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At least 595 records · Page 33

Better together: Elements of successful scientific software development in a distributed collaborative community

Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities

97 MATHEMATICS AND COMPUTING↗

Multi-objective Bayesian optimization of ferroelectric materials with interfacial control for memory and energy storage applications

Optimization of materials’ performance for specific applications often requires balancing multiple aspects of materials’ functionality. Even for the cases where a generative physical model of material behavior is known and reliable, this often requires search over multidimensional function space to identify low-dimensional manifold corresponding to the required Pareto front. In this work, we introduce the multi-objective Bayesian optimization (MOBO) workflow for the ferroelectric/antiferroelectric performance optimization for memory and energy storage applications based on the numerical solution of the Ginzburg–Landau equation with electrochemical or semiconducting boundary conditions. MOBO is a low computational cost optimization tool for expensive multi-objective functions, where we update posterior surrogate Gaussian process models from prior evaluations and then select future evaluations from maximizing an acquisition function. Using the parameters for a prototype bulk antiferroelectric (PbZrO 3 ), we first develop a physics-driven decision tree of target functions from the loop structures. We further develop a physics-driven MOBO architecture to explore multidimensional parameter space and build Pareto-frontiers by maximizing two target functions jointly—energy storage and loss. This approach allows for rapid initial materials and device parameter selection for a given application and can be further expanded toward the active experiment setting. The associated notebooks provide both the tutorial on MOBO and allow us to reproduce the reported analyses and apply them to other systems (https://github.com/arpanbiswas52/MOBO_AFI_Supplements).

36 MATERIALS SCIENCE↗

Pathways for Electron Transfer at MgO–Water Interfaces from Ab Initio Molecular Dynamics

The nature of electron transfer across metal oxide–water interfaces depends significantly on the band gap of the oxide and its band edge energies relative to the potentials of relevant aqueous redox couples. Here we focus on the water interface with MgO, a prototypical wide band gap oxide whose conduction band edge is close in energy to that of water. We investigate the behavior of an excess electron at and out of equilibrium near the interface using ab initio molecular dynamics based on hybrid density functional theory. Our simulations show that under equilibrium conditions the excess electron (donated by an Al impurity in MgO) localizes to a midgap defect state comparable in energy and shape to a hydrated electron in bulk water. To characterize the electron transfer from the conduction band of MgO to interfacial product states, we dope near-equilibrium configurations of the pristine MgO–water system with Al and run short trajectories of these instantaneously out-of-equilibrium systems. Here we observe two distinct products associated with the excess electron: a surface-localized electron (e surf –) and an aqueous hydrogen radical (H • ). The H • pathway exhibits a much higher activation barrier despite being more exoergic, making e surf – the kinetic product. Our characterization of the pathways on the basis of Marcus theory is consistent with the poor observed utility of MgO for water radiolysis. Moreover, we anticipate that the computational framework employed here will be broadly applicable to assessing electron transfer mechanisms at aqueous, photocatalytic interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Kokkos Ecosystem [Brief]

