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NeuNorm is a scipp-based Python library for neutron imaging normalization and time-of-flight (TOF) data processing at Oak Ridge National Laboratory imaging facilities (MARS at HFIR and VENUS at SNS). NeuNorm 2.0 is a complete, scipp-based rewrite of the original NeuNorm normalization library, adding HDF5 output, automatic uncertainty propagation, and TOF/event-mode processing.
SkyPy is an open-source Python package for simulating the astrophysical sky. It comprises a library of physical and empirical models across a range of observables and a command-line script to run end-to-end simulations. The library provides functions that sample realisations of sources and their associated properties from probability distributions. Simulation pipelines are constructed from these models using a YAML-based configuration syntax, while task scheduling and data dependencies are handled internally and the modular design allows users to interface with external software. SkyPy is developed and maintained by a diverse community of domain experts with a focus on software sustainability and interoperability. By fostering development, it provides a framework for correlated simulations of a range of cosmological probes including galaxy populations, large scale structure, the cosmic microwave background, supernovae and gravitational waves. Version 0.4 implements functions that model various properties of galaxies including luminosity functions, redshift distributions and optical photometry from spectral energy distribution templates. Future releases will provide additional modules, for example, to simulate populations of dark matter halos and model the galaxy-halo connection, making use of existing software packages from the astrophysics community where appropriate.
Spatial optimization is a major spatial analytical tool in management and planning, the significance of which cannot be overstated. Spatial optimization models play an important role in designing and managing effective and efficient service systems such as transportation, education, public health, environmental protection, and commercial investment among others. To this end, spopt (spatial optimization) is under active development for the inclusion of newly proposed models and methods for regionalization, facility location, and transportation-oriented solutions (Feng et al., 2021). Spopt is a submodule in the open-source spatial analysis library PySAL (Python Spatial Analysis Library) founded by Dr. Sergio J. Rey and Dr. Luc Anselin in 2005 (Rey et al., 2015, 2021; Rey & Anselin, 2007). The goal of developing spopt is to provide management and decision-making support to all relevant practitioners and to further promote the appropriate and meaningful application of spatial optimization models in practice.
The Transformer eXplainability and eXploration (Martindale & Stewart, 2021), or TX 2 software package, is a library designed for artificial intelligence researchers to better understand the performance of transformer models (Vaswani et al., 2017) used for sequence classification. The tool is capable of integrating with a trained transformer model and a dataset split into training and testing populations to produce an ipywidget (Project Jupyter Contributors, 2021) dashboard with a number of visualizations to understand model performance with an emphasis on explainability and interpretability. The TX 2 package is primarily intended to integrate into a workflow centered around Jupyter Notebooks (Kluyver et al., 2016), and currently assumes the use of PyTorch (Paszke et al., 2019) and Hugging Face transformers library (Wolf et al., 2020). The dashboard includes visualization and data exploration features to aid researchers, including an interactive UMAP embedding graph (McInnes et al., 2018) to understand classification clusters, a word salience map that can be updated as researchers alter textual entries in near real time, a set of tools to understand word frequency and importance based on the clusters in the UMAP embedding graph, and a set of traditional confusion matrix analysis tools.
The Interactive Corpus Analysis Tool (ICAT) is a Python library for creating dashboards to explore textual datasets and build simple binary classification models to help filter through them and focus on entries of interest. This tool uses a form of interactive machine learning (IML), a paradigm of “machine teaching” (Simard et al., 2017) that sits at the intersection of the fields of human computer interaction (HCI), visual analytics, and machine learning. The intent of ICAT is to allow subject matter experts (SME) with limited to no experience in machine learning to benefit from an iterative human-in-the-loop (HITL) approach to building their own model without needing to understand the details of the underlying algorithm. This interactivity is achieved by allowing the user to create features, label data points, and visually manipulate a representation of the features to manually cluster and investigate data, while a model is trained on the fly based on these actions. ICAT is built on top of the Panel (Holoviz, 2018) library, using a combination of Vega, a custom IPyWidget using D3, and ipyvuetify, and is intended to be used inside of a Jupyter environment.
