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DOE OSTI2014

The NIFTY way of Bayesian signal inference

We introduce NIFTY, 'Numerical Information Field Theory', a software package for the development of Bayesian signal inference algorithms that operate independently from any underlying spatial grid and its resolution. A large number of Bayesian and Maximum Entropy methods for 1D signal reconstruction, 2D imaging, as well as 3D tomography, appear formally similar, but one often finds individualized implementations that are neither flexible nor easily transferable. Signal inference in the framework of NIFTY can be done in an abstract way, such that algorithms, prototyped in 1D, can be applied to real world problems in higher-dimensional settings. NIFTY as a versatile library is applicable and already has been applied in 1D, 2D, 3D and spherical settings. A recent application is the D{sup 3}PO algorithm targeting the non-trivial task of denoising, deconvolving, and decomposing photon observations in high energy astronomy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

SharP Data Constructs: Data Constructs to Enable Data-Centric Computing

Extreme-scale applications (i.e., Big-Compute) are becoming increasingly data-intensive, i.e., producing and consuming increasingly large amounts of data. The HPC systems traditionally used for these applications are now used for Big-Data applications such as data analytics, social network analysis, machine learning, and genomics. As a consequence of these trends, the system architecture should be flexible and data-centric. This can already be witnessed in the pre-exascale systems with TBs of on-node hierarchical and heterogeneous memories, PBs of system memory, low-latency, high-throughput networks, and many threaded cores. As such, the pre-exascale systems suit the needs of both Big-Compute and Big-Data applications. Though the system architecture is flexible enough to support both Big-Compute and Big-Data, we argue there is a software gap. Particularly, we need data-centric abstractions to leverage the full potential of the system, i.e., there is a need for native support for data resilience, the ability to express data locality and affinity, mechanisms to reduce data movement, the ability to share data, and abstractions to express User's data usage and data access patterns. In this paper, we (i) show the need for taking a holistic approach towards data-centric abstractions, (ii) show how these approaches were realized in the SHARed data-structure centric Programming abstraction (SharP) library, a data-structure centric programming abstraction, and (iii) apply these approaches to a variety of applications that demonstrate its usefulness. Particularly, we apply these approaches to QMCPack and the Graph500 benchmark and demonstrate the advantages of this approach on extreme-scale systems.

Aderholdt, William Ferrol↗

NASA NTRS2013

Enhanced Schapery Theory Software Development for Modeling Failure of Fiber-Reinforced Laminates

Progressive damage and failure analysis (PDFA) tools are needed to predict the nonlinear response of advanced fiber-reinforced composite structures. Predictive tools should incorporate the underlying physics of the damage and failure mechanisms observed in the composite, and should utilize as few input parameters as possible. The purpose of the Enhanced Schapery Theory (EST) was to create a PDFA tool that operates in conjunction with a commercially available finite element (FE) code (Abaqus). The tool captures the physics of the damage and failure mechanisms that result in the nonlinear behavior of the material, and the failure methodology employed yields numerical results that are relatively insensitive to changes in the FE mesh. The EST code is written in Fortran and compiled into a static library that is linked to Abaqus. A Fortran Abaqus UMAT material subroutine is used to facilitate the communication between Abaqus and EST. A clear distinction between damage and failure is imposed. Damage mechanisms result in pre-peak nonlinearity in the stress strain curve. Four internal state variables (ISVs) are utilized to control the damage and failure degradation. All damage is said to result from matrix microdamage, and a single ISV marks the micro-damage evolution as it is used to degrade the transverse and shear moduli of the lamina using a set of experimentally obtainable matrix microdamage functions. Three separate failure ISVs are used to incorporate failure due to fiber breakage, mode I matrix cracking, and mode II matrix cracking. Failure initiation is determined using a failure criterion, and the evolution of these ISVs is controlled by a set of traction-separation laws. The traction separation laws are postulated such that the area under the curves is equal to the fracture toughness of the material associated with the corresponding failure mechanism. A characteristic finite element length is used to transform the traction-separation laws into stress-strain laws. The ISV evolution equations are derived in a thermodynamically consistent manner by invoking the stationary principle on the total work of the system with respect to each ISV. A novel feature is the inclusion of both pre-peak damage and appropriately scaled, post-peak strain softening failure. Also, the characteristic elements used in the failure degradation scheme are calculated using the element nodal coordinates, rather than simply the square root of the area of the element.

