C.

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve

Structure Prediction of Ionic Epitaxial Interfaces with Ogre Demonstrated for Colloidal Heterostructures of Lead Halide Perovskites

Colloidal epitaxial heterostructures are nanoparticles composed of two different materials connected at an interface, which can exhibit properties different from those of their individual components. Combining dissimilar materials offers exciting opportunities to create a wide variety of functional heterostructures. However, assessing structural compatibility–the main prerequisite for epitaxial growth–is challenging when pairing complex materials with different lattice parameters and crystal structures. This complicates both the selection of target heterostructures for synthesis and the assignment of interface models when new heterostructures are obtained. Here, we demonstrate Ogre as a powerful tool to accelerate the design and characterization of colloidal heterostructures. To this end, we implemented developments tailored for the high-efficiency prediction of epitaxial interfaces between ionic/polar materials, which encompass most colloidal semiconductors. These include the use of pre-screening candidate models based on charge balance at the interface and the use of a classical potential for fast energy evaluations, with parameters automatically calculated based on the input bulk structures. These developments are validated for perovskite-based CsPbBr 3 /Pb 4 S 3 Br 2 heterostructures, where Ogre produces interface models in excellent agreement with density functional theory and experiments. Furthermore, we use Ogre to rationalize the templating effect of CsPbCl 3 on the growth of lead sulfochlorides, where perovskite seeds induce the formation of Pb 4 S 3 Cl 2 rather than Pb 3 S 2 Cl 2 due to better epitaxial compatibility. Finally, combining Ogre simulations with experimental data enables us to unravel the structure and composition of the hitherto unsolved CsPbBr 3 /Bi x Pb y S z interface, and to assign a structure to several other reported metal halide- and oxide-based interfaces. The Ogre package is available on GitHub or via the OgreInterface desktop application, available for Windows, Linux, and Mac.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Thoroughly testing and integrating hundreds of Pull Requests per month: ROOT’s new Cost-efficient and Feature Rich GitHub-based CI

ROOT is an open source framework, freely available on GitHub, at the heart of data acquisition, processing and analysis of HE(N)P experiments, and beyond. It is developed collaboratively: contributions are not authored only by ROOT team members, but also by the user community at large: developers and scientists from universities, labs as well as the private sector. More than 1500 GitHub Pull Requests are merged on average per year. It is in this context that code integration acquires a primary role. The review of code contributions isn’t enough: not only they need to be thoroughly reviewed, they also need to be thoroughly tested through a powerful CI infrastructure on several different platforms to comply with the high code quality standards of the project. Since the end of 2023, ROOT moved its continuous integration system from Jenkins to GitHub Actions. In this contribution, we characterise the transition to the GitHub CI, focussing on our strategy, its implementation and the lessons learned, as well as the advantages the new system offers with respect to the previous one. Particular emphasis will be given to the evaluation of the cost-benefit ratio for Jenkins and GitHub Actions for the ROOT project. We also describe how we manage to run in less than one hour thousands of unit, integration, functional and end-to-end tests on different flavours of Windows, four versions of macOS, as well as about ten of the most used Linux distributions, taking advantage of the CERN computing infrastructure.

Piparo, Danilo [CERN]

Poplar: a phylogenomics pipeline

Motivation Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist. Results We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline. Availability and implementation Freely available on GitHub at https://github.com/sandialabs/poplar. Implemented using Python and supported on Linux.

Koning, Elizabeth [Sandia National Laboratories (S

GenomeDepot: data management system for microbial comparative genomics

Summary GenomeDepot is an open-source web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of websites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, Basic Local Alignment Search Tool (BLAST) search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools. Availability and implementation GenomeDepot is open source and distributed under the GNU General Public License via GitHub (https://github.com/aekazakov/genome-depot). GenomeDepot is implemented in Python and was tested in Ubuntu Linux. Full installation instructions and documentation are available at https://aekazakov.github.io/genome-depot/. GenomeDepot demo server is freely accessible at https://iseq.lbl.gov/demogd/.

