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At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Maskman

SAND2025-04369O Maskman is a user-friendly tool designed to create hex masks, which are essential for optimizing application performance in high-performance computing environments. By converting a list of integers into binary and then hex masks, Maskman simplifies the process of setting application affinity. This ensures that software runs efficiently on specific nodes within a computing cluster. Ideal for researchers and developers, Maskman streamlines the preparation of inputs for HPC schedulers, enhancing resource management and improving overall system performance. 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.

Pase, Douglas [Sandia National Lab. (SNL-CA), Live↗
DOE OSTI2025

MiniMOD

SAND2025-03854O MiniMod is a user-friendly software tool designed to assess the performance of high-performance computing (HPC) systems. Researchers can use the program to test communication methods and computational tasks to understand how different setups can affect application efficiency. This software is particularly useful for optimizing network performance in scientific research, simulations, and data analysis. MiniMod‘s flexible design allows users to make informed decisions about their computing environments, which can enhance productivity and results in real-world applications. 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.

Dosanjh, Matthew [Sandia National Lab. (SNL-CA), L↗
DOE OSTI2025

Hiperclust

This software leverages transfer learning to analyze atom probe tomography (APT) data. It is trained on synthetic data and then applies this knowledge to predict the optimal number of clusters for a given APT dataset. Initially, the software used preliminary clustering to estimate the general structure of the data. Based on this, it provides suggestions for key parameters like minimum cluster size and minimum number of points. These parameters are critical for algorithms like HDBSCAN, ensuring accurate cluster formation without the need for trial-and-error testing. The software runs on High-Performance computing (HPC) systems, enabling fast, scalable analysis of large APT datasets, ultimately saving time and improving the reliability of clustering outcomes.

Tang, Yalei [Idaho National Laboratory (INL), Idah↗
DOE OSTI2026

Roadrunner

SAND2026-17073O Roadrunner software provides a comprehensive platform for simulating the mechanical behavior of crystalline materials under various loading conditions, allowing users to investigate the effects of dislocation slip hardening and damage evolution. Developed as a fork of the Multiphysics Object Oriented Simulation Environment (MOOSE) software from Idaho National Laboratory, Roadrunner is optimized for high-performance computing and can simulate large-scale problems, enabling researchers to explore complex scenarios. Its applications include material design and optimization in aerospace and automotive industries, investigation of failure mechanisms in structural materials, and development of predictive models for crystalline materials under various loading conditions. 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.

Lim, Hojun [Sandia National Lab. (SNL-CA), Livermo↗
DOE OSTI2026

ExaGO v2

ExaGO is a high-performance computing power systems modeling suite providing models for different power flow analyses. It supports forward AC power flow, multiperiod AC and DC optimal power flow analyses, contingency analysis, as well as stochastic optimal power flow analysis. ExaGO can use HiOp and Ipopt optimization engines. It supports Matpower and PSS/E input file formats. ExaGO v2 includes code from ExaGO 1.6.0.

Peles, Slaven [Oak Ridge National Laboratory (ORNL↗
DOE OSTI2026

panhandle

A project to provide user activity monitoring for High Performance Computing systems and clusters. The goal is to provide effective user activity monitoring with minimal performance impact on the host running this service.

McGee, David [@LANL @USMC @DoD]↗
DOE OSTI2026

wastewater_virus

This repo contains software used to clean and assemble high-throughput sequencing data containing viruses. The input is raw illumina sequencing reads and the output is a database of high-quality viral genomes. The specific application is to wastewater viral concentrates but it is not restricted to that sample type. The software is composed of Nextflow workflows and a set of custom Python and bash scripts that call publicly available bioinformatics tools to accomplish obvious tasks in data analysis in a high performance computing environment. For detailed information, please see the repo's README file.

Kantor, Rose [Lawrence Livermore National Laborato↗
DOE OSTI2025

Ocean Model for E3SM Global Applications (OMEGA)

This ocean model is the next generation version of the previous LANL developed MPAS-Ocean (Model for Prediction Across Scales) Ocean model. It is specifically designed to be used effectively on high performance computing, in particular GPU enabled architectures.

Van Roekel, Luke↗
DOE OSTI2025

An HPC benchmark survey and taxonomy for characterization

The field of High-Performance Computing (HPC) is defined by providing computing devices with highest performance for a variety of demanding scientific users. The tight co-design relationship between HPC providers and users propels the field forward, paired with technological improvements, achieving continuously higher performance and resource utilization. A key device for system architects, architecture researchers, and scientific users are benchmarks, allowing for well-defined assessment of hardware, software, and algorithms. Many benchmarks exist in the community, from individual niche benchmarks testing specific features, to large-scale benchmark suites for whole procurements. We survey the available HPC benchmarks, summarizing them in table form with key details and concise categorization, also through an interactive website. For categorization, we present a benchmark taxonomy for well-defined characterization of benchmarks.

