Object-Centric Data Management in HPC Workflows - A Case Study
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Computer science↗
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From Cloud to Clarity: Basement Fault Mapping in CO2 Storage Using a Machine Learning-Assisted Workflow
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Geosciences↗
Predictive Execution of Workflows in a HPC+Cloud Environment
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Behera, Subhendu [North Carolina State University,↗
State Machine Orchestration of an HPC Workflow in Cloud
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Sochat, V. [Lawrence Livermore National Laboratory↗
Building a new multiphysics workflow in MOOSE: application to tritium migration, trapping and advection in TMAP8
Fusion devices are anticipated to produce and consume several kilograms of tritium per year. This rare fuel resource is both highly mobile and radioactive, making tracking inventories a priority for operation and safety. The fusion safety program at the Idaho National Laboratory has been developing the Tritium Migration and Analysis Program (TMAP), of which the latest version is a MOOSE-based application. TMAP8 is verified against its predecessors and possesses additional multi-dimensional tritium migration modeling capabilities. As we extend its capabilities towards both whole device (in multiple dimensions) and whole plant (with multiple components) simulations, the syntax of inputs must become compact, descriptive, compatible with quality assurance processes, and as error-proof as achievable. The new Physics system developed MOOSE can set up equations and instantiating them on plant components. The system permits the automatic definition of complex discretization with a consistency between object parameters achieved programmatically. The Physics system can currently instantiate the equations for heat conduction and Navier Stokes weakly compressible flow. In MOOSE-terms, it automates the definition of kernels, boundary conditions, and several core and helper materials and fields. As part of this effort, Physics classes were developed for tritium migration, trapping and advection within either a multi-dimensional Navier Stokes fluid dynamics simulation, or a 1D thermal hydraulics piping system. In this presentation, we will showcase the new syntax, its application to several verification and validation cases which were already studied using the classical TMAP8 syntax, and a demonstration of the new coupling capabilities for the migration of tritium into blanket coolant channels and the subsequent advection into the coolant loop.
70 - PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Improved Workflow and Productivity Tools for NCS at Sandia National Laboratories
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Raster, Ashley Rachel [Sandia National Laboratorie↗
Darshan for HEP applications
Modern HEP workflows must manage increasingly large and complex data collections. HPC facilities may be employed to help meet these workflows’ growing data processing needs. However, a better understanding of the I/O patterns and underlying bottlenecks of these workflows is necessary to meet the performance expectations of HPC systems.Darshan is a lightweight I/O characterization tool that captures concise views of HPC application I/O behavior. It intercepts application I/O calls at runtime, records file access statistics for each process, and generates log files detailing application I/O access patterns.Typical HEP workflows include event generation, detector simulation, event reconstruction, and subsequent analysis stages. A study of the I/O behavior of the ATLAS simulation and filtering stage, and the CMS simulation workflow using Darshan is presented, including insights into the I/O operations and data access size.
Wang, Rui↗
Adaptive elasticity policies for staging-based in situ visualization
In situ processing aims to alleviate the growing gap between computation and I/O capabilities by performing data processing close to the data source. In situ processing is widely used to process data generated by multiple data sources, including observation data from edge devices or scientific observational facilities and the simulation data generated by scientific computation on a high-performance computing (HPC) platform. For a scientific workflow that is run on an HPC platform and composed of a simulation program and an in situ data analytics or visualization (abbreviated as ana/vis) task, there is an implicit assumption that the computing resources assigned to the workflow keep static during the workflow execution. However, with the converging trend between the HPC and cloud computing platform, running the in situ ana/vis task in an elastic way is promising to decrease its overhead and improve its resource utilization rate. Resource elasticity represents the ability to change resource configurations such as the number of computing nodes/processes during workflow execution. An elastic job may dynamically adjust resource configurations; it may use a few resources at the beginning and more resources toward the end of the job when interesting data appear. However, it is hard to predict a priori how many computing nodes/processes need to be added/removed during the workflow execution to adapt to changing workflow needs. How to efficiently guide elasticity operations, such as growing or shrinking the number of processes used for in situ analysis during workflow execution, is an open-ended research question. In this article, we present adaptive elasticity policies that adopt workflow runtime information collected during workflow execution to predict how to trigger the addition/removal of processes in order to minimize in situ processing overhead. Taking in situ visualization tasks as an example, we integrate the presented elasticity policies into a staging-based elastic workflow and evaluate its efficiency in multiple elasticity scenarios. Compared with the situation without elasticity or with a static elasticity policy that uses a fixed number of processes for each rescaling operation, the adaptive elasticity policy can save overhead in finding a proper resource configuration and improve resource utilization efficiency. Furthermore, one experiment illustrates that the adaptive elasticity policy saves 41% of core-hours compared with the situation without the resource elasticity.