Kazakov, Alexey [Lawrence Berkeley National Labora

Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE

Summary Protein property prediction via machine learning with and without labeled data is becoming increasingly powerful, yet methods are disparate and capabilities vary widely over applications. The software presented here, “Artificial Intelligence Driven protein Estimation (AIDE)”, enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods for variants and variable length homologs in a single, reproducible notebook or script by defining a modular, standardized application programming interface (API), i.e. drop-in compatible with scikit-learn transformers and pipelines. Availability and implementation AIDE is an installable, importable python package inheriting from scikit-learn classes and API and is installable on Windows, Mac, and Linux. Many of the wrapped models internal to AIDE will be effectively inaccessible without a GPU, and some assume CUDA. The newest stable, tested version can be found at https://github.com/beckham-lab/aide_predict and a full user guide and API reference can be found at https://beckham-lab.github.io/aide_predict/. Static versions of both at the time of writing can be found on Zenodo.

36 MATERIALS SCIENCE

SAIGE-GPU: accelerating genome- and phenome-wide association studies using GPUs

Genome-wide association studies (GWAS) at biobank scale are computationally intensive, especially for admixed populations requiring robust statistical models. SAIGE is a widely used method for generalized linear mixed-model GWAS but is limited by its CPU-based implementation, making phenome-wide association studies impractical for many research groups. We developed SAIGE-GPU, a GPU-accelerated version of SAIGE that replaces CPU-intensive matrix operations with GPU-optimized kernels. The core innovation is distributing genetic relationship matrix calculations across GPUs and communication layers. Applied to 2068 phenotypes from 635 969 participants in the Million Veteran Program, including diverse and admixed populations, SAIGE-GPU achieved a 5-fold speedup in mixed model fitting on supercomputing infrastructure and cloud platforms. We further optimized the variant association testing step through multi-core and multi-trait parallelization. Deployed on Google Cloud Platform and Azure, the method provided substantial cost and time savings. Source code and binaries are available for download at https://github.com/saigegit/SAIGE/tree/SAIGE-GPU-1.3.3. A code snapshot is archived at Zenodo for reproducibility (DOI: [10.5281/zenodo.17642591]). SAIGE-GPU is available in a containerized format for use across HPC and cloud environments and is implemented in R/C++ and runs on Linux systems.

Rodriguez, Alex [Argonne National Laboratory (ANL)

Gaia: segmented germanium detector for high-energy X-ray fluorescence and spectroscopic imaging

We present Gaia, a monolithic array of 96 high-purity germanium pixel detectors integrated with a custom low-noise application-specific integrated circuit (ASIC) and a field-programmable gate array (FPGA)-based data acquisition system. The sensor operates at ∼100 K using a commercial closed-cycle cryocooler, with the in-vacuum electronics thermally isolated from the cold finger to ensure thermal stability. The system demonstrates an average energy resolution of 711 eV at 122 keV, measured using a 57 Co source, and 253 eV at 5.89 keV, measured with 55 Fe across all channels. The readout architecture incorporates a high-performance FPGA paired with a dual-core ARM processor, forming a complete embedded Linux-based computing platform. Communication between the processor and FPGA is handled via memory-mapped I/O, and data are streamed over high-speed gigabit Ethernet. A full-scale 384-pixel Gaia detector, based on this 96-element module, is currently under fabrication.

