Final Technical Report: Towards Scalable Precision Tuning of Numerical Software
Final Technical Report for Award SC0020286.
Rubio Gonzalez, Cindy [University of California, D↗
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Elaenia: Automated Error Analysis of Numerical Software
DAHCS Demo day poster for LDRD 25-0103
Pollard, Samuel Douglas [Sandia National Laborator↗
A numerical study of process complexity in permafrost dominated regions
Numerical modeling of permafrost dynamics requires adequate representation of atmospheric and surface processes, a reasonable parameter estimation strategy, and site-specific model development. The three main research objectives of the study are: (i) to propose a novel methodology that determines the required level of surface process complexity of permafrost models by conducting parameter sensitivity and calibration, (ii) to design and compare three numerical models of increasing surface process complexity, and (iii) to calibrate and validate the numerical models at the Yakou catchment on the Qinghai-Tibet Plateau as an exemplary study site. The calibration was carried out by coupling the Advanced Terrestrial Simulator (numerical model) and PEST (calibration tool). Simulation results showed that (i) A simple numerical model that considers only subsurface processes can simulate active layer development with the same accuracy as other more complex models that include surface processes. (ii) Peat and mineral soil layer permeability, Van Genuchten alpha, and porosity are highly sensitive. (iii) Liquid precipitation aids in increasing the rate of permafrost degradation. (iv) Deposition of snow insulated the subsurface during the thaw initiation period. We have developed and released an integrated code that couples the numerical software ATS to the calibration software PEST. The numerical model can be further used to determine the impacts of climate change on permafrost degradation.
Calibration↗
Combining diagnostics, modeling, and control systems for automated alignment of the TES beamline
X-ray beamlines are essential components of all synchrotron light sources. Practical operations involve frequent variation in beamline component positions and orientation, particularly when photon beam parameters shift due to experimental needs, or due to variations in the incoming photon beam. The alignment process can be time consuming and takes away from valuable beam time for experimental data collection. We describe progress in the automation of certain alignment tasks on the tender-energy X-ray spectroscopy (TES) beamline at the National Synchrotron Light Source II (NSLS-II). The beamline is controlled using the BlueSky software in which high level experimental plans guide the beamline components during an experiment. Numerous software packages exist for beamline modeling, and they may be tied to the beamline control system using a package we are continuing to develop called Sirepo-Bluesky. The photon beam distribution may be measured with fluorescent screens, and a relation between beam and machine state can be found by varying the mirror and aperture settings over a multi-dimensional range. We describe the results of such parameter varying measurements and how we are combining Sirepo-Bluesky with machine learning methods and reduced models to automate mirror alignment on the TES beamline.
36 MATERIALS SCIENCE↗
Guiding the choice of informatics software and tools for lipidomics research applications
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
59 BASIC BIOLOGICAL SCIENCES↗
Neuromorphic intermediate representation: A unified instruction set for interoperable brain-inspired computing
Abstract Spiking neural networks and neuromorphic hardware platforms that simulate neuronal dynamics are getting wide attention and are being applied to many relevant problems using Machine Learning. Despite a well-established mathematical foundation for neural dynamics, there exists numerous software and hardware solutions and stacks whose variability makes it difficult to reproduce findings. Here, we establish a common reference frame for computations in digital neuromorphic systems, titled Neuromorphic Intermediate Representation (NIR). NIR defines a set of computational and composable model primitives as hybrid systems combining continuous-time dynamics and discrete events. By abstracting away assumptions around discretization and hardware constraints, NIR faithfully captures the computational model, while bridging differences between the evaluated implementation and the underlying mathematical formalism. NIR supports an unprecedented number of neuromorphic systems, which we demonstrate by reproducing three spiking neural network models of different complexity across 7 neuromorphic simulators and 4 digital hardware platforms. NIR decouples the development of neuromorphic hardware and software, enabling interoperability between platforms and improving accessibility to multiple neuromorphic technologies. We believe that NIR is a key next step in brain-inspired hardware-software co-evolution, enabling research towards the implementation of energy efficient computational principles of nervous systems. NIR is available atneuroir.org
Science & Technology - Other Topics↗
Automatic Differentiation of C++ Codes on Emerging Manycore Architectures with Sacado
Automatic differentiation (AD) is a well-known technique for evaluating analytic derivatives of calculations implemented on a computer, with numerous software tools available for incorporating AD technology into complex applications. However, a growing challenge for AD is the efficient differentiation of parallel computations implemented on emerging manycore computing architectures such as multicore CPUs, GPUs, and accelerators as these devices become more pervasive. In this work, we explore forward mode, operator overloading-based differentiation of C++ codes on these architectures using the widely available Sacado AD software package. In particular, we leverage Kokkos, a C++ tool providing APIs for implementing parallel computations that is portable to a wide variety of emerging architectures. Here we describe the challenges that arise when differentiating code for these architectures using Kokkos, and two approaches for overcoming them that ensure optimal memory access patterns as well as expose additional dimensions of fine-grained parallelism in the derivative calculation. We describe the results of several computational experiments that demonstrate the performance of the approach on a few contemporary CPU and GPU architectures. We then conclude with applications of these techniques to the simulation of discretized systems of partial differential equations.
