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At least 559 records · Page 31

Catalyst: Fast and flexible modeling of reaction networks

We introduce Catalyst.jl, a flexible and feature-filled Julia library for modeling and high-performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating stochastic chemical kinetics (jump process), chemical Langevin equation (stochastic differential equation), and reaction rate equation (ordinary differential equation) representations for CRNs. Through comprehensive benchmarks, we demonstrate that Catalyst simulation runtimes are often one to two orders of magnitude faster than other popular tools. More broadly, Catalyst acts as both a domain-specific language and an intermediate representation for symbolically encoding CRN models as Julia-native objects. This enables a pipeline of symbolically specifying, analyzing, and modifying CRNs; converting Catalyst models to symbolic representations of concrete mathematical models; and generating compiled code for numerical solvers. Leveraging ModelingToolkit.jl and Symbolics.jl, Catalyst models can be analyzed, simplified, and compiled into optimized representations for use in numerical solvers. Finally, we demonstrate Catalyst’s broad extensibility and composability by highlighting how it can compose with a variety of Julia libraries, and how existing open-source biological modeling projects have extended its intermediate representation.

59 BASIC BIOLOGICAL SCIENCES↗

Integration of energy storage with diesel generation in remote communities

Highlights Battery energy storage may improve energy efficiency and reliability of hybrid energy systems composed by diesel and solar photovoltaic power generators serving isolated communities. In projects aiming update of power plants serving electrically isolated communities with redundant diesel generation, battery energy storage can improve overall economic performance of power supply system by reducing fuel usage, decreasing capital costs by replacing redundant diesel generation units, and increasing generator system life by shortening yearly runtime. Fast-acting battery energy storage systems with grid-forming inverters might have potential for improving drastically the reliability indices of isolated communities currently supplied by diesel generation. Abstract This paper will highlight unique challenges and opportunities with regard to energy storage utilization in remote, self-sustaining communities. The energy management of such areas has unique concerns. Diesel generation is often the go-to power source in these scenarios, but these systems are not devoid of issues. Without dedicated maintenance crews as in large, interconnected network areas, minor interruptions can be frequent and invasive not only for those who lose power, but also for those in the community that must then correct any faults. Although the immediate financial benefits are perhaps not readily apparent, energy storage could be used to address concerns related to reliability, automation, fuel supply concerns, generator degradation, solar utilization, and, yes, fuel costs to name a few. These ideas are shown through a case study of the Levelock Village of Alaska. Currently, the community is faced with high diesel prices and a difficult supply chain, which makes temporary loss of power very common and reductions in fuel consumption very impactful. This study will investigate the benefits that an energy storage system could bring to the overall system life, fuel costs, and reliability of the power supply. The variable efficiency of the generators, impact of startup/shutdown process, and low-load operation concerns are considered. The technological benefits of the combined system will be explored for various scenarios of future diesel prices and technology maintenance/replacement costs as well as for the avoidance of power interruptions that are so common in the community currently. Graphic abstract Discussion In several cases, energy storage can provide a means to promote energy equity by improving remote communities’ power supply reliability to levels closer to what the average urban consumer experiences at a reduced cost compared to transmission buildout. Furthermore, energy equity represents a hard-to-quantify benefit achieved by the integration of energy storage to isolated power systems of under-served communities, which suggests that the financial aspects of such projects should be questioned as the main performance criterion. To improve battery energy storage system valuation for diesel-based power systems, integration analysis must be holistic and go beyond fuel savings to capture every value stream possible.

25 ENERGY STORAGE↗

LLM Benchmarking with LLaMA2: Evaluating Code Development Performance Across Multiple Programming Languages

The rapid evolution of large language models (LLMs) has opened new possibilities for automating various tasks in software development. This paper evaluates the capabilities of the LLaMA 2-70B model in automating these tasks for scientific applications written in commonly used programming languages. Using representative test problems, we assess the model's capacity to generate code, documentation, and unit tests, as well as its ability to translate existing code between commonly used programming languages. Our comprehensive analysis evaluates the compilation, runtime behavior, and correctness of the generated and translated code. Additionally, we assess the quality of automatically generated code, documentation, and unit tests. Here, our results indicate that while LLaMA 2-70B frequently generates syntactically correct and functional code for simpler numerical tasks, it encounters substantial difficulties with more complex, parallelized, or distributed computations, requiring considerable manual corrections. We identify key limitations and suggest areas for future improvements to better leverage AI-driven automation in scientific computing workflows.