In 2016/2017, the field of High-Performance Computing (HPC) entered a new era driven by fundamental physics challenges to produce ever more energy and cost-efficient processors. Since the convergence on the Message-Passing Interface (MPI) standard in the mid-1990s, application developers enjoyed a seemingly static view of the underlying machine — that of a distributed collection of homogeneous nodes executing in collaboration. However, after almost two decades of dominance, the sole use of MPI to derive parallelism acted as a limiter to improved future performance. While MPI is widely expected to continue to function as the basic mechanism for communication between compute nodes for the immediate future, additional parallelism is required on the computing node itself if high performance and efficiency goals are to be realized. When reviewing the architectures of the top HPC systems today, the change in paradigm is clear: the compute nodes of the leading machines in the world are either powered by many-core chips with a few dozen cores each, or use heterogeneous designs, where traditional CPUs marshal work to massively parallel compute accelerators which has as many as 200,000 processing threads in flight simultaneously. Complicating matters further for application developers, each processor vendor has its own preferred way of writing code for their architecture.The Kokkos EcoSystem was released by Sandia in 2017 to address this new era in HPC system design by providing a vendor independent performance portable programming system for scientific, engineering, and mathematical software applications written in the C++ programming language. Using Kokkos, application developers can be more productive because they will not have to create and maintain separate versions of their software for each architecture, nor will they have to be experts in each architecture's peculiar requirements. Instead, they will have a single method of programming for the diverse set of modern HPC architectures. While Kokkos started in 2011 as a programming model only, it soon became clear that complex applications needed more. It is also critical to have a portable mathematical functions and developers need tools to debug their applications, gain insight into the performance characteristics of their codes and tune algorithm performance parameters through automated processes. The Kokkos EcoSystem addresses those needs through its three main components: the Kokkos Core programming model, the Kokkos Kernels math library, and the Kokkos Tools project.

97 MATHEMATICS AND COMPUTING↗

A simple analytical function for bidirectional reflectance

A simple bidirectional reflectance model based on physical scattering laws is developed to calculate the bidirectional reflectance of a wide variety of surfaces. Chandrasekhar's radiative transfer solution, obtained for the anisotropically scattering semi-infinite medium, is used to compute the multiple-scattered radiances. However, since the radiative transfer solution does not take architectural effects into consideration, we adopt Hapke's (1986) approach and add an empirical term to explain the hot-spot phenomenon and use Cox and Munk's (1954) formulation to take into account the specular reflection. The physical parameters of the model are retrieved from bidirectional reflectance measurements. For each surface, only one set of model parameters is needed for application to all illumination and viewing geometries. The validity of the model is established by comparing the computed and measured reflectances for sets of viewing and illumination angles that were not included in the inversion algorithm. Good agreement is shown between the model-computed and the observed reflectances for dense prairie vegetation canopies, a sparse desert scrub community, a plowed agricultural field, and an alkali flat.

Ahmad, Suraiya P.↗

NSFnets (Navier-Stokes flow nets): Physics-informed neural networks for the incompressible Navier-Stokes equations

In the last 50 years there has been a tremendous progress in solving numerically the Navier-Stokes equations using finite differences, finite elements, spectral, and even meshless methods. Yet, in many real cases, we still cannot incorporate seamlessly (multi-fidelity) data into existing algorithms, and for industrial-complexity applications the mesh generation is time consuming and still an art. Moreover, solving ill-posed problems (e.g., lacking boundary conditions) or inverse problems is often prohibitively expensive and requires different formulations and new computer codes. Here, we employ physics-informed neural networks (PINNs), encoding the governing equations directly into the deep neural network via automatic differentiation, to overcome some of the aforementioned limitations for simulating incompressible laminar and turbulent flows. We develop the Navier-Stokes flow nets (NSFnets) by considering two different mathematical formulations of the Navier-Stokes equations: the velocity-pressure (VP) formulation and the vorticity-velocity (VV) formulation. Since this is a new approach, we first select some standard benchmark problems to assess the accuracy, convergence rate, computational cost and flexibility of NSFnets; analytical solutions and direct numerical simulation (DNS) databases provide proper initial and boundary conditions for the NSFnet simulations. The spatial and temporal coordinates are the inputs of the NSFnets, while the instantaneous velocity and pressure fields are the outputs for the VP-NSFnet, and the instantaneous velocity and vorticity fields are the outputs for the VV-NSFnet. This is unsupervised learning and, hence, no labeled data are required beyond boundary and initial conditions and the fluid properties. The residuals of the VP or VV governing equations, together with the initial and boundary conditions, are embedded into the loss function of the NSFnets. No data is provided for the pressure to the VP-NSFnet, which is a hidden state and is obtained via the incompressibility constraint without extra computational cost. Unlike the traditional numerical methods, NSFnets inherit the properties of neural networks (NNs), hence the total error is composed of the approximation, the optimization, and the generalization errors. Here, we empirically attempt to quantify these errors by varying the sampling (“residual”) points, the iterative solvers, and the size of the NN architecture. For the laminar flow solutions, we show that both the VP and the VV formulations are comparable in accuracy but their best performance corresponds to different NN architectures. The initial convergence rate is fast but the error eventually saturates to a plateau due to the dominance of the optimization error. For the turbulent channel flow, we show that NSFnets can sustain turbulence at , but due to expensive training we only consider part of the channel domain and enforce velocity boundary conditions on the subdomain boundaries provided by the DNS data base. We also perform a systematic study on the weights used in the loss function for balancing the data and physics components, and investigate a new way of computing the weights dynamically to accelerate training and enhance accuracy. In the last part, we demonstrate how NSFnets should be used in practice, namely for ill-posed problems with incomplete or noisy boundary conditions as well as for inverse problems. We obtain reasonably accurate solutions for such cases as well without the need to change the NSFnets and at the same computational cost as in the forward well-posed problems. As a result, we also present a simple example of transfer learning that will aid in accelerating the training of NSFnets for different parameter settings.

