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Biofuels Information Center

The purpose of the Biofuels Information Center (BIC) task is to provide relevant data, information, reports, and web-based tools to all bioenergy stakeholders. The BIC task began in FY08 to meet the requirement under Title II, Sec. 229 of the Energy Independence and Security Act of 2007 (EISA) requires DOE to develop a "Biofuels and Biorefinery Information Center". The BIC task supports biofuels pages content on the EERE's most visited website - the Alternative Fuels Data Center (AFDC http://www.afdc.energy.gov) and the Bioenergy Atlas tools (currently archived) (previous address https://maps.nrel.gov). This task results in more than 1.7 million web pageviews (an instance of an internet user visiting a webpage) per year. In FY22, the task completed the final year of the 5 year USDA Biofuels Infrastructure Partnership (BIP). The USDA BIP expanded infrastructure for E15 and/or E85 to approximately 850 stations and NREL received and reviewed data for quality analyzed all infrastructure and sales data collected by USDA. Stations are privately held and previously it was difficult to ascertain infrastructure and sales data. This unique dataset allows insight into infrastructure data (number of pumps and tanks, costs to install new equipment) and sales data (price and volume for E10, E15, E85, and diesel by month). The 2021 USDA BIP National Summary Report is with DOE for review prior to publication. Future work will include the biannual Bioenergy Industry Status Report (4 previous versions have been published) . The task also supports the principal investigator's time to engage stakeholders on infrastructure and deployment of biofuels. This includes leading, membership, and participation in the following roles: member Board of Advisors at the Fuels Institute, voting member for multiple UL standards committees, Co-Chair of the Infrastructure team at Agriculture/Auto/Ethanol, Member of Coordination Research Council's ULSD Corrosion Committee. The Principal investigator routinely responds to industry inquires to assist in deployment of biofuels regularly.

biofuels↗

Three practical workflow schedulers for easy maximum parallelism

Runtime scheduling and workflow systems are an increasingly popular algorithmic component in HPC because they allow full system utilization with relaxed synchronization requirements. There are so many special-purpose tools for task scheduling, one might wonder why more are needed. Use cases seen on the Summit supercomputer needed better integration with MPI and greater flexibility in job launch configurations. Preparation, execution, and analysis of computational chemistry simulations at the scale of tens of thousands of processors revealed three distinct workflow patterns. A separate job scheduler was implemented for each one using extremely simple and robust designs: file-based, task-list based, and bulk-synchronous. Comparing to existing methods shows unique benefits of this work, including simplicity of design, suitability for HPC centers, short startup time, and well-understood per-task overhead. All three new tools have been shown to scale to full utilization of Summit, and have been made publicly available with tests and documentation. This work presents a complete characterization of the minimum effective task granularity for efficient scheduler usage scenarios. Here, these schedulers have the same bottlenecks, and hence similar task granularities as those reported for existing tools following comparable paradigms.

97 MATHEMATICS AND COMPUTING↗

Information Processing Capacity of Spintronic Oscillator

Physical reservoir computing is a framework that enables energy‐efficient information processing by using physical systems. Nonlinear dynamics in physical systems provide a computational capability that is unique to reservoirs. It is, however, difficult to find an appropriate task for a reservoir because of the complexity of nonlinear information processing. The information processing capacity has recently been used to clarify systematically the tasks that are solved by reservoirs; it quantifies the memory capacity of reservoirs in accordance with the order of nonlinearity. Herein, an experimental evaluation of the information processing capacity of a spintronic oscillator consisting of nanostructured ferromagnets is reported. The spintronic reservoir state is electrically manipulated by adding a delayed‐feedback circuit. The total capacity reaches a maximum of 5.6 at the edge of the echo state property. A trade‐off between the linear and nonlinear components of the capacity is also found. The result can be used to better understand the nonlinear information processing in reservoirs and to find good matches between reservoirs and tasks. As an example, a function‐approximation task is performed and it is found that it can be efficiently solved when the reservoir state is appropriately tuned so that its information processing capacity matches that of the task.