Pineda, Evan J.↗

DOE OSTI2020

Accelerating Radiation Computations for Dynamical Models With Targeted Machine Learning and Code Optimization

Abstract Atmospheric radiation is the main driver of weather and climate, yet due to a complicated absorption spectrum, the precise treatment of radiative transfer in numerical weather and climate models is computationally unfeasible. Radiation parameterizations need to maximize computational efficiency as well as accuracy, and for predicting the future climate many greenhouse gases need to be included. In this work, neural networks (NNs) were developed to replace the gas optics computations in a modern radiation scheme (RTE+RRTMGP) by using carefully constructed models and training data. The NNs, implemented in Fortran and utilizing BLAS for batched inference, are faster by a factor of 1–6, depending on the software and hardware platforms. We combined the accelerated gas optics with a refactored radiative transfer solver, resulting in clear‐sky longwave (shortwave) fluxes being 3.5 (1.8) faster to compute on an Intel platform. The accuracy, evaluated with benchmark line‐by‐line computations across a large range of atmospheric conditions, is very similar to the original scheme with errors in heating rates and top‐of‐atmosphere radiative forcings typically below 0.1 K day −1 and 0.5 W m −2 , respectively. These results show that targeted machine learning, code restructuring techniques, and the use of numerical libraries can yield material gains in efficiency while retaining accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

SU-F-I-53: Coded Aperture Coherent Scatter Spectral Imaging of the Breast: A Monte Carlo Evaluation of Absorbed Dose

Purpose: Coherent scatter based imaging has shown improved contrast and molecular specificity over conventional digital mammography however the biological risks have not been quantified due to a lack of accurate information on absorbed dose. This study intends to characterize the dose distribution and average glandular dose from coded aperture coherent scatter spectral imaging of the breast. The dose deposited in the breast from this new diagnostic imaging modality has not yet been quantitatively evaluated. Here, various digitized anthropomorphic phantoms are tested in a Monte Carlo simulation to evaluate the absorbed dose distribution and average glandular dose using clinically feasible scan protocols. Methods: Geant4 Monte Carlo radiation transport simulation software is used to replicate the coded aperture coherent scatter spectral imaging system. Energy sensitive, photon counting detectors are used to characterize the x-ray beam spectra for various imaging protocols. This input spectra is cross-validated with the results from XSPECT, a commercially available application that yields x-ray tube specific spectra for the operating parameters employed. XSPECT is also used to determine the appropriate number of photons emitted per mAs of tube current at a given kVp tube potential. With the implementation of the XCAT digital anthropomorphic breast phantom library, a variety of breast sizes with differing anatomical structure are evaluated. Simulations were performed with and without compression of the breast for dose comparison. Results: Through the Monte Carlo evaluation of a diverse population of breast types imaged under real-world scan conditions, a clinically relevant average glandular dose for this new imaging modality is extrapolated. Conclusion: With access to the physical coherent scatter imaging system used in the simulation, the results of this Monte Carlo study may be used to directly influence the future development of the modality to keep breast dose to a minimum while still maintaining clinically viable image quality.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

funnel v0.0.1

fcompare is a software package that applies for comparing two curves generated from datasets in csv format. A funnel is generated around the reference curve and the other curve is checked to verify if it is inside the funnel. The funnel can be reshaped by setting a tolerance. One potential application is to verify the development of building HVAC control sequence, in which it compares data curves from real operation with data curves from simulation using developed control sequences, to verify if the developed control sequences have been implemented correctly. In addition, it can be used for Modelica library developer to do the unit test that verifies new model developments.

