Significant Advances in Computational Simulation Workflow for National Security Applications.
Abstract not provided.
Witkowski, Walter R.↗
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Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows
The 2024 Workflows Community Summit report presents the outcomes of a three-day international gathering that brought together 109 experts from 18 countries to discuss future trends and challenges in scientific workflows. The summit focused on six key areas: time-sensitive workflows, convergence of AI and HPC workflows, multi-facility workflows, heterogeneous HPC environments, user experience and interfaces, and FAIR computational workflows. Discussions highlighted emerging challenges such as integrating AI with traditional HPC, managing workflows across diverse facilities, addressing heterogeneity in computing environments, and ensuring workflows are findable, accessible, interoperable, and reusable (FAIR). The report outlines recent advances, ongoing challenges, and provides recommendations for each topic area, emphasizing the need for standardization, improved interoperability, and the development of more sophisticated tools and frameworks to support the evolving landscape of scientific workflows in the era of exascale computing and AI integration.
97 MATHEMATICS AND COMPUTING↗
Joint Genome Institute Analysis Workflow Service (JAWS) v2.7
The U.S. Department of Energy Joint Genome Institute (JGI) has developed the JGI Analysis Workflow Service (JAWS) as a distributed framework to run computational workflows across diverse high-performance computing (HPC) and cloud environments. JAWS enhances the reusability, scalability, and robustness of scientific workflows by orchestrating data movement, code execution, and results retrieval across multiple DOE facilities. At its core, JAWS integrates the Cromwell workflow engine to run workflows expressed in the Workflow Description Language (WDL), ensuring portability and interoperability. To provide consistent runtime environments, JAWS employs container technologies such as Shifter, Apptainer, and Docker. Workflow tasks are managed via HTCondor on HPC backends, while Globus ensures secure and efficient data transfer between sites. JAWS is deployed as a multi-site workflow manager across national laboratory computing facilities, with dedicated instances supporting community projects such as the National Microbiome Data Collaborative (NMDC) and KBase. This distributed, service-oriented architecture enables users to "write once, run anywhere," providing scalable, production-quality workflow execution.
Kirton, Edward↗
Computational Tools and Workflows for Quantitative Risk Assessment and Decision Support for Geologic Carbon Storage Sites: Progress and Insights from the U.S. DOE’s National Risk Assessment Partnership
The 2005 Intergovernmental Panel on Climate Change (IPCC) Special Report on CCS raised the profile of CO2 capture and storage (CCS) as an important technology for reducing greenhouse gas (GHG) emissions. CCS is now recognized as a key component of most climate change mitigation scenarios. Since publication of that report the international research, development, and deployment (RD&D) community has advanced key technical aspects, clarified regulatory requirements, explored value chain and infrastructure solutions, and developed incentive paradigms to enable and promote large-scale deployment of CCS. These efforts have included research to better characterize geologic storage resources, to improve injection performance and storage efficiency, to assess and manage subsurface environmental risks, and to advance monitoring technologies to assure system conformance. These efforts have helped to build confidence in the viability of geologic carbon storage (GCS), but stakeholder concerns about long-term risks and liability associated with GCS remain a hurdle to broad acceptance and large-scale deployment of CCS. Since 2010, the U.S. DOE’s National Risk Assessment Partnership (NRAP) – a research collaboration between five contributing national laboratories – has worked to establish and demonstrate methods and tools to quantify and manage the subsurface environmental risks associated with GCS, amidst uncertainty. This work supports the Office of Fossil Energy and Carbon Management Carbon Transport and Storage Program’s goal of advancing safe and secure commercial-scale GCS deployment. To address the technical challenge of simulating the physical response of the GCS site to large-scale CO2 injection, NRAP has adopted an approach that relies on coupling computationally efficient reduced-order and/or data-driven proxy models of important system components (i.e., storage reservoir, sealing caprock, leakage pathways, intermediate formations, overlying groundwater aquifers, and the atmosphere) in integrated assessment framework. That integrated model of the physical system is complemented with fit-for purpose functionality to support site characterization and risk-related decisions. The recently released NRAP Phase II toolset includes the Open-Source Integrated Assessment Model (NRAP-Open-IAM) for evaluation of trends in leakage risk and potential impact, tools to support monitoring design optimization (Designs for Risk Evaluation and Management – DREAM v3.0 and Passive Seismic Monitoring Tool - PSMT), and tools for state of stress evaluation (State-of-Stress Analysis Tool - SOSAT) and forecasting induced seismicity risk. The NRAP team has also released a pair of reports describing conceptual workflows to incorporate physics-based, quantitative risk assessment into many of the design, planning, operation, and closure decisions for GCS projects. An online catalogue highlights published studies where these tools and methods are demonstrated. In this presentation, the utility of these products to assess risks and address key stakeholder questions will be highlighted through examples, and related insights about the safety and security of geologic carbon storage in qualified storage sites will be discussed. The prospect of rapid, large-scale deployment of GCS technology to aggressively reduce anthropogenic CO2 emissions requires careful consideration of interference between multiple commercial-scale storage projects within a basin. Going forward, NRAP is expanding and adapting site-scale risk quantification tools and methods to enable assessment of risks and inform management decisions for basin-scale deployment. Increasingly, this work will leverage next-generation approaches for surrogate modelling, fast prediction, and advanced visualization enabled by machine learning and artificial intelligence to promote virtual learning, scenario evaluation, and augment risk-based decision making.