Benchmarking↗
DOE OSTI2023

Galba: genome annotation with miniprot and AUGUSTUS

The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Providing Geospatial Intelligence through a Scalable Imagery Pipeline

This chapter describes ORNL’s (Oak Ridge National Laboratory’s) contributions to imagery preprocessing for geospatial intelligence research and development (R&D) in four sections. First, we discuss challenges involved in building an effective imagery preprocessing workflow and the world-class high-performance computing (HPC) resources at ORNL available to process petabytes of imagery data. Second, we highlight how we developed imagery preprocessing tools over three decades while paving the way for our current cutting-edge machine learning and computer vision algorithms that are impacting humanitarian and disaster response efforts. Third, we discuss how PIPE modules work together to turn raw images into analysis-ready datasets. Fourth, we look toward the future and discuss planned advancements to PIPE and computing trends that will affect geospatial intelligence R&D.

Reith, Andrew↗
DOE OSTI2025

If We Build Them, They Will Run: Automated HPC Apps Deployment and Profiling with eBPF in Cloud

The high performance computing (HPC) community is in a period of transition. The rise of AI/ML coupled with a changing landscape of resources deems portability a new metric of performance, and methods to move between on-premises and cloud environments and assess compatibility are paramount. Here we design and test a strategy for bridging the gap between traditional HPC and Kubernetes environments – first containerizing applications, providing automated orchestration to run studies, and packaging the setup with automated means to assess performance using low overhead eXtended Berkeley Packet Filter (eBPF) programs. We first assess different designs for eBPF collection, demonstrating a tradeoff between number of programs deployed on a node and overhead added. We develop 5 low overhead eBPF programs that combine with streaming ML models to assess CPU, futex, TCP, shared memory, and file access across four different builds of an HPC application for CPU and GPU. We use eBPF data to generate insights into the possible underlying etiology of scaling issues. We then assess compatibility of a well-known benchmark, HPCG, across matrices of micro-architectures and optimization levels (217 containers across 24 instance types and over 7500 runs). We provide to the community 30 applications to deploy in our automated setup and perform a scaling study from 4 to a maximum of 256 nodes for both CPU and GPU applications. Finally, we use our gained knowledge about performance to generate compatibility artifacts that are used by a newly developed Kubernetes controller to intelligently select instance type based on optimizing a figure of merit. Along with insights to scaling in this environment with a collection of applications and templates to work from, we provide an overall strategy for approaching HPC application deployment and image selection based on compatibility in cloud.

Computer science↗
DOE OSTI2021

SMC 2021 : Analyzing Resource Utilization and User Behavior on Titan Supercomputer

Resource utilization statistics of submitted jobs on a supercomputer can help us understand how users from various scientific domains use HPC platforms and better design a job scheduler. We explore to generate insight regarding workload distribution and usage pattern domains from job scheduler trace, GPU failure information, and project-specific information collected from Titan supercomputer. Furthermore, we want to know how the scheduler performance varies over time and how the users' scheduling behavior changes following a system failure. These observations have the potential to provide valuable insight, which is helpful to prepare for system failures. These practices will help us develop and apply novel machine learning algorithms in understanding system behavior, requirement, and better scheduling of HPC systems. There are two datasets, RUR and GPU. RUR: This dataset is the job scheduler traces collected from the Titan supercomputerfrom 01/01/2015 to 07/31/2019 (2015.csv - 2019.csv). These were collected usingResource Utilization Report (RUR), a Cray-developed resource-usage data collectionand reporting system. It contains the usage information of its critical resources (CPU,Memory, GPU, and I/O) of each running job on Titan during that period [2]. ProjectAreas: Every job is associated with a project ID. TheProjectAreas.csvdatasetprovides a mapping of the project ID to its domain science. GPU: There have been some hardware-related issues in the GPUs in Titan that caused some GPUs to fail, sometimes irrecoverably during some job runs. This dataset provides information regarding these failures during the execution of the submitted jobs. GPUs on Titan are uniquely identified by a serial number (SN), and they are installed in a location. A GPU can be installed in a location, then removed from that location following a failure, and then re-installed in a different location after fixing the problem. If the failure can't be recovered, the GPU might be removed entirely from Titan. There are two prominent types of failures that resulted in the removal of GPUs from Titan: Double Bit Error (DBE) and Out of the Bus (OTB). The dataset (gc_full.csv) has the following fields: 1. SN : Serial number of a GPU 2. location : The location where it is installed 3. insert : The time when it was inserted into that location 4. remove : The time when it was removed from that location 5. duration : Amount of time the GPU spent in this location 6. out : If the device was taken out entirely w/o a re-installment into a new location. 7. event : If the GPU was taken out entirely, the reason for its removal. To learn more about this dataset, please refer to the git repositoryhttps://github.com/olcf/TitanGPULifeand the related publication [1]. References [1] George Ostrouchov, Don Maxwell, Rizwan A Ashraf, Christian Engelmann, MallikarjunShankar, and James H Rogers. Gpu lifetimes on titan supercomputer: Survival analysisand reliability. InSC20: International Conference for High Performance Computing,Networking, Storage and Analysis, pages 1-14. IEEE, 2020. [2] Feiyi Wang, Sarp Oral, Satyabrata Sen, and Neena Imam. Learning from five-yearresource-utilization data of titan system. In2019 IEEE International Conference onCluster Computing (CLUSTER), pages 1-6. IEEE, 2019.

