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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2021

LocOO3D User's Manual

LocOO3D is a software tool that computes geographical locations for seismic events at regional to global scales. This software has a rich set of features, including the ability to use custom 3D velocity models, correlated observations and master event locations. The LocOO3D software is especially useful for research related to seismic monitoring applications, since it allows users to easily explore a variety of location methods and scenarios and is compatible with the CSS3.0 data format used in monitoring applications. The LocOO3D software, User's Manual, and Examples are available on the web at: https://github.com/sandialabs/LocOO3D For additional information on GeoTess, SALSA3D, RSTT, and other related software, please see: https://github.com/sandialabs/GeoTessJava, www.sandia.gov/geotess, www.sandia.gov/salsa3d, and www.sandia.gov/rstt

58 GEOSCIENCES↗
DOE OSTI2023

Normality of I-V Measurements Using ML

There is an increased interest in instrument-computing ecosystems (ICEs) that support science workflows empowered by AI-automated experiments and computations in diverse areas. In particular, electrochemistry ICEs are promising for accelerating the design and discovery of electrochemical systems for energy storage and conversion, by automating significant parts of workflows that combine synthesis and characterization experiments with computations. They require the integration of flow controllers, solvent containers, pumps, fraction collectors, and potentiostats, all connected to an electrochemical cell, as illustrated in Fig. 1. These are specialized instruments with custom software that is not originally designed for network integration. We developed network and software solutions for electrochemical workflows that adapt system and instrument settings in real-time for multiple rounds of experiments. In particular, we developed Python wrappers for Application Programming Interfaces (APIs) of instrument commands and Pyro client-server modules that enable them to be executed from remote computers. The entire workflow is orchestrated by a Jupyter notebook running on a remote computer.

Al Najjar, Anees↗
DOE OSTI2022

Mesoflow: An Open-Source Reacting Flow Solver for Catalysis at Mesoscale

We present the capabilities and software performance metrics of our open-source continuum solver for catalysis, Mesoflow, developed specifically for modeling transport and chemistry at the mesoscale. Our solver utilizes Cartesian block-structured adaptive mesh refinement to resolve complex catalyst surface morphologies directly obtained from X-ray tomography data. An immersed boundary based formulation enables rapid representation of complex geometries prevalent in most mesoporous catalyst interfaces. The solver is developed on top of open-source performance portable library, AMReX, providing parallel execution capabilities on current and upcoming high-performance-computing (HPC) architectures. Our flexible software framework enables integration of complex chemical mechanisms at heterogenous interfaces and time-split algorithms for circumventing highly disparate reaction and flow time-scales. Our current studies indicate a ten-fold performance gain by using graphics-processing-units (GPUs) compared to a single processor for representative problem sizes (2 million cell mesh). We will also present a brief introduction on how to build and use this software for application problems pertaining to catalytic upgrading and gas transport within porous catalyst particles.

adaptive meshing↗
DOE OSTI2023

Autonomy Loops for Monitoring, Operational Data Analytics, Feedback, and Response in HPC Operations

Many High Performance Computing (HPC) facilities have developed and deployed frameworks in support of continuous monitoring and operational data analytics (MODA) to help improve efficiency and throughput. Because of the complexity and scale of systems and workflows and the need for low-latency response to address dynamic circumstances, automated feedback and response have the potential to be more effective than current human-in-the-loop approaches which are laborious and error prone. Progress has been limited, however, by factors such as the lack of infrastructure and feedback hooks, and successful deployment is often site- and case-specific. In this position paper we report on the outcomes and plans from a recent Dagstuhl Seminar, seeking to carve a path for community progress in the development of autonomous feedback loops for MODA, based on the established formalism of similar (MAPE-K) loops in autonomous computing and self-adaptive systems. By defining and developing such loops for significant cases experienced across HPC sites, we seek to extract commonalities and develop conventions that will facilitate interoperability and interchangeability with system hardware, software, and applications across different sites, and will motivate vendors and others to provide telemetry interfaces and feedback hooks to enable community development and pervasive deployment of MODA autonomy loops.

autonomy loops↗
DOE OSTI2020

Holistic Measurement Driven Resilience: Combining Operational Fault and Failure Measurements and Fault Injection for Quantifying Fault Detection, Propagation and Impact. Final report

