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DOE OSTI2023

Visualizing the NIOSH Pocket Guide: Open-source web application for accessing and exploring the NIOSH Pocket Guide to Chemical Hazards

The NIOSH Pocket Guide to Chemical Hazards is a trusted resource that displays key information for a collection of chemicals commonly encountered in the workplace. Entries contain chemical structures—occupational exposure limit information ranging from limits based on full-shift time-weighted averages to acute limits such as short-term exposure limits and immediately dangerous to life or health values, as well as a variety of other data such as chemical-physical properties and symptoms of exposure. The NIOSH Pocket Guide (NPG) is available as a printed, hardcopy book, a PDF version, an electronic database, and a downloadable application for mobile phones. All formats of the NIOSH Pocket Guide allow users to access the data for each chemical separately, however, the guide does not support data analytics or visualization across chemicals. This project reformatted existing data in the NPG to make it searchable and compatible with exploration and analysis using a web application. The resulting application allows users to investigate the relationships between occupational exposure limits, the range and distribution of occupational exposure limits, and the specialized sorting of chemicals by health endpoint or to summarize information of particular interest. These tasks would have previously required manual extraction of the data and analysis. The usability of this application was evaluated among industrial hygienists and researchers and while the existing application seems most relevant to researchers, the open-source code and data are amenable to modification by users to increase customization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

A review of non-cognitive applications for neuromorphic computing

Abstract Though neuromorphic computers have typically targeted applications in machine learning and neuroscience (‘cognitive’ applications), they have many computational characteristics that are attractive for a wide variety of computational problems. In this work, we review the current state-of-the-art for non-cognitive applications on neuromorphic computers, including simple computational kernels for composition, graph algorithms, constrained optimization, and signal processing. We discuss the advantages of using neuromorphic computers for these different applications, as well as the challenges that still remain. The ultimate goal of this work is to bring awareness to this class of problems for neuromorphic systems to the broader community, particularly to encourage further work in this area and to make sure that these applications are considered in the design of future neuromorphic systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Addressing Load Imbalance in Bioinformatics and Biomedical Applications: Efficient Scheduling across Multiple GPUs

Computational bioinformatics and biomedical applications frequently contain heterogeneously sized units of work or tasks, for instance due to variability in the sizes of biological sequences and molecules. Variable-sized workloads lead to load imbalances in parallel implementations which detract from efficiency and performance. Many modern computing resources now have multiple graphics processing units(GPUs) per computer for acceleration. These multiple GPU resources need to be used efficiently through balancing of workloads across the GPUs. OpenMP is a portable directive-based parallel programming API used ubiquitously in bioscience applications to program CPUs; recently, the use of OpenMP directives for GPU acceleration has become possible. Here, motivated by experiences with imbalanced loads in GPU-accelerated bioinformatics applications, we address the load balancing problem using OpenMP task-to-GPU scheduling combined with OpenMP GPU offloading for multiply heterogeneous workloads – loads with both variable input sizes, and simultaneously, variable convergence rates for algorithms with a stochastic component – scheduled across multiple GPUs. We aim to develop strategies which are both easy to use and have lower overheads, and may be incorporated incrementally in existing programs which already make use of OpenMP for CPU-based threading in order to make use of multi-GPU computers. We test different combinations of input size variability and convergence rate variability, and characterize the effects of these different scenarios on the performance of scheduling strategies across multiple GPUs with OpenMP. We present several dynamic scheduling solutions for different parallel patterns, explore optimizations, and provide publicly available example computational kernels to make these strategies easy to use in programs. This work will enable application developers to efficiently and easily use multiple GPUs for imbalanced workloads found in bioinformatics and biomedical applications.

Thavappiragasam, Mathialakan↗

DOE OSTI2021

DynPaC: Coarse-Grained, Dynamic, and Partially Reconfigurable Array for Streaming Applications

Coarse-grained reconfigurable arrays (CGRAs) provide higher flexibility than application-specific integrated circuits (ASICs) and higher efficiency than fine-grained reconfigurable devices such as Field Programmable Gate Arrays (FPGAs). However, CGRAs are generally designed to support offloading of a single kernel. While their design, based on communicating functional units, appears to naturally suit streaming applications composed of multiple cooperating kernels, current approaches only statically partition the resources across kernels. However, streaming applications often are data-dependent, leading to variable kernel execution times depending on the input data and impacting the throughput of the entire pipeline if resources are statically allocated. Therefore, in this paper, we discuss the design of DynPaC — a coarse-grained, dynamically, and partially reconfigurable array for data-dependent streaming applications. We discuss the required software and hardware components to manage partial dynamic reconfiguration. We demonstrate that by supporting partial dynamic reconfiguration, we can obtain an average speedup of 1.44X for a representative set of applications w.r.t. static partitioning, with a limited area overhead (6.4% of the entire chip).

