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At least 19 records

Comparing cross-platform performance via node-to-node scaling studies

Due to the increasing diversity of high-performance computing architectures, researchers and practitioners are increasingly interested in comparing a code’s performance and scalability across different platforms. However, there is a lack of available guidance on how to actually set up and analyze such cross-platform studies. In this paper, we contend that the natural base unit of computing for such studies is a single compute node on each platform and offer guidance in setting up, running, and analyzing node-to-node scaling studies. In conclusion, we propose templates for presenting scaling results of these studies and provide several case studies highlighting the benefits of this approach.

cross-platform studies

Generic and ML Workloads in an HPC Datacenter: Node Energy, Job Failures, and Node-Job Analysis

HPC datacenters offer a backbone to the modern digital society. Increasingly, they run Machine Learning (ML) jobs next to generic, compute-intensive workloads, supporting science, business, and other decision-making processes. However, understanding how ML jobs impact the operation of HPC datacenters, relative to generic jobs, remains desirable but understudied. In this work, we leverage long-term operational data, collected from a national-scale production HPC datacenter, and statistically compare how ML and generic jobs can impact the performance, failures, resource utilization, and energy consumption of HPC datacenters. Our study provides key insights, e.g., ML-related power usage causes GPU nodes to run into temperature limitations, median/mean runtime and failure rates are higher for ML jobs than for generic jobs, both ML and generic jobs exhibit highly variable arrival processes and resource demands, significant amounts of energy are spent on unsuccessfully terminating jobs, and concurrent jobs tend to terminate in the same state. We open-source our cleaned-up data traces on Zenodo (https://doi. org/10.5281/zenodo.13685426), and provide our analysis toolkit as software hosted on GitHub (https://github.com/atlarge-research/2024-icpads-hpc-workload-characterization). This study offers multiple benefits for data center administrators, who can improve operational efficiency, and for researchers, who can further improve system designs, scheduling techniques, etc.

crossanalysis

NLR HPC Eagle GPU Node Metrics

Ganglia node metrics and iLO (Integrated Lights Out) power data captured from six representative Eagle GPU nodes The Eagle HPC operated at NLR from 2019 through 2024. Eagle was a 2,000-node, 8-petaflop system. This dataset is a representative sample of metrics for 6 of the GPU nodes. Each GPU node contained 2 CPUs and 2 GPUs. Data provided in compressed CSV format. Ganglia and iLO Power Time Series Fields ts: Timestamp dv: Device / Node - Rack and Unit - r103u17 == r(ack)103u(nit)17 mt: Metric (only present for Ganglia) vl: Value - Value in watts for iLO power (instantaneous value at sampling time) or specified Ganglia metric below Ganglia Metrics Metric name -- Metric description -- Unit cpu_aidle -- Percent of time since boot idle CPU -- Percent cpu_idle -- Percent CPU idle -- Percent cpu_nice -- Percent CPU nice -- Percent cpu_speed -- Speed in MHz of CPU -- MHz cpu_user -- Percent CPU user -- Percent cpu_wio -- The percentage of CPU Wait I/O -- Percent gpu0_bar1_memory -- Used GPU bar1 memory -- MB gpu0_decoder_util -- GPU decoder utilization -- Percent gpu0_ecc_db_error -- Total ECC error counts for the GPU -- Number gpu0_encoder_util -- GPU encoder utilization -- Percent gpu0_fan -- Fan speed -- RPM gpu0_fb_memory -- Used GPU framebuffer memory -- MB gpu0_graphics_clock_report -- Current clock speeds for the device -- MHz gpu0_mem_total -- Memory total -- MB gpu0_mem_util -- Memory utilization -- Percent gpu0_power_usage_report -- Power usage report -- Watts gpu0_temp -- GPU 1 temperature -- Celsius gpu1_bar1_memory -- Used GPU bar1 memory -- MB gpu1_decoder_util -- GPU decoder utilization -- Percent gpu1_ecc_db_error -- Total ECC error counts for the GPU -- Number gpu1_encoder_util -- GPU encoder utilization -- Percent gpu1_fan -- Fan speed -- RPM gpu1_fb_memory -- Used GPU framebuffer memory -- MB gpu1_graphics_clock_report -- Current clock speeds for the GPU -- MHz gpu1_mem_total -- Memory total -- MB gpu1_mem_util -- Memory utilization -- MB gpu1_power_usage_report -- Power usage report -- Watts gpu1_temp -- GPU 1 temperature -- Celsius ipmi_cpu1_temp -- CPU 1 temperature -- Celsius ipmi_cpu2_temp -- CPU 2 temperature -- Celsius ipmi_inlet_ambient_temp -- Temperature measured at intake -- Celsius ipmi_vr_p1_temp -- CPU 1 voltage regulator temperature -- Celsius ipmi_vr_p2_temp -- CPU 2 voltage regulator temperature -- Celsius mem_buffers -- Amount of buffered memory -- Bytes mem_cached -- Amount of cached memory -- Bytes mem_free -- Amount of available memory -- Bytes mem_shared -- Amount of shared memory -- Bytes mem_total -- Amount of available memory -- Bytes