97 MATHEMATICS AND COMPUTING↗
Milestone 49 Report: Batched Sparse LA Phase 5 Implementation
Batched sparse linear algebra operations in general, and solvers in particular, have become the major algorithmic development activity and foremost performance engineering effort in the numerical software libraries work on modern hardware with accelerators such as GPUs. Many applications, ECP and non-ECP alike, require simultaneous solutions of many small linear systems of equations that are structurally sparse in one form or another. In order to move towards high hardware utilization levels, it is important to provide these applications with appropriate interface designs to be both functionally efficient and performance portable and give full access to the appropriate batched sparse solvers running on modern hardware accelerators prevalent across DOE supercomputing sites since the inception of ECP. To this end, we present here a summary of recent advances on the interface designs in use by HPC software libraries supporting batched sparse linear algebra and the development of sparse batched kernel codes for solvers and preconditioners. We also address the potential interoperability opportunities to keep the corresponding software portable between the major hardware accelerators from AMD, Intel, and NVIDIA, while maintaining the appropriate disclosure levels conforming to the active NDA agreements. The presented interface specifications include a mix of batched band, sparse iterative, and sparse direct solvers with their accompanying functionality that is already required by the application codes or we anticipated to be needed in the near future. This report summarizes progress in Kokkos Kernels and the xSDK libraries MAGMA, Ginkgo, hypre, PETSc, and SuperLU.
97 MATHEMATICS AND COMPUTING↗
SAM User's Guide
The System Analysis Module (SAM) is a modern system analysis tool being developed at Argonne National Laboratory for advanced non-LWR safety analysis. It aims to provide fast-running, whole-plant transient analyses capability with improved-fidelity for Sodium-cooled Fast Reactors (SFR), Lead-cooled Fast Reactors (LFR), and Molten Salt Reactors (MSR) or Fluoride-cooled High-temperature Reactors (FHR). SAM takes advantage of advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability. It utilizes an object-oriented application framework (MOOSE), and its underlying meshing and finite-element library (libMesh) and linear and non-linear solvers (PETSc), to leverage the modern advanced software environments and numerical methods. This document provides a user’s guide, which will help users understand the input description and core capabilities of the SAM code. A brief overview of the code is presented, as well as how to obtain and run it. The input syntax for various parts of the code is provided. Additionally, a number of example problems, starting with simple unit component problems to problems with increasing complexity, are provided. Because the code is still under active development, this SAM User’s Guide will evolve with periodic updates.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Enabling New Flexibility in the SUNDIALS Suite of Nonlinear and Differential/Algebraic Equation Solvers
In recent years, the SUite of Nonlinear and DIfferential/ALgebraic equation Solvers (SUNDIALS) has been redesigned to better enable the use of application-specific and third-party algebraic solvers and data structures. Throughout this work, we have adhered to specific guiding principles that minimized the impact to current users while providing maximum flexibility for later evolution of solvers and data structures. The redesign was done through the addition of new linear and nonlinear solvers classes, enhancements to the vector class, and the creation of modern Fortran interfaces. The vast majority of this work has been performed “behind-the-scenes,” with minimal changes to the user interface and no reduction in solver capabilities or performance. These changes allow SUNDIALS users to more easily utilize external solver libraries and create highly customized solvers, enabling greater flexibility on extreme-scale, heterogeneous computational architectures.
97 MATHEMATICS AND COMPUTING↗
Simulation of Transport Phenomena in Bubble Column Reactors
The production of carbon and hydrogen from methane is a viable pathway for monetizing the vast reserves of US natural gas. Liquid (metals and/or salts) bubble column reactors operating at temperatures greater than 1000° C allow the conversion of methane into hydrogen without CO 2 emission. The low-density carbon floats on top of the liquid surface, allowing an easier removal, compared to other reactor concepts for methane pyrolysis. In this current report, we present results from simulations of transport phenomena in a liquid bubble column reactor. The goal is to investigate and understand parameters that are crucial for bubble column reactor design and scale up. The report presents the formulation and numerical methods used in the multiphase direct numerical simulation software, Quilt. This software was validated for the bubbly flow using numerical and physics based test problems. Quilt was then used to perform simulations of the bubble column reactor as a parametric study, varying the bubble injection parameters. The simulations were visualized for qualitative analysis and followed up with a quantitative analysis. The effect of injection parameters on various quantitative measures of the bubble residence time, interfacial area and motion through the column are presented.