Tan, Cheng↗

DOE OSTI2021

An Application for Validation of Power Distribution System Models in an ADMS Environment

An accurate model of a power distribution system is the foundation for model-based applications that ensure efficient and reliable grid operation in an advanced distribution management system (ADMS) environment. However, these models are error-prone and comprehensive model validation is challenging due to lack of standards-based systems, data originating from disparate databases and other sources, and the constantly evolving nature of modern power distribution systems. In this paper, a novel framework for comprehensive model validation is described. The proposed application, the Model Validator, ensures that a model is both consistent and feasible by validating the derivative static and operational network model. A modular architecture for the application has been implemented and integrated with an open-source standards-based platform for ADMS application development, GridAPPS-D, allowing new validation capability to be added with minimal time and effort. The Model Validator application is demonstrated on the IEEE 13-bus, 123-bus, and 8500-node test cases over three validation scenarios.

Poudel, Shiva↗

DOE OSTI2022

Superconducting Shuttle-Flux Shift Register for Race Logic and Its Applications

Here this paper presents a superconducting, magnetically-coupled, shuttle-flux shift register (SF-SR) that stores single flux quantum (SFQ) pulses. This shift register has a DC bias operating margin of ±34% at 10 GHz, with a power dissipation of 3.6 μW and 38% fewer Josephson junctions (JJs) when scaled up to multiple stages compared to a data flip-flop (DFF) based shift register. The clock input is inductively coupled and is independent from the data input. We then present three applications for our SF-SR. In the first application, we add two non-destructive readout (NDRO) cells to construct a buffer that temporarily stores the temporal information of a series of race logic (RL) pulses. The second application is a pseudo-random number generator based on a linear function shift register (LFSR). The third application is N parallel SF-SRs that can act similar to a deserializer or instead can emulate a single SF-SR of N times higher clock frequency. These three applications motivate deep shift registers with many shifting intervals, which our SF-SR can implement with fewer JJs and lower power consumption compared to DFF-based shift registers.

42 ENGINEERING↗

DOE OSTI2020

Evaluation and Demonstration of Blockchain Applicability Framework

Blockchain technology has been gaining great interest from a variety of industry sectors, including financial, food processing, and power and energy markets. Realizing the strength of blockchain technology beyond the successful application in the cryptocurrency arena, researchers have been evaluating and using blockchain for applications such as supply chain management, transactive industry (both financial and energy), system integrity, device cybersecurity, identity management, and much more. One of the unique elements of the blockchain technology that made it such a captivating technology to researchers is its plethora of features. Some of the features include smart contracts, cryptocurrency and tokenizing, immutable distributed ledger, cryptographic hashing, and digital signature. In addition, there are multiple types of blockchains, such as permissioned/private and permissionless/public, and various consensus models, such as proof-of-work, proof-of-authority, proof-of-burn, and proof-of-stake. Therefore, it is often non-trivial to determine if an application requires a blockchain. If so, what kind of blockchain and consensus is most appropriate? This paper discusses the blockchain applicability framework (BAF), which was specifically designed with the purpose to answer those questions. BAF is divided into five domains, 18 subdomains, and about 100 controls. It is designed to ingest detailed user requirements to perform a weighted evaluation that is built on mathematical constructs to determine the ideal combination of blockchain that is appropriate for an application. Along with the core logical formulation of BAF, this paper depicts the efficacy of BAF through two use cases

Gourisetti, Sri Nikhil G.↗

DOE OSTI2021

Reconfigurable Framework for Resilient Semantic Segmentation for Space Applications