Wetter, Michael↗

NASA NTRS1990

Solar Astronomy Data Base: Packaged Information on Diskette

In its role as a library, the National Geophysical Data Center has transferred to diskette a collection of small, digital files of routinely measured solar indices for use on an IBM-compatible desktop computer. Recording these observations on diskette allows the distribution of specialized information to researchers with a wide range of expertise in computer science and solar astronomy. Every data set was made self-contained by including formats, extraction utilities, and plain-language descriptive text. Moreover, for several archives, two versions of the observations are provided - one suitable for display, the other for analysis with popular software packages. Since the files contain no control characters, each one can be modified with any text editor.

Mckinnon, John A.↗

DOE OSTI2020

A fully unprivileged CernVM-FS

The CernVM File System provides the software and container distribution backbone for most High Energy and Nuclear Physics experiments. It is implemented as a file system in user-space (Fuse) module, which permits its execution without any elevated privileges. Yet, mounting the file system in the first place is handled by a privileged suid helper program that is installed by the Fuse package on most systems. The privileged nature of the mount system call is a serious hindrance to running CernVM-FS on opportunistic resource and supercomputers. Fortunately, recent developments in the Linux kernel and in the Fuse user-space libraries enabled fully unprivileged mounting for Fuse file systems (as of RHEL 8), or at least outsourcing the privileged mount system call to a custom, external process. This opens the door to several, very appealing new ways to use CernVM-FS, such as a generally usable “super pilot” consisting of the pilot code bundled with Singularity and CernVM-FS, or the on-demand instantiation of unprivileged, ephemeral containers to publish new CernVM-FS content from anywhere. In this contribution, we discuss the integration of these new Linux features with CernVM-FS and show some of its most promising, new applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Hindsight logging for model training

In modern Machine Learning, model training is an iterative, experimental process that can consume enormous computation resources and developer time. To aid in that process, experienced model developers log and visualize program variables during training runs. Exhaustive logging of all variables is infeasible, so developers are left to choose between slowing down training via extensive conservative logging, or letting training run fast via minimalist optimistic logging that may omit key information. As a compromise, optimistic logging can be accompanied by program checkpoints; this allows developers to add log statements post-hoc, and "replay" desired log statements from checkpoint---a process we refer to as hindsight logging. Unfortunately, hindsight logging raises tricky problems in data management and software engineering. Done poorly, hindsight logging can waste resources and generate technical debt embodied in multiple variants of training code. In this paper, we present methodologies for efficient and effective logging practices for model training, with a focus on techniques for hindsight logging. Our goal is for experienced model developers to learn and adopt these practices. To make this easier, we provide an open-source suite of tools for Fast Low-Overhead Recovery (flor) that embodies our design across three tasks: (i) efficient background logging in Python, (ii) adaptive periodic checkpointing, and (iii) an instrumentation library that codifies hindsight logging for efficient and automatic record-replay of model-training. Model developers can use each flor tool separately as they see fit, or they can use flor in hands-free mode, entrusting it to instrument their code end-to-end for efficient record-replay. Our solutions leverage techniques from physiological transaction logs and recovery in database systems. Evaluations on modern ML benchmarks demonstrate that flor can produce fast checkpointing with small user-specifiable overheads (e.g. 7%), and still provide hindsight log replay times orders of magnitude faster than restarting training from scratch.