For HPC systems to date, application resilience to faults and failures has been accomplished by the brute- force method of checkpoint/restart, which allows an application to make forward progress in the face of system and application faults, errors, and failures independent of root cause or end result. It has remained the primary resilience mechanism because we lack a way to identify faults and anticipate consequences early enough to take meaningful mitigating action. However, checkpoint/restart implementations put a tremendous burden on system resources and on the applications themselves and is becoming less feasible at scale. Because we have not yet operated at scales at which checkpoint/restart fails to provide forward progress, despite increasing costs, vendors have had little motivation to provide the instrumentation necessary for early identification of faults and failures. However, as we move from petascale to exascale, component mean time to failure (MTTF) will render the existing techniques ineffectual and/or too expensive. Furthermore, fault recovery mechanisms such as failover and/or error correction introduce performance inconsistency. Instrumentation allowing early indication of problems and tools to enable use of such information by systems, operating systems, and applications offer an alternative, more scalable and less costly solution. In the HMDR project, we built on our experience and expertise developed and accumulated over years of research on design, monitoring, measurement, and assessment of resilient computing systems. Analysis of field data on the current and past generations of extreme-scale systems revealed several challenges that, if not addressed in increasingly larger and more complex systems, may hinder the effectiveness of future exascale computing systems. Specifically, i) file systems and interconnects in current-generation large-scale systems already operate at the margins of resiliency, including consistent performance, and may not scale to larger deployments; ii) automated, software-based failover mechanisms are frequently inadequate and can introduce wider failures, such that failures during recovery may lead to system/application failures, including system-wide outages; and iii) silent data corruption represents a critical fault mode and will require efficient detection mechanisms if next-generation applications are to take full advantage of exascale hardware. To address the above challenges, we assembled a team of world-renowned experts in resilient extreme- scale computing from the University of Illinois (Electrical and Computer Engineering, Computer Science, and NCSA), SNL, LANL, NERSC, and Cray. Our team includes representatives from centers that house many of the largest HPC resources in the world, both today and over the coming years. The team has a unique track record of research in i) system and application failure characterization based on the analysis of field data, ii) data-driven design of fault/error detection mechanisms, and iii) experimental characterization of system/application resiliency. The team includes system owners/operators who provide continuous data collection and access and ensure installation of appropriate analysis tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Resilience and fault tolerance in high-performance computing for numerical weather and climate prediction

Progress in numerical weather and climate prediction accuracy greatly depends on the growth of the available computing power. As the number of cores in top computing facilities pushes into the millions, increased average frequency of hardware and software failures forces users to review their algorithms and systems in order to protect simulations from breakdown. This report surveys hardware, application-level and algorithm-level resilience approaches of particular relevance to time-critical numerical weather and climate prediction systems. A selection of applicable existing strategies is analysed, featuring interpolation-restart and compressed checkpointing for the numerical schemes, in-memory checkpointing, user-level failure mitigation and backup-based methods for the systems. Numerical examples showcase the performance of the techniques in addressing faults, with particular emphasis on iterative solvers for linear systems, a staple of atmospheric fluid flow solvers. The potential impact of these strategies is discussed in relation to current development of numerical weather prediction algorithms and systems towards the exascale. Trade-offs between performance, efficiency and effectiveness of resiliency strategies are analysed and some recommendations outlined for future developments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Gaussian Process Optimization of Sensitivity-Based Similarity Metrics between New Nuclear Applications and New/Existing Benchmarks

Confidently designing safe, new nuclear criticality experiments requires expert judgement, which could take years of experience. Sensitivity/uncertainty (S/U) analysis can be utilized by less experienced individuals to conservatively estimate uncertainties in important parameters, such as k eff , in newly proposed nuclear applications. This type of analysis relies on matching new nuclear applications with existing benchmark experiments. The Whisper-1.1 software package included in MCNP6.2 ®1 contains more than 1,100 International Criticality Safety Benchmark Evaluation Project (ICSBEP) benchmarks. These benchmarks however rarely match new nuclear applications. The number of benchmarks available to match a given set of materials or geometric configurations varies significantly. Furthermore, recently performed benchmark experiments may not have had enough time to be properly documented and published. Benchmarks are vital for determining the accuracy of nuclear data and can assist nuclear physics and evaluators in improving nuclear data libraries. Exhaustively exploring the parameter space using simulations with software such as MCNP is too computationally expensive. In this work, Gaussian process optimization was implemented to reduce the number of simulations needed for optimization over multiple parameters. This optimization scheme was designed to selectively generate new benchmarks with high sensitivity-based similarity metrics to user-defined nuclear applications. Two benchmark models of spherically nested shells containing plutonium, uranium, tantalum, and water were used in the optimization to match an application containing plutonium plates, stacked in a tantalum reflector, surrounded by water.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Building an Integrated Ecosystem of Computational and Observational Facilities to Accelerate Scientific Discovery