97 MATHEMATICS AND COMPUTING↗

IDAES-PSE 2.6.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.6.0 Release Highlights Upcoming Changes IDAES will be switching to the new Pyomo solver interface in the next release. Whilst this will hopefully be a smooth transition for most users, there are a few important changes to be aware of. The new solver interface uses a different version of the IPOPT writer (“ipopt_v2”) and thus any custom configuration options you might have set for IPOPT will not carry over and will need to be reset. By default, the new Pyomo linear presolver will be activated with ipopt_v2. Whilst are working to identify any bugs in the presolver, it is possible that some edge cases will remain. IDAES will begin deploying a new set of scaling tools and APIs over the next few releases that make use of the new solver writers. The old scaling tools and APIs will remain for backward compatibility but will begin to be deprecated. New Models, Tools and Features New Intersphinx extension automatically linking Jupyter notebook examples to project documentation New end-to-end diagnostics example demonstrated on a real problem New complementarity formulation for VLE with cubic equations of state, backward compatibility for old formulation New solver interface with presolve (ipopt_v2) in support of upcoming changes to the initialization and APIs methods, with default set to ipopt to maintain backwards compatibility; this will deprecate once all examples have been updated New forecaster and parameterized bidder methods within grid integration library Updated surrogates API and examples to support Keras 3, with backwards compatibility for older formats such as TensorFlow SavedModel (TFSM) Updated costing base dictionary to include the 2023 cost year index value Updated ProcessBlock to include information on the constructing block class Updated Flowsheet Visualizer to allow visualize() method to return value and functions Bug Fixes Fixed bug in the Modular Property Framework that would cause errors when trying to use phase-based material balances with phase equilibria. Fixed bug in Modular Properties Framework that caused errors when initializing models with non-vapor-liquid phase equilibria. Fixed typos flagged by June update to crate-ci/typos and removed DMF-related exceptions Minor corrections of units of measurement handling in power plant waste/transport costing expressions, control volume material holdup expressions, and BTX property package parameters Fixed throwing >7500 numpy deprecation warnings by replacing scalar value assignment with element extraction and item iteration calls Testing and Robustness Migrated slow tests (>10s) to integration, impacting test coverage but also yielding a nearly 30% decrease in local test runtime Pinned pint to avoid issues with older supported Python versions Pinned codecov versions to avoid tokenless upload behavior with latest version Bumped extensions to version 3.4.2 to allow pointing to non-standard install location Deprecations and Removals Python 3.8 is no longer supported. The supported Python versions are 3.9 through 3.12 The Data Management Framework (DMF) is no longer supported. Importing idaes.core.dmf will cause a deprecation warning to be displayed until the next release The SOFC Keras surrogates have been removed. The current version of the SOFC surrogate model in the examples repository is a PySMO Kriging model.

AS↗

EspressoDB: A scientific database for managing high-performance computing workflows

EspressoDB is a programmatic object-relational mapping (ORM) data management framework implemented in Python and based on the Django web framework. EspressoDB was developed to streamline data management, centralize and promote data integrity, while providing domain flexibility and ease of use. It is designed to directly integrate in utilized software to allow dynamical access to vast amount of relational data at runtime.

Chang, Chia↗

libEnsemble: A complete Python toolkit for dynamic ensembles of calculations

Almost all science and engineering applications eventually stop scaling: their runtime no longer decreases as available computational resources increase. Therefore, many applications will struggle to efficiently use emerging extreme-scale high-performance, parallel, and distributed systems. libEnsemble is a complete Python toolkit and workflow system for intelligently driving ensembles of experiments or simulations at massive scales. It enables and encourages multidisciplinary design, decision, and inference studies portably running on laptops, clusters, and supercomputers.

97 MATHEMATICS AND COMPUTING↗

SDA: a symbolic differential algebra package in C++

Truncated Power Series Algebra (TPSA), or Differential Algebra (DA), is a well-established tool in accelerator physics, commonly used for generating high-order maps of dynamic systems, as well as in symplectic tracking, normal form analysis, verified integration, optimization, and fast multipole methods. This package is the first to perform symbolic DA computations, enabling traceability of initial condition contributions and runtime reduction for repeated DA calculations, potentially expanding DA’s applications.

