GLANCED-IO: Taming IO Optimization for Deep Learning at Scale
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Computer science↗
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Crystal field splittings and magnetic ground state of the square-lattice antiferromagnets YbBi 2 ClO 4 and YbBi 2 IO 4 with J eff = $\frac{1}{2}$
Here, we report on the crystal field level splitting and magnetic ground state of the J eff = $\frac{1}{2}$ square lattice antiferromagnets YbBi 2 ClO 4 and YbBi 2 IO 4 using powder inelastic neutron scattering (INS) and neutron diffraction measurements. Both compounds exhibit a well-isolated Γ 7 doublet ground state under a tetragonal crystal field environment, confirming a robust J eff = $\frac{1}{2}$ picture with slight XY-type anisotropic character in the g-tensor. Notably, the ground state wave functions closely resemble the Γ 7 doublet expected in the perfect cubic limit, consistent with the nearly cubic ligand configuration of eight O 2- ions surrounding Yb 3+ . Below T N = 0.21 K, YbBi 2 IO 4 exhibits a stripe long-range magnetic order characterized by an ordering wave vector q m = (1/2, 0, 0) or its symmetry-equivalent (0, 1/2, 0), with magnetic moments aligned along q m . The ordered moment is approximately 79% of the classical prediction, significantly larger than expected from the isotropic J 1 -J 2 model, suggesting the possible involvement of exchange anisotropy in explaining this observation. We show that symmetry-allowed XXZ and bond-dependent anisotropic exchange terms in a square lattice can play a critical role in stabilizing the stripe order and suppressing the moment reduction as observed. These findings establish YbBi 2 ClO 4 and YbBi 2 IO 4 as unique platforms for exploring rich J eff = $\frac{1}{2}$ magnetism from two less investigated perspectives: (i) on a square lattice and (ii) within a (nearly) cubic ligand environment.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Phlex-io-granularity-test
Granularity test stand for storing Phlex type data product in RNTupe.
Canal, Philippe [Fermilab]↗
Why is my IO Slow. Rethinking Storage Systems for Explainability
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Computer science↗
GLANCED-IO: Taming I/O Optimization for Deep Learning at Scale
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Computer science↗
Investigation of the iodate sorption mechanism by CoAl LDH through experiments and ab initio molecular dynamics simulations
Radioiodine released during the nuclear-fuel cycle constitutes a persistent radiological hazard. In this study, the IO 3 – uptake mechanism of CoAl LDH was resolved by combining pH-controlled sorption experiments, synchrotron XAFS, and DFT-based AIMD simulations. At pH close to 6, approximately 90% of IO 3 – was removed, and the equilibrium distribution coefficient reached about 1.7 × 10 4 mL g –1 . EXAFS analysis indicated an average iodine–oxygen bond length of 1.81 Å and a coordination number near 3, with the fit R-factor equal to 0.002. The simulations faithfully reproduced the experimental spectrum and revealed transient proton hopping events that generated metastable I–O–H species inside the interlayer, thereby confirming nitrate-to-iodate exchange as the controlling capture pathway. Atomic density profiles and radial distribution functions further showed that IO 3 – adopt an end-on orientation perpendicular to the hydroxide sheets, while water molecules mediate proton migration without disturbing the host lattice. In conclusion, the integrated experimental–computational evidence demonstrates that CoAl LDH can rapidly and selectively sequester IO 3 – under near-neutral conditions, offering atomic scale guidance for the rational engineering of layered sorbents for advanced radioactive-waste treatment.
Kang, Jaehyuk [Jeju National Univ. (Korea, Republi↗
A Performance Model of In-Situ Techniques
The computational capacity of High-Performance Computing (HPC) systems increases continuously with the rapid development of central processing units (CPUs) and graphic processing units (GPUs), while the in-/output (IO) subsystem develops relatively slowly and storage capacity is also limited. Data-intensive applications, which are designed to leverage the high computational capacity of HPC resources, typically generate a considerable amount of data for post-processing visualizations and data analytics. The limited IO speed and storage space could lead to constraints in the actual performance of these applications and, therefore, scientific discovery. In-situ techniques, where data is visualized/analysed while still in memory rather than through disk, can contribute to alleviating these problems as they can reduce or even fully avoid data writing/reading through the IO subsystem to/from storage. However, the overall efficiency of insitu techniques crucially depends on the characteristics of both the in-situ tasks and the applications, and the resource distribution among them. Therefore, choosing the right in-situ approach (synchronous, asynchronous, or hybrid) and resource allocation is essential to minimize overhead and maximize the benefits of concurrent execution. In this paper, we present a performance model of in-situ techniques to find the most beneficial in-situ approach and the preferred resource configuration. We verify the high accuracy of our approach with over 6800 measurements and provide use cases with different applications.