quantitative risk assessment, geologic carbon stor↗
Frontiers in Scientific Workflows: Pervasive Integration With High-Performance Computing
Herein we address the increasing complexity of scientific workflows in the context of high-performance computing (HPC) and their associated need for robust, adaptable, and flexible computational support systems. We explore five key trends as well as future challenges and opportunities for scientific workflows and HPC technologies.
97 MATHEMATICS AND COMPUTING↗
Robust In-Situ Strain Measurements to Monitor CO 2 Storage
The goal of this project was to develop and demonstrate robust instrumentation to monitor the in-situ strain tensor in order to improve the reliability and security of CO 2 storage in geologic formations. We met the original goals of the project and the major overarching accomplishment is the advancement of strain tensor monitoring from an intriguing concept to a commercially available technology with a solid foundation of novel instruments supported by theoretical analyses and validation experiments. The main accomplishments of the project are summarized below. We designed, built and evaluated nine new optical fiber strainmeters and tiltmeters using Michelson interferometers to measure deformation with ultra-high resolution at both shallow and deep point locations in the subsurface. These are the robust strainmeters that motivated the title of the project. We designed, built and evaluated a novel method of measuring distributed strain in optical fibers with nanostrain resolution, and cm-scale location, and sampling into the seismic band. The new method is called Coherence-length-gated Microwave Photonics Interfereometry (CMPI). CMPI technology has advantages over existing commercial DAS and DSS methods. We developed and demonstrated capabilities to deploy instruments in the field and used them to measure strain caused by ambient signals like barometric pressure and tides, as well as induced signals like surface loading and pore pressure changes from pumping tests. We deployed a working strainmeter at 1,700 ft depth, slightly above an active reservoir. This is to our knowledge the greatest depth a strainmeter has been deployed and the techniques we used can readily be extended to greater depths. Optical fiber borehole tensor strainmeter techology was advanced from a TRL 4 at the start, to a TRL of 7 at the conclusion of the project. The project included advances in simulations and theoretical analyses. We developed and demonstrated a computational workflow that uses machine learning to reduce the computational requirements and make it practical to use Bayesian inversion to solve large numerical poroelastic analyses needed to interpret strain tensor field data. We evaluated the strain tensor fields and time series that would be caused by leaks of CO 2 or other fluids from reservoirs. These simulations demonstrated that signals from leaks could be measured with instruments developed for the project, opening a potentially new method for ensuring storage security. We showed that strains in caprock can be used to estimate pressure in a reservoir. This avoids the need to drill monitoring wells into the reservoir, and it expands the capabilities of monitoring in the caprock. The project includes a derivation and application of a novel analytical solution to the strains in the vicinity of a pressurized poroelastic inclusion. This solution explains field data measured during injeciton tests at the North Avant Field, and it will simplify future interpretation of strain tensor data. The project included a broad range of experiments, and of the most significant is the characterization of the strain tensor at an array three strainmeters during six injection tests at the North Avant Field, Oklahoma. This demonstrated repeatability of the strain signal measured by the new instruments developed for the project, and it showed similarities between the strain signal at shallow depths and pressure in the underlying reservoir. We also demonstrated that useful strain data can be measured at reservoir depths. This confirms that strain tensor data can be measured throughout the caprock over a reservoir. The project demonstrated the feasibility of using the strain tensor and distributed strain measured in caprock during a variety of different well tests where the pumping rate was constant, sinusoidal and positive, or a periodic square wave with zero net rate. This further strengthens the validity of using strain data to characterize reservoirs and aquifers. We also demonstrated that strain caused be fluctuations of air pressure and water pressure in the vadose zone can be measured and interpreted, suggesting that high resolution distributed strain measurements hold promise for monitoring the vadose zone. The project partially supported nine graduate students in the Environmental Engineering, Hydrogeology, Electrical Engineering programs at Clemson University. The research was described in nine journal papers, 23 talks and conference abstracts. Additional journal papers are in preparation. A new company called Tensora was started to provide strainmeter technology for commercial applications.