Sigma is a header-only C++-17 library for uncertainty propagation, inspired by uncertainties for Python and Measurements.jl for Julia. The library tracks the functional correlation between dependent and independent variables, ensuring that the uncertainty of the independent variables is properly considered in the calculation of the dependent variables’ uncertainties. It is intended as a near drop-in replacement for the standard floating point types (aside from uncertainty specification), and aims to be easily interoperable with the existing standard types.
kokkos-fft provides a unified, performance-portable interface for Fast Fourier Transforms (FFTs) within the Kokkos ecosystem (C. Trott et al., 2021). It seamlessly integrates with leading local FFT libraries including FFTW, cuFFT, rocFFT, and oneMKL. Designed for simplicity and efficiency, kokkos-fft offers a user experience akin to numpy.fft for in-place and out-of-place transforms, while leveraging the raw speed of vendor-optimized libraries. A demonstration solving 2D Hasegawa-Wakatani turbulence with the Fourier spectral method illustrates how kokkos-fft can deliver significant speedups over Python-based alternatives without drastically increasing code complexity, empowering researchers to perform high-performance FFTs simply and effectively.
The U. S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility began a pilot project in May 2015 to design a routine, high-resolution modeling capability to complement ARM’s extensive suite of measurements. This modeling capability has evolved into the Large-Eddy Simulation (LES) ARM Symbiotic Simulation and Observation (LASSO) datastream. The datastream, broadly termed data bundles, contains high-resolution model output, input files, observations for evaluation, and skill scores for the simulations. The initial focus of LASSO is on shallow convection at the ARM Southern Great Plains (SGP) atmospheric observatory. The availability of LES simulations with concurrent observations serves many purposes. LES helps bridge the scale gap between DOE ARM observations and models, and the use of routine LES adds value to observations. It provides a self-consistent representation of the atmosphere and a dynamical context for the observations. Further, it elucidates unobservable processes and properties. LASSO generates a simulation library for researchers that enables statistical approaches beyond a single-case mentality. It also provides tools necessary for modelers to reproduce the LES and conduct their own sensitivity experiments. The LASSO library of data bundles is designed to facilitate a wide range of research. For an observationalist, LASSO can help inform instrument remote-sensing retrievals, conduct observation system simulation experiments (OSSEs), and test implications of radar scan strategies or flight paths. For a theoretician, LASSO can help calculate estimates of fluxes and co-variability of values, and test relationships without having to run the model personally. For a modeler, LASSO can help one know ahead of time which days have good forcing, have co-registered observations at high-resolution scales, and have simulation inputs and corresponding outputs to test parameterizations. Further details on the overall LASSO project are available at https://www.arm.gov/capabilities/modeling/lasso.
The use of high-throughput virtual screening (HTVS) tools is a powerful tool to expedite the materials discovery of commercially relevant materials. In previous years, our group has developed a molecular discovery platform to generate libraries in order to obtain suitable candidates for different applications, starting from the Harvard Clean Energy Project. This platform is suitable to test in-silico on traditional supercomputing clusters and shared resources, for example, in the IBM World Community Grid. In this project, we used the molecular discovery platform to create and screen a library of candidates of organic photovoltaic (OPVs) molecules. Based on a set of candidates created with combinations of molecular moieties, we were able to filter, by conformation stability, the energy of electronic orbitals and approximated power conversion efficiencies (PCE). To improve the predictions of orbital energies calculated and the PCEs, we used Gaussian Process regression and two sets of molecules. These sets correspond to electronic structure calculations of a higher level of theory and experimental PCE values, respectively. Finally, we selected a subset of the best candidates (molecules with a PCE higher than 10%) to understand its absorbance properties with TD-DFT. This project has demonstrated the capabilities of our molecular discovery platform for HTVS. Finally, machine learning can help us to introduce more complex effects included in bulk conditions and computational intensive calculations on models.