Computer Science↗

DOE OSTI2026

Westcott g factors extended to arbitrary neutron energy spectra

Westcott 𝑔 factors are used in Neutron Activation Analysis (NAA) and Prompt Gamma-ray Activation Analysis (PGAA) to evaluate the impact of non-1∕𝑣 behavior in the neutron-capture cross sections of certain nuclei on activation product yields. This non-1∕𝑣 behavior arises from the presence of neutron resonances in the neutron- capture cross sections that overlap with the source neutron spectrum at low (< 5 eV) energies. Historically, Westcott 𝑔 factors that have been cataloged for NAA and PGAA applications are the result of calculations that assume a Maxwellian neutron flux distribution with a given temperature. In this work, we use this approach with updated neutron-capture cross sections from the Evaluated Nuclear Data File, version VIII.1 (ENDF/B-VIII.1) to tabulate Westcott 𝑔 factor values for a broad range of Maxwellian distribution temperatures, comparing the results against currently-available 𝑔 factors from International Atomic Energy Agency tables and other sources. Here, it was discovered during this analysis that the use of guided thermal and cold-neutron beams at certain facilities necessitates an approach for evaluating Westcott 𝑔 factors based on arbitrary non-Maxwellian spectra. In this paper, we present an approach for calculating 𝑔 factors with user-specified neutron spectra, and we demonstrate these methods to obtain Westcott 𝑔-factors for guided- and cold-neutron beams at the Budapest Research Reactor and the Forschungsreaktor München II reactor. As part of this work, open-source software has been developed that can be used to perform these calculations for applications in PGAA and NAA experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2017

Dynamic equation-based thermo-hydraulic pipe model for district heating and cooling systems

Simulation and optimisation of district heating and cooling networks requires efficient and realistic models of the individual network elements in order to correctly represent heat losses or gains, temperature propagation and pressure drops. Due to more recent thermal networks incorporating meshing decentralised heat and cold sources, the system often has to deal with variable temperatures and mass flow rates, with flow reversal occurring more frequently. This paper presents the mathematical derivation and software implementation in Modelica of a thermo-hydraulic model for thermal networks that meets the above requirements and compares it to both experimental data and a commonly used model. Good correspondence between experimental data from a controlled test set-up and simulations using the presented model was found. Compared to measurement data from a real district heating network, the simulation results led to a larger error than in the controlled test set-up, but the general trend is still approximated closely and the model yields results similar to a pipe model from the Modelica Standard Library. However, the presented model simulates 1.7 (for low number of volumes) to 68 (for highly discretized pipes) times faster than a conventional model for a realistic test case. A working implementation of the presented model is made openly available within the IBPSA Modelica Library. The model is robust in the sense that grid size and time step do not need to be adapted to the flow rate, as is the case in finite volume models.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

Real-Time Automated Pathogen Identification by Enhanced Ribotyping (RAPIER) LDRD Final Report

Funded through the IHNS/E&HS investment area for FY16-18, the RAPIER LDRD sought to evaluate the potential benefits and applicability of the new Oxford MinION nanopore sequencer to pathogen diagnostic applications in biodefense, biosurveillance, and global/public health. The project had four primary objectives: 1) to investigate the performance of the MinION sequencer while building facility with its operation, 2) to develop microfluidic library prep automation facilitating the use of the MinION in field-forward or point-of-care applications, 3) to leverage CRISPR/Cas9 technology to enable targeted identification of bacterial pathogens, and 4) to capitalize on the real- time data output capabilities of the MinION to enable rapid sequence-based diagnostics. While the rapid evolution of the MinION sequencing technology during the course of the project posed a number of challenges and required a reassessment of initial project priorities, it also provided unique opportunities, notably culminating in our development of the RUBRIC real-time selective sequencing software.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Agile Acceleration of LLVM Flang Support for Fortran 2018 Parallel Programming

The LLVM Flang compiler ("Flang") is currently Fortran 95 compliant, and the frontend can parse Fortran 2018. However, Flang does not have a comprehensive 2018 test suite and does not fully implement the static semantics of the 2018 standard. We are investigating whether agile software development techniques, such as pair programming and test-driven development (TDD), can help Flang to rapidly progress to Fortran 2018 compliance. Because of the paramount importance of parallelism in high-performance computing, we are focusing on Fortran’s parallel features, commonly denoted “Coarray Fortran.” We are developing what we believe are the first exhaustive, open-source tests for the static semantics of Fortran 2018 parallel features, and contributing them to the LLVM project. A related effort involves writing runtime tests for parallel 2018 features and supporting those tests by developing a new parallel runtime library: the CoArray Fortran Framework of Efficient Interfaces to Network Environments (Caffeine).