97 MATHEMATICS AND COMPUTING↗

Kuang's Semi-Classical Formalism for Calculating Electron Capture Cross Sections: A Space- Physics Application

Accurate estimates of electroncapture cross sections at energies relevant to the modeling of the transport, acceleration, and interaction of energetic neutral atoms (ENA) in space (approximately few MeV per nucleon) and especially for multi-electron ions must rely on detailed, but computationally expensive, quantum-mechanical description of the collision process. Kuang's semi-classical approach is an elegant and efficient way to arrive at these estimates. Motivated by ENA modeling efforts for apace applications, we shall briefly present this approach along with sample applications and report on current progress.

Barghouty, A. F.↗

DLIO: A DATA-CENTRIC BENCHMARK FOR DEEP LEARNING APPLICATIONS

SF-22-136 Deep learning has been shown as a successful method for various tasks, and its popularity results in numerous open-source deep learning software tools. Deep learning has been applied to a broad spectrum of scientific domains such as cosmology, particle physics, computer vision, fusion, and astrophysics. Scientists have performed a great deal of work to optimize the computational performance of deep learning frameworks. However, the same cannot be said for I/O performance. As deep learning algorithms rely on big-data volume and variety to effectively train neural networks accurately, I/O is a significant bottleneck on large-scale distributed deep learning training. DLIO, is a novel representative benchmark suite built based on the I/O profiling of the selected workloads. DLIO can be utilized to accurately emulate the I/O behavior of modern deep learning applications. Using DLIO, application developers and system software solution architects can identify potential I/O bottlenecks in their applications and guide optimizations to boost the I/O performance leading to lower training times. The storage vendor can also use DLIO as a guide for designing and optimize the storage and filesystem targeting at deep learning application.

ZHENG, HUIHUO↗

Computational Characterization and Boundary Condition Models of a Jet Interaction Fluidic Oscillator

Fluidically oscillating jet actuators that generate sweeping jets when supplied with a pressurized fluid have been used to mitigate separation and reduce drag in a range of flow control applications. Their implementation in future flight vehicles would require fundamental understanding and accurate predictive techniques of the physics of their internal flow and jet formation. The present investigations focus on high-fidelity, time-accurate simulations to characterize the flow physics of the actuator in quiescent conditions. An important element of the present simulations is to demonstrate the ability of the computational fluid dynamics (CFD) solver to predict the jet characteristics and provide a basis for the development of improved boundary conditions (BC) without entirely resolving the geometrical features of the fluidic device. The CFD-predicted oscillation frequencies of the engendered jets were found to be in excellent agreement with experiments, even on two-dimensional meshes. The study revealed that three-dimensional simulations are required to capture some of the flow features of the sweeping jet such as the double peak in time-averaged velocity distributions downstream of the actuator’s orifice that were measured in experiments. Furthermore, several approaches for modeling the actuator were implemented and assessed in quiescent conditions. The evaluation of a boundary condition at the device throat, based on the phase-averaged flow variables, provides the basis for devising surface-based boundary conditions. The influence and necessity of including turbulent characteristics as part of the boundary conditions have also been identified.