36 MATERIALS SCIENCE

Quantum/AI Topology-Aware Latency-Adaptive HPC Workflow Scheduling Optimization

The growing demand for more powerful high-performance computing (HPC) systems has led to a steady rise in energy consumption by supercomputing worldwide. This study is focused on comparing our Application-Topology Mapper (ATMapper) to the popular Simple Linux Utility for Resource Management (SLURM) for the purpose of exploring methods that can further optimize job-scheduling within HPC systems. ATMapper is an Artificial-Intelligence based approach to job-scheduling that is currently being enhanced with quantum annealing (QA) to generate optimal schedules faster. We are applying QA to speedup our ATMapper process to achieve higher computing efficiency, thereby reducing HPC energy consumption. Here, we examine how four job-scheduling approaches perform in processor node assignment when using an example network architecture of 4 interconnected nodes. Using a specialized script, we are assessing the schedule of a computation flow with 11 interdependent tasks. The data movements among nodes were tracked to count for the number of interactions (network hops) between nodes needed to complete the tasks. The total number of hops and the job completion time were then used to quantify the efficiency of the different mapping approaches. In addition to SLURM, we also compare our ATMapper to the QA-enabled LBNL TIGER and the D-Wave Distributed Computing processor assignment approaches. The preliminary results showed that our topology-aware, latency-adaptive ATMapper is significantly more efficient when compared to the other scheduling approaches due to its load-imbalance network allocation. The scheduler displayed a computing efficiency of 53% by performing significantly fewer network hops than its alternatives. By reducing the number of hops, ATMapper was able to perform all 11 tasks by using only 3 nodes out of given 4. This research indicates the potential to use QA/AI for HPC job-scheduling. Later, we will test a SLURM simulator program to draw further comparisons on the effectiveness of ATMapper's scheduling approach. The results of this comparison will serve as a baseline for later improving SLURM's performance using a QA-enhanced ATMapper approach.

Caraveo, Braulio [University of Huston - Clear Lak

Real-Time Ethernet Interface for NSTX-U’s Thomson Scattering Diagnostic (2023)

Here, the multipoint Thomson scattering (MPTS) diagnostic system at the National Spherical Torus Experiment Upgrade (NSTX-U) facility is undergoing an upgrade to operate in real-time and interface with the plasma control system (PCS) for NSTX-U. Previous prototyping efforts have shown that spectral analysis and rapid calculations of electron temperature and density are possible on a real-time Linux machine when using up to a 100-Hz laser pulse repetition rate. A remaining challenge was transferring the real-time data to NSTX-U’s PCS, which utilizes the front panel data port (FPDP) protocol. The original proposed method was to convert the real-time data into analog values, but a new solution was developed to keep the output format digital by using an Ethernet controller with a field-programmable gate array (FPGA). This article focuses on a new input module that has been developed to accept incoming user datagram protocol (UDP) packets sent over Ethernet, convert into FPDP format, and integrate into the existing data stream under NSTX-U’s real-time framework.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND

Preliminary Study on Fine-Grained Power and Energy Measurements on Grace Hopper GH200 with Open-Source Performance Tools

The increasing adoption of tightly integrated, heterogeneous architectures, combined with the slowdown of Moore’s law, has made application power and energy-driven optimizations critical to efficiently use high-performance computing systems. This paper introduces a newly developed open-source toolkit that seamlessly integrates the Linux real-time hardware monitoring program hwmon with the Performance Application Programming Interface and the Score-P performance measurement system, thereby enabling fine-grained power and energy measurements for high-performance computing applications. Our primary target platform is the Wombat test bed, which is a system based on the NVIDIA GH200 superchip. The toolkit can capture transient power peaks with high temporal resolution (50 ms) and, thanks to Score-P integration, can map power metrics to specific code regions, thereby providing actionable information on power-intensive operations and inefficiencies. The toolkit also provides a holistic view of both the power and the energy consumption of the entire GH200 superchip by covering all major components: the Grace CPU, the Hopper GPU, and the I/O subsystem. Experiments that use Locally Self-consistent Multiple Scattering, which is an application for first-principles calculations of materials developed at Oak Ridge National Laboratory, have demonstrated the tool’s ability to identify transient power spikes and uncover opportunities for energy-aware optimizations. Additionally, we introduce a Python-based utility for converting Open Trace Format 2 traces to Parquet format, thus enabling advanced data analysis for numerical integration methods applied to power data for accurate energy profiling.

Hernandez Mendoza, Oscar [ORNL] (ORCID:00000002538