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DOE OSTI2017

UNITY: Unified Memory and File Space

This paper describes the vision for UNITY, a new high-performance computing focused data storage abstraction that places the entire memory hierarchy, including both traditionally separated memoryand file-based data storage, into one storage continuum. Through the use of a novel API and a set of services centered around a smart runtime system, UNITY is able to provide a number of valuable and interesting benefits. The unified storage space provides a scalable and resilient data environment that dynamically manages the mapping of data onto available resources based on multiple factors, including desired persistence and energy budget considerations. By eliminating the need for high-performance computing domain scientists to develop architecture-dependent optimizations for rapidly evolving data storage technologies, UNITY addresses both ease-of-use and performance.

Otstott, Douglas↗

DOE OSTI2017

UNITY: Unified Memory and File Space. In: ROSS '17 Proceedings of the 7th International Workshop on Runtime and Operating Systems for Supercomputers ROSS 2017, Article No. 6

This paper describes the vision for UNITY, a new high-performance computing focused data storage abstraction that places the entire memory hierarchy, including both traditionally separated memory-and file-based data storage, into one storage continuum. Through the use of a novel API and a set of services centered around a smart runtime system, UNITY is able to provide a number of valuable and interesting benefits. The unified storage space provides a scalable and resilient data environment that dynamically manages the mapping of data onto available resources based on multiple factors, including desired persistence and energy budget considerations. By eliminating the need for high-performance computing domain scientists to develop architecture-dependent optimizations for rapidly evolving data storage technologies, UNITY addresses both ease-of-use and performance.

Jones, Terry↗

DOE OSTI2023

BMX: Biological modelling and interface exchange

Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Uncovering I/O demands on HPC platforms: Peeking under the hood of Santos Dumont

High-Performance Computing (HPC) platforms are required to solve the most diverse large-scale scientific problems in various research areas, such as biology, chemistry, physics, and health sciences. Researchers use a multitude of scientific softwares, which have different requirements. These include input and output operations, which directly impact performance due to the existing difference in processing and data access speeds. Thus, supercomputers must efficiently handle mixed workload when storing data from the applications. Understanding the set of applications and their performance running in a supercomputer is paramount to understanding the storage system's usage, pinpointing possible bottlenecks, and guiding optimization techniques. This research proposes a methodology and visualization tool to evaluate a supercomputer's data storage infrastructure's performance, taking into account the diverse workload and demands of the system over a long period of operation. As a study case, we focus on the Santos Dumont supercomputer, identifying inefficient usage, problematic performance factors, and providing guidelines on how to tackle those issues.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Defining quantum-ready primitives for hybrid HPC-QC supercomputing: a case study in Hamiltonian simulation

As computational demands in scientific applications continue to rise, hybrid high-performance computing (HPC) systems integrating classical and quantum computers (HPC-QC) are emerging as a promising approach to tackling complex computational challenges. One critical area of application is Hamiltonian simulation, a fundamental task in quantum physics and other large-scale scientific domains. This paper investigates strategies for quantum-classical integration to enhance Hamiltonian simulation within hybrid supercomputing environments. By analyzing computational primitives in HPC allocations dedicated to these tasks, we identify key components in Hamiltonian simulation workflows that stand to benefit from quantum acceleration. To this end, we systematically break down the Hamiltonian simulation process into discrete computational phases, highlighting specific primitives that could be effectively offloaded to quantum processors for improved efficiency. Our empirical findings provide insights into system integration, potential offloading techniques, and the challenges of achieving seamless quantum-classical interoperability. We assess the feasibility of quantum-ready primitives within HPC workflows and discuss key barriers such as synchronization, data transfer latency, and algorithmic adaptability. These results contribute to the ongoing development of optimized hybrid solutions, advancing the role of quantum-enhanced computing in scientific research.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

High-Accuracy Simulations to Model Pyrometallurgical Processes in a Secondary Lead Reverberatory Furnace

The US manufacturing industry produces about 1.3 million tons of refined lead each year using secondary sources consisting mainly of lead batteries. ORNL is partnering with Gopher resource, the second largest lead recycling company in the United States, and GTI, to develop a high-fidelity CFD model of a directly fired, reverberatory-style, secondary lead furnace. These High Performance Computing (HPC) simulations are aimed to use first principles modeling for combustion and melting processes of the secondary lead feed while accounting for complex interphase interactions between the gas, solid charge (lead) material, slag, and metal phases. Through validation against operating plant data, this effort will enable significant improvements in design, operational parameters, and energy efficiency, thus improving productivity and refractory lifetime of secondary lead melting furnaces. Estimated savings/reduction of, at least, 1 trillion BTU, 1 million ton/year of greenhouse gas emissions, and $\$50$ million/year to the US lead industry can be expected. ORNL resources and expertise in high-performance computing and multicomponent, multiphase flows were utilized to realize this goal while advancing the understanding of the smelting and melting processes occurring within the furnace.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