42 ENGINEERING↗

PanDA: Production and Distributed Analysis System

The Production and Distributed Analysis (PanDA) system is a data-driven workload management system engineered to operate at the LHC data processing scale. The PanDA system provides a solution for scientific experiments to fully leverage their distributed heterogeneous resources, showcasing scalability, usability, flexibility, and robustness. The system has successfully proven itself through nearly two decades of steady operation in the ATLAS experiment, addressing the intricate requirements such as diverse resources distributed worldwide at about 200 sites, thousands of scientists analyzing the data remotely, the volume of processed data beyond the exabyte scale, dozens of scientific applications to support, and data processing over several billion hours of computing usage per year. PanDA’s flexibility and scalability make it suitable for the High Energy Physics community and wider science domains at the Exascale. Beyond High Energy Physics, PanDA’s relevance extends to other big data sciences, as evidenced by its adoption in the Vera C. Rubin Observatory and the sPHENIX experiment. As the significance of advanced workflows continues to grow, PanDA has transformed into a comprehensive ecosystem, effectively tackling challenges associated with emerging workflows and evolving computing technologies. The paper discusses PanDA’s prominent role in the scientific landscape, detailing its architecture, functionality, deployment strategies, project management approaches, results, and evolution into an ecosystem.

97 MATHEMATICS AND COMPUTING↗

CLAS12 remote data-stream processing using ERSAP framework

Implementing a physics data processing application is relatively straightforward with the use of current containerization technologies and container image runtime services, which are prevalent in most high-performance computing (HPC) environments. However, the process is complicated by the challenges associated with data provisioning and migration, impacting the ease of workflow migration and deployment. Transitioning from traditional file-based batch processing to data-stream processing workflows is suggested as a method to streamline these workflows. This transition not only simplifies file provisioning and migration but also significantly reduces the necessity for extensive disk space. Data-stream processing is particularly effective for real-time processing during data acquisition, thereby enhancing data quality assurance. This paper introduces the integration of the JLAB CLAS12 event reconstruction application within the ERSAP data-stream processing framework that facilitates the execution of streaming event reconstruction at a remote data center and enables the return streaming of reconstructed events to JLAB while circumventing the need for temporary data storage throughout the process.

Gyurjyan, Vardan↗

Quick response targeting program

Computer program generates and verifies operational launch vehicle targeting presettings for lunar free-return missions and lunar landing missions. Program is applicable in astronomy and nuclear physics, and in areas where improved targeting techniques are valuable.

Bosley, J. T.↗

Sharp-Focus Composite Microscope Imaging by Computer

Enhanced depth of focus aids medical analysis. Computer image-processing system synthesizes sharply-focused composite picture from series of photomicrographs of same object taken at different depths. Computer rejects blured parts of each photomicrograph. Remaining in focus portions form focused composite. System used to study alveolar lung tissue and has applications in medicine and physical sciences.

Wall, R. J.↗

Proceedings of the 4th International Conference and Exhibition: World Congress on Superconductivity, volume 1

The papers presented at the 4th International Conference Exhibition: World Congress on Superconductivity held at the Marriott Orlando World Center, Orlando, Florida, are contained in this document and encompass the research, technology, applications, funding, political, and social aspects of superconductivity. Specifically, the areas covered included: high-temperature materials; thin films; C-60 based superconductors; persistent magnetic fields and shielding; fabrication methodology; space applications; physical applications; performance characterization; device applications; weak link effects and flux motion; accelerator technology; superconductivity energy; storage; future research and development directions; medical applications; granular superconductors; wire fabrication technology; computer applications; technical and commercial challenges, and power and energy applications.