97 MATHEMATICS AND COMPUTING↗

A review of machine learning in building load prediction

The surge of machine learning in recent years has been empowering engineer modeling in various fields. The decreasing hardware cost, increasing data accessibility, and advances of building automation system (BAS) allow the collection and storage of a significant amount of building operation data. The two facts provide great opportunities of applying machine learning to building energy systems modeling and analysis. There are a great number of research papers on this topic but there lacks a comprehensive and general review to summarize the current development, limitations, gaps and future trend. In this review paper series, machine learning techniques in building energy system modeling and analysis are reviewed under the organization and logic of the machine learning definition by Tom M. Mitchell: a computer program is said to learn from experience E with respect to some class of tasks T and performance measure P if its performance at tasks in T, as measured by P, improves with experience E. This paper is the first part of the review paper series, which focuses on building load prediction. First, the applications of building load prediction model (task T) are reviewed. Then, the modeling algorithms improving machine learning performance and accuracy (performance P) are reviewed. At the same time, the literature on the data perspective for modeling (experience E), including data engineering from sensors level to data level, pre-processing, feature extraction and selection, is reviewed. Finally, what is well-studied and what is lacking but with great potential are concluded; the gaps between present and future utilization of machine learning techniques are identified; the future trend and development are also predicted. The target readers of this paper are not only researchers from the building side who can get exposed to cutting edge machine learning tools, but also those from machine learning side who can understand the potential and challenge to apply machine learning in buildings.

Liang, Zhang↗

An OpenMP GPU-offload implementation of a non-equilibrium solidification cellular automata model for additive manufacturing

Here, in this paper, performance strategies on GPU-based HPC platforms of a cellular automata (CA) simulation code for non-equilibrium solidification, including nucleation, grain growth, solute partitioning and transport for the metal additive manufacturing (AM) process are investigated using OpenMP 4.5. To accurately report the speed-up for multicore CPUs and GPUs, a rigorous performance analysis employed optimizations appropriate for both CPU-only code (baseline) and GPU offload codes for an isothermal test problem. The performance results on Summit at the Oak Ridge Leadership Computing Facility indicate that using a precomputed list of interface cells significantly decreased the wall-clock time on GPUs. The speedup due to GPU acceleration was evaluated for a full Summit node and measured to be 1.8X when comparing a 6 MPI tasks run with 6 GPUs versus 36 MPI tasks on the CPU only. That speed-up was found to be 7.9X when comparing 6 MPI tasks with 6 GPUs versus the 6 MPI tasks running on the CPU only. Performance measurements showed that system total time is almost constant for runs with more than 96 MPI tasks (or GPUs), indicating that the GPU-accelerated code showed an excellent weak scaling performance. Finally, a rapid directional solidification problem was considered to demonstrate the CA code capability on Summit. It was found that a mesh size of at least 0.05 μm is recommended for the AM-like simulations in order to obtain accurate elongated grain microstructure and elongated subgrain features, which are in qualitative good agreement with experimental data. The results presented in this study indicate that the performance strategies on GPU-based HPC platforms for the CA code are appropriate for novel HPC exascale platforms.

36 MATERIALS SCIENCE↗

Enabling machine learning-ready HPC ensembles with Merlin

With the growing complexity of computational and experimental facilities, many scientific researchers are turning to machine learning (ML) techniques to analyze large scale ensemble data. With complexities such as multi-component workflows, heterogeneous machine architectures, parallel file systems, and batch scheduling, care must be taken to facilitate this analysis in a high performance computing (HPC) environment. Here, we present Merlin, a workflow framework to enable large ML-friendly ensembles of scientific HPC simulations. By augmenting traditional HPC with distributed compute technologies, Merlin aims to lower the barrier for scientific subject matter experts to incorporate ML into their analysis. As a producer–consumer workflow model, Merlin enables multi-machine, cross-batch job, dynamically allocated yet persistent workflows capable of utilizing surge-compute resources. Key features of Merlin are a flexible HPC-centric interface, low per-task overhead, multi-tiered fault recovery, and a hierarchical sampling algorithm that allows for $\mathscr{O}$(N) task execution and $\mathscr{O}$(N ln N) task queuing to ensembles of millions of tasks. In addition to Merlin’s design, we test the algorithm’s performance in an HPC center and demonstrate the ability to enqueue 40 million simulations in 100 s, with a 30 millisecond per-task overhead that is independent of ensemble size. Finally, we describe some example applications that Merlin has enabled on leadership-class HPC resources, such as the ML-augmented optimization of nuclear fusion experiments and the calibration of infectious disease models to study the progression of and possible mitigation strategies for COVID-19.

97 MATHEMATICS AND COMPUTING↗

KEBLM: Knowledge-Enhanced Biomedical Language Models

Pretrained language models (PLMs) have demonstrated strong performance on many natural language processing (NLP) tasks. Despite their great success, these PLMs are typically pretrained only on unstructured free texts without leveraging existing structured knowledge bases that are readily available for many domains, especially scientific domains. As a result, these PLMs may not achieve satisfactory performance on knowledge-intensive tasks such as biomedical NLP. Comprehending a complex biomedical document without domain-specific knowledge is challenging, even for humans. Inspired by this observation, we propose a general framework for incorporating various types of domain knowledge from multiple sources into biomedical PLMs. We encode domain knowledge using lightweight adapter modules, bottleneck feed-forward networks that are inserted into different locations of a backbone PLM. For each knowledge source of interest, we pretrain an adapter module to capture the knowledge in a self-supervised way. We design a wide range of self-supervised objectives to accommodate diverse types of knowledge, ranging from entity relations to description sentences. Once a set of pretrained adapters is available, we employ fusion layers to combine the knowledge encoded within these adapters for downstream tasks. Each fusion layer is a parameterized mixer of the available trained adapters that can identify and activate the most useful adapters for a given input. Our method diverges from prior work by including a knowledge consolidation phase, during which we teach the fusion layers to effectively combine knowledge from both the original PLM and newly-acquired external knowledge using a large collection of unannotated texts. After the consolidation phase, the complete knowledge-enhanced model can be fine-tuned for any downstream task of interest to achieve optimal performance. Extensive experiments on many biomedical NLP datasets show that our proposed framework consistently improves the performance of the underlying PLMs on various downstream tasks such as natural language inference, question answering, and entity linking. These results demonstrate the benefits of using multiple sources of external knowledge to enhance PLMs and the effectiveness of the framework for incorporating knowledge into PLMs. Finally, while primarily focused on the biomedical domain in this work, our framework is highly adaptable and can be easily applied to other domains, such as the bioenergy sector.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

MechBERT: Language Models for Extracting Chemical and Property Relationships about Mechanical Stress and Strain

Language models are transforming materials-aware naturallanguage processing by enabling the extraction of dynamic, context-rich information from unstructured text, thus, moving beyond the limitations of traditional information-extraction methods. Moreover, small language models are on the rise because some of them can perform better than large language models (LLMs) when given domain-specific questionanswer tasks, especially about an application area that relies on a highly specialized vernacular, such as materials science. We therefore present a new class of MechBERT language models for understanding mechanical stress and strain in materials. These employ Bidirectional Encoder Representations for transformer (BERT) architectures. We showcase four MechBERT models, all of which were pretrained on a corpus of documents that are textually rich in chemicals and their stress–strain properties and were fine-tuned on question-answering tasks. We evaluated the level of performance of our models on domain-specific as well as general English-language question-answer tasks and also explored the influence of the size and type of BERT architectures on model performance. We find that our MechBERT models outperform BERT-based models of the same size and maintain relevancy better than much larger BERT-based models when tasked with domain-specific question-answering tasks within the stress–strain engineering sector. These small language models also enable much faster processing and require a much smaller fraction of data to pretrain them, affording them greater operational efficiency and energy sustainability than LLMs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive stretching of representations across brain regions and deep learning model layers

Prefrontal cortex (PFC) is known to modulate the visual system to favor goal-relevant information by accentuating task-relevant stimulus dimensions. Does the brain broadly re-configures itself to optimize performance by stretching visual representations along task-relevant dimensions? We considered a task that required monkeys to selectively attend on a trial-by-trial basis to one of two dimensions (color or motion direction) to make a decision. Although effects were most prominent in frontal areas, representations stretched along task-relevant dimensions in all sites considered: V4, MT, lateral PFC, frontal eye fields (FEF), lateral intraparietal cortex (LIP), and inferotemporal cortex (IT). Spike timing was crucial to this code. A deep learning model was trained on the same visual input and rewards as the monkeys. Despite lacking an explicit selective attention or other control mechanism, by minimizing error during learning, the model’s representations stretched along task-relevant dimensions, indicating that stretching is an adaptive strategy.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancing generative molecular design via uncertainty-guided fine-tuning of variational autoencoders

In recent years, deep generative models have been successfully applied to various molecular design tasks, particularly in the life and materials sciences. One critical challenge for pre-trained generative molecular design (GMD) models is to fine-tune them to be better suited for downstream design tasks that aim at optimizing specific molecular properties. However, redesigning and training an existing effective generative model from scratch for each new design task are impractical. Furthermore, the black-box nature of typical downstream tasks that involve property prediction makes it nontrivial to optimize the generative model in a task-specific manner. In this work, we propose an uncertainty-guided fine-tuning strategy that can effectively enhance a pre-trained variational autoencoder (VAE) for GMD through performance feedback in an active learning setting. The strategy begins by quantifying the model uncertainty of the generative model using an efficient active subspace-based UQ (uncertainty quantification) scheme. Next, the decoder diversity within the characterized model uncertainty class is explored to expand the viable space of molecular generation. The low-dimensionality of the active subspace makes this exploration tractable using a black-box optimization scheme, which in turn enables us to identify and leverage a diverse set of high-performing models to generate enhanced molecules. Empirical results across six target molecular properties using multiple VAE-based generative models demonstrate that our uncertainty-guided fine-tuning strategy consistently leads to improved models that outperform the original pre-trained models.

97 MATHEMATICS AND COMPUTING↗

The ICRP, MELODI, and ALLIANCE workshop on effects of ionizing radiation exposure in offspring and next generations: a summary of discussions

Task Group 121 – Effects of ionizing radiation exposure in offspring and next generations – is a task group under the Committee 1 of the International Commission on Radiological Protection (ICRP), approved by the Main Commission on 18th November 2021. The main goals of Task Group 121 are to (1) review and update the scientific literature of relevance to radiation-related effects in the offspring of parent(s) exposed to ionizing radiation in both human and non-human biota; (2) to assess preconceptional and intrauterine effects of radiation exposure and related morbidity and mortality; and, (3) to provide advice about the level of evidence and how to consider these preconceptional and postconceptional effects in the system of radiological protection for humans and non-human biota. The Task Group is reviewing relevant literature since Publication 90 ‘Biological effects after prenatal irradiation (embryo and fetus)’ (2003) and will include radiation-related effects on future generations in humans, animals, and plants. This review will be conducted to account for the health effects on offspring and subsequent generations in the current system of radiological protection. Radiation detriment calculation will also be reviewed. Finally, preliminary recommendations will be made to update the integration of health effects in offspring and next generations in the system of radiological protection. A Workshop, jointly organized by ICRP Task Group 121 and European Radiation Protection Research Platforms MELODI and ALLIANCE was held in Budapest, Hungary, from 31st May to 2nd June 2022. Participants discussed four important topics: (1) hereditary and epigenetic effects due to exposure of the germ cell line (preconceptional exposure), (2) effects arising from exposure of the embryo and fetus (intrauterine exposure), (3) transgenerational effects on biota, and (4) its potential impact on the system of radiological protection. Based on the discussions and presentations during the breakout sessions, newer publications, and gaps on the current scientific literature were identified. For instance, there are some ongoing systematic reviews and radiation epidemiology reviews of intrauterine effects. There are newer methods of Monte Carlo simulation for fetal dosimetry, and advances in radiation genetics, epigenetics, and radiobiology studies. While the current impact of hereditary effects on the global detriment was reported as small, the questions surrounding the effects of radiation exposure on offspring and the next generation are crucial, recurring, and with a major focus on exposed populations. Here, this article summarizes the workshop discussions, presentations, and conclusions of each topic and introduces the special issue of the International Journal of Radiation Biology resulting from the discussions of the meeting.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Opening band gaps of low-dimensional materials at the meta-GGA level of density functional approximations

The quasiparticle band structure can be properly described by Hedin's GW approximation (GW), at a high computational cost. For band gaps, semilocal density functionals up to the generalized gradient approximation (GGA) level cannot compete with the accuracy of hybrid-based approximations or GW. Meta-GGA density functionals with a strong dependence on the kinetic energy density ingredient can potentially give wider band gaps compared with GGAs. The recent TASK meta-GGA density functional from Aschebrock and Kümmel [ Phys. Rev. Research 1 , 033082 (2019) ], is constructed with an enhanced nonlocality in the generalized Kohn-Sham scheme and therefore harbors great opportunities for band gap prediction. Although this approximation was found to yield excellent band gaps of bulk solids, this accuracy cannot be straightforwardly transferred to low-dimensional materials. Additionally, the reduced screening of these materials results in larger band gaps compared with their bulk counterparts, as an additional barrier to overcome. In this paper we demonstrate how the alteration of this functional affects the band gaps of monolayers and nanoribbons and present accurate band gaps competing with the revised Heyd-Scuseria-Ernzerhof (HSE06) approximation. In order to achieve this goal, we have modified the TASK functional (a) by changing the tight upper bound for one- or two-electron systems ( h X 0 ) from 1.174 to 1.29 and (b) by changing the limit of the interpolation function f X ( α → ∞ ) of the TASK functional that interpolates the exchange enhancement factor F X ( s , α ) from α = 0 to 1. The resulting modified TASK (mTASK) was tested for various materials from three dimensions to two dimensions to one dimension (nanoribbons) and was compared with the results of the higher-level hybrid functional HSE06 or with the G 0 W 0 approximation within many-body perturbation theory. We find that mTASK systematically improves the band gaps and band structures of two-dimensional (2D) and 1D systems, without significantly affecting the accuracy of the original TASK for the bulk 3D materials, when compared with the Perdew-Burke-Ernzerhof (PBE) GGA and the strongly constrained and appropriately normed (SCAN) meta-GGA. We further demonstrate the applicability of mTASK by assessing the band structures of transition metal dichalcogenide nanoribbons with respect to various bending curvatures.

36 MATERIALS SCIENCE↗

HCPerf: Driving Performance-Directed Hierarchical Coordination for Autonomous Vehicles

The rapid development of autonomous driving poses new research challenges to the on-vehicle computing system. In particular, the execution time of autonomous driving tasks highly depends on the specific driving environment. For instance, the execution time of configurable sensor fusion increases significantly as the scene becomes complex, which leads to end-to-end deadline misses from sensing to control and may cause accidents. Thus, a framework that can effectively utilize the system resources to guarantee the end-to-end deadlines of autonomous driving tasks as well as effectively prioritize the responsiveness and throughput of the control commands is crucial for autonomous driving. In this paper, we propose HCPerf, a performance-directed hierarchical coordination framework that intelligently coordinates the autonomous driving tasks with high execution time variation and complex dependencies according to the driving performance in real-time. Specifically, HCPerf mainly consists of two coordinators. The internal coordinator intelligently schedules the tasks according to the driving performance of the vehicle in order to help them meet the end-to-end deadlines while well prioritizing the responsiveness and throughput of the control commands. At the same time, the external coordinator dynamically tunes the rates of tasks according to the schedulability in order to efficiently utilize the system resource. We conduct extensive experiments on both simulation and hardware testbeds with the representative autonomous driving application. The results show that HCPerf can effectively improve the driving performance by 7.69%-45.94% in different driving scenarios.

Ma, Jialiang↗

Design and Performance Characterization of RADICAL-Pilot on Leadership-Class Platforms

Many extreme scale scientific applications have workloads comprised of a large number of individual highperformance tasks. The Pilot abstraction decouples workload specification, resource management, and task execution via job placeholders and late-binding. As such, suitable implementations of the Pilot abstraction can support the collective execution of large number of tasks on supercomputers. We introduce RADICAL-Pilot (RP) as a portable, modular and extensible Pilot enabled runtime system. We describe RP's design, architecture and implementation. We characterize its performance and show its ability to scalably execute workloads comprised of tens of thousands heterogeneous tasks on DOE and NSF leadership-class HPC platforms. Specifically, we investigate RP's weak/strong scaling with CPU/GPU, single/multi core, (non)MPI tasks and python functions when using most of ORNL Summit and TACC Frontera. RADICAL-Pilot can be used stand-alone, as well as the runtime for third-party workflow systems.

97 MATHEMATICS AND COMPUTING↗

CoordNet: Data Generation and Visualization Generation for Time-Varying Volumes via a Coordinate-Based Neural Network

Although deep learning has demonstrated its capability in solving diverse scientific visualization problems, it still lacks generalization power across different tasks. To address this challenge, we propose CoordNet, a single coordinate-based framework that tackles various tasks relevant to time-varying volumetric data visualization without modifying the network architecture. The core idea of our approach is to decompose diverse task inputs and outputs into a unified representation (i.e., coordinates and values) and learn a function from coordinates to their corresponding values. We achieve this goal using a residual block-based implicit neural representation architecture with periodic activation functions. We evaluate CoordNet on data generation (i.e., temporal super-resolution and spatial super-resolution) and visualization generation (i.e., view synthesis and ambient occlusion prediction) tasks using time-varying volumetric data sets of various characteristics. Here, the experimental results indicate that CoordNet achieves better quantitative and qualitative results than the state-of-the-art approaches across all the evaluated tasks. Source code and pre-trained models are available at https://github.com/stevenhan1991/CoordNet.

97 MATHEMATICS AND COMPUTING↗

Tandem Predictions for HPC Jobs

At the core of the predictive analytics applied to High Performance Computing (HPC), the most prominent tasks are the prediction of job runtimes and the prediction of job queue times, both of which have the potential for informing HPC users during their every-day decision making. Accurate runtime predictions can help users better choose so-called wallclock times at job submission, decreasing the odds of their jobs waiting in queues longer than necessary. The accurate and timely queue time predictions offered for the available partitions can inform the favorable selection of partitions for running jobs. This potential is well understood as we see in the abundance of research studies that propose solutions for these tasks, including the work published in the last several years. These tasks are seemingly receptive to the Machine Learning (ML) solutions, considering that there is no shortage of training data where HPC centers over time run millions and millions of jobs. However, we study the existing research literature, as well as look for examples in the toolchains supported on the exemplar HPC facilities, and, surprisingly, do not find any practical solutions that are ready to be adopted. We interpret this as a manifestation of the shortage of UX/UI efforts that support HPC analytics and also as a sign that the research has not come to the consensus on solving these tasks. In this study, we aim to shed new light on the long-running task of job queue time prediction by exploring the utility of runtime predictions in improving prediction accuracy and, actually, predicting these two metrics together, in tandem. In other words, we show how runtime predictions become valuable input in the queue time modeling. We challenge the existing approaches to feature engineering for the queue time prediction and describe promising results we obtained for a large dataset of HPC jobs from a supercomputer at the National Renewable Energy Laboratory.

HPC↗

Serial2Parallel

In the era of machine learning, we often need to run the same code/script many times with little or no variations (e.g., performance evaluation, data preprocessing, data generation, hyperparameter tuning, etc.). It is not a problem when you just need to do that a few times, but when the number of repetitions becomes very large, it can be a daunting task. The code “Serial2Parallel” provides an easy way for users to be able to run many numbers of any serial code/scripts in a parallel manner across multiple nodes in an message passing interface (MPI) cluster. The code includes the server program that deals with task pool management and client program that processes task. The server gets the tasks ready and waits for clients' connections. The client code pulls tasks from the server and processes them. The client code will run in parallel.

Sangkeun, MattLee↗

TaskWorks v1.0

TaskWorks is a portable, high-level, task engine designed for HPC workloads. Applications can create tasks and define dependencies between them with the task engine. Once the task is defined and submitted to TaskWorks, the TaskWorks engine will execute it according to the specified dependencies, without additional input from the application. TaskWorks has an integrated event manager monitors files, sockets, timers, and MPI operations, and these events can be used as task dependencies. TaskWorks is compatible with MPI and is designed to work efficiently with HPC applications that perform.

Koziol, Quincey↗