This work focuses on estimation of unknown states and parameters in a discrete-time, stochastic, SEIR model using reported case counts and mortality data. An SEIR model is based on classifying individuals with respect to their status in regards to the progression of the disease, where S is the number individuals who remain susceptible to the disease, E is the number of individuals who have been exposed to the disease but not yet infectious, I is the number of individuals who are currently infectious, and R is the number of recovered individuals. For convenience, we include in our notation the number of infections or transmissions, T, that represents the number of individuals transitioning from compartment S to compartment E over a particular interval. Similarly, we use C to represent the number of reported cases.
The propagation of a wave pulse due to low-speed impact on a one-dimensional, heterogeneous bar is studied. Due to the dispersive character of the medium, the pulse attenuates as it propagates. This attenuation is studied over propagation distances that are much longer than the size of the microstructure. A homogenized peridynamic material model can be calibrated to reproduce the attenuation and spreading of the wave. The calibration consists of matching the dispersion curve for the heterogeneous material near the limit of long wavelengths. It is demonstrated that the peridynamic method reproduces the attenuation of wave pulses predicted by an exact microstructural model over large propagation distances.
The June 15, 1991 Mt. Pinatubo eruption is simulated in E3SM by injecting 10 Tg of SO2 gas in the stratosphere, turning off prescribed volcanic aerosols, and enabling E3SM to treat stratospheric volcanic aerosols prognostically. This experimental prognostic treatment of volcanic aerosols in the stratosphere results in some realistic behaviors (SO2 evolves into H2SO4 which heats the lower stratosphere), and some expected biases (H2SO4 aerosols sediment out of the stratosphere too quickly). Climate fingerprinting techniques are used to establish a Mt. Pinatubo fingerprint based on the vertical profile of temperature from the E3SMv1 DECK ensemble. By projecting reanalysis data and preindustrial simulations onto the fingerprint, the Mt. Pinatubo stratospheric heating anomaly is detected. Projecting the experimental prognostic aerosol simulation onto the fingerprint also results in a detectable heating anomaly, but, as expected, the duration is too short relative to reanalysis data.
Achieving efficient learning for AI systems was identified as a major challenge in the DOE's recently released, AI for Science, report. The human brain is capable of efficient and low-powered learning. It is likely that implementing brain-like principles will lead to more efficient AI systems. In this LDRD, I aim to contribute to this goal by creating a foundation for implementing and studying a brain phenomenon termed short term plasticity (STP) in spiking artificial neural networks within Sandia. First, data collected by the Allen Institute for Brain Science (AIBS) was analyzed to see if STP could be classified into types using the data collected. Although the data was inadequate at the time, AIBS has updated their database and created models that could be utilized in the future. Second, I began creating a software package to assess the ability of a Boltzmann machine utilizing STP to sample from national security data.
State-of-the-art engineering and science codes have grown in complexity dramatically over the last two decades. Application teams have adopted more sophisticated development strategies, leveraging third party libraries, deploying comprehensive testing, and using advanced debugging and profiling tools. In today's environment of diverse hardware platforms, these applications also desire performance portability-avoiding the need to duplicate work for various platforms. The Kokkos EcoSystem provides that portable software stack. Based on the Kokkos Core Programming Model, the EcoSystem provides math libraries, interoperability capabilities with Python and Fortran, and Tools for analyzing, debugging, and optimizing applications. In this article, we overview the components, discuss some specific use cases, and highlight how codesigning these components enables a more developer friendly experience.
Swiler, Laura P.; Becker, Dirk-Alexander; Brooks, Dusty M.; Govaerts, Joan; Koskinen, Lasse; Plischke, Elmar; Rohlig, Klaus-Jurgen; Saveleva, Elena; Spiessl, Sabine M.; Stein, Emily; Svitelman, Valentina
Over the past four years, an informal working group has developed to investigate existing sensitivity analysis methods, examine new methods, and identify best practices. The focus is on the use of sensitivity analysis in case studies involving geologic disposal of spent nuclear fuel or nuclear waste. To examine ideas and have applicable test cases for comparison purposes, we have developed multiple case studies. Four of these case studies are presented in this report: the GRS clay case, the SNL shale case, the Dessel case, and the IBRAE groundwater case. We present the different sensitivity analysis methods investigated by various groups, the results obtained by different groups and different implementations, and summarize our findings.