Krishen, Kumar↗

Proceedings of the 4th International Conference and Exhibition: World Congress on Superconductivity, Volume 2

This document contains papers presented at the 4th International Conference Exhibition: World Congress on Superconductivity held June 27-July 1, 1994 in Orlando, Florida. These documents encompass research, technology, applications, funding, political, and social aspects of superconductivity. The areas covered included: high-temperature materials; thin films; C-60 based superconductors; persistent magnetic fields and shielding; fabrication methodology; space applications; physical applications; performance characterization; device applications; weak link effects and flux motion; accelerator technology; superconductivity energy; storage; future research and development directions; medical applications; granular superconductors; wire fabrication technology; computer applications; technical and commercial challenges; and power and energy applications.

Krishen, Kumar↗

Effect of Discontinuities and Uncertainties on the Response and Failure of Composite Structures

The overall goal of this research was to assess the effect of discontinuities and uncertainties on the nonlinear response and failure of composite structures subjected to combined mechanical and thermal loads. The four key elements of the study were: (1) development of simple and efficient procedures for the accurate determination of transverse shear and transverse normal stresses in structural sandwiches as well as in unstiffened and stiffened composite panels and shells; (2) study the effects of transverse stresses on the response, damage initiation and propagation in composite and sandwich structures; (3) use of hierarchical sensitivity coefficients to identify the major parameters that affect the response and damage in each of the different levels in the hierarchy (micro-mechanical, layer, panel, subcomponent and component levels); and (4) application of fuzzy set techniques to identify the range and variation of possible responses. The computational models developed were used in conjunction with experiments, to understand the physical phenomena associated with the nonlinear response and failure of composite and sandwich structures. A toolkit was developed for use in conjunction with deterministic analysis programs to help the designer in assessing the effect of uncertainties in the different computational model parameters on the variability of the response quantities.

Noor, Ahmed K.↗

Nonlinear and Failure Analysis of Composite Structures

The overall goal of this research is to assess the effect of discontinuities and uncertainties on the nonlinear response and failure of stiffened composite panels subjected to combined mechanical and thermal loads. The key elements of the study are: (a) study of the effects of stiffener geometry and of transverse stresses on the response, damage initiation and propagation in stiffened composite panels; (b) use of hierarchical sensitivity coefficients to identify the major parameters that affect the response and damage in each of the different levels in the hierarchy (micromechanical, layer, panel, subcomponent and component levels); and, (c) application of fuzzy set techniques to identify the range and variation of possible responses. The computational models developed are used in conjunction with experiments to understand the physical phenomena associated with the nonlinear response and failure of stiffened composite panels. A toolkit is developed for use in conjunction with deterministic analysis programs to help the designer in assessing the effect of uncertainties in the different computational model parameters on the variability of the response quantities.

Noor, Ahmed K.↗

A Deep Learning Approach to Fast Radiative Transfer

Due to the sheer volume of data, leveraging satellite instrument observations effectively in a data assimilation context for numerical weather prediction or for remote sensing requires a radiative transfer model as an observation operator that is both fast and accurate at the same time. Physics-based line-by-line radiative transfer (RT) models fulfil the requirement for accuracy, but are too slow and too costly in computational terms for operational applications. Therefore, fast methods were developed to be able to perform fast RT calculations using techniques such as spectral sampling or pre-computed look-up tables. The operational fast models currently calculate the absorption and scattering coefficients from the pre-computed regression coefficients and atmospheric state and cloud profiles. As a novel solution to this problem, this work investigates a deep learning approach to replace the regression coefficients in the fast RT models. A selection of hidden-layer neural network configurations is trained against atmospheric transmittance profile data computed by an accurate line-by-line model and their performance is evaluated and their advantages and disadvantages are discussed.

Machine learning↗