Ju, Yi [Max Planck Computing and Data Facility, Ga↗
Preliminary proof-of-concept of real-time divertor heat flux control from infrared cameras with nitrogen injection in the DIII-D tokamak
In future tokamak reactors like ITER and the Fusion Pilot Plant (FPP), real-time feedback control of heat flux to the plasma-facing components (PFC) will be critical for steady-state operation. This work presents the first experimental demonstration of real-time divertor heat flux estimation with infrared thermography and feedback control with impurity seeding on the DIII-D tokamak. The flexible infrastructure of the Plasma Control System (PCS) on DIII-D makes this new capability possible. The PCS software runs on a gateway computer system, and five real-time compute nodes. An array of low latency streaming digitizers from D-TACQ Solutions connects to these real-time computers to collect and process data, and send commands to actuators during plasma discharges. This system handles the signal IO from the tokamak and allows the PCS to utilize the diagnostic data necessary to perform control in real-time. Feedback control on heat flux was accomplished by feeding infrared camera data from the “Infrared TV” (IRTV) camera to a custom-developed User Datagram Protocol (UDP) server. This server transmits infrared data to a newly developed PCS algorithm that estimates the heat flux to PFC. Here, a proportional integral derivative (PID) controller minimizes the error between a heat flux reference and the real-time estimate by injecting nitrogen gas into the divertor.
Algorithm development↗
Geophysical Impacts and Spectroscopic Identification of a Hydrous Iron Sulfate on Icy Worlds
Over geologic time-scales, large volumes of exogenic sulfur ions from Io's plasma torus have been supplied to the surface of Europa and Ganymede, which, combined with recent interpretations of orbiter images, dynamical modeling, and surface-subsurface exchange, suggests further sulfur transport into the interior of the icy worlds. These observations motivate mixed-phase spectral modeling for interpreting orbiter spectroscopy data and determination of hydration states of candidate surface materials including hydrous sulfates. In this work, we present a combined experimental and theoretical study of the low temperature and high pressure vibrational spectral signature of the iron-sulfate monohydrate endmember, szomolnokite (FeSO 4 ·H 2 O). By employing synchrotron Fourier-transform infrared spectroscopy (FTIR) in the diamond anvil cell up to 23 GPa and down to 20 K, we explore the extreme range of pressure-temperature domains relevant to icy environments throughout our solar system and beyond. Combined with our density-functional theory quantum-mechanics molecular dynamics results, we demonstrate that experimentally observed infrared features in the O-H stretching region commonly associated with nH 2 O (n > 1) hydration states can be attributed to a pure monohydrate without the need for pressure-induced exsolved ice, other coexisting hydrous iron sulfates, or strong overtone and combination modes. We further discuss the possibility of lateral variations in density and shear properties on icy worlds associated with temperature variations and the high-pressure phases of kieserite group monohydrated sulfates.
Geosciences↗
Integrated operation scenarios: Chapter 6 of the special issue: on the path to tokamak burning plasma operation
Here we report the progress of the development and optimization of operational scenarios for ITER and beyond, focusing upon baseline, hybrid, and steady-state scenarios since 2007. This includes advancements made by the integrated operation scenarios (IOS) topical group of the international tokamak physical activity as well as contributions from the broader tokamak community. The key area of research involves developing IOSs that encompass tokamak physics, operation, and technology by utilizing integrated modeling and control strategies. This requires leveraging available actuators to simultaneously control plasma position and shape, MHD activities that could lead to disruptions, transport, plasma-wall interaction and power exhaust, fuel cycle, fusion burn, and tritium breeding. The control extends from the plasma initiation phase, through the current ramp-up, flattop, start and end of the fusion burn, and current ramp-down, to the plasma termination phase. A review of the currently developed scenarios and modeling is provided in terms of (i) optimizing plasma initiation in ITER, (ii) preparing for the low activation phase to fully commission all tokamak systems and establish and validate physics and scenario conditions in preparation for deuterim-tritium (DT) operation, (iii) developing and preparing baseline and hybrid scenarios to demonstrate the feasibility of achieving these regimes within device constraints, (iv) exploring steady-state scenarios to meet ITER’s steady-state goals, (v) evaluating and preparing actuators for ITER, (vi) developing integrated control solutions using shared actuators. The most notable achievements include; (i) the development of ITER demonstration discharges by matching various dimensionless parameters, (ii) the development of scenarios in an ITER-like tungsten environment and DT operation, and (iii) the development of scenarios in superconducting tokamaks, enabling long-pulse operations with similar coil constraints to ITER. Along with these significant achievements, outstanding issues and recommendations for further research and development are provided. Importantly, this study goes beyond simply updating the ITER Physics Basis; it carries profound implications for the broader field of burning plasma research, offering valuable insights and guidance for the next generation of fusion experiments and devices.