97 MATHEMATICS AND COMPUTING

Improving Property Graph Layouts by Leveraging Attribute Similarity for Structurally Equivalent Nodes

Many real-world networks contain structurally-equivalent nodes. These are defined as vertices that share the same set of neighboring nodes, making them interchangeable with a traditional graph layout approach. However, many real-world graphs also have properties associated with nodes, adding additional meaning to them. We present an approach for swapping locations of structurally-equivalent nodes in graph layout so that those with more similar properties have closer proximity to each other. This improves the usefulness of the visualization from an attribute perspective without negatively impacting the visualization from a structural perspective. We include an algorithm for finding these sets of nodes in linear time, as well as methodologies for ordering nodes based on their attribute similarity, which works for scalar, ordinal, multidimensional, and categorical data.

graph drawing, network visualization, property gra

NLR HPC Eagle Node Power Data

Power time series captured from all Eagle nodes using iLO (Integrated Lights Out) The Eagle HPC operated at NLR from 2019 through 2024. Eagle was a 2,000-node, 8-petaflop system. This dataset is a comprehensive time series of instantaneous snapshots of power usage at 1 minute intervals from all nodes at the node level. Data provided in compressed Hive dataset/Parquet format. iLO Power Time Series Fields ts: Timestamp dv: Device / Node - Rack and Unit - r103u17 == r(ack)103u(nit)17 vl: Value - Value in watts (instantaneous value at sampling time) day month year

97 MATHEMATICS AND COMPUTING

Unexpected Photodriven Linker-to-Node Hole Transfer in a Zirconium-Based Metal–Organic Framework

Zr 6 (μ 3 -O) 4 (μ 3 -OH) 4 node cores are indispensable building blocks for almost all zirconium-based metal–organic frameworks. Consistent with the insulating nature of zirconia, they are generally considered electronically inert. Contrasting this viewpoint, we present spectral measurements and calculations indicating that emission from photoexcited NU-601, a six-connected Zr-based MOF, comes from both linker-centric locally excited and linker-to-node charge-transfer (CT) states. The CT state originates from a hole transfer process enabled by favorable energy alignment of the HOMOs of the node and linker. This alignment can be manipulated by changing the pH of the medium, which alters the protonation state of multiple oxy groups on the Zr-node. Thus, the acid–base chemistry of the node has a direct effect on the photophysics of the MOF following linker-localized electronic excitation. In conclusion, these new findings open opportunities to understand and exploit, for energy conversion, unconventional mechanisms of exciton formation and transport in MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Dirac Node Pinning from Dzyaloshinskii-Moriya Interactions in a Kagome Spin Liquid

Recent experiments on the Kagome spin liquid candidate material YCu 3 ⁢(OH) 6 ⁢Br 2 ⁢[Br 1−𝑦 ⁢(OH) 𝑦 ] suggest the presence of Dirac fermionic spinons near the magnetization plateau at 1/9. Theories suggest that the spinons are charge neutral spin-1/2 excitations, in a 2⁢𝜋/3 flux, which triples the unit cell. Generally a gap is expected, and there is no symmetry protection for the Dirac nodes in this system. The question arises as to what causes the nodes and stabilizes them. In this work, we propose a node-creation and node-pinning mechanism driven by Dzyaloshinskii-Moriya (DM) interactions. Employing Gutzwiller-projected variational Monte Carlo calculations, we demonstrate that DM interactions induce a band closing phase transition in the spinon spectrum. There is a change in the Chern number when the bands are inverted. Together with the DM-generated internal gauge flux, the coupling to the spinon orbital magnetization counteracts the band reopening. Furthermore, this interplay energetically pins the Dirac nodes over a range of parameters, resulting in a pinning mechanism distinct from the usual one from symmetry protection.