97 MATHEMATICS AND COMPUTING↗

A Graphics Processing Unit–Based, Industrial Grade Compositional Reservoir Simulator

Summary Recently, graphics processing units (GPUs) have been demonstrated to provide a significant performance benefit for black-oil reservoir simulation, as well as flash calculations that serve an important role in compositional simulation. A comprehensive approach to compositional simulation based on GPUs has yet to emerge, and the question remains as to whether the benefits observed in black-oil simulation persist with a more complex fluid description. We present a positive answer to this question through the extension of a commercial GPU-based black-oil simulator to include a compositional description based on standard cubic equations of state (EOSs). We describe the motivations for the selected nonlinear formulation, including the choice of primary variables and iteration scheme, and support for both fully implicit methods (FIMs) and adaptive implicit methods (AIMs). We then present performance results on an example sector model and simplified synthetic case designed to allow a detailed examination of runtime and memory scaling with respect to the number of hydrocarbon components and model size, as well as the number of processors. We finally show results from two complex asset models (synthetic and real) and examine performance scaling with respect to GPU generation, demonstrating that performance correlates strongly with GPU memory bandwidth. NOTE: This paper is also published as part of the 2021 SPE Reservoir Simulation Conference Special Issue.

Engineering↗

ECP Software Technology Capability Assessment Report

The Exascale Computing Project Software Technology (ECP ST) focus area represents the key bridge between Exascale systems and the scientists developing applications that will run on those platforms. ECP offers a unique opportunity to build a coherent set of software (often referred to as the "software stack") that will allow application developers to maximize their ability to write highly parallel applications, targeting multiple Exascale architectures with runtime environments that will provide high performance and resilience. But applications are only useful if they can provide scientific insight, and the unprecedented data produced by these applications require a complete analysis work ow that includes new technology to scalably collect, reduce, organize, curate, and analyze the data into actionable decisions. This requires approaching scientific computing in a holistic manner, encompassing the entire user workflow - from conception of a problem, setting up the problem with validated inputs, performing high-fidelity simulations, to the application of uncertainty quantification to the final analysis. The software stack plan defined here aims to address all of these needs by extending current technologies to Exascale where possible, by performing the research required to conceive of new approaches necessary to address unique problems where current approaches will not suffice, and by deploying high-quality and robust software products on the platforms developed in the Exascale systems project. The ECP ST portfolio has established a set of interdependent projects that will allow for the research, development, and delivery of a comprehensive software stack,

97 MATHEMATICS AND COMPUTING↗

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↗

Implementing Software Resiliency in HPX for Extreme Scale Computing

The DOE Office of Science Exascale Computing Project (ECP) outlines the next milestones in the supercomputing domain. The target computing systems under the project will deliver 10x performance while keeping the power budget under 30 megawatts. With such large machines, the need to make applications resilient has become paramount. The benefits of adding resiliency to mission critical and scientific applications, includes the reduced cost of restarting the failed simulation both in terms of time and power. Most of the current implementation of resiliency at the software level makes use of a Coordinated Checkpoint and Restart (C/R). This technique of resiliency generates a consistent global snapshot, also called a checkpoint. Generating snapshots involves global communication and coordination and is achieved by synchronizing all running processes. The generated checkpoint is then stored in some form of persistent storage. On failure detection, the runtime initiates a global rollback to the most recent previously saved checkpoint. This involves aborting all running processes, rolling them back to the previous state and restarting them.

97 MATHEMATICS AND COMPUTING↗

Multiclass classification experiments

We seek a multiclass classifier that can satisfy the following requirements. 1. Predict among at least three classes. 2. Handle a moderately large number of correlated predictors. 3. Handle mixed categorical and continuous predictors. 4. Handle missing values (in some way). 5. Be trained with about n = 1,000 responses, and 6. Quantify prediction uncertainty. Based on 5. above, it is assumed that accuracy of prediction is paramount (relative to, say, runtime). All methods considered in this document take on the order of minutes (most take seconds) on a 2.8 GHz Quad-Core Intel Core i7 processor with 16GB RAM. Secondly, quantification of uncertainty is assumed to be a secondary task, since, with this small data size, resampling methods (i.e. bootstrapping) are possible. Further studies should quantify the feasibility and accuracy of resampling methods, and/or other methods, for quantifying uncertainty. R was used for all software.