Deep learning (DL) presents new opportunities for enabling spacecraft autonomy, onboard analysis, and intelligent applications for space missions. However, DL applications are computationally intensive and often infeasible to deploy on radiation-hardened (rad-hard) processors, which traditionally harness a fraction of the computational capability of their commercial-off-the-shelf counterparts. Commercial FPGAs and system-on-chips present numerous architectural advantages and provide the computation capabilities to enable onboard DL applications; however, these devices are highly susceptible to radiation-induced single-event effects (SEEs) that can degrade the dependability of DL applications. In this article, we propose Reconfigurable ConvNet (RECON), a reconfigurable acceleration framework for dependable, high-performance semantic segmentation for space applications. In RECON, we propose both selective and adaptive approaches to enable efficient SEE mitigation. In our selective approach, control-flow parts are selectively protected by triple-modular redundancy to minimize SEE-induced hangs, and in our adaptive approach, partial reconfiguration is used to adapt the mitigation of dataflow parts in response to a dynamic radiation environment. Combined, both approaches enable RECON to maximize system performability subject to mission availability constraints. We perform fault injection and neutron irradiation to observe the susceptibility of RECON and use dependability modeling to evaluate RECON in various orbital case studies to demonstrate a 1.5–3.0× performability improvement in both performance and energy efficiency compared to static approaches.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Exploring the Use of Novel Spatial Accelerators in Scientific Applications

Driven by the need to find alternative accelerators which can viably replace GPUs in next-generation Supercomputing systems, this paper proposes a methodology to enable agile application/hardware co-design. The application-first methodology provides the ability to come up with design of accelerators while working with real-world workloads, available accelerators, and system software. The iterative design process targets a set of kernels in a workload for performance estimates that can prune the design space for later phases of detailed architectural evaluations. To this effect, in this paper, a novel data-parallel device model is introduced that simulates the latency of performance-sensitive operations in an accelerator including data transfers and kernel computation using multi-core CPUs. The use of off-the-shelf simulators, such as pre-RTL simulator Aladdin or multiple tools available for exploring the design of deep neural network accelerators (e.g., Timeloop) is demonstrated for evaluation of various accelerator designs using applications with realistic inputs. Examples of multiple device configurations that are instantiable in a system are explored to evaluate the performance benefit of deploying novel accelerators. The proposed device is integrated with a programming model and system software to potentially explore the impacts of high-level programming languages/compilers and low-level effects such as task scheduling on multiple accelerators. We analyze our methodology for a set of applications that represent high-performance computing (HPC) and graph analytics. The applications include a computational chemistry kernel realized using tensor contractions, triangle counting, GraphSAGE and Breadth-first Search. These applications include kernels such as dense matrix-dense matrix multiplication, sparse matrix-spare matrix multiplication, and sparse matrix-dense vector multiplication. Our results indicate potential performance benefits and insights for system design by including accelerators that realize these kernels along-side general purpose accelerators.

AI, codesign, Accelerated Computing, Modeling and ↗

DOE OSTI2023

Is Knowledge about Running Applications Helping Improve Runtime Prediction of HPC Jobs?

High-performance computing systems rely upon scheduling algorithms to achieve high utilization. These schedulers rely upon user estimates of job resource requirements, such as runtime, to determine optimal scheduling of incoming jobs. These user estimates, however, are prone to error. To mitigate this error, significant research has been directed at providing better estimates of job runtime, usually employing machine learning techniques. These techniques are dependent upon the input features selected. Among the possible features is the primary application used by the job. In a survey of more than 20 papers directed at improving runtime prediction, only four included primary application as an input feature. We focus this investigation specifically on the value of adding primary application as an input feature, and find that it does improve model performance, especially for jobs with longer runtimes, though this improvement varies based on the application used. We recommend further research to determine the cause of this variability as well as an optimal strategy for employing a mixture of models both including and not including primary application as a feature.

MATHEMATICS AND COMPUTING↗

DOE OSTI2023

SeeQ: A Programming Model for Portable Data-Driven Building Applications

This paper introduces SeeQ, a programming model and an abstraction framework that facilitates the development of portable data- driven building applications. Data-driven approaches can provide insights into building operations and guide decision-making to achieve operational objectives. Yet the configuration of such applications per building requires extensive effort and tacit knowledge. In SeeQ, we propose a portable programming model and build a software system that enables self-configuration and execution across diverse buildings. The configuration of each building is captured in a unified data model - in this paper, we work with the Brick ontology without loss of generality. SeeQ focuses on the distinction between the application logic and the configuration of an application against building-specific data inputs and systems. We test the proposed approach by configuring and deploying a diverse range of applications across five heterogeneous real-world buildings. The analysis shows the potential of SeeQ to significantly reduce the efforts associated with the delivery of building analytics.