ITER↗
Gene-Metabolite Association Prediction with Interactive Knowledge Transfer Enhanced Graph for Metabolite Production
Identifying gene targets for enhancing metabolite production in metabolic engineering is challenging due to the vast research literature and the approximation in genome-scale metabolic model (GEM) simulations. Here, to address this, we propose the Gene-Metabolite Association Prediction task, which automates gene discovery for given metabolite-gene pairs, accompanied by a benchmark dataset of 2474 metabolites and 1947 genes for Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is complicated by incomplete metabolic graphs and metabolic heterogeneity. We introduce an Interactive Knowledge Transfer mechanism based on Metabolism Graphs (IKT4Meta) to enhance prediction accuracy by integrating cross-metabolism knowledge. Using Pretrained Language Models (PLMs) to generate inter-graph links mitigates heterogeneity issues, while intra-graph links are propagated via these anchors. Gene-metabolite predictions are then performed on the enriched graphs integrating multiple microorganisms’ knowledge. Experiments show that IKT4Meta outperforms baselines by up to 12.3% in link prediction.
59 BASIC BIOLOGICAL SCIENCES↗
Advanced Photovoltaic Module Characterization: Using Image Transformers for Current–Voltage Curve Prediction From Electroluminescence Images
Individual photovoltaic (PV) module health monitoring can be a daunting task for operation and maintenance of solar farms. Modules can be inspected through luminescence, thermal imaging, and current–voltage (I–V) curve analyzes for identification of damage and power loss. I–V curves provide easily interpretable data to determine module health as they directly provide electrical performance metrics. However, in order to obtain these curves, modules must be disconnected from the array and either removed to a solar simulator or characterized in situ with corrections for module temperature, the incident solar spectrum, and intensity. Luminescence or thermal images of a module are relatively easy to acquire in situ. Electroluminescence (EL) images highlight physical defects in the modules but do not provide easily interpretable features to correlate with electrical performance. This work presents a SWin transformer network to predict I–V curves for PV modules from their corresponding EL images. The predicted I–V curves allow the accurate prediction of the maximum power point (MPP), short-circuit current I sc , and open-circuit voltage V oc with a mean error less of than 1%. Comparing single diode model (SDM) parameters extracted from the predicted curves to those extracted from the true curves, the series resistance R s demonstrates a mean error of 5.19%, and the photocurrent I a mean error of 0.197%. The shunt resistance R sh and dark current Io parameters are predicted with larger errors because of their sensitivity to small changes in the I–V curve.
Byford, Brandon K. [New Mexico State Univ., Las Cr↗
HPC Campaign Management: Remote data access with user-defined error bound using ADIOS and ZFP
Remote access to large-scale scientific datasets, like those generated by combustion simulations or other high-performance computing (HPC) applications, presents a significant challenge. Downloading entire datasets is often impractical due to their size and the bandwidth limitations of typical networks. To address this challenge, we propose a novel approach that enables efficient remote access to large datasets distributed across multiple facilities. Our method enables technologies to download only the data values of a select variable, in a select region of interest, to a user-defined accuracy. For this purpose, we extended the ADIOS IO library to provide read functions with user-defined accuracy, a remote data server that understands multidimensional selections of specific variables, steps and accuracy from an ADIOS dataset, and which uses lossy compression on the remote site to reduce the data to be transferred back to the client. In addition, our extension of the ADIOS library collects metadata from multiple datasets in small files called Campaign Archives, which can be shared among project participants on any HPC, cloud or laptop, and which can easily facilitate the discovery of content and pointers to the data location as well as remote access to the data by local tools as if data was local. This feature called Campaign Management, enables a group of scientists to manage related datasets stored in multiple files, across multiple facilities as if it was in a single file/database. We demonstrate the effectiveness of our approach using a 1.5 TB dataset from the S3D combustion simulation on Frontier at the Oak Ridge Leadership Facility. Even a single variable from this dataset, at 64 GB, is too large to be processed on a standard laptop. We show two different reading patterns for 2D plots and 3D visualization, with careful settings that a scientist studying combustion data would do and show that running the same Python scripts on Frontier directly takes comparable time than running them on the local laptop with remote access to the data on Frontier.