Although many software teams across the laboratories comply with yearly software quality engineering (SQE) assessments, the practice of introducing quality into each phase of the software lifecycle, or the team processes, may vary substantially. Even with the support of a quality engineer, many teams struggle to adapt and right-size software engineering best practices in quality to fit their context, and these activities aren’t framed in a way that motivates teams to take action. In short, software quality is often a “check the box for compliance” activity instead of a cultural practice that both values software quality and knows how to achieve it. In this report, we present the results of our 6600 VISTA Innovation Tournament project, "Incentivizing and Motivating High Confidence and Research Software Teams to Adopt the Practice of Quality." We present our findings and roadmap for future work based on 1) a rapid review of relevant literature, 2) lessons learned from an internal design thinking workshop, and 3) an external Collegeville 2021 workshop. These activities provided an opportunity for team ideation and community engagement/feedback. Based on our findings, we believe a coordinated effort (e.g. strategic communication campaign) aimed at diffusing the innovation of the practice of quality across Sandia National Laboratories could over time effect meaningful organizational change. As such, our roadmap addresses strategies for motivating and incentivizing individuals ranging from early career to seasoned software developers/scientists.
The final review for the FY21 Advanced Simulation and Computing (ASC) Computational Systems and Software Environments (CSSE) L2 Milestone #7840 was conducted on August 25th, 2021 at Sandia National Laboratories in Albuquerque, New Mexico. The review committee/panel unanimously agreed that the milestone has been successfully completed, exceeding expectations on several of the key deliverables.
Abdelfattah, Ahmad; Anzt, Hartwig; Ayala, Alan; Boman, Erik G.; Carson, Erin C.; Cayrols, Sebastien; Cojean, Terry; Dongarra, Jack J.; Falgout, Rob; Gates, Mark; G, R\{U}Tzmacher; Higham, Nicholas J.; Kruger, Scott E.; Li, Sherry; Lindquist, Neil; Liu, Yang; Loe, Jennifer A.; Nayak, Pratik; Osei-Kuffuor, Daniel; Pranesh, Sri; Rajamanickam, Sivasankaran; Ribizel, Tobias; Smith, Bryce; Swirydowicz, Kasia; Thomas, Stephen J.; Tomov, Stanimire; Tsai, Yaohung M.; Yamazaki, Ichitaro; Yang, Urike M.
Over the last year, the ECP xSDK-multiprecision effort has made tremendous progress in developing and deploying new mixed precision technology and customizing the algorithms for the hardware deployed in the ECP flagship supercomputers. The effort also has succeeded in creating a cross-laboratory community of scientists interested in mixed precision technology and now working together in deploying this technology for ECP applications. In this report, we highlight some of the most promising and impactful achievements of the last year. Among the highlights we present are: Mixed precision IR using a dense LU factorization and achieving a 1.8× speedup on Spock; results and strategies for mixed precision IR using a sparse LU factorization; a mixed precision eigenvalue solver; Mixed Precision GMRES-IR being deployed in Trilinos, and achieving a speedup of 1.4× over standard GMRES; compressed Basis (CB) GMRES being deployed in Ginkgo and achieving an average 1.4× speedup over standard GMRES; preparing hypre for mixed precision execution; mixed precision sparse approximate inverse preconditioners achieving an average speedup of 1.2×; and detailed description of the memory accessor separating the arithmetic precision from the memory precision, and enabling memory-bound low precision BLAS 1/2 operations to increase the accuracy by using high precision in the computations without degrading the performance. We emphasize that many of the highlights presented here have also been submitted to peer-reviewed journals or established conferences, and are under peer-review or have already been published.