Future scientific discoveries will rely on flexible ecosystems that incorporate modern scientific instruments, high performance computing resources, parallel distributed data storage, and performant networks across multiple, independent facilities. In addition to connecting physical resources, such an ecosystem presents many challenges in logistics and accessibility, especially in orchestrating computations and experiments that span across leadership computing systems and experimental instruments. Past efforts have typically been application-specific or limited to interfaces for computing resources. This paper proposes a general framework for integrating computation resources and instrument operations, addressing challenges in code development/execution, data staging and collection, software stack, control mechanisms, resource authorization and governance, and hardware integration. We also describe a demonstration use case wherein a Bayesian optimization algorithm running on an edge computing resource guides a scanning probe microscope to autonomously and intelligently characterize a material sample. This science edge ecosystem framework will provide a blueprint for federating multi-institutional, disparate resources and orchestrating scientific workflows across them to enable next-generation discoveries.

Somnath, Suhas↗
DOE OSTI2021

PyGDH: Python Grid Discretization Helper

Mathematical models expressed in the form of discretized equations play an important role inmany scientific disciplines. In our experience, few domain scientists have sufficient backgroundin numerical computing (or the time required to acquire such a background) to use manyflexible and powerful but complex open source packages, such as FEniCS (Alnæs et al., 2015)and OpenFOAM (The OpenFOAM Foundation Ltd, n.d.). Many user-friendly open sourcepackages, such as FiPy (J. E. Guyer & Warren, 2009), and many commercial packages, suchas COMSOL Multiphysics (COMSOL AB, n.d.) and Simcenter STAR-CCM+ (Siemens DigitalIndustries Software, n.d.), provide limited flexibility in the equations that users can express.Additionally, the use of commercial packages, which by nature do not perform calculationstransparently, can hinder reproducibility, which is vital to the scientific process. PyGDH(“pigged”) is a Python 2 / Python 3 (Python Software Foundation, 1991–2020) package thatis meant to be accessible to scientists who might not be specialists in scientific computing,while approaching the level of flexibility associated with writing dedicated programs tailoredto solving specific problems. The PyGDH User’s Guide provides detailed instructions forcreating numerical models, including a brief introduction to necessary command line andPython (Python Software Foundation, 1991–2020) skills, and discussions of discretization andvalidation. Note that PyGDH emphasizes flexibility and simplicity over performance, and wasnot designed for high-performance applications or models describing complex spatial domains.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Software Deployment Process at NERSC: Deploying the Extreme-scale Scientific Software Stack (E4S) Using Spack at the National Energy Research Scientific Computing Center (NERSC)

One of the many benefits of using a high-performance computing (HPC) system at a Department of Energy (DOE) Office of Science (SC) HPC facility is the large number of software products, built and optimized for the system. The HPC center staff and HPC vendors provide optimized software such as libraries and even full scientific applications, ready to be used by users as building blocks to accelerate scientific discovery. Behind each provided packaged software module are a large number of decisions - which compiler, optimizations, variants/options - to build the software on the target system. And, even before the software gets deployed, the software must be developed, tested, and maintained, including deprecating old versions and ensuring compatibility across versions. The software lifecycle is complex and is further convoluted by a web of interdependencies on other software.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A workflow for segmenting soil and plant X-ray computed tomography images with deep learning in Google’s Colaboratory

X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google’s Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Improving the performance of medical imaging applications using SYCL

As opposed to the Open Computing Language (OpenCL) programming model, in which host and device codes are generally written in different programming languages, SYCL can combine host and device codes for an application in a type-safe way to improve development productivity and performance portability. Hence, this report shows the experimental results of applying the SYCL programming model to medical imaging applications for a study on performance portability and programming productivity between OpenCL and SYCL. Rodinia is a widely used open-source benchmark suite for heterogeneous computing. We choose two medical imaging applications (Heart Wall and Particle Filter) in the benchmark suite, migrate the OpenCL implementations of the applications to the SYCL implementations, and evaluate their performance and productivity on Intel® microprocessors that contain a central processing unit (CPU) and an integrated graphics processing unit (GPU). The maturing SYCL compilers, which are based on a conformant implementation of the SYCL 1.2.1 Khronos specification, have been actively optimized for Intel® computing platforms. The experimental results are promising in terms of the raw performance and productivity. Although the SYCL implementation of the Heart Wall application does not execute successfully on a CPU, the SYCL implementations of the application can achieve comparable or better performance than the OpenCL implementation on Intel® integrated GPUs. For the Particle Filter application, the performance difference between the SYCL and OpenCL implementations is comparable on the GPUs for most cases, but the SYCL implementations are on average 4X faster than the OpenCL implementations on Intel® Xeon® CPUs. For programming productivity, we arguably use lines of code as a way to measure programming productivity in software. The SYCL programs reduce the lines of code of the OpenCL programs by 52% and 38% for the Heart Wall and Particle Filter, respectively. The results indicate that SYCL is a promising programming model for heterogeneous computing with the maturing compilers. We organize the remainder of the report as follows. Section II introduces the SYCL programming model, compares the major differences between an OpenCL program and a SYCL program, and describes the characteristics of the two applications. Section III describes the SYCL programming model in more details, and shows the SYCL implementation of a kernel function in the Particle Filter application as an example. In Section IV, we evaluate the performance of the applications on the CPUs and GPUs. Section V concludes the report.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A survey of nonlinear robust optimization