03 NATURAL GAS↗
SAM Theory Manual
The System Analysis Module (SAM) is an advanced and modern system analysis tool under development at Argonne National Laboratory for advanced non-LWR reactor safety analysis. It aims to provide fast-running, modest-fidelity, whole-plant transient analyses capabilities, which are essential for fast turnaround design scoping and engineering analyses of advanced reactor concepts. While SAM is being developed as a system-level modeling and simulation tool, advanced modeling techniques being implemented include a reduced-order three-dimensional module, pseudo 3-D conjugate heat transfer modeling in reactor core, flexible and multi-scale modeling of heat transfer between fluid and structures, in addition to the advances in software environments and design, and numerical methods. SAM aims to be a generic system-level safety analysis tool for advanced non-LWRs, including Liquid-Metal-cooled fast Reactors (LMR), Molten Salt Reactors (MSR), Fluoride-salt-cooled High-temperature Reactors (FHR), and High-Temperature Gas-cooled Reactors (HTGR). SAM takes advantage of advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability. It utilizes an object-oriented computational framework (MOOSE), and its underlying meshing and finite-element library and linear and non-linear solvers, to leverage the modern advanced software environments and numerical methods. This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As new code capabilities and features are added, the SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Strengthening the Security of Operational Technology: Understanding Contemporary Bill of Materials
The evolution of cyber-physical infrastructure has made its security more challenging. The last few years have witnessed a convergence of hardware and software segments in various domains, including operational technology (OT) which is responsible for carrying out critical tasks such as monitoring and controlling power grids, nuclear plants, transportation, and emergency services. Both hardware and software encapsulate numerous open source and proprietary subcomponents, making it crucial for end-users to understand the composition of the products they are using. For example, wind turbines incorporate thousands of lines of code (software) used for the turbine's design, planning, operation, and analytics in addition to the numerous hardware subcomponents that construct it. Due to the highly complex nature of software and hardware, knowledge of the components and subcomponents is required to mitigate cyber vulnerabilities and defend against cyberattacks. There has also been a transformation from a traditional linear supply chain into a global, dynamic, diverse, and interconnected system. The digitization of the supply chain makes it easier to find and exploit vulnerabilities. Critical infrastructures (e.g., power grids, oil, natural gas, water, and wastewater) rely on OT to function, and if the OT is compromised, equipment damage and potential interruption of services could result. A significant security measure to protect OT systems from disruption is to develop a supply chain bill of materials (BoM) corresponding to the software and hardware used in OT, along with attestations amongst vendors and asset owners. A supply chain BoM is a proactive way to understand the inherent vulnerabilities in the system and mitigate them in advance of being exploited. BoMs bolster the trust placed in the digital infrastructure and enhance software supply chain security by sustaining the management of component obsolescence and compliance, along with the seclusion of unsafe segments of a specific product. Adopting BoM tools is becoming increasingly important across various government sectors, as evidenced by the recent U.S. executive order on cybersecurity (NIST 2021). This paper aims to classify BoMs based on structure, functionality, component type, and architecture. The work also discusses case studies to further highlight the benefits of BoMs. In addition, it identifies missing pieces in existing BoM implementations so that future research may identify bounds on where it could expect to make improvements and directly enable researchers to identify promising areas for exploration. Further, the authors provide valuable recommendations to tool developers, researchers, and standardizing organizations (policymakers), additionally benefitting critical infrastructure owners and government executives. This aids in paving a path for future work, thereby, providing suggestions to determine a tool for consumers that best suit their needs.