97 MATHEMATICS AND COMPUTING↗
FORCE Update 2024
The Framework for Optimization of Resources and Economics (FORCE) tool suite is the U.S. Department of Energy’s Nuclear Integrated Energy Systems (IES) Program flagship tool suite for technoeconomic IES analysis of IES. This tool suite is useful for analysis designed to evaluate and improve the technoeconomics of energy production systems, particularly for systems including nuclear technology. In this report, we document the development activity for the FORCE tool suite to extend its capabilities as performed during fiscal year 2024. In addition to reliability and accessibility, capability is one of the three standards guiding the development of the FORCE tool suite and the software codes that are its constituent parts. Extending the capabilities of the FORCE tool suite allows analysis both within the IES program as well as industry, university, and laboratory partners to perform analysis with more accuracy, insight, and impactful narrative. Four areas of capability development were the focus of activity this year: economic parameter uncertainty quantification, multiresolution analysis, components-to-optimization workflow automation, and statespace construction workflows for real-time optimal control. In economic parameter uncertainty quantification, the ability of HERON to capture risk due to scenarios (weather and energy demand uncertainty) was expanded to also include uncertainties in financial parameters such as capital cost or operation and maintenance costs. By including these sources of uncertainty, which are sometimes very large compared with scenario uncertainty, HERON is better able to capture the risk posed by investment in various IES technology. Because of this, analysts can also consider the reduction in risks that can be realized by choice of some technologies. In multiresolution analysis, development activity extended on work completed previously. In fiscal year 2023, methods for decomposing time series signals, such as demand, solar and wind availability, and price profiles, were analyzed and down-selected to those most effective at splitting signals into different resolutions. These resolutions allow considering the influence of different energy demand and supply behaviors across different time scales. For example, energy demand might be divided into seasonal, weekly, and hourly profiles. In fiscal year 2024, this preliminary work was extended and implemented within the Risk Analysis Virtual Environment (RAVEN) risk and uncertainty analysis platform, which is used throughout the FORCE framework. This development of the “multi-resolution time series analysis” (MR-TSA) module in RAVEN allows training synthetic history generators on complex time series. These synthetic history generators can then be used in HERON for generating scenarios that represent possible market and weather scenarios that can be analyzed on different time scales. We envision completing this work in the future, implementing multiresolution dispatch optimization strategies that can make the most beneficial use of these stratified time histories. In components-to-optimization workflow development, workflows for translating user inputs of components into algorithms for algebraic optimization were selected and implemented. Similar algorithms within the Holistic Energy Resource Optimization Network (HERON) were separated from the main code base of HERON and gathered with the components-to-optimization workflows in the new Dispatch Optimization Variable Engine (DOVE) software library. This modularization allows FORCE users to analyze dispatch optimization and energy system duty cycles independently of HERON, which previously was a burdensome task. Additionally, these dispatch optimization algorithms, set up in an independent library, can now be used across all software applications within FORCE, especially including the real-time optimal control software Optimization of Real-time Capacity Allocation (ORCA). Allowing FORCE software to share dispatch optimization algorithms within a single library allows for improved software maintenance and reliability. In statespace characterization workflow development, alternative workflows for optimizing dispatch with additional technical accuracy was the focus, particularly to improve the real-time optimization decision making in ORCA. Using algorithms and workflows initially developed for the Feasible Actuator Range Modifier (FARM), workflows for determining the statespace representation of IES were identified and demonstrated. The resulting dispatch optimization required a more robust optimization algorithm than that originally used in HERON (and moved to DOVE), which required adding an alternate workflow to DOVE that can more accurately match the behavior of physical systems using a partial differential equation representation. In conclusion, capability developments in the FORCE tool suite in fiscal year 2024 have improved the ability of the FORCE tool suite to perform
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Observing System Simulation Experiment (OSSE) for the HyspIRI Spectrometer Mission