analytics↗

DOE OSTI2024

Studying CPU and memory utilization of applications on Fujitsu A64FX and Nvidia Grace Superchip

ARM-based manycore CPU architectures are well-positioned to provide the rising memory throughput requirements of modern data intensive scientific applications in High Performance Computing (HPC). The Fujitsu A64FX CPU platform is based on the ARM v8.2A architecture, and is the processor of the flagship Japanese supercomputer - "Fugaku", which was previously ranked as the #1 supercomputer in the world according to the Top500 list. The Nvidia Grace superchip features 144 Neoverse V2 cores based on the ARMv9 architecture with 4x128b SVE2, providing exceptional computational power. The chip supports up to 480GB of memory, making it ideal for AI, machine learning, and scientific computing workloads. In this paper, we conduct a thorough performance exploration of a variety of parallel bandwidth-sensitive benchmarks and applications compiled with the native Fujitsu compiler on a Fugaku A64FX compute node and ARM (LLVM) Compiler on an NVIDIA Grace superchip compute node, engaging all the computational cores per cluster using OpenMP multithreading (assuming the cores can drive the available bandwidth). Our ultimate goals are to study the resource utilization of scientific applications and benchmarks on A64FX and Grace superchip, considering graph application scenarios ( GAP Benchmark suite) and eleven appli- cation proxies from the Rodinia heterogeneous benchmark suite (considering domains such as Data Mining, Bioinformatics, Fluid Dynamics, Pattern Recognition, etc.). Through exhaustive performance monitoring, we quantify the resource utilization of diverse OpenMP-based HPC applications on both the Fujitsu A64FX and the Nvidia Grace Superchip platforms.

benchmarking, Performance Analysis, High performan↗

DOE OSTI2023

Inl Open Ondemand Applications

Open OnDemand is a software tool that is used to access HPC resources. It provides a framework for organizations to create apps and other additional functionality that may be useful to the organization. This code expands upon the pre-existing INL applications, including the NEAMS Workbench application, MOOSE Herd applications, and others. These changes significantly expand upon the functionality originally provided. Due to the extensive functionality that we added, these changes would not be added to the original application but would function as a standalone application that other organizations would be able to utilize on their own systems.

Biggs, BrandonS.↗

DOE OSTI2021

Blockchain Applicability and Cybersecurity Frameworks (BAF)

The Blockchain Applicability and Cybersecurity Frameworks is the implementation of an earlier invention disclosure and Provisional Patent Application: S-146,805, Battelle IPID 31608-E. —BAF walks a user (or an interested party) through ~100 controls to determine various factors, including: 1. Does the application need a blockchain? 2. If the application needs a blockchain, does it need a private blockchain or permissionless/public blockchain? 3. What kind of consensus is most suitable for the application? The current version of BAF evaluates between four consensus mechanisms: proof-of-work, proof-of-stake, proof-of-burn, and proof-of-authority.

Gourisetti, Sri Nikhil Gupta↗

DOE OSTI2022

Advances in the Application and Utility of Subseasonal-to-Seasonal Predictions

The subseasonal-to-seasonal (S2S) predictive time scale, encompassing lead times ranging from 2 weeks to a season, is at the frontier of forecasting science. Forecasts on this time scale provide opportunities for enhanced application-focused capabilities to complement existing weather and climate services and products. There is, however, a “knowledge–value” gap, where a lack of evidence and awareness of the potential socioeconomic benefits of S2S forecasts limits their wider uptake. To address this gap, here we present the first global community effort at summarizing relevant applications of S2S forecasts to guide further decision-making and support the continued development of S2S forecasts and related services. Focusing on 12 sectoral case studies spanning public health, agriculture, water resource management, renewable energy and utilities, and emergency management and response, we draw on recent advancements to explore their application and utility. These case studies mark a significant step forward in moving from potential to actual S2S forecasting applications. We show that by placing user needs at the forefront of S2S forecast development—demonstrating both skill and utility across sectors—this dialogue can be used to help promote and accelerate the awareness, value, and cogeneration of S2S forecasts. We also highlight that while S2S forecasts are increasingly gaining interest among users, incorporating probabilistic S2S forecasts into existing decision-making operations is not trivial. Nevertheless, S2S forecasting represents a significant opportunity to generate useful, usable, and actionable forecast applications for and with users that will increasingly unlock the potential of this forecasting time scale.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Interactive Web Application for Traffic Simulation Data Management and Visualization