DuoModel: Leveraging Reduced Model for Data Reduction and Re-Computation on HPC Storage

High-performance computing (HPC) applications generate large amounts of floating-point data that need to be stored and analyzed efficiently to extract the insights and advance knowledge discovery. With the growing disparities between compute and I/O, optimizing the storage stack alone may not suffice to cure the I/O problem. There has been a strong push in the HPC communities to perform data reduction before data is transmitted to storage in order to lower the I/O cost. However, as of now, neither lossless nor lossy compressors can achieve the adequate reduction ratio that is desired by applications. This paper proposes DuoModel, a new approach that leverages the similarity between the full and reduced application models, and further improve the data reduction ratio. DouModel further improves the compression ratio of state-of-the-art compressors via compressing the differences (termed as delta) between the data products of the two models. For data analytics, the high fidelity data can be re-computed by launching the reduced model and applying the compressed delta. Our evaluations confirm that DuoModel can further push the limit of data reduction while the high fidelity of data is maintained.

Luo, Huizhang (ORCID:0000000323920267)↗

DOE OSTI2023

Multi-Model Future Typical Meteorological (fTMY) Weather Files for nearly every US County

Exploring climate-induced impacts on building energy consumption can provide valuable insights for sustainable energy planning and environmental management in the face of a changing climate. By utilizing future weather data statistically downscaled from the Intergovernmental Panel on Climate Change (IPCC) General Circulation Models (GCMs) from 2020-2100, this paper presents a broadening industry-consensus approach for generating future Typical Meteorological Year (fTMY) weather files through a combination of statistical downscaling and high-performance computing that generalizes across decades, multiple locations for a region, and varying climate models. Furthermore, these fTMY files have been generated for 3,128 US counties for capturing potential weather on a 20-year basis.

Building↗

DOE OSTI2020

PtychoShelves , a versatile high-level framework for high-performance analysis of ptychographic data

Over the past decade, ptychography has been proven to be a robust tool for non-destructive high-resolution quantitative electron, X-ray and optical microscopy. It allows for quantitative reconstruction of the specimen's transmissivity, as well as recovery of the illuminating wavefront. Additionally, various algorithms have been developed to account for systematic errors and improved convergence. With fast ptychographic microscopes and more advanced algorithms, both the complexity of the reconstruction task and the data volume increase significantly. PtychoShelves is a software package which combines high-level modularity for easy and fast changes to the data-processing pipeline, and high-performance computing on CPUs and GPUs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Design and implementation of I/O performance prediction scheme on HPC systems through large-scale log analysis

Abstract Large-scale high performance computing (HPC) systems typically consist of many thousands of CPUs and storage units used by hundreds to thousands of users simultaneously. Applications from large numbers of users have diverse characteristics, such as varying computation, communication, memory, and I/O intensity. A good understanding of the performance characteristics of each user application is important for job scheduling and resource provisioning. Among these performance characteristics, I/O performance is becoming increasingly important as data sizes rapidly increase and large-scale applications, such as simulation and model training, are widely adopted. However, predicting I/O performance is difficult because I/O systems are shared among all users and involve many layers of software and hardware stack, including the application, network interconnect, operating system, file system, and storage devices. Furthermore, updates to these layers and changes in system management policy can significantly alter the I/O behavior of applications and the entire system. To improve the prediction of the I/O performance on HPC systems, we propose integrating information from several different system logs and developing a regression-based approach to predict the I/O performance. Our proposed scheme can dynamically select the most relevant features from the log entries using various feature selection algorithms and scoring functions, and can automatically select the regression algorithm with the best accuracy for the prediction task. The evaluation results show that our proposed scheme can predict the write performance with up to 90% prediction accuracy and the read performance with up to 99% prediction accuracy using the real logs from the Cori supercomputer system at NERSC.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1991

Robo-line storage: Low latency, high capacity storage systems over geographically distributed networks

Rapid advances in high performance computing are making possible more complete and accurate computer-based modeling of complex physical phenomena, such as weather front interactions, dynamics of chemical reactions, numerical aerodynamic analysis of airframes, and ocean-land-atmosphere interactions. Many of these 'grand challenge' applications are as demanding of the underlying storage system, in terms of their capacity and bandwidth requirements, as they are on the computational power of the processor. A global view of the Earth's ocean chlorophyll and land vegetation requires over 2 terabytes of raw satellite image data. In this paper, we describe our planned research program in high capacity, high bandwidth storage systems. The project has four overall goals. First, we will examine new methods for high capacity storage systems, made possible by low cost, small form factor magnetic and optical tape systems. Second, access to the storage system will be low latency and high bandwidth. To achieve this, we must interleave data transfer at all levels of the storage system, including devices, controllers, servers, and communications links. Latency will be reduced by extensive caching throughout the storage hierarchy. Third, we will provide effective management of a storage hierarchy, extending the techniques already developed for the Log Structured File System. Finally, we will construct a protototype high capacity file server, suitable for use on the National Research and Education Network (NREN). Such research must be a Cornerstone of any coherent program in high performance computing and communications.