Robust optimization (RO) has attracted great attention from the optimization community over the past decade. RO is dedicated to solving optimization problems subject to uncertainty: design constraints must be satisfied for all the values of the uncertain parameters within a given uncertainty set. Uncertainty sets may be modeled as deterministic sets (boxes, polyhedra, ellipsoids), in which case the RO problem may be reformulated via worst-case analysis, or as families of distributions. The challenge of RO is to reformulate or approximate robust constraints so that the uncertain optimization problem is transformed into a tractable deterministic optimization problem. Most reformulation methods assume linearity of the robust constraints or uncertainty sets of favorable shape, which represents only a fraction of real-world applications. This survey addresses nonlinear RO and includes problem formulations and applications, solution approaches, and available software with code samples.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Algorithms and file structures to enhance software workflows for ion mobility mass spectrometry (IM-MS): CRADA 410 (Final Report)

This document is the final report for CRADA 410 (Project No. 72496). The purpose of this project was supporting customizations of algorithms and raw data file structures to enhance software workflows for liquid chromatography (LC), mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS)-based metabolite characterization. PNNL worked with Agilent to evaluate and improve the integration of ion mobility into existing MS data analysis methods of Agilent software tools. The project augmented PNNL’s capabilities to analyze complex omics samples. These capabilities are directly beneficial to DOE and PNNL efforts to characterize and analyze compounds in microbial and plant communities. The project assisted Agilent in further developing improved instrument-software solutions combining ion mobility with mass spectrometry for widespread applications in life sciences and other fields.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Cooperative Education

Los Alamos National Laboratory (LANL) is a multidisciplinary national laboratory that conducts research and development in national security, engineering, materials science, computational modeling, and advanced manufacturing. The laboratory develops innovative technologies to address complex scientific and engineering challenges. This project focuses on the development and evaluation of high-performance absorbing structures through computational design, simulation, and engineering analysis. Absorbing structures are used in applications where damage mitigation, structural protection, and material efficiency are critical performance requirements. The increasing demand for lightweight, high-strength, and highly efficient structural systems has created a need for improved design methodologies capable of maximizing absorption while minimizing weight and material usage. The project utilizes advanced engineering software, including 3D CAD software and FEA, to generate and optimize structural concepts. Computational simulations are performed to evaluate structural behavior under loading conditions, while mathematical analyses are conducted using Python-based tools as well as established analytical equations from material and structural mechanics. The project benefits LANL by supporting the development of advanced design methodologies and improving the understanding of material and structural performance. During the internship term, a significant portion of the design development, simulation, and data analysis activities will be completed. Success of the project depends on collaboration among engineering mentors and technical staff members. Work will be conducted at Los Alamos National Laboratory using laboratory computing resources and engineering software.

42 ENGINEERING↗
DOE OSTI2022

The SODA Approach: Leveraging High-Level Synthesis for Hardware/Software Co-design and Hardware Specialization: Invited

Novel "converged" applications combine phases of scientific simulation with data analysis and machine learning. Each computational phase can benefit from specialized accelerators. However, algorithms evolve so quickly that mapping them on existing accelerators is suboptimal or even impossible. This paper presents the SODA (Software Defined Accelerators) framework, a modular, multi-level, open-source, no-human-in-the-loop, hardware synthesizer that enables end-to-end generation of specialized accelerators. SODA is composed of SODA-Opt, a high-level frontend developed in MLIR that interfaces with domain-specific programming frameworks and allows performing system level design, and Bambu, a state-of-the-art high-level synthesis engine that can target different device technologies. The framework implements design space exploration as compiler optimization passes. We show how the modular, yet tight, integration of the high-level optimizer and lower-level HLS tools enables the generation of accelerators optimized for the computational patterns of converged applications. We then discuss some of the research opportunities that such a framework allows, including system-level design, profile driven optimization, and supporting new optimization metrics.

Bohm Agostini, Nicolas↗
DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