01 COAL, LIGNITE, AND PEAT↗
Evaluation of Portable Programming Models to Accelerate LArTPC Detector Simulations
The Liquid Argon Time Projection Chamber (LArTPC) technology is widely used in high energy physics experiments, including the upcoming Deep Underground Neutrino Experiment (DUNE). Accurately simulating LArTPC detector responses is essential for analysis algorithm development and physics model interpretations. Accurate LArTPC detector response simulations are computationally demanding, and can become a bottleneck in the analysis workflow. Compute devices such as General-Purpose Graphics Processing Units (GPGPUs) have the potential to substantially accelerate simulations compared to traditional CPU-only processing. The software development for these compute accelerators often carries the cost of specialized code refactorization and porting to match the target hardware architecture. With the rapid evolution and increased diversity of the computer architecture landscape, it is highly desirable to have a portable solution that also maintains reasonable performance. We report our ongoing effort in evaluating Kokkos as a basis for this portable programming model using LArTPC simulations in the context of the Wire-Cell Toolkit, a C++ library for LArTPC simulations, data analysis, reconstruction and visualization.
47 OTHER INSTRUMENTATION↗
Evaluation of Portable Programming Models to Accelerate LArTPC Detector Simulations
The Liquid Argon Time Projection Chamber (LArTPC) technology is widely used in high energy physics experiments, including the upcoming Deep Underground Neutrino Experiment (DUNE). Accurately simulating LArTPC detector responses is essential for analysis algorithm development and physics model interpretations. Accurate LArTPC detector response simulations are computationally demanding, and can become a bottleneck in the analysis workflow. Compute devices such as General-Purpose Graphics Processing Units (GPGPUs) have the potential to substantially accelerate simulations compared to traditional CPU-only processing. The software development that requires often carries the cost of specialized code refactorization and porting to match the target hardware architecture. With the rapid evolution and increased diversity of the computer architecture landscape, it is highly desirable to have a portable solution that also maintains reasonable performance. We report our ongoing effort in evaluating Kokkos as a basis for this portable programming model using LArTPC simulations in the context of the Wire-Cell Toolkit, a C++ library for LArTPC simulations, data analysis, reconstruction and visualization.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Diaspora: Resilience-Enabling Services for Real-Time Distributed Workflows
The need for real-time processing to enable automated decision making and experimental steering has driven a shift from high-performance computing workflows on a centralized system to a distributed approach that integrates remote data sources, edge devices, and diverse compute facilities. Under this paradigm, data can be processed close to the source where it is generated, thus reducing latency and bandwidth usage. System resilience is thus a key challenge, requiring distributed workflows to survive component failures and to meet stringent quality-of-service requirements, which results in the need to mitigate anomalies such as congestion and low availability of resources. To address these challenges, we propose Diaspora, a unified resilience framework that is inspired by event-driven communication patterns used in public clouds. Specifically, we propose an event fabric that extends across sites, facilities, and computations to provide timely, reliable, and accurate information about data, application, and resource status. On top of the event fabric, we build resilience-enabling services that combine QoS-aware data streaming, resilient data views, resilient compute and data resources, and anomaly detection and prediction, all of which collectively enhance workflow resilience for these scientific cases.