42 ENGINEERING↗
DOE OSTI2020

GPU Lifetimes on Titan Supercomputer: Survival Analysis and Reliability

George Ostrouchov, Don Maxwell, Rizwan Ashraf, Mallikarjun Shankar, and James Rogers. 2020. GPU Lifetimes on Titan Supercomputer: Survival Analysis and Reliability. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '20). Association for Computing Machinery, New York, NY, USA. Data and code for SC20 paper about Titan GPU reliability analysis: https://github.com/olcf/TitanGPULife. Includes R code to generate graphics for paper and additional analyses. See code/README for instructions. Includes original Titan GPU reliability data on over 100,000 collective hours of operation: data/titan.gpu.history.txt - history data, data/titan.service.txt - service nodes for exclusion. Includes output data files produced by code/TitanGPUmodel.Rmd: data/gc_full.csv - cleaned up data (see paper and R code); data/gc_summary_loc.csv - one record per GPU (variables: SN, time, nlife, nloc, last, col, row, cage, slot, node, max_loc_events, time_max_loc, dbe, dbe_loc, otb, otb_loc, out, batch, days, years, dead, dead_otb, dead_dbe) (see paper and R code). Includes .Rmd analysis document as TitanGPUmode.html. Includes Python code to process data/gc_full.csv into graphics from time-between-failure analyses: See code/tbf-analyses/README for instructions.

42 ENGINEERING↗
DOE OSTI2021

Model America - data and models of every U.S. building

The 5-year goal of the 'Model America' concept was to generate a model of every building in the United States. This data repository delivers on that goal. Oak Ridge National Laboratory (ORNL) has developed the Automatic Building Energy Modeling (AutoBEM) software suite to process multiple types of data, extract building-specific descriptors, generate building energy models, and simulate them on High Performance Computing (HPC) resources. For more information, see AutoBEM-related publications (bit.ly/AutoBEM). There were 125,714,640 buildings detected in the United States and this dataset contains 122,930,327 (97.8%) buildings which resulted in a successful simulation. Future, annual updates have been proposed that may include additional buildings, data improvements, or other algorithmic enhancements. This dataset of 122.9 million buildings includes: Models (state_county.zip) - OpenStudio (v3.1.0) and EnergyPlus (v9.4) building energy models. Please note that the download requires the free Globus Connect Personal (https://www.globus.org/globus-connect-personal); Each model has approximately 3,000 building input descriptors that can be extracted. Please see the EnergyPlus(v9.4) 2,784-page Input/Output Reference Guide (https://energyplus.net/sites/all/modules/custom/nrel_custom/pdfs/pdfs_v9.4.0/InputOutputReference.pdf) for everything that can be retrieved or simulated from these models. These models were derived from the following metadata, which is not included in this dataset: 1. ID - unique building ID 2. County - county name 3. State - state name 4. CZ - ASHRAE Climate Zone designation 5. Clim_Zone - text label of climate zone 6. est_year - estimated year of construction 7. est_commercial - estimated building type (0=residential, 1=commercial) 8. Centroid - building center location in latitude/longitude (from Footprint2D) 9. Footprint2D - building polygon of 2D footprint (lat1/lon1_lat2/lon2_...) 10. Height - building height (meters) 11. Area2D - footprint area (ft2) 12. BuildingType - DOE prototype building designation (IECC=residential) as implemented by OpenStudio-standards 13. WWR_surfaces - percent of each facade (pair of points from Footprint2D) covered by fenestration/windows (average 14.5% for residential, 40% for commercial buildings) 14. NumFloors - number of floors (above-grade) 15. Area - estimate of total conditioned floor area (ft2) 16. Standard - building vintage. These models are made free and openly available in hopes of stimulating any simulation-informed use case. Data is provided as-is with no warranties, express or implied, regarding fitness for a particular purpose. We wish to thank our sponsors which include Oak Ridge National Laboratory (ORNL) Laboratory Directed Research and Development (LDRD), U.S. Dept. of Energy's (DOE) Building Technologies Office (BTO), Office of Electricity (OE), Biological and Environmental Research (BER), and National Nuclear Security Administration (NNSA). This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357. Please cite as: New, Joshua R., Adams, Mark, Bass, Brett, Berres, Anne, and Clinton, Nicholas (2021). 'Model America - data and models of every U.S. building. [Data set].' Constellation, doi.ccs.ornl.gov/ui/doi/339, April 14, 2021