97 MATHEMATICS AND COMPUTING↗

BEE - FY20 P6-2: Support for HPC resource managers 2.3.6.01 – LANL ATDM ST / STNS01-6 P6 Milestone Completion Documentation

BEE uses abstract interfaces between core functionality and specific driver code. An example of this is the worker_interface. The worker_interface is used by the BEETaskManager to communicate with the HPC system-specific resource manager (e.g. Slurm) and container runtime (e.g. Charliecloud). BEE initially only supported the Slurm HPC resource manager. This activity will make HPC resource manager support a configurable option. When this activity is complete BEE will support both the Slurm and LSF resource managers.

97 MATHEMATICS AND COMPUTING↗

Parameter Sensitivity Analysis of the SparTen High Performance Sparse Tensor Decomposition Software (Extended Analysis)

Tensor decomposition models play an increasingly important role in modern data science applications. One problem of particular interest is fitting a low-rank Canonical Polyadic (CP) tensor decomposition model when the tensor has sparse structure and the tensor elements are nonnegative count data. SparTen is a high-performance C++ library which computes a low-rank decomposition using different solvers: a first-order quasi-Newton or a second-order damped Newton method, along with the appropriate choice of runtime parameters. Since default parameters in SparTen are tuned to experimental results in prior published work on a single real-world dataset conducted using MATLAB implementations of these methods, it remains unclear if the parameter defaults in SparTen are appropriate for general tensor data. Furthermore, it is unknown how sensitive algorithm convergence is to changes in the input parameter values. This report addresses these unresolved issues with large-scale experimentation on three benchmark tensor data sets. Experiments were conducted on several different CPU architectures and replicated with many initial states to establish generalized profiles of algorithm convergence behavior.

97 MATHEMATICS AND COMPUTING↗

Pulsed Thermal Tomography Nondestructive Examination of Additively Manufactured Reactor Materials (Second Annual Progress Report)

Additive manufacturing (AM) is an emerging method for cost-efficient fabrication of nuclear reactor parts. AM of metallic structures for nuclear energy applications is currently based on laser powder bed fusion (LPBF) process, which can introduce internal material flaws, such as pores and anisotropy. Integrity of AM structures needs to be evaluated nondestructively because material flaws could lead to premature failures due to exposure to high temperature, radiation and corrosive environment in a nuclear reactor. Thermal tomography (TT) provides a capability for non-destructive evaluation of sub-surface defects in arbitrary size structures. Thermal tomography is a computational method for heat diffusion-based imaging of solids, which provides 3D visualization of data from flash thermography measurements. We investigate thermal tomography imaging and nondestructive evaluation of stainless steel and nickel super alloy metallic structures produced with laser powder bed fusion (LPBF) additive manufacturing (AM) process. Metallic structures produced with LPBF contain defects, and there are limited capabilities to evaluate these structures non-destructively. Thermal tomography reconstruction of 3D apparent spatial effusivity provides information about AM structure geometry and internal material flaws. We study performance of thermal tomography in imaging of metallic structures through COMSOL computer simulations of transient heat transfer, and through reconstruction of data obtained from experimental measurements. Reconstruction of internal defects is investigated using a stainless steel 316L specimen with flat bottom hole (FBH) indentations, and Inconel 718 plate produced with laser powder bed fusion (LPBF) method, which contains imprinted hemispherical shape low density regions containing non-sintered metallic powder. The FBH’s have the same sizes as the imprinted defects in the LPBF specimens, but offer better imaging contrast. Thermal tomography reconstructions provide visualizations of internal defects, and allow for estimation of their sizes and locations. Detection sensitivity of TT is limited by noises. We investigate separation of signal from noise in thermography images using several machine learning (ML) methods, including new spatio-temporal blind source separation (STBSS) and spatio-temporal sparse dictionary learning (STSDL) methods. Performance of the ML methods is benchmarked using thermography data obtained from imaging stainless steel 316L and Inconel 718 specimens produced LPBF method with imprinted calibrated porosity defects. The ML methods are ranked by F-score and execution runtime. Finally, we investigate TT of AM stainless steel 316L specimen with imprinted internal porosity defects using relatively low-cost, small form factor infrared (IR) camera based on uncooled micro bolometer detector. Sparse coding related K-means singular value decomposition (SVD) machine learning, image processing algorithms are developed to improve quality of TT images through removal of Additive white Gaussian noise without blurring the images. Following initial qualification of an AM component for deployment in a nuclear reactor, a compact TT can also be used for in-service nondestructive evaluation (NDE). With capability to perform in-service NDE of the AM component lifecycle, TT data can be used for development of a component digital twin.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Vitrification of Hanford Tank 241-AP-107 with Recycled Condensate