Katz, Randy H.↗

NASA NTRS2018

Smallholder Crop Area Mapped with Wall-To-Wall WorldView Sub-Meter Panchromatic Image Texture: A Test Case for Tigray, Ethiopia

Global food production in the developing world occurs within sub-hectare fields that are difficult to identify with moderate resolution satellite imagery. Knowledge about the distribution of these fields is critical in food security programs. We developed a semi-automated image segmentation approach using wall-to-wall sub-meter imagery with high-performance computing to map crop area (CA) throughout Tigray, Ethiopia that encompasses over 41,000 km (exp 2). Multiple processing streams were tested to minimize mapping error while applying five unique smoothing kernels to capture differences in land surface texture associated to CA. Typically, very-small fields (mean < 2 ha) have a smooth image roughness compared to natural scrub/shrub woody vegetation at the ~1m scale and these features can be segmented in panchromatic imagery with multi-level histogram thresholding. Multi-temporal very-high resolution (VHR) panchromatic imagery with multi-spectral VHR are sufficient in extracting critical CA information needed in food security programs. A 2011 to 2015 CA map was produced, using over 3000 WorldView-1 panchromatic images wall-to-wall in 1/2 deg mosaics for Tigray, Ethiopia. CA was evaluated with nearly 3000 WorldView-2 2m multispectral 250 X 250 m image subsets by seven expert interpretations, and with in-situ global positioning system photography. CA estimates ranged from 32 to 41% in sub regions of Tigray with median maximum per bin commission and omission errors of 11% and 1% respectively, with most of the error occurring in bins <15%. This empirical, simple, and low direct cost approach via U.S. government license agreement to access commercial VHR data, could be a viable big-data high-performance computing methodology to extract wall-to-wall CA for other regions of the world that have very-small agriculture fields with similar image texture."

Ethiopia↗

DOE OSTI2025

VA EDH Advanced Software Pipeline Framework Report: Enhancing Automation and Scalability

The VA Environmental Determinants of Health (EDH) Advanced Software Pipeline Framework is designed to enhance the efficiency, scalability, and security of geospatial data processing workflows. This framework integrates modern data orchestration and containerization technologies, including Prefect for workflow automation, Docker for containerization, and PostgreSQL/PostGIS for geospatial data storage and analysis. It ensures standardized, reproducible, and automated data processing, supporting VA objectives related to substance use risk assessment and recovery research. The pipeline addresses key scalability and performance challenges through horizontal and vertical scaling, high-performance computing (HPC) integration, parallel processing, task caching, and dynamic resource allocation. These optimizations improve throughput and reduce latency, allowing the system to efficiently manage large and complex datasets. Additionally, security and compliance measures—such as data encryption (SSL), Role-Based Access Control (RBAC), and adherence to GDPR and HIPAA standards—safeguard sensitive information throughout data transmission and storage. A key implementation of this framework includes the automation of shelter list geolocation workflows, ensuring that up-to-date data is readily available for VA decision-making. Lessons learned from this project include the transition from in-memory processing to incremental storage writes, improving resource management and reliability. Future enhancements aim to expand automation, integrate AI-driven anomaly detection, and incorporate high-performance computing resources. This framework provides a scalable, secure, and adaptable solution for managing geospatial datasets, reinforcing the VA’s ability to support clinical and strategic initiatives through data-driven decision-making.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Learning from Five-year Resource-Utilization Data of Titan System

Titan was the flagship supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). It was deployed in late 2012, became the fastest supercomputer in the world and was retired on August 2, 2019. With Titan's mission complete, this paper provides a first-order examination of the usage of its critical resources (CPU, Memory, GPU, and I/O) over a five-year production period (2015-2019). In particular, we show quantitatively that the majority of CPU time was spent on the large-scale jobs, which is consistent with the policy of driving ground-breaking science through leadership computing. We also corroborate the general observation of the low CPU-memory usage with 95% jobs utilizing only 15% or less available memory. Additionally, we correlate the increase of total job submissions and the decrease of GPU-enabled jobs during 2016 with the GPU reliability issue which impacted the large-scale runs. We further show the surprising read/write ratio over the five-year period, which contradicts the general mindset of the large-scale simulation machines being “write-heavy”. This understanding will have potential impact on how we design our next-generation large-scale storage systems. We believe that our analyses and findings are going to be of great interest to the high-performance computing (HPC) community at large.