The OSSE software provides an integrated end-to-end environment to simulate an Earth observing system by iteratively running a distributed modeling workflow based on the HyspIRI Mission, including atmospheric radiative transfer, surface albedo effects, detection, and retrieval for agile exploration of the mission design space. The software enables an Observing System Simulation Experiment (OSSE) and can be used for design trade space exploration of science return for proposed instruments by modeling the whole ground truth, sensing, and retrieval chain and to assess retrieval accuracy for a particular instrument and algorithm design. The OSSE in fra struc ture is extensible to future National Research Council (NRC) Decadal Survey concept missions where integrated modeling can improve the fidelity of coupled science and engineering analyses for systematic analysis and science return studies. This software has a distributed architecture that gives it a distinct advantage over other similar efforts. The workflow modeling components are typically legacy computer programs implemented in a variety of programming languages, including MATLAB, Excel, and FORTRAN. Integration of these diverse components is difficult and time-consuming. In order to hide this complexity, each modeling component is wrapped as a Web Service, and each component is able to pass analysis parameterizations, such as reflectance or radiance spectra, on to the next component downstream in the service workflow chain. In this way, the interface to each modeling component becomes uniform and the entire end-to-end workflow can be run using any existing or custom workflow processing engine. The architecture lets users extend workflows as new modeling components become available, chain together the components using any existing or custom workflow processing engine, and distribute them across any Internet-accessible Web Service endpoints. The workflow components can be hosted on any Internet-accessible machine. This has the advantages that the computations can be distributed to make best use of the available computing resources, and each workflow component can be hosted and maintained by their respective domain experts.
Turmon, Michael J.↗
Building a Wide-Area File Transfer Performance Predictor: An Empirical Study
Wide-area data transfer is central to geographically distributed scientific workflows. Faster delivery of data is important for these workflows. Predictability is equally (or even more) important. With the goal of providing a reasonably accurate estimate of data transfer time to improve resource allocation & scheduling for workflows and enable end-to-end data transfer optimization, we apply machine learning methods to develop predictive models for data transfer times over a variety of wide area networks. To build and evaluate these models, we use 201,388 transfers, involving 759 million files totaling 9 PB transferred, over 115 heavily used source-destination pairs (“edges”) between 135 unique endpoints. We evaluate the models for different retraining frequencies and different window size of history data. In the best case, the resulting models have a median prediction error of ≤21% for 50% of the edges, and ≤32% for 75% of the edges. We present a detailed analysis of these results that provides insights into the cause of some of the high errors. We envision that the performance predictor will be informative for scheduling geo-distributed workflows. The insights also suggest obvious directions for both further analysis and transfer service optimization.
Liu, Zhengchun↗
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↗
Equilibrium reconstruction of DIII-D plasmas using predictive modeling of the pressure profile
New workflows have been developed for predictive modeling of magnetohydrodynamic (MHD) equilibrium in tokamak plasmas. The goal of this work is to predict the MHD equilibrium in tokamak discharges without having measurements of the kinetic profiles. The workflows include a cold start tool, which constructs all the profiles and power flows needed by transport codes; a Grad–Shafranov equilibrium solver; and various codes for the sources and sinks. For validation purposes, a database of DIII-D tokamak discharges has been constructed that is comprised of scans in the plasma current, toroidal magnetic field, and triangularity. Initial efforts focused on developing a workflow utilizing an empirically derived pressure model tuned to DIII-D discharges with monotonic safety factor profiles. This workflow shows good agreement with experimental kinetic equilibrium calculations, but is limited in that it is a single fluid (equal ion and electron temperatures) model and lacks H-mode pedestal predictions. The best agreement with the H-mode database is obtained using a theory-based workflow utilizing pressure profile predictions from a coupled TGLF turbulent transport and EPED pedestal models together with external magnetics and Motional Stark Effect (MSE) data to construct the equilibrium. Here, we obtain an average root mean square error of 5.1% in the safety factor profile when comparing the predicted and experimental kinetic equilibrium. We also find good agreement with the plasma stored energy, internal inductance, and pressure profiles. Including MSE data in the theory-based workflow results in noticeably improved agreement with the q-profiles in high triangularity discharges in comparison with the results obtained with magnetic data only. The predictive equilibrium workflow is expected to have wide applications in experimental planning, between-shot analysis, and reactor studies.