UNITY is a 36-month project focused on providing design and evaluate a new distributed storage paradigm that unifies the traditionally distinct application views of memory- and file-based data storage into a single scalable and resilient environment. The project is a collaboration among Oak Ridge National Laboratory (ORNL, Lead institution), Los Alamos National Labs (LANL), and Georgia Tech (GT). The main contributions of the GT team have been around development of low level systems software for best leveraging the capabilities of new types of persistent memory technologies, and for development of methods for intelligent data management across memory/storage substrates with heterogeneous components. GT contributed the Phoenix library for optimized checkpoint/restart for HPC I/O for systems with non-volatile memory (NVM), the NVStream library for NVM-specialized streaming I/O for HPC workflows, the CoMerge, Mnemo and Kleio solutions for intelligent data management on NVM-based systems. These contributions result in significant improvements in both application performance and system efficiency.
This document details the development and current state of MGMC: a proxy Multi-Group Monte Carlo transport application. The goal of this work was to develop a light-weight Monte Carlo transport solver that could be easily reconfigured to test parallelization strategies targeting advanced architectures and heterogeneous computing environments. Additionally, MGMC is able to act as a proxy-app for testing the development of algorithms and the integration of other libraries and into Monte Carlo transport codes. MGMC is currently able to run in parallel using OpenMP for CPU threads or CUDA for NVIDIA GPUs. MGMC was also used to investigate the using SYCL for portable parallelization targeting either CPU threads, vender-agnostic GPUs, and ARM chips, detailed in Section II. In the process of developing MGMC, several other C++ libraries have been created with the intent for re-use in future research projects and potential inclusion in production-level codes, detailed in Section III. The physics capabilities in MGMC are detailed in Section IV, code verification is detailed in Section V, and performance results are detailed in Section VI.
Siera/SolidMechanics (Sierra / SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra / SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra / SM has a versatile library of continuum and structural elements, and a large library of material models. The code is written for parallel computing environments enabling scalable solutions of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes . This document describes the functionality and input syntax for Sierra/SM.
This report provides a summary of notes for building and running the Sandia Computational Engine for Particle Transport for Radiation Effects (SCEPTRE) code. SCEPTRE is a general purpose C++ code for solving the Boltzmann transport equation in serial or parallel using unstructured spatial finite elements, multigroup energy treatment, and a variety of angular treatments including discrete ordinates and spherical harmonics. Either the first-order form of the Boltzmann equation or one of the second-order forms may be solved. SCEPTRE requires a small number of open-source Third Party Libraries (TPL) to be available, and example scripts for building these TPL's are provided. The TPL's needed by SCEPTRE are Trilinos, boost, and netcdf. SCEPTRE uses an autoconf build system, and a sample configure script is provided. Running the SCEPTRE code requires that the user provide a spatial finite-elements mesh in Exodus format and a cross section library in a format that will be described. SCEPTRE uses an xml-based input, and several examples will be provided.
This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear solvers, nonlinear solvers, and time integrators that may be used in application codes written in Fortran, C, C++, and Python. PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than \rolling them" yourself.