97 MATHEMATICS AND COMPUTING↗
Field Laboratory for Emerging Stacked Unconventional Plays in Central Appalachia
The goal of the Field Laboratory for Emerging Stacked Unconventional Plays (ESUP) in Central Appalachia project was to investigate and characterize the resource potential for multi-play production of emerging unconventional reservoirs in Central Appalachia. Project activities included drilling, logging and coring of a vertical characterization well drilled to basement to approximately 15,000 feet in depth. The data from drilling and well logs as well recovered core samples were used by the research team to support characterization of the geology and potential pay zones within the Nora Gas Field of southwestern Virginia and the greater Central Appalachian Basin. This project was led by Dr. Nino Ripepi of the Virginia Center for Coal and Energy Research (VCCER) in close collaboration with EnerVest Operating LLC (EnerVest). VCCER is housed in the Department of Mining and Minerals Engineering at Virginia Tech and was created by an Act of the Virginia General Assembly on March 30, 1977, as an interdisciplinary study, research, information, and resource facility for the Commonwealth of Virginia. EnerVest is a top tier, low-cost oil and natural gas company with a long history of traditional operating relationships with institutional investors as well as public and private companies. This report summarizes two major research activities: 1) Log and Core Analysis and 2) Numerical Modeling. Core analysis comprises the characterization efforts of the ESUP Field Laboratory and includes a discussion of the well logs run in the deep characterization wells, an initial analysis of those, the number, size and location of cores recovered, core testing and analysis done to date as well as plans for future analysis. Numerical modeling is comprised of seven major modeling efforts, including (1) Multiphysics shale transport modeling work, (2) the developed in-house compositional simulator studies, (3) reservoir modeling studies using GEM software, (4) fracture modeling work using EFRAC3D software and (5) numerical modeling efforts with ABAQUS software, (6) Numerical modeling efforts using FLAC3D and PFC3D, and (7) Automatic Machine Learning (AutoML) Studies.
02 PETROLEUM↗
Next-Generation Marine Energy Software Needs Assessment
The U.S. Department of Energy (DOE) Water Power Technologies Office’s (WPTO) initial investment in marine energy software was driven by needs identified over a decade ago. WPTO-funded research was first launched because of a U.S. congressional mandate that called for the DOE to officially research marine energy technologies, which also established the DOE WPTO in 2008. A congressional mandate requested the WPTO to evaluate a variety of marine energy devices, establish baseline levelized cost of energy estimates, and provide an overall report to Congress. This congressional mandate led to the Reference Model Project (RMP), for which WPTO funded a national multi-laboratory team to develop these reference models, based on state-of-the-art designs of six marine energy converter archetypes that consisted of three current energy converters and three wave energy converters (WEC). Each device was designed to operate for a specific marine resource, thus allowing the devices to serve as reference models for future studies. The RMP congressional report cited the need for improved marine energy software to handle a variety of device designs, as well as a need to standardize performance outputs. Without validated software packages and established metrics, information presented to the WPTO by technology developers could be incorrect or inaccurate and result in misleading conclusions. The recommendation to coordinate WPTO investment in software for numerical modeling and analysis was given a high priority because it would directly fill needs at the time, and focused funding would amplify impact. By sponsoring software development, WPTO would provide industry developers, university researchers, and national laboratories software that could be used, customized, and advanced, thus supporting the overall advancement of marine energy.
16 TIDAL AND WAVE POWER↗
Numerical relativity higher order gravitational waveforms of eccentric, spinning, nonprecessing binary black hole mergers
We use the open source, community-driven, numerical relativity software, the EINSTEIN TOOLKIT to study the physics of eccentric, spinning, nonprecessing binary black hole mergers with mass-ratios q = {2; 4; 6}, individual dimensionless spin parameters chi 1z = +/- 0.6, chi 2z = +/- 0.3, that include higher order gravitational wave modes l <= 4, except for memory modes. Assuming stellar mass binary black hole mergers that may be detectable by the advanced LIGO detectors, we find that including modes up to l = 4 increases the signal-to-noise of compact binaries between 3.5% to 35%, compared to signals that only include the l = ImI = 2 mode. We use two waveform models, TEOBResumS and SEOBNRE, which incorporate spin and eccentricity corrections in the waveform dynamics, to quantify the orbital eccentricity of our numerical relativity catalog in a gauge-invariant manner through fitting factor calculations. Our findings indicate that the inclusion of higher order wave modes has a measurable effect in the recovery of moderately and highly eccentric black hole mergers, and thus it is essential to develop waveform models and signal processing tools that accurately describe the physics of these astrophysical sources.
Joshi, Abhishek V.↗
Toward performance-portable PETSc for GPU-based exascale systems
The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization. The PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that used by the library, and it enables application developers to use their preferred programming model, such as Kokkos, RAJA, SYCL, HIP, CUDA, or OpenCL, on upcoming exascale systems. Furthermore, a blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems.
97 MATHEMATICS AND COMPUTING↗
Enabling GPU accelerated computing in the SUNDIALS time integration library
Not Available
97 MATHEMATICS AND COMPUTING↗