Kinsey, J. E. (ORCID:0000000193347473)↗
An XML Representation for Crew Procedures
NASA ensures safe operation of complex systems through the use of formally-documented procedures, which encode the operational knowledge of the system as derived from system experts. Crew members use procedure documentation on the ground for training purposes and on-board space shuttle and space station to guide their activities. Investigators at JSC are developing a new representation for procedures that is content-based (as opposed to display-based). Instead of specifying how a procedure should look on the printed page, the content-based representation will identify the components of a procedure and (more importantly) how the components are related (e.g., how the activities within a procedure are sequenced; what resources need to be available for each activity). This approach will allow different sets of rules to be created for displaying procedures on a computer screen, on a hand-held personal digital assistant (PDA), verbally, or on a printed page, and will also allow intelligent reasoning processes to automatically interpret and use procedure definitions. During his NASA fellowship, Dr. Simpson examined how various industries represent procedures (also called business processes or workflows), in areas such as manufacturing, accounting, shipping, or customer service. A useful method for designing and evaluating workflow representation languages is by determining their ability to encode various workflow patterns, which depict abstract relationships between the components of a procedure removed from the context of a specific procedure or industry. Investigators have used this type of analysis to evaluate how well-suited existing workflow representation languages are for various industries based on the workflow patterns that commonly arise across industry-specific procedures. Based on this type of analysis, it is already clear that existing workflow representations capture discrete flow of control (i.e., when one activity should start and stop based on when other activities start and stop), but do not capture the flow of data, materials, resources or priorities. Existing workflow representation languages are also limited to representing sequences of discrete activities, and cannot encode procedures involving continuous flow of information or materials between activities.
Simpson, Richard C.↗
Earth Science Data Processing With Nextflow
Earth science data processing tasks present many challenges. These tasks often process large input datasets and require scores of CPU-hours to generate results. All but the simplest tasks will be decomposed into a series of computational or data manipulation steps, also known as a scientific workflow. In order to reduce the burden of orchestrating and running the dependent processing steps, a workflow execution engine is required. This poster describes the lessons learned by the CLARREO Pathfinder (CPF) team while developing multiple scientific workflows and utilizing the open-source Nextflow engine to execute them in a cloud computing environment. The Nextflow engine is designed with the following stated goals: first, the engine does not dictate how individual steps in the task are implemented (i.e. it is language and interface agnostic); second, the engine supports easy configuration and modularity at the workflow level so that others can easily execute our workflows to reproduce results; lastly, the engine eases development by transparently scaling execution from local to remote environments. Nextflow was developed for the bioinformatics domain but is a good fit for other scientific workflows where the overall task is well-described by a dataflow diagram. The CPF team has developed Nextflow pipelines (i.e. scientific workflows) to simulate CLARREO radiance, generate large look-up tables for inter-calibration algorithms, and generate L4 intercalibration data products. These pipelines consume from single-digits to hundreds of thousands of CPU-hours. In the development and evolution of these pipelines we have discovered many design patterns, pitfalls, and solutions to common problems. Our goal is to demonstrate important aspects of how to design, implement, run, and ultimately share Nextflow pipelines in the domain of Earth science.