We present an approach for constructing a surrogate from ensembles of information sources of varying cost and accuracy. The multifidelity surrogate encodes connections between information sources as a directed acyclic graph, and is trained via gradient-based minimization of a nonlinear least squares objective. While the vast majority of state-of-the-art assumes hierarchical connections between information sources, our approach works with flexibly structured information sources that may not admit a strict hierarchy. The formulation has two advantages: (1) increased data efficiency due to parsimonious multifidelity networks that can be tailored to the application; and (2) no constraints on the training data—we can combine noisy, non-nested evaluations of the information sources. Finally, numerical examples ranging from synthetic to physics-based computational mechanics simulations indicate the error in our approach can be orders-of-magnitude smaller, particularly in the low-data regime, than single-fidelity and hierarchical multifidelity approaches.
The advanced materials team investigated the use of additively manufactured metallic lattice structures for mitigating impact response in a Davis gun earth penetrator impact experiment. High-fidelity finite element models were developed and validated with quasistatic experiments. These models were then used to simulate the response of such lattices when subjected to the acceleration loads expected in the Davis gun experiment. Results reveal how the impact mitigation performance of lattices can change drastically at a certain relative density. Based on these observations, an experiment deck was designed to probe the response of lattices with different relative densities during the Davis gun phase 2 shots. The expected performance of these lattices is predicted before testing based on simulation results. The results of the Davis gun phase 2 shots are expected to provide data which will be used to assess the predictive capability of the finite element simulations in such a complex impact environment.
The Spent Fuel and Waste Science and Technology (SFWST) Campaign of the U.S. Department of Energy (DOE) Office of Nuclear Energy (NE), Office of Fuel Cycle Technology (FCT) is conducting research and development (R&D) on geologic disposal of spent nuclear fuel (SNF) and high-level nuclear waste (HLW). Two high priorities for SFWST disposal R&D are design concept development and disposal system modeling. These priorities are directly addressed in the SFWST Geologic Disposal Safety Assessment (GDSA) control account, which is charged with developing a geologic repository system modeling and analysis capability, and the associated software, GDSA Framework, for evaluating disposal system performance for nuclear waste in geologic media. GDSA Framework is supported by SFWST Campaign and its predecessor the Used Fuel Disposition (UFD) campaign. This report fulfills the GDSA Uncertainty and Sensitivity Analysis Methods work package (SF-21SN01030404) level 3 milestone, Uncertainty and Sensitivity Analysis Methods and Applications in GDSA Framework (FY2021) (M3SF-21SN010304042). It presents high level objectives and strategy for development of uncertainty and sensitivity analysis tools, demonstrates uncertainty quantification (UQ) and sensitivity analysis (SA) tools in GDSA Framework in FY21, and describes additional UQ/SA tools whose future implementation would enhance the UQ/SA capability of GDSA Framework. This work was closely coordinated with the other Sandia National Laboratory GDSA work packages: the GDSA Framework Development work package (SF-21SN01030405), the GDSA Repository Systems Analysis work package (SF-21SN01030406), and the GDSA PFLOTRAN Development work package (SF-21SN01030407). This report builds on developments reported in previous GDSA Framework milestones, particularly M3SF 20SN010304032.
The representation of material heterogeneity (also referred to as "spatial variation") plays a key role in the material failure simulation method used in ALEGRA. ALEGRA is an arbitrary Lagrangian-Eulerian shock and multiphysics code developed at Sandia National Laboratories and contains several methods for incorporating spatial variation into simulations. A desirable property of a spatial variation method is that it should produce consistent stochastic behavior regardless of the mesh used (a property referred to as "mesh independence"). However, mesh dependence has been reported using the Weibull distribution with ALEGRA's spatial variation method. This report describes efforts towards providing additional insight into both the theory and numerical experiments investigating such mesh dependence. In particular, we have implemented a discrete minimum order statistic model with properties that are theoretically mesh independent.
The generalized singular value decomposition (GSVD) is a valuable tool that has many applications in computational science. However, computing the GSVD for large-scale problems is challenging. Motivated by applications in hyper-differential sensitivity analysis (HDSA), we propose new randomized algorithms for computing the GSVD which use randomized subspace iteration and weighted QR factorization. Detailed error analysis is given which provides insight into the accuracy of the algorithms and the choice of the algorithmic parameters. We demonstrate the performance of our algorithms on test matrices and a large-scale model problem where HDSA is used to study subsurface flow.