Rasmussen, Katherine↗

NASA NTRS1993

Software to model AXAF image quality

This draft final report describes the work performed under this delivery order from May 1992 through June 1993. The purpose of this contract was to enhance and develop an integrated optical performance modeling software for complex x-ray optical systems such as AXAF. The GRAZTRACE program developed by the MSFC Optical Systems Branch for modeling VETA-I was used as the starting baseline program. The original program was a large single file program and, therefore, could not be modified very efficiently. The original source code has been reorganized, and a 'Make Utility' has been written to update the original program. The new version of the source code consists of 36 small source files to make it easier for the code developer to manage and modify the program. A user library has also been built and a 'Makelib' utility has been furnished to update the library. With the user library, the users can easily access the GRAZTRACE source files and build a custom library. A user manual for the new version of GRAZTRACE has been compiled. The plotting capability for the 3-D point spread functions and contour plots has been provided in the GRAZTRACE using the graphics package DISPLAY. The Graphics emulator over the network has been set up for programming the graphics routine. The point spread function and the contour plot routines have also been modified to display the plot centroid, and to allow the user to specify the plot range, and the viewing angle options. A Command Mode version of GRAZTRACE has also been developed. More than 60 commands have been implemented in a Code-V like format. The functions covered in this version include data manipulation, performance evaluation, and inquiry and setting of internal parameters. The user manual for these commands has been formatted as in Code-V, showing the command syntax, synopsis, and options. An interactive on-line help system for the command mode has also been accomplished to allow the user to find valid commands, command syntax, and command function. A translation program has been written to convert FEA output from structural analysis to GRAZTRACE surface deformation file (.dfm file). The program can accept standard output files and list files from COSMOS/M and NASTRAN finite analysis programs. Some interactive options are also provided, such as Cartesian or cylindrical coordinate transformation, coordinate shift and scale, and axial length change. A computerized database for technical documents relating to the AXAF project has been established. Over 5000 technical documents have been entered into the master database. A user can now rapidly retrieve the desired documents relating to the AXAF project. The summary of the work performed under this contract is shown.

Ahmad, Anees↗

NASA NTRS2014

Using SpF to Achieve Petascale for Legacy Pseudospectral Applications

Pseudospectral (PS) methods possess a number of characteristics (e.g., efficiency, accuracy, natural boundary conditions) that are extremely desirable for dynamo models. Unfortunately, dynamo models based upon PS methods face a number of daunting challenges, which include exposing additional parallelism, leveraging hardware accelerators, exploiting hybrid parallelism, and improving the scalability of global memory transposes. Although these issues are a concern for most models, solutions for PS methods tend to require far more pervasive changes to underlying data and control structures. Further, improvements in performance in one model are difficult to transfer to other models, resulting in significant duplication of effort across the research community. We have developed an extensible software framework for pseudospectral methods called SpF that is intended to enable extreme scalability and optimal performance. Highlevel abstractions provided by SpF unburden applications of the responsibility of managing domain decomposition and load balance while reducing the changes in code required to adapt to new computing architectures. The key design concept in SpF is that each phase of the numerical calculation is partitioned into disjoint numerical kernels that can be performed entirely inprocessor. The granularity of domain decomposition provided by SpF is only constrained by the datalocality requirements of these kernels. SpF builds on top of optimized vendor libraries for common numerical operations such as transforms, matrix solvers, etc., but can also be configured to use open source alternatives for portability. SpF includes several alternative schemes for global data redistribution and is expected to serve as an ideal testbed for further research into optimal approaches for different network architectures. In this presentation, we will describe our experience in porting legacy pseudospectral models, MoSST and DYNAMO, to use SpF as well as present preliminary performance results provided by the improved scalability.