Rao, Nageswara↗
Prescriptive provenance for streaming analysis of workflows at scale
Abstract- We extend our approach capturing and relating the provenance and performance metrics of computational workflows as a diagnostic tool for runtime optimization and placement. One important challenge is the volume of extracted data, both for performance metrics and provenance, even when specifying filters and focusing on quantities of interest in a simulation. We reduce this data by performing anomaly detection on streaming data and store provenance for the detected anomalies, an approach we call prescriptive provenance. This paper discusses the Chimbuko architecture enabling the approach. We present the use of a protein structure propagation workflow based on NWChemEx. We are testing algorithms for anomaly detection and present preliminary results here obtained with Local Outlier Factor. While scaling remains a challenge, these results show that our robust Chimbuko architecture for streaming analysis with prescriptive provenance is a promising approach.
97 MATHEMATICS AND COMPUTING↗
Official Report on the 2021 Computational and Autonomous Workflows Workshop (CAW 2021)
This technical report documents the Computational and Autonomous Workflows (CAW) workshop held at ORNL (Oak Ridge National Laboratory) in July 2021. The theme of the workshop was "FAIR workflows". This document describes the workshop and takeaways for the Department of Energy, for ORNL, and for the Oak Ridge Leadership Computing Facility.
42 ENGINEERING↗
Workflows Community Summit: Tightening the Integration between Computing Facilities and Scientific Workflows
Scientific workflows are used almost universally across science domains for solving complex and largescale computing and data analysis problems. The importance of workflows is highlighted by the fact that they have underpinned some of the most significant discoveries of the past decades. Many of these workflows have significant computational, storage, and communication demands, and thus must execute on a range of large-scale computer systems, from local clusters to public clouds and upcoming exascale HPC platforms. Managing these executions is often a significant undertaking, requiring a sophisticated and versatile software infrastructure. Historically, infrastructures for workflow execution consisted of complex, integrated systems, developed in-house by workflow practitioners with strong dependencies on a range of legacy technologies—even including sets of ad hoc scripts. Due to the increasing need to support workflows, dedicated workflow systems were developed to provide abstractions for creating, executing, and adapting workflows conveniently and efficiently while ensuring portability. While these efforts are all worthwhile individually, there are now hundreds of independent workflow systems. These workflow systems are created and used by thousands of researchers and developers, leading to a rapidly growing corpus of workflows research publications. The resulting workflow system technology landscape is fragmented, which may present significant barriers for future workflow users due to many seemingly comparable, yet usually mutually incompatible, systems that exist. In order to tackle some of the challenges described above, the DOE-funded ExaWorks and NSF-funded WorkflowsRI projects have organized in 2021 a series of events entitled the “Workflows Community Summit”. The third edition of the “Workflows Community Summit” explored workflows challenges and opportunities from the perspective of computing centers and facilities. This third summit builds on two prior summits (https://workflowsri.org/summits) that (i) established a high level vision for workflows research; and (ii) explored technical approaches for realizing that vision. The third summit brought together a small group of facilities representatives with the aim to understand how workflows are currently being used at each facility, how facilities would like to interact with workflow developers and users, how workflows fit with facility roadmaps, and what opportunities there are for tighter integration between facilities and workflows. This report documents and organizes the wealth of information provided by the participants before, during, and after the summit.