Kagome lattice

Organophosphorus Binding Thermodynamics in Metal–Organic Frameworks: Interplay between Oxidation State, Lewis Acidity, and Node Structure

Organophosphorus compounds, including nerve agents and pesticides, represent a class of toxic chemicals causing harm to troops, civilians, and the environment. Metal–organic frameworks (MOFs) have emerged as a class of highly porous, crystalline, tunable materials adept at both capturing and catalytically neutralizing these harmful toxins. In particular, MOFs whose nodes display strong Lewis acidic character can hydrolyze such chemicals nearly instantaneously. However, without the help of a basic buffer to regenerate the active site, the benign organophosphorus product strongly binds to the node and prevents catalyst turnover. Here, we investigate a series of MOFs whose nodes contain metals of varying Lewis acidities and employ isothermal titration calorimetry (ITC) to directly measure the heat from the binding of an organophosphorus probe molecule, allowing the construction of a full thermodynamic binding profile (ΔH, ΔS, ΔG, K a ). We couple this with potentiometric titrations and solid state 31 P magic angle spinning (MAS) NMR to gain a clearer picture of how node identity, structure, and Lewis acidity interplay to impact binding strength and favorability. Furthermore, this study is the first to integrate these three complementary techniques to investigate binding interactions in MOFs, further showcasing the viability of ITC for probing MOF systems, which is still relatively underexplored.

Lewis acidity

Node Distortions as a Means of Defect Engineering in Zr-Based MOFs

Defect engineering in Zr-based metal–organic frameworks (Zr-MOFs) has focused primarily on missing-linker defects. However, recent studies suggest that node dehydroxylation–which creates distortions and coordinatively unsaturated Zr sites (Zr cus )–may have a more significant impact on properties. The present work uses pair distribution function (PDF) and thermogravimetric analysis coupled with systematic defect manipulation to study the effect of node dehydroxylation and missing-linker defects in UiO-66. By employing rapid heat treatment (RHT) under humid flow, we tracked the transition from high-symmetry [Zr 6 O 4 (OH) 4 ] 12+ to distorted [Zr 6 O 6 ] 12+ nodes. This structural evolution significantly improves As(V) uptake, whereas increasing the number of missing linkers–via chemical treatment or RHT of mixed-ligand frameworks–fails to enhance performance. Crucially, our detection of distorted nodes in as-synthesized UiO-66 also raises the possibility that these defects were silently present in many earlier studies that span various applications, where their role in governing performance may have been inadvertently overlooked. The present study challenges the prevailing “missing-linker” paradigm and establishes cluster dehydroxylation as a defect-engineering strategy to enhance Lewis-acidic performance in Zr-MOFs.

Adsorption

Metal–Organic Frameworks at the Edge of Stability: Mediating Node Distortion to Access Metastable Nanoparticle Polymorphs

Metal-organic frameworks (MOFs) are emerging as unconventional precursors for nanoparticle synthesis, with potential to leverage their tunable structures and chemistry to achieve nanomaterials with structures and compositions inaccessible via traditional synthetic routes. Here we use in situ synchrotron X-ray diffraction and pair distribution function (PDF) measurements to investigate how the dynamic structure of MOFs at the edge of stability influences their transformation into different metastable polymorphs. Our study reveals that the local structural features of metal-oxo MOF nodes at elevated temperatures are linked to the resulting nanoparticle structures formed under mild conditions. Focusing on the titanium-based MOF MIL-125, we demonstrate that manipulating the chemical environment to facilitate transformation of the Ti8 node geometry promotes formation of metastable, nanometer-scale TiO2 brookite rather than the more common anatase and rutile TiO2 polymorphs typically produced through MOF pyrolysis at high temperature. These findings highlight the potential to harness the MOF topology and chemical environment to design and control node distortions and enable access to exotic metastable nanoparticle states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Node-Solution Microenvironment Governs the Selectivity of Thioanisole Oxidation within Catalytic Zr-Based Metal–Organic Framework