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Machine Learning assisted optimization and parameter space exploration dataset of spin ice Hamiltonian

This repository contains both simulated and experimental structure factor data for the data challenge involving the inverse scattering problem. The simulated data were generated during a machine-learning-assisted optimization routine described in ref[1]. The experimental structure factor was measured on a rare-earth oxide, Dy2Ti2O7 using diffuse neutron scattering from time-of-flight techniques on the CORELLI instrument at the Spallation Neutron Source, Oak Ridge National Laboratory. A Metropolis Monte Carlo code implemented to run in a High-performance computing setting was used to calculated simulated structure factors for the spin-ice Hamiltonian at 680 mK, which is the same temperature as for the experimental data. The total size of all the files in this repository is 5.12 GB. A detailed description of the files is given below. ExperimentalData_630mK.dat – A linearized version of 3-dimensional experimental data of size 61×81×21. This data was processed to remove an estimation of non-magnetic background, including nuclear scattering signal and instrumentation background. Parameters.dat – 6700 samples were evaluated over the 4-dimensional parameter space (J_1, J_2, J_3 and J_(3^' )). There is an additional parameter, D in the spin Hamiltonian to mimic the dipolar interaction between magnetic ions. However, this parameter, D was fixed to a value determined by prior work. This file contains five columns for the parameters J_1, J_2, J_3, J_(3^' ) and D respectively. 3D_Simulation_Data.dat – The simulated structure factor, S(Q) data are included in this file. Each raw contains a linearized array of 3D volumes of S(Q) calculated for the parameter set given in the corresponding row of the file Parameters.dat. The size of the volume data was matched to the experimental data. Qx(h,-h,0).dat, Qy(k,k,-2k).dat, Qz(l,l,l).dat – These files contain the h, k, and l values along with the reciprocal vectors [h,-h,0], [k,k,-2k] and [l,l,l] respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Flexspander: augmenting expander networks in high-performance systems with optical bandwidth steering

Communication efficiency is one of the deciding factors in determining many of today’s high-performance computing (HPC) applications. Traditionally, HPC systems have been on static network topologies, making them inflexible to the variety of skewed traffic demands that may arise due to the spatial locality inherent in many applications. To handle traffic locality, researchers have proposed integrating optical circuit switches (OCSs) into the network architecture, which reconfigures the network topology to alter and dynamically adapt to the predicted traffic. In this paper, we present a novel reconfigurable network topology called Flexspander. Beyond offering a flexible interconnect, Flexspander also offers full flexibility in terms of construction and can be built with any arbitrary combination of commercial electrical packet switches and OCSs. We evaluate Flexspander performance through extensive simulations with multiple network traces, and our results show improved performance for Flexspander over currently proposed static and reconfigurable topologies in terms of the flow completion time.

Teh, Min Yee↗
DOE OSTI2022

Toward higher-radix switches with co-packaged optics for improved network locality in data center and HPC networks [Invited]

In this work, we study the network locality improvements that can be achieved by using co-packaged optics in data center and high-performance computing (HPC) networks. The increased escape bandwidth offered by co-packaged optics can enable switches with speeds of 51.2 Tb/s and beyond. From a network architecture perspective, the key advantages of introducing co-packaged optics at the switch points include the implementation of large-scale topologies of >12,000 end points with 4× higher bisection bandwidth and the reduction of the required number of switches by >40% compared with state-of-the-art approaches. From a network operation perspective, improved network locality and faster operation can be achieved since the higher-radix switches can mitigate the impact of network contention. Placing applications under fewer leaf switches reduces the number of packets that cross the spine switches in a leaf-spine topology. The proposed scheme is evaluated via discrete-event simulations: we initially evaluate the network locality properties of the system by using virtual-machine traces from a production data center, and we subsequently quantify the performance improvements by simulating an all-to-all pattern for a variety of message sizes over a number of nodes. The results suggest that co-packaged optics form a promising solution for keeping up with bandwidth scaling in future networks. The virtual-machine analysis shows that large-scale applications can be placed under up to 50% fewer first-level switches, while the network analysis shows speedups of up to 7.1, which translates to execution time reductions of up to 26% and 42.7% for applications with communication ratios of 0.3 and 0.5, respectively.

99 GENERAL AND MISCELLANEOUS↗