DYNAMO↗

DOE OSTI2019

Scalable PETSc Implementation of the Three-Phase Unbalanced AC Power Flow Solver

A revolutionary transition of energy infrastructure, spanning across supply and demand sectors, is happening all around the world. Integration of renewable energy sources into our ever-complex power distribution networks is central to the infrastructure planning of the future. One step towards achieving this goal is to solve unbalanced transmission and distribution systems. Traditional approaches and software tools are not suitable because they assume a completely balanced 3-phase system, hence a single-phase equivalent can be solved. Renewable energy such as wind and solar power are intermittent and can pose a challenge when integrating into an already unbalanced power grid. Furthermore, these power grids can be quite large at scale consisting of potentially thousands of buses, which can be computationally demanding. This poster presents preliminary work on designing a robust and scalable 3-phase unbalanced AC power flow solver. The proposed power flow solver will eventually be built on top of the PETSc library and utilizes state-of-the-art parallel data structures like the DMNetwork as well as iterative solvers and preconditioners.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

Development, validation, and verification of multi-pass thermo-mechanical welding simulations using the open-source MOOSE framework: NeT TG4 benchmark weldment

This study develops and validates a sequentially coupled thermo-mechanical welding simulation for the three-pass 316L stainless steel NeT TG4 benchmark weldment using the open-source Multiphysics Object-Oriented Simulation Environment (MOOSE) and the Nuclear Engineering Material model Library (NEML). A diffused ellipsoidal heat source was calibrated against thermocouple data and weld macrographs to accurately model the fusion zone geometry and transient thermal fields. Material hardening is represented using the Lemaitre-Chaboche mixed isotropic-kinematic hardening model, while four annealing models - no annealing, single-stage at 1050 °C and 1300 °C, and two-stage at 800 °C/1300 °C - were implemented to assess the impact of annealing models on the accuracy of the predicted welding-induced plasticity, distortions, and residual stresses. The predictions were validated against experimental measurements and benchmarked against results from commercial software, demonstrating that thermo-mechanical MOOSE welding simulations achieve comparable accuracy with enhanced computational efficiency. This work highlights the potential of using open-source finite element frameworks like MOOSE for advanced manufacturing simulations.

Ji, Wendy [Australian Nuclear Science and Technolo↗

NASA NTRS1992

How to handle 6GBytes a night and not get swamped

The Macho Project has undertaken a 5 year effort to search for dark matter in the halo of the Galaxy by scanning the Magellanic Clouds for micro-lensing events. Each evening's raw image data will be reduced in real-time into the observed stars' photometric measurements. The actual search for micro-lensing events will be a post-processing operation. The theoretical prediction of the rate of such events necessitates the collection of a large number of repeated exposures. The project designed camera subsystem delivers 64 Mbytes per exposure with exposures typically occurring every 500 seconds. An ideal evening's observing will provide 6 Gbytes of raw image data and 40 Mbytes of reduced photometric measurements. Recognizing the difficulty of digging out from a snowballing cascade of raw data, the project requires the real-time reduction of each evening's data. The software team's implementation strategy centered on this non-negotiable mandate. Accepting the reality that 2 full time people needed to implement the core real-time control and data management system within 6 months, off-the-shelf vendor components were explored to provide quick solutions to the classic needs for file management, data management, and process control. Where vendor solutions were lacking, state-of-the-art models were used for hand tailored subsystems. In particular, petri nets manage process control, memory mapped bulletin boards provide interprocess communication between the multi-tasked processes, and C++ class libraries provide memory mapped, disk resident databases. The differences between the implementation strategy and the final implementation reality are presented. The necessity of validating vendor product claims are explored. Both the successful and hindsight decisions enabling the collection and processing of the nightly data barrage are reviewed.

Allsman, R.↗