Advanced reactor concepts currently being developed throughout the industry are significantly different from light water reactor (LWR) designs with respect to geometry, materials, and operating conditions, and consequently, with respect to their reactor physics behavior. Given the limited operating experience with non-LWRs, the accurate simulation of reactor physics and the quantification of associated uncertainties are critical for ensuring that advanced reactor concepts operate within the appropriate safety margins. Nuclear data are a major source of input uncertainties in reactor physics analysis. As part of an ongoing project at Oak Ridge National Laboratory (ORNL), the effects of nuclear data uncertainties on key figures of merit associated with advanced reactor safety are being assessed for selected advanced reactor technologies. Key nuclear data relevant for reactor safety analysis for each selected advanced reactor technology were identified, and their impact on important key figures of merit was assessed. Available advanced reactor specifications were reviewed, results from studies performed at ORNL and other research institutions were consulted, and available evaluated nuclear data libraries were analyzed. This report summarizes the key nuclear data for nuclides in the fuel, as well as other significant data, including scattering and neutron capture in various materials for the moderator, coolant, and structure of the considered advanced reactors. For the considered advanced reactors that use low-enriched uranium (LEU) fuel, results from LWR studies provided insight into relevant nuclear data given the lack of available studies specifically addressing these new systems. The major nominal missing data that were identified consist of thermal scattering data and 135m Xe cross section data for molten salt reactor (MSR) analysis. The identified major gaps with respect to nuclear data uncertainties are missing uncertainties of thermal scattering data for high temperature gas-cooled reactors and moderated MSR systems, and incomplete uncertainties on angular distributions in particular for fast spectrum systems, such as sodiumcooled fast reactors, fast molten salt reactors, and heat pipe reactors. Furthermore, it was found that special attention should be paid to cross section and uncertainty differences between different evaluated nuclear data library releases, because significant differences in nuclear data that can lead to major differences in reactivity calculations were found, even for well-known nuclides.
Sierra / SolidMechanics (Sierra / SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra / SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra / SM has a versatile library of continuum and structural elements, an d a large library of material models. The code is written for parallel computing environments enabling scalable solutions of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes . This document describes the functionality and input syntax for Sierra / SM.
Productivity and Sustainability Improvement Planning (PSIP) is a lightweight, incremental and iterative approach (much in the same spirit as Agile methodologies) for making routine software process improvements in software projects. It is designed to be easily applied in existing development workflows. Quoting from a November 2019 workshop paper describing PSIP. PSIP breaks from classic software process improvement approaches such as CMM(I), SPICE, ISO 9000 or Six Sigma, in that it trades comprehensive standards and certification-driven assessment for self-defined, internally driven goals. It does, however, carry forward such ideas as having staged models of improvement (like CMM(I)) in the form of progress tracking cards. Additionally, PSIP is more aligned with lean and agile methods; it adopts their emphasis on iterative improvement and continuous learning. At its core, PSIP is an instantiation of the Plan-Do-Check-Act management cycle (PDCA, also known as Plan-Do-Study-Adjust) which provides the foundation for much of the modern software process improvement literature. This situates PSIP within a constellation of bottom-up, inductive software process improvement methods. PSIP is designed around the notion that already overburdened teams can define and carry out a series of small, incremental steps of progression towards improvement goals without significant (there will be some, but the goal is to avoid significant) disruption to ongoing development activities. A key enabling tool in PSIP is the use of Progress Tracking Cards (PTCs) which define the steps of progression towards a given improvement goal. This is the theory of PSIP. The PSIP for HDF5 project was aimed at putting PSIP into practice with the purpose of evaluating its effectiveness in planning and facilitating quality and process improvements in a scientific software project as well as its associated artifacts. The HDF5 project was chosen as a use case to evaluate PSIP for several reasons. First, NNSA labs and LLNL in particular have a keen interest in how HDF5 quality impacts its uptake and sustainability as a community adopted and supported code. Next, HDF5 is a foundational library, a key substrate in the HPC/CSE software stack, and any improvements there realized through this contract will have benefits to many DOE applications depending on it. HDF5 also represents an older, legacy code with technical debts to pay down. These characteristics are similar to many NNSA and even some ECP code projects. But, because HDF5 is an I/O library, it represents a simpler use case within which to study PSIP than a full-fledged and significantly more complex PDE simulation code. We believe these attributes make HDF5 an ideal use case for evaluating PSIP.
The auxiliary field quantum Monte Carlo algorithm in QMCPACK was ported to run on AMD GPUs using HIP. Initial performance measurements on early access hardware indicate a 4x slowdown compared to NVIDIA V100s. The slowdown was determined to be a result of suboptimal ROCM libraries for small matrix sizes coupled with some poorly performing hipified CUDA kernels. Through a preliminary analysis of HIP kernel performance we determined a strategy for pro ling and tuning kernels. We request that ROCM libraries are optimized for smaller problem sizes particularly for batched operations.