Podhorszki, Norbert [ORNL] (ORCID:000000019647542X↗
Streaming Data in HPC Workflows Using ADIOS
The “IO Wall” problem, in which the gap between computation rate and data access rate grows continuously, poses significant problems to scientific workflows which have traditionally relied upon using the filesystem for intermediate storage between workflow stages. One way to avoid this problem in scientific workflows is to stream data directly from producers to consumers and avoiding storage entirely. However, the manner in which this is accomplished is key to both performance and usability. This paper presents the Sustainable Staging Transport, an approach which allows direct streaming between traditional file writers and readers with few application changes. SST is an ADIOS “engine”, accessible via standard ADIOS APIs, and because ADIOS allows engines to be chosen at run-time, many existing file-oriented ADIOS workflows can utilize SST for direct application-to-application communication without any source code changes. This paper describes the design of SST and presents performance results from various applications that use SST, for feeding model training with simulation data with substantially higher bandwidth than the theoretical limits of Frontier’s file system, for strong coupling of separately developed applications for multiphysics multiscale simulation, or for in situ analysis and visualization of data to complete all data processing shortly after the simulation finishes.
Podhorszki, Norbert [ORNL] (ORCID:000000019647542X↗
exnehilo7/fielddata-lite-iOS-app
Field Expedition Routing and Navigation (FERN) is an IOS app funded by the Center for Bioenergy Innovation (CBI). It allows an end user to make trips to collect novel data points. It allows user to return to previously surveyed points to collect more data. It calculates the optimal route to use to sample points needed for return trips. A companion php/database application is required for full functionality. Links to this open source project are in the README. FERN can use the default GPS on an Iphone but it also optimized for Arrow Gold GPS. Other external GPS could be supported by modifying this code and adding the proper routines.
Hopp, Daniel↗
VerifyIO: Verifying Adherence to Parallel I/O Consistency Semantics
VerifyIO is a tool designed for verifying I/O consistency semantics in High-Performance Computing (HPC) applications. It addresses the challenges of ensuring correctness and portability across different I/O consistency models, such as POSIX, Commit, Session, and MPI-IO. By analyzing execution traces, detecting conflicts, and verifying synchronization adherence, VerifyIO provides actionable insights for both application developers and I/O library designers.
Wang, Chen [Lawrence Livermore National Laboratory↗
OPET Hardware (Open PV Electrical Tool Hardware) [SWR-25-42]
OPET (Open-source Photovoltaic Electrical Tool) is used for performance measurements of solar photovoltaic (PV) devices in the field under natural sunlight or in the lab under artificial light. Its primary use is in research and development of solar cells and modules, specifically in reliability and durability research of PV devices. Some features and functions include: -IV curve measurements with linear or cosine distributed measurement points -PV device active loading at open circuit voltage (Voc), short circuit current (Isc) and maximum power point (Pmp) -Bias power supply to overcome series resistance in contact wires for Isc measurements and loading -PV voltage input in five ranges from 1V to 100V -PV current input ranges -Low current version, six current ranges from 1.1mA to 340mA -High current version, six current ranges from 50mA to 15A -IO ports for I2C and SPI temperature sensor Arduino extension boards -Integrated fan control This repository contains everything relating to the hardware of the OPET device. If you are looking for the firmware or software repositories, links are below: https://github.com/NREL/opet-firmware https://github.com/NREL/opet-control
McDanold, Byron [National Renewable Energy Laborat↗
radkit base v1.6
The radkit (base) software suite (python) consists of three primary libraries: stark, trajan, and curie. The trajan library provides the tools to analyze and manipulate data from lidar and inertial measurement unit (IMU) devices, cameras, as well as trajectories from algorithms such as simultaneous localization and mapping (SLAM). These components allow reading and writing standard data formats, performing rigid affine transformations, discretizing three-dimensional space, and visualizing data products. The curie library comprises a standard set of object-oriented tools for radiation data and analysis in the following modules: (1) listmode and binmode data classes with methods for manipulation, plotting, slicing and file IO; (2) radiological/nuclear source detection/identification analysis results; (3) source encounters of correlated analyses and (4) energy-dependent angular detector response functions. The stark package provides low-level tools that are leveraged by both curie and trajan. The tools are flexible for offline analysis as well as performant for real-time integrations.
Salathe, Marco [Lawrence Berkeley National Laborat↗