97 MATHEMATICS AND COMPUTING↗
Computational multiphysics modeling of radioactive aerosol deposition in diverse human respiratory tract geometries
The evaluation of aerosol exposure relies on generic mathematical models that assume uniform particle deposition profiles over the human respiratory tract and do not account for subject-specific characteristics. Here we introduce a hybrid-automated computational workflow that generates personalized particle deposition profiles in 3D reconstructed human airways from computed tomography scans using Computational Fluid and Particle Dynamics simulations. This is the first large-scale study to consider realistic airways variability, where 380 lower and 40 upper human respiratory tract 3D geometries are reconstructed and parameterized. The data is clustered into nine groups using random forest regression. Computational fluid and particle dynamics simulations are conducted on these representative geometries using a realistic heavy-breathing respiratory cycle and radioactive iodine-131 as a source term. Monte Carlo radiation transport simulations are performed to obtain detailed energy deposition maps. Our findings emphasize the importance of personalized studies, as minor respiratory tract variations notably influence deposition patterns rather than global parameters of the lower airways, observing more than 30% variance in the mass deposition fraction.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Petascale supercomputing to accelerate the design of high-temperature alloys
Recent progress in high-performance computing and data informatics has opened up numerous opportunities to aid the design of advanced materials. Herein, we demonstrate a computational workflow that includes rapid population of high-fidelity materials datasets via petascale computing and subsequent analyses with modern data science techniques. We use a first-principles approach based on density functional theory to derive the segregation energies of 34 microalloying elements at the coherent and semi-coherent interfaces between the aluminium matrix and the θ '-Al 2 Cu precipitate, which requires several hundred supercell calculations. We also perform extensive correlation analyses to identify materials descriptors that affect the segregation behaviour of solutes at the interfaces. Finally, we show an example of leveraging machine learning techniques to predict segregation energies without performing computationally expensive physics-based simulations. As a result, the approach demonstrated in the present work can be applied to any high-temperature alloy system for which key materials data can be obtained using high-performance computing.
36 MATERIALS SCIENCE↗
MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME
Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. In conclusion, MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.
97 MATHEMATICS AND COMPUTING↗
Roadmap on methods and software for electronic structure based simulations in chemistry and materials
This Roadmap article provides a succinct, comprehensive overview of the state of electronic structure methods and software for molecular and materials simulations. Seventeen distinct sections collect insights by 51 leading scientists in the field. Each contribution addresses the status of a particular area, as well as current challenges and anticipated future advances, with a particular eye towards software related aspects and providing key references for further reading. Foundational sections cover density functional theory and its implementation in real-world simulation frameworks, Green's function based many-body perturbation theory, wave-function based and stochastic electronic structure approaches, relativistic effects and semiempirical electronic structure theory approaches. Subsequent sections cover nuclear quantum effects, real-time propagation of the electronic structure, challenges for computational spectroscopy simulations, and exploration of complex potential energy surfaces. The final sections summarize practical aspects, including computational workflows for complex simulation tasks, the impact of current and future high-performance computing architectures, software engineering practices, education and training to maintain and broaden the community, as well as the status of and needs for electronic structure based modeling from the vantage point of industry environments. Overall, the field of electronic structure software and method development continues to unlock immense opportunities for future scientific discovery, based on the growing ability of computations to reveal complex phenomena, processes and properties that are determined by the make-up of matter at the atomic scale, with high precision.
36 MATERIALS SCIENCE↗
Improving climate model coupling through a complete mesh representation: a case study with E3SM (v1) and MOAB (v5.x)
One of the fundamental factors contributing to the spatiotemporal inaccuracy in climate modeling is the mapping of solution field data between different discretizations and numerical grids used in the coupled component models. The typical climate computational workflow involves evaluation and serialization of the remapping weights during the preprocessing step, which is then consumed by the coupled driver infrastructure during simulation to compute field projections. Tools like Earth System Modeling Framework (ESMF) and TempestRemap offer capability to generate conservative remapping weights, while the Model Coupling Toolkit (MCT) that is utilized in many production climate models exposes functionality to make use of the operators to solve the coupled problem. However, such multistep processes present several hurdles in terms of the scientific workflow and impede research productivity. In order to overcome these limitations, we present a fully integrated infrastructure based on the Mesh Oriented datABase (MOAB) library, which allows for a complete description of the numerical grids and solution data used in each submodel. Through a scalable advancing-front intersection algorithm, the supermesh of the source and target grids are computed, which is then used to assemble the high-order, conservative, and monotonicity-preserving remapping weights between discretization specifications. The Fortran-compatible interfaces in MOAB are utilized to directly link the submodels in the Energy Exascale Earth System Model (E3SM) to enable online remapping strategies in order to simplify the coupled workflow process. We demonstrate the superior computational efficiency of the remapping algorithms in comparison with other state-of-the-science tools and present strong scaling results on large-scale machines for computing remapping weights between the spectral element atmosphere and finite volume discretizations on the polygonal ocean grids.
58 GEOSCIENCES↗