As traffic simulation software becomes more effective for realistically simulating and analyzing traffic dynamics and vehicle interactions on the mesoscopic and microscopic level, the management, dissemination, and collaborative visualization of traffic simulation results produced by individual transportation planners presents a significant challenge. Existing online content management systems have a very limited capability in allowing users to query specific traffic simulation scenarios and geospatially visualize simulation results through shareable and interactive web interfaces. This paper presents a web-based application for promoting the archiving, sharing, and visualization of large-scale traffic simulation outputs. The application is developed to enhance cyber-physical controls, communications, and public education for collaborative transportation planning. Unique features of the web application include: (a) allowing users to upload their new traffic simulation scenarios (parameters and outputs), as well as search existing scenarios using easily accessible interfaces; (b) optimizing simulation output files with heterogeneous data formats and projected coordinate systems for web-based storage and management using a scalable and searchable data/metadata standard; (c) standardizing user-uploaded simulation outputs using web interfaces and data processing libraries with parallel computing capacity; and (d) providing shareable web visual interfaces for visualizing the traffic flow and signal information stored in simulation outputs (e.g., regional traffic patterns and individual vehicle interactions) and visually comparing multiple simulation outputs both spatially and temporally. Furthermore, the paper presents the conceptual design and implementation of this application, and demonstrates the application’s performance for sharing, comparing, and visualizing simulation outputs from VISSIM and SUMO, two commonly used traffic simulation software programs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2024

Ginkgo - A math library designed to accelerate Exascale Computing Project science applications

Large-scale simulations require efficient computation across the entire computing hierarchy. A challenge of the Exascale Computing Project (ECP) was to reconcile highly heterogeneous hardware with the myriad of applications that were required to run on these supercomputers. Mathematical software forms the backbone of almost all scientific applications, providing efficient abstractions and operations that are crucial to harness the performance of computing systems. Ginkgo is one such mathematical software library, nurtured by ECP, providing high-performance, user-friendly, and performance portable interfaces for applications in ECP and beyond. In this paper, we elaborate on Ginkgo’s philosophy of high-performance software that is sustainable, reproducible, and easy to use. We showcase the wide feature set of solvers and preconditioners available in Ginkgo and the central concepts involved in their design. We elaborate on four different ECP software integrations: MFEM, PeleLM + SUNDIALS, XGC, and ExaSGD that use Ginkgo to accelerate their science runs. Performance studies of different problems from these applications highlight the effectiveness of Ginkgo and the benefits incurred by these ECP applications.

Cojean, Terry↗

DOE OSTI2025

Parallelizing autotuning for HPC applications: Unveiling the potential of the speculation strategy in Bayesian optimization

In the exascale computing era, tuning High-Performance Computing (HPC) applications has become a significant computational challenge. Although Bayesian optimization (BO) has emerged as a promising tool for HPC performance tuning, the BO workflow is inherently sequential (i.e., one function evaluation at a time) and cannot leverage the huge amount of parallel resources present in modern supercomputers, resulting in a considerable underutilization of their computational capabilities. This paper explores the trade-off between search quality and parallelism in BO, investigating a diverse set of methods. Building upon both previous approaches from the literature and novel methodologies introduced in this work, our study provides a deep analysis to accelerate BO performance tuning. By examining a set of synthetic functions and practical HPC applications, our exploration analyzes the interaction among various BO methods for parallelization, the quantity of parallel resources, the runtime distribution of target HPC applications, and the costs associated with different search orchestration mechanisms that have been overlooked in previous studies. Compared to sequential BO, our novel methodology achieves comparable quality while demonstrating robust scalability in search time as the amount of parallel resources increases; it also outperforms a state-of-the-art tuner, which supports parallelization, achieving up to 3.67x faster search time. We provide high-value insights for practitioners seeking to leverage the power of parallel computing for efficient HPC application tuning. Additionally, to further assist researchers in accelerating the performance tuning of their HPC applications, we provide an extension of an existing open-source tuning framework that incorporates our methods.

Bayesian optimization↗