Lewis acidic metal oxides, including zirconia (ZrO 2 ), are catalytically active toward oxidative reactions in the presence of sacrificial oxidants like t-butyl hydroperoxide (TBHP). The structural ambiguity and heterogeneity of the ZrO 2 surface impose challenges to chemists in understanding the reaction mechanism down to atomic-level precision. The inorganic, Zr-oxo nodes of many crystalline metal–organic frameworks (MOFs) structurally mimic ZrO 2 . Herein, we report three novel findings: (A) Zr-based MOF, Zr-MOF-808 is catalytically competent in activating TBHP to induce oxygen atom transfer (OAT) reactions to a model substrate, thioanisole, at room temperature, (B) its reaction mechanism can be derived with greater structural precision owing to the crystallinity of the MOF, and (C) the node-binding agent and other reaction conditions significantly impact the selectivity between the singly oxidized methyl phenyl sulfoxide vs the doubly oxidized sulfone. These findings suggest that both the activity and selectivity of OAT reactions within Zr-MOF-808 are governed by the chemistry occurring at the interface of the node and the surrounding reaction medium. Implications of these findings in OAT reactions and other MOF/metal oxide-catalyzed relevant catalysis are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Nodeman: A Node Management Tool For Hpc Clusters

NodeMan is a command line tool to manage nodes in an HPC cluster. At it's core, it is an extensible framework composed of bash scripting and GNU parallel. HPC System Administrator will find it useful in that it encapsulates desired functions and allows them to be assembled in a way familiar to administrators - through pipes. In fact, NodeMan functions can work with common command line tools as long as they use stdin/stdout. System Administrators can construct moderately complex logic and filtering on a compact command line that would normally require a substantial shell script. In the spirit of clush and pdsh, it is able to run commands remotely on nodes. Additionally, NodeMan is more flexible. For example, it can interact with IPMI and naturally processes node lists for orchestrating different tools. The library of useful pre-built functions is growing. System administrators can easily create new functions and make it their own.

Serr, ScottM

Respiration Signal Pattern Analysis for Doppler Radar Sensor with Passive Node and Its Application in Occupancy Sensing of a Stationary Subject

Doppler radar node occupancy sensors are promising for applications in smart buildings due to their simple circuits and price advantage compared to quadrature radar sensors. However, single-channel sensitivity limitations may result in low sensitivity and misinterpreted motion rates if the detected subject is at or close to “null” points. We designed and tested a novel method to eliminate such limits, demonstrating that passive nodes can be used to detect a sedentary person regardless of position. This method is based on characteristics of chest motion due to respiration, found via both simulations and experiments based on a sinusoidal model and a more realistic model of cardiorespiratory motion. In addition, respiratory rate variability is considered to distinguish a true human presence from a mechanical target. Sensor node data were collected simultaneously with an infrared camera system, which provided a respiration signal reference, to test the algorithm with 19 human subjects and a mechanical target. The results indicate that a human presence was detected with 100% accuracy and successfully differentiated from a mechanical target in a controlled environment. The developed method can greatly improve the occupancy detection accuracy of single-channel radar-based occupancy sensors and facilitate their adoption in smart building applications.

Song, Chenyan

SympGNNs: Symplectic Graph Neural Networks for identifying high-dimensional Hamiltonian systems and node classification

Existing neural network models to learn Hamiltonian systems, such as SympNets, although accurate in low-dimensions, struggle to learn the correct dynamics for high-dimensional many-body systems. Herein, we introduce Symplectic Graph Neural Networks (SympGNNs) that can effectively handle system identification in high-dimensional Hamiltonian systems, as well as node classification. SympGNNs combine symplectic maps with permutation equivariance, a property of graph neural networks. Specifically, we propose two variants of SympGNNs: (i) G-SympGNN and (ii) LA-SympGNN, arising from different parameterizations of the kinetic and potential energy. We demonstrate the capabilities of SympGNN on two physical examples: a 40-particle coupled Harmonic oscillator, and a 2000-particle molecular dynamics simulation in a two-dimensional Lennard-Jones potential. Furthermore, we demonstrate the performance of SympGNN in the node classification task, achieving accuracy comparable to the state-of-the-art. Finally, we also empirically show that SympGNN can overcome the oversmoothing and heterophily problems, two key challenges in the field of graph neural networks.

Deep learning

Exploring the Computational Aspects of Propylene Oligomerization Catalysis Using M′ 2 M Type Trimetallic MOF Nodes