Aron D Bartle↗
Mind the Gap: Building Simulation in the Architectural Design Studio
Building modelling and simulation approaches are increasingly being utilized in architectural design studios to guide and inform the design process and offer evidence-based feedback on proposed building performance. The development of intuitive and simplified simulation interfaces has greatly contributed to achieving this integration. One aspect that is often overlooked is the workflow that governs and regulates integrated design, which can have significant impacts on final design outcomes. Currently there are numerous software packages available for building performance simulations. This makes it challenging to select an appropriate tool that provides accurate results yet allows a designer to make informed architectural decisions with a designer-friendly interface. Furthermore, workflows to incorporate simulations into the design process proved to highly impact student’s project design integration. Yet, it is not clear what type of workflows are successful to achieve this goal, under what conditions, and/or for which building and site typologies. This paper addresses these issues by first reviewing three different workflows for integrating building performance simulation processes and highlighting their strengths and weaknesses. Second, a comparative case study approach was employed to test three of the most common workflows in three different integrated design architectural studios at the senior and vertical studio levels as well as in two courses that run parallel and complementary to the design studios. The workflows, processes, and the resultant student projects were further analyzed based on criteria for better integrated design and architectural excellence as outlined in the American Institute of Architects Committee on the Environment (AIA COTE) Top 10 Student’s Competition. Third, to situate the pedagogical case studies’ results within a larger context, a survey of the AIA COTE Top 10 student competition award recipients over the last five years was conducted. The results are summarized in a pedagogical framework that outlines best strategies of the type of workflows, software, design process used, methods to achieve desired interaction between design process and analytical feedback, and metrics for educators to evaluate the success of this integration and their learning outcomes in the design studio. The goal is to help bridge the gap between the building design and simulation within the design studio’s creative process for more integrated design outcomes.
Elzeyadi, Ihab↗
Performance analysis and optimization for scalable deployment of deep learning models for country-scale settlement mapping on Titan supercomputer
Here, we present a scalable object detection workflow for detecting objects, such as settlements, from remotely sensed (RS) imagery. We have successfully deployed this workflow on Titan supercomputer and utilized it for the task of mapping human settlement at a country scale. The performance of various stages in the workflow was analyzed before making it operational. The workflow implemented various strategies to address issues such as suboptimal resource utilization and long-tail effects due to unbalanced image workload, data loss due to runtime failures, and maximum wall-time constraints imposed by Titan's job scheduling policy. A mean shift clustering–based static load balancing strategy was implemented, which partitions the image load such that each partition contained similar-sized images. Furthermore, a checkpoint-restart strategy was added in the workflow as a fault-tolerance mechanism to prevent the data losses due to unforeseen runtime failures. The performance of the above-mentioned strategies was observed in various scenarios, such as node failure, exceeding wall time, and successful completion. Using this workflow, we have examined an RS data set that has a spatial resolution of 0.31 m and is comprised of 685 675 km 2 of area of the Republic of Zambia in under six hours using 5426 nodes of the Titan supercomputer.
97 MATHEMATICS AND COMPUTING↗
DART-PFLOTRAN: An ensemble-based data assimilation system for estimating subsurface flow and transport model parameters
Ensemble-based Data Assimilation (EDA), based on the Monte Carlo approach, has been effectively applied to estimate model parameters through inverse modeling in subsurface flow and transport problems. However, implementation of EDA approach involves a complicated workflow that include setting up and executing ensemble forward model simulations, processing observations and model simulation results for parameter updates, and repeat for sequential or iterative EDA. To facilitate the management of such workflow and lower the barriers for adopting EDA-based parameter estimation in subsurface science, we develop a generic software frame-work linking the Data Assimilation Research Testbed (DART) with a massively parallel subsurface FLOw and TRANsport code PFLOTRAN. The new DART-PFLOTRAN leverages both the core data assimilation engines in DART and the computational power afforded by PFLOTRAN. In addition to the standard smoother and filtering options, DART-PFLOTRAN enables an iterative EDA workflow based on the Ensemble Smoother for Multiple Data Assimilation method (ES-MDA) to improve estimation accuracy for nonlinear forward problems. Here, we verify the implementation of ES-MDA in DART-PFLOTRAN using two synthetic cases designed to estimate static permeability and dynamic exchange fluxes across the riverbed, respectively, from continuous temperature measurements made across a depth profile. One-dimensional hydro-thermal simulations are performed in both cases to relate temperature responses with the parameters of interest. In the case of estimating dynamic parameters, we demonstrate the flexibility of DART-PFLOTRAN in automating sequential ES-MDA workflow, which will significantly reduce the time researchers spend on managing complex workflows in similar applications. Both studies yield accurate estimations of the parameters compared to their synthetic truth, while ES-MDA leads to more accurate estimation when a high level of nonlinearity exist between observed responses and unknown parameters. With a code base in Python and Fortran, DART-PFLOTRAN paves the way for applications in large-scale subsurface inverse modeling by automating the complex workflow of sequential ES-MDA that can be executed on various computing platforms.
97 MATHEMATICS AND COMPUTING↗