Wang, Feiyi↗

NASA NTRS2012

Social Networking Adapted for Distributed Scientific Collaboration

Share is a social networking site with novel, specially designed feature sets to enable simultaneous remote collaboration and sharing of large data sets among scientists. The site will include not only the standard features found on popular consumer-oriented social networking sites such as Facebook and Myspace, but also a number of powerful tools to extend its functionality to a science collaboration site. A Virtual Observatory is a promising technology for making data accessible from various missions and instruments through a Web browser. Sci-Share augments services provided by Virtual Observatories by enabling distributed collaboration and sharing of downloaded and/or processed data among scientists. This will, in turn, increase science returns from NASA missions. Sci-Share also enables better utilization of NASA s high-performance computing resources by providing an easy and central mechanism to access and share large files on users space or those saved on mass storage. The most common means of remote scientific collaboration today remains the trio of e-mail for electronic communication, FTP for file sharing, and personalized Web sites for dissemination of papers and research results. Each of these tools has well-known limitations. Sci-Share transforms the social networking paradigm into a scientific collaboration environment by offering powerful tools for cooperative discourse and digital content sharing. Sci-Share differentiates itself by serving as an online repository for users digital content with the following unique features: a) Sharing of any file type, any size, from anywhere; b) Creation of projects and groups for controlled sharing; c) Module for sharing files on HPC (High Performance Computing) sites; d) Universal accessibility of staged files as embedded links on other sites (e.g. Facebook) and tools (e.g. e-mail); e) Drag-and-drop transfer of large files, replacing awkward e-mail attachments (and file size limitations); f) Enterprise-level data and messaging encryption; and g) Easy-to-use intuitive workflow.

Karimabadi, Homa↗

DOE OSTI2025

An Efficient Storage-Driven Machine Learning Model for Performance in the Era of Multimodal Scientific Data

Scientific workflows are increasingly relying on machine learning (ML), simulation, and hybrid techniques to predict, understand, and optimize the behavior of complex experiments. High-performance computing has greatly improved researchers’ ability to acquire diverse data modalities in these workflows. Recent studies suggest that the performance of machine learning models can be improved by integrating data from various sources. Unfortunately, these workloads pose unprecedent pressure on the network storage to meet the demands associated with accessing these multimodal data. To mitigate the impact of intensive IO, we propose a solution that utilizes a multi-tier High-Performance Computing (HPC) distributed storage and data processing framework, placing computation where the data resides for better performance. By adopting this project, the scientific community will gain new opportunities to explore multimodal storage-driven possibilities, integrating multiple scientific data sources with advanced streaming frameworks. Additionally, our framework effectively utilizes computing resources and bridges the gaps identified by HPC experts. Our proposed approach tackles scalability and persistence challenges by leveraging native persistency, which has posed difficulties in traditional approaches. Furthermore, we seek to enhance fault-tolerance and load-balance of computations by leveraging real-time streaming in diverse scientific computing environments, thereby propelling advanced scientific computing research into the next generation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

HyperSpace: Distributed Bayesian Hyperparameter Optimization

As machine learning models continue to increase in complexity, so does the potential number of free model parameters commonly known as hyperparameters. While there has been considerable progress toward finding optimal configurations of these hyperparameters, many optimization procedures are treated as black boxes. We believe optimization methods should not only return a set of optimized hyperparameters, but also give insight into the effects of model hyperparameter settings. To this end, we present HyperSpace, a parallel implementation of Bayesian sequential model-based optimization. HyperSpace leverages high performance computing (HPC) resources to better understand unknown, potentially non-convex hyperparameter search spaces. We show that it is possible to learn the dependencies between model hyperparameters through the optimization process. By partitioning large search spaces and running many optimization procedures in parallel, we also show that it is possible to discover families of good hyperparameter settings over a variety of models including unsupervised clustering, regression, and classification tasks.

Computer Science↗

DOE OSTI2017

Distributed Workflows for Modeling Experimental Data

Modeling helps explain the fundamental physics hidden behind experimental data. In the case of material modeling, running one simulation rarely results in output that reproduces the experimental data. Often one or more of the force field parameters are not precisely known and must be optimized for the output to match that of the experiment. Since the simulations require high performance computing (HPC) resources and there are usually many simulations to run, a workflow is very useful to prevent errors and assure that the simulations are identical except for the parameters that need to be varied. These workflows are usually distributed because the simulations require HPC, but the optimization and steps to compare the simulation results and experimental data are done on a local workstation. We will present results from force field refinement of data collected at the Spallation Neutron Source using Kepler, Pegasus, and Beam workflows and discuss what we have learned from using these workflows.

Lynch, Vickie E.↗