During the vitrification of nuclear waste at the Hanford Waste Treatment and Immobilization Plant (WTP) – the primary mission of the U.S. Department of Energy Office of River Protection – the offgas condensate generated from the waste-to-glass conversion is currently planned to be concentrated by evaporation in the Effluent Management Facility (EMF). This concentrated condensate can then be recycled back to the incoming waste and vitrified. To test the recycle process, a test apparatus was designed to mimic the EMF evaporator and used to concentrate a volume of condensate that had been previously produced during the vitrification of Hanford tank 241-AP-107 (referred to herein as AP-107) waste in a continuous laboratory-scale melter (CLSM). The test apparatus successfully concentrated the AP-107 condensate by a factor of 10 while retaining over 90 % of the technetium-99 ( 99 Tc), Cs, and I inventory. A second portion of AP-107 waste was retrieved by Washington River Protection Solutions, LLC, given to Pacific Northwest National Laboratory, and combined with the AP-107 condensate concentrate after undergoing solids filtration and cesium removal by ion exchange. This combination served to approximate the recycling action to be performed at the WTP. After the addition of glass-forming chemicals (GFCs), the combined AP-107 waste and AP-107 condensate concentrate were processed in the CLSM to produce a glass, called AP-107-1R, that was designed to satisfy the WTP baseline requirements (Kim et al. 2012). During the 8.87 hours of processing, 7.27 kg of AP-107-1R glass were produced for an average glass production rate of 1739 kg m 2 d -1 . Compared to the previous run in the CLSM without recycled condensate, the run with the recycle had a greater average glass production rate, but the rate was within the potential range of variability when processing melter feeds with similar composition in the CLSM. The glass produced from the AP-107 recycle run in the CLSM was within 10 % of the target AP-107-1R glass composition with respect to the primary glass components. Analysis of the minor component impurities revealed that their content in the glass product had approached their nominal target after 2 turnovers of the glass inventory in the CLSM while the activity of the minor radionuclides was retained in the glass product. The 99 Tc and total cesium content in the combined AP-107 waste and recycled condensate were maintained at concentrations expected to be experienced at the WTP. During processing in the CLSM, at discrete sampling time periods, the target 99 Tc/Cs mass ratio in the glass formulation varied from 0.9 to 62.9. Across this range, the Cs retention in the glass ranged from 53 to 60 %, while the retention from the entire runtime totaled 68 %, values which align with Cs retention in other scaled melter systems while processing LAW melter feeds at 99 Tc/Cs mass ratios ranging from 1 to 100. The 99 Tc retention in the glass ranged from 22 to 32 %, primarily due to the cold-cap coverage on the glass melt surface, the area covered by reacting melter feed, varying from ~80 % to ~95 % during processing, demonstrating greater volatility of 99 Tc from the glass while more surface was exposed, as expected based on previous 99 Tc volatility studies.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

A Multi-Scale Inference, Estimation, and Prediction Engine for Earth System Modeling

We posit that AI methods can be leveraged to significantly enhance the predictive skill of forward Earth system modeling (ESM) activities. A hybrid framework incorporating traditional ESM modeling, inference methods, and AI techniques could make better use of both measured and computed information as well as computational resources by targeting inference tasks at program priorities, such as the predictability of precipitation extremes. This runtime pathway to closing the simulation/analysis-data/model improvement loop will streamline the traditional offline pathway to model improvement, which is based on domain science expertise, while suggesting guidance for further observations and measurements.

58 GEOSCIENCES↗