Metal-organic frameworks have emerged as promising materials in the field of catalysis. They offer an optimal ground for screening catalysts and tailoring their catalytic properties. Here, in this work, via density functional theory (DFT) calculations, we investigated the catalytic activity of the trimetallic MOF nodes, M' 2 M for propylene oligomerization, by varying the active metal M from Sc to Cu with M' being Fe, aiming to grasp the impact of altering the active atoms on the catalyst's activity. Additionally, we examined how substituting the spectator atom, M', with other transition metals, i.e., from Sc to Cu, affects these energy barriers, keeping Ni as the active metal. We proposed several cases with lower or comparable energy barriers to the experimentally reported Fe 2 Ni trimetallic MOF node. In addition, we found a correlative relationship between spin-density from natural population analysis and energy barriers in the realm of C-C bond formation, whereby an elevation in spin-density is found to be inversely proportional to the magnitude of the energy barriers. Moreover, we calculated the energy barriers for C-C coupling and beta-hydride elimination using multireference NEVPT2 calculations on top of the CASSCF wave function to validate the rate-determining step that is predicted by DFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Reproducibility of fixed-node diffusion Monte Carlo across diverse community codes: The case of water–methane dimer

Fixed-node diffusion quantum Monte Carlo (FN-DMC) is a widely trusted many-body method for solving the Schrödinger equation, known for its reliable predictions of material and molecular properties. Furthermore, its excellent scalability with system complexity and near-perfect utilization of computational power make FN-DMC ideally positioned to leverage new advances in computing to address increasingly complex scientific problems. Even though the method is widely used as a computational gold standard, reproducibility across the numerous FN-DMC code implementations has yet to be demonstrated. This difficulty stems from the diverse array of DMC algorithms and trial wave functions, compounded by the method’s inherent stochastic nature. Here, this study represents a community-wide effort to assess the reproducibility of the method, affirming that yes, FN-DMC is reproducible (when handled with care). Using the water–methane dimer as the canonical test case, we compare results from eleven different FN-DMC codes and show that the approximations to treat the non-locality of pseudopotentials are the primary source of the discrepancies between them. In particular, we demonstrate that, for the same choice of determinantal component in the trial wave function, reliable and reproducible predictions can be achieved by employing the T-move, the determinant locality approximation, or the determinant T-move schemes, while the older locality approximation leads to considerable variability in results. These findings demonstrate that, with appropriate choices of algorithmic details, fixed-node DMC is reproducible across diverse community codes—highlighting the maturity and robustness of the method as a tool for open and reliable computational science.

Della Pia, Flaviano [Univ. of Cambridge (United Ki

Fine-Grained Power and Energy Attribution on AMD GPU/APU-Based Exascale Nodes

Modern exascale GPU- and APU-based systems provide multiple power and energy sensors, but differences in scope, update rate, timing, and filtering complicate the attribution of short-lived accelerator activity. This paper presents a methodology to characterize and correct these effects on Cray EX systems with AMD Instinct MI250X GPUs (Frontier) and MI300A APUs (Portage). Using controlled square-wave workloads, we quantify update intervals, delay, aliasing, and variability across up to 512 GPUs and 480 APUs with on-chip (rocm-smi/amd-smi) and off-chip Cray Power Management sensors. We reconstruct power from cumulative energy counters to achieve faster response times, validate it against on-chip, off-chip, and node-level sensors, and integrate the resulting streams into a Score-P/PAPI-based tool for time-aligned, phase-level attribution. Applied to rocHPL, rocHPL-MxP, and HPG-MxP, the method separates energy savings due to reduced runtime from changes in power. Mixed precision reduces node energy on Frontier by 79% for rocHPL-MxP and 31% for HPG-MxP, with similar trends on Portage. These results provide portable guidance for sensor validation and power-aware optimization on current and future exascale systems.

Mcdaniel, Adam [ORNL] (ORCID:000000016926028X)

Multiple-amplifier sensing charged-coupled device: model and improvement of the node removal efficiency

The multiple-amplifier sensing charge-coupled device (MAS-CCD) has emerged as a promising technology for astronomical observation, quantum imaging, and low-energy particle detection due to its ability to reduce the readout time for the same readout noise level compared with its predecessor, the skipper-CCD, by reading out the same charge packet through multiple inline amplifiers. Previous works identified a new parameter in this sensor, called node removal inefficiency (NRI), related to inefficiencies in charge transfer and residual charge removal from the sense node of each amplifier after readout. These inefficiencies can lead to distortions in the measured signals similar to those produced by the charge transfer inefficiencies in standard CCDs. We introduce more details in the mathematical model of the NRI mechanism and provide techniques to quantify its magnitude from the measured data. It also proposes a new operation strategy that significantly reduces its effect with minimal alterations of the timing sequences or voltage settings for the other signals of the sensor. The proposed technique is demonstrated experimentally on a 16-amplifier MAS-CCD. At the same time, the experimental data demonstrate that this approach minimizes the NRI effect to levels comparable with other sources of distortion such as the charge transfer inefficiency in scientific devices.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND