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At least 541 records · Page 30

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↗

An evaluation of GPT models for phenotype concept recognition

Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. The best run, using in-context learning, achieved 0.58 document-level F1 score on publication abstracts and 0.75 document-level F1 score on clinical observations, as well as a mention-level F1 score of 0.7, which surpasses the current best in class tool. Without in-context learning, however, performance is significantly below the existing approaches. Our experiments show that gpt-4.0 surpasses the state of the art performance if the task is constrained to a subset of the target ontology where there is prior knowledge of the terms that are expected to be matched. While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.

59 BASIC BIOLOGICAL SCIENCES↗

Foundation Models of Scientific Knowledge for Chemistry: Opportunities, Challenges and Lessons Learned

Foundation models pre-trained on large corpora demonstrate significant gains across many natural language processing tasks and domains e.g., law, healthcare, education, etc. However, only limited efforts have investigated the opportunities and limitations of applying these powerful models to science and security applications. In this work we develop foundation models of scientific knowledge for chemistry to augment scientists with the advanced ability to perceive and reason at scale previously unimagined. Specifically, we build large-scale (1.47B parameter) general-purpose models for chemistry that can be effectively used to perform a wide range of in-domain and out-of-domain tasks. Evaluating these models in a zero-shot setting, we analyze the effect of model and data scaling, knowledge depth, and temporality on model performance in context of model training efficiency. Our novel findings demonstrate that (1) model size significantly contributes to the task performance when evaluated in a zero-shot setting; (2) data quality (aka diversity) affects model performance more than data quantity; (3) similarly, unlike previous work (Luu et al., 2021) temporal order of the documents in the corpus boosts model performance only for specific tasks, e.g., SciQ; and (4) models pre-trained from scratch perform better on in-domain tasks than those tuned from general-purpose models like Open AI’s GPT-2.

Foundation Models, Chemistry↗

BEE - FY20 P6-3: Release BEEWorkflowManager, BEETaskManager, and client application 2.3.6.01 – LANL ATDM ST / STNS01-4 P6 Milestone Completion Documentation

Release BEEWorkflowManager, BEETaskManager, and client software. The BEEWorkflowManager daemon runs on the HPC cluster login node. It accepts workflows submitted by the BEE client. These workflows are specified using the Common Workflow Language (CWL) standard. The BEEWorkflowManager loads workflows into the Neo4j graph database to create the workflow directed acyclic graph (DAG), and submits the workflow tasks to the BEETaskManager for execution. The BEEWorkflowManager records the state of the workflow and its tasks, and communicates this state to the BEE client. The BEEWorkflowManager will start, pause, and cancel a running workflow and its tasks at the command of the BEE client. The BEETaskManager daemon runs on the HPC cluster login node. It accepts tasks from the BEEWorkflowManager, turns those tasks into HPC resource manager jobs (e.g. a slurm job script), and submits the job to the cluster resource manager. The BEETaskManager then tracks the status of the job (pending, running, complete) and updates the BEEWorkflowManager. The BEETaskManager will also cancel a queued or running job when commanded to do so by the BEEWorkflowManager. The first release of the BEETaskManager will support the Slurm resource manager and the Charliecloud linux container runtime.

97 MATHEMATICS AND COMPUTING↗

NRC Multiphysics Analysis Capability Deployment FY2020 - Part 4

This report details progress and activities of Idaho National Laboratory (INL) on the Nuclear Regulatory Commission (NRC) project “Development and Modeling Sup- port for Advanced Non-Light Water Reactors.” The tasks completed for this report are: • Task 3a: This task demonstrates the effectiveness of Griffin’s methods for interpolating cross sections and SPH correction factors as a function of control drum rotation. The Monte Carlo code Serpent is used to generate reference results. The accuracy of Griffin-calculated eigenvalues and reaction rates are studied as a function of control drum rotation for cross section and SPH factor libraries of varying fidelity. Higher-fidelity libraries require less interpolation and are therefore inherently more accurate; however, they require more computational resources to create. Overall, Griffin is able to accurately model eigenvalue and reaction rates over the full range of drum rotation using a library generated from three to five discrete drum rotations for a particular microreactor design. • Task 3c: This preliminary task successfully demonstrates the performance of a coupled neutron-photon transport calculation with Griffin using the spherical harmonics approximation. The Griffin solutions are compared to reference solutions from the continuous energy Monte Carlo codes MCNP and Serpent. Furthermore, this work also demonstrates how to prepare the neutron and photon libraries using NJOY, MCNP, and Serpent with the latest ENDF/B-VIII data for 235 U and graphite. The Griffin total energy deposition in the active core region is calculated within 0.3% of the reference, but it degrades in the reflector regions with a maximum difference of -1.5%. Overall, the results look promising and future analysis should use an improved data stream and focus on determining the potential cancellation of error within each energy group.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