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At least 469 records · Page 26

Developing an Automated Uncertainty Quantification Tool to Improve Watershed-Scale Predictions of Water and Nutrient Cycling

Managing the flow of water, nutrients, and contaminants in watersheds is vital to addressing pressing issues related to water scarcity, access to clean drinking water, energy production, resilience to natural and anthropogenic perturbations, and ecological restoration. Decisions about the management of watersheds critically depend on the accuracy with which the flow of water and chemicals through the watershed can be predicted by computer models. Prediction uncertainty can be reduced by matching the model to data, which are collected in the field at great expense. The contribution of watershed characterization data to reducing uncertainty of relevant model predictions can be evaluated in a so-called data-worth analysis, which provides transparent, quantitative metrics about a data set’s value for the support of relevant watershed management objectives. To achieve this goal, we developed a software package that implements the data-worth analysis approach for use with state-of-the-art watershed models. The purpose of the proposed data-worth analysis is to help decision-makers allocate resources for watershed characterization such that the uncertainty in model predictions can be significantly reduced, which leads to better, more effective management decisions. At the same time, watershed characterization costs can be reduced. The specific technical objectives of this SBIR/STTR Phase II project were to develop a framework and associated software toolsets that implement the uncertainty quantification and data-worth analysis approach for use with state-of-the-art watershed models. This goal was achieved by (A) developing a user-friendly, robust software package that is accessible to a wide audience, including watershed managers, policy-makers, and public stakeholders; (B) by demonstrating application of the prototype on several use cases that are representative of complex watershed management challenges spanning a range of scales and that consider different open-source, DOE-based codes and other modeling platforms; and (C) by gathering information about the needs and requirements from potential users to help guide future developments, ensuring that the final product will be commercially viable. The developed software consists of a graphical user interface that guides the user through a sequence of analysis steps, supported by toolsets that leverage state-of-the-art computational simulation-optimization capabilities. A prototype of the software runs on multiple platforms (PC, Mac, multi-processor Linux environment), is linked to diverse watershed simulators (e.g., ECOSYS, TOUGH2, TOUGHREACT, Amanzi-ATS), performs multiple analysis tasks (predictive simulations, sensitivity analysis, uncertainty analysis, automatic parameter estimation, and data-worth analysis, multicomponent geothermometry), and is readily extensible to include external simulators and analysis tools. The software is being commercialized and will be continually updated to address user needs.

58 GEOSCIENCES↗

Status of the NEAMS and ARC fast reactor tools integration to the NEAMS Workbench

The Workbench initiative was launched in FY-2017 within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to facilitate the transition from conventional tools to high-fidelity tools. The NEAMS Workbench provides a common user interface for model creation, real-time validation, execution, output processing, and visualization for integrated codes. The integration of the Argonne Reactor Computation (ARC) suite of codes into the NEAMS Workbench through the PyARC module was initiated in FY-2017. The ARC codes, which focus on fast reactor multiphysics analysis, contain both legacy codes like DIF3D and REBUS-3 that were developed with over 30 years of experience, and newer NEAMS additions like MC 2 -3, PERSENT, and PROTEUS. Recent work expended this integration to other tools to support the U.S. fast reactor community such as DASSH for sub-channel thermal-hydraulics, Griffin for high-fidelity deterministic transport calculations, and OpenMC for Monte Carlo simulations (with Shift integration planned for FY-2023). The integration of the “extended ARC” suite of codes into the NEAMS Workbench interface relies on the PyARC and PyGriffin modules to handles the pre- and post-processing of these codes input, and the runtime environment. The PyARC module together with the NEAMS Workbench interface are both released under Open Source Software licenses.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Science & Technology Review: The Road to Exascale Computing

At Lawrence Livermore National Laboratory, we focus on science and technology research to ensure our nation’s security. We also apply that expertise to solve other important national problems in energy, bioscience, and the environment. Science & Technology Review is published eight times a year to communicate, to a broad audience, the Laboratory’s scientific and technological accomplishments in fulfilling its primary missions. The publication’s goal is to help readers understand these accomplishments and appreciate their value to the individual citizen, the nation, and the world. The Department of Energy’s Exascale Computing Project (ECP) and Lawrence Livermore’s RADIUSS (Rapid Application Development via an Institutional Universal Software Stack) initiative benefit from strategically developed software tools. The front cover shows a simulation of advection under twisting rotation that uses high-order finite elements from Livermore’s Modular Finite Element Methods (MFEM) software library and GLVis visualization tool. On the back cover, the logo (also created with GLVis) for the MFEM project illustrates the curved mesh and sub-element resolution used in high-order simulations. MFEM and GLVis are key components of the ECP’s co-design Center for Efficient Exascale Discretizations (CEED) and RADIUSS. MFEM is also part of ECP’s Extreme-Scale Scientific Software Development Kit (xSDK).

97 MATHEMATICS AND COMPUTING↗

OpenCHAMI Introduction: Cloud-like HPC Management for the Composable future [Slides]

OpenCHAMI is: An independent partnership of large HPC operators and vendor(s); Based on the APIs and Microservices from the Cray System Manager; A set of governance standards for developing HPC system management software aligned with cloud principles; A github organization; A set of software repositories in active development to enable sites to solve their own problems in a shareable way.

97 MATHEMATICS AND COMPUTING↗

Sierra/SD – User's Manual – 5.18

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high-fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a user’s guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

97 MATHEMATICS AND COMPUTING↗

POEM

User manual for software POEM (Platform of Optimal Experiment Management).

42 ENGINEERING↗

Preliminary Thermoluminescent Dosimeter Glow Curve Analysis with Automated Glow Peak Identification for LiF Mg,Ti

When appropriately analyzed, thermoluminescent dosimeter glow curve analysis allows for improved quantification of thermoluminescent material behavior while flagging abnormalities. The mathematical separation of a glow curve into contributions from energetically unique trap states, or glow curve analysis, may be used to remove undesired effects of signal fading for complex materials. A generalized glow curve analysis software for the separation of glow curves is presented in this paper. Written in C ++ , the software uses the first-order kinetics model with automatic peak identification. The automatic identification of peaks is achieved through a unique peak-finding algorithm. Here, the program was performance tested using experimental glow curve data from LiF:Mg,Ti, and comparative results are presented.

47 OTHER INSTRUMENTATION↗

An extension to V ORO ++ for multithreaded computation of Voronoi cells

V ORO ++ is a software library written in C++ for computing the Voronoi tessellation, a technique in computational geometry that is widely used for analyzing systems of particles. V ORO ++ was released in 2009 and is based on computing the Voronoi cell for each particle individually. Here, we take advantage of modern computer hardware, and extend the original serial version to allow for multithreaded computation of Voronoi cells via the OpenMP application programming interface. We test the performance of the code, and demonstrate that it can achieve parallel efficiencies greater than 95% in many cases. Further, the multithreaded extension follows standard OpenMP programming paradigms, allowing it to be incorporated into other programs. We provide an example of this using the VoroTop software library, performing a multithreaded Voronoi cell topology analysis of up to 102.4 million particles.

97 MATHEMATICS AND COMPUTING↗

DSPS: Differentiable stellar population synthesis

ABSTRACT Models of stellar population synthesis (SPS) are the fundamental tool that relates the physical properties of a galaxy to its spectral energy distribution (SED). In this paper, we present DSPS: a python package for SPS. All of the functionality in DSPS is implemented natively in the JAX library for automatic differentiation, and so our predictions for galaxy photometry are fully differentiable, and directly inherit the performance benefits of JAX, including portability onto GPUs. DSPS also implements several novel features, such as i) a flexible empirical model for stellar metallicity that incorporates correlations with stellar age, ii) support for the Diffstar model that provides a physically-motivated connection between the star formation history of a galaxy (SFH) and the mass assembly of its underlying dark matter halo. We detail a set of theoretical techniques for using autodiff to calculate gradients of predictions for galaxy SEDs with respect to SPS parameters that control a range of physical effects, including SFH, stellar metallicity, nebular emission, and dust attenuation. When forward modelling the colours of a synthetic galaxy population, we find that DSPS can provide a factor of 5 speed-up over standard SPS codes on a CPU, and a factor of 300-400 on a modern GPU. When coupled with gradient-based techniques for optimization and inference, DSPS makes it practical to conduct expansive likelihood analyses of simulation-based models of the galaxy–halo connection that fully forward model galaxy spectra and photometry.

79 ASTRONOMY AND ASTROPHYSICS↗

Converged Computing: A Best of Both Worlds of High-Performance Computing and Cloud

Collaboration between Cloud and High Performance Computing (HPC) communities has accelerated in the last half decade. A common goal to run batch workloads combined with a desire for reproducibility, automation, and optimization has led to successful projects that range from container technologies to workload management and security. This span of current and future work defines a novel “Converged Computing” paradigm that aims to combine the best of both worlds, both from a technological and cultural standpoint. Furthermore, in this Special Issue, we review common themes in the space, showcasing current work and encouraging a continued effort toward innovative ideas that will enable the next generations of scientific discovery.

97 MATHEMATICS AND COMPUTING↗

QASMBench: A Low-Level Quantum Benchmark Suite for NISQ Evaluation and Simulation

The rapid development of quantum computing (QC) in the NISQ era urgently demands a low-level benchmark suite and insightful evaluation metrics for characterizing the properties of prototype NISQ devices, the efficiency of QC programming compilers, schedulers and assemblers, and the capability of quantum system simulators in a classical computer. In this work, we fill this gap by proposing a low-level, easy-to-use benchmark suite called QASMBench based on the OpenQASM assembly representation. It consolidates commonly used quantum routines and kernels from a variety of domains including chemistry, simulation, linear algebra, searching, optimization, arithmetic, machine learning, fault tolerance, cryptography, and so on, trading-off between generality and usability. To analyze these kernels in terms of NISQ device execution, in addition to circuit width and depth, we propose four circuit metrics including gate density, retention lifespan, measurement density, and entanglement variance, to extract more insights about the execution efficiency, the susceptibility to NISQ error, and the potential gain from machine-specific optimizations. Applications in QASMBench can be launched and verified on several NISQ platforms, including IBM-Q, Rigetti, IonQ and Quantinuum. For evaluation, we measure the execution fidelity of a subset of QASMBench applications on 12 IBM-Q machines through density matrix state tomography, comprising 25K circuit evaluations. In addition we also compare the fidelity of executions among the IBM-Q machines, the IonQ QPU and the Rigetti Aspen M-1 system.

97 MATHEMATICS AND COMPUTING↗

FY19 Status Report on the Computing Systems for the Yucca Mountain Project TSPA-LA Models and Preliminary Testing of a Selected Process Model

Sandia National Laboratories continued evaluation of total system performance assessment (TSPA) computing systems for the previously considered Yucca Mountain Project. This was done to maintain the operational readiness of the computing infrastructure (computer hardware and software) and knowledge capability for total system performance assessment) type analysis, as directed by the National Nuclear Security Administration (NNSA), DOE 2010. The FY19 task included continued operation of the cluster; maintenance of the TSPA-LA models (with Gold Sim 9.60.300); preliminary assessment of the status of the Infiltration Model (a process model that feeds the TSPA-LA). In addition, precautionary actions were needed to extend the life of the cluster hardware. To do that, three new nodes were added to the cluster. In the event any of the original nodes fail they will be replaced with the new nodes, thereby maintaining the core capability. The 2014 cluster and supporting software systems are currently fully operational to support TSPA-LA type analysis.

97 MATHEMATICS AND COMPUTING↗

Research software engineering: Professionalization, roles, and identity

This report summarizes the results of a study of research software professionals based on 17 interviews conducted at U.S. national laboratories and academic institutions. The study focuses on understanding the emerging professional role of research software engineer (RSE) and examining how the history of software engineering might be relevant to the emergence of research software engineering as a professional movement. The report first uses interview data to identify several models of professional identity for research software professionals. These include dominance models in which a person strongly identifies with a single professional identity (such as RSE), and multiplicity models in which an individual sees an identity like RSE as just one facet of their overall professional role. Next, it identifies three types of work situations for software professionals at national laboratories, covering those who work in dedicated RSE organizations, those who play an integral role in large multiphysics code projects, and those who work in a more isolated capacity to provide software development support for less computationally intensive research projects. It then reviews some key ideas from the sociology of professions in the context of the software engineering profession, suggesting parallels between the current RSE professional movement and aspects of the history of software engineering. It concludes by suggesting some potential practical implications of these findings for the RSE movement and professional organizations.

97 MATHEMATICS AND COMPUTING↗

VC3: Virtual Clusters for Community Computation

A traditional HPC computing facility provides a large amount of computing power but has a fixed environment designed to satisfy local needs. This makes it very challenging for users to deploy complex applications that span multiple sites and require specific application software, scheduling middleware, or sharing policies. This project addressed many of these challenges by making it possible for researchers to easily aggregate and share resources, install custom software environments, and deploy clustering frameworks across multiple HPC facilities through the concept of “virtual clusters”. We designed and implemented a prototype virtual cluster facility that enabled unprivileged users to create dynamic aggregations of computing power across multiple sites, deployed with custom middleware and complex software dependencies. This service is hosted at the University of Chicago and available through the site virtualclusters.org.

97 MATHEMATICS AND COMPUTING↗

Agilent AgileBioFoundry CRADA (Final Report)

The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOF-MS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Therefore, our accomplishment in this CRADA improved the efficiency and accuracy of strain testing by developing and implementing fast analytical methods, robust processing tools, and software for predicting the best methods for UHPLC analysis.

97 MATHEMATICS